From 65119929968c101b355d18783dcb781e636c70d3 Mon Sep 17 00:00:00 2001 From: Dominik Maszczyk Date: Thu, 25 Jan 2024 11:01:52 +0100 Subject: [PATCH] Lifelike staging az deployment becomes master (#2213) * Convert `get_genes_to_organisms` to AQL * Convert `get_proteins_to_organisms` to AQL * Convert `get_global_inclusions_count` to AQL * Convert `get_global_inclusions` to AQL * Convert `get_global_inclusions_paginated` to AQL * Convert `get_docs_by_ids` to AQL * Convert `get_mesh_by_ids` to AQL * Convert `get_node_labels_and_relationship` to AQL * Convert `global_inclusions_by_type` queries to AQL * Convert `_global_annotation_exists_in_kg` to AQL * Update goc queries for globals * Fix linting * Skip annotations pytests This is a temporary measure to allow CI to pass without needing to refactor every annotations test which previously used Neo4j. * Fix bug in `get_global_inclusions_by_type_query` * Remove unnecessary graph services from annotations * Update ET to use Arango * Resolve mypy & pycodestyle issues * Update organism search to use AQL * Update visualizer search to use AQL * Update synonym search to use AQL * Remove `SearchService` No longer needed as it isn't used anywhere. * Update viz expansion/snippets queries to use AQL * Fix bug in batch uri request api * Ignore failing visualizer tests Just silencing these until after the arango integration is complete. * Fix lint issues * Update id properties to use `IdType` This should help if in the future we decide to go back to using numbers, we won't have to change every single instance of a type definition. * Fix bad type definition in sidenav-type view * Move import to correct group * Add `verify_override` argument to ArangoClient * Remove KgService and Pathway Browser Since this feature is mostly a prototype and we're moving away from Neo4j anyway, doesn't really make sense to keep it. * Remove remaining references to neo4j package Removes (almost) all remaining references to the neo4j python driver in the appserver. There are still a few references in the pytests, these can be ironed out when the tests themselves are updated in the near future. * Add arango driver to stats-enrichment pipfile * Update SE to use arango * Remove neo4j & py2neo from SE pipfile * Fix pagination bug in visualizer search * Fix bug in visualizer expansion query * Update cache-invalidator to use Arango * Add correct sorting to visualizer search query * Fix sorting in misc. visualizer snippet queries * Remove possibly unnecessary `exec $@` call * Add sanity check log after dbs have started * Remove n4j container & update startup w/ arango * Test ansible workflow changes (add verbosity) * Re-format relevant visualizer JS files * Update expand to bulk create reference tables * Fix input/output errors in visualization cmp * Fix direction bug in reference table creation * Improve visualizer expand timing Consolidates the expand/reference table requests into a single one. Also adds some small performance improvements on the client. * Add improved association matching to viz queries * Add very slight perf improvement to snippets query * Add starts-with phrase search to viz search * Add perf update to node pair snippets query * Fix domain labels not appearing in viz search * Fix mypy errors * Remove accidental workflow changes * Fix ChEBI typo in constants * Fix pagination issue in viz search * Clean up a few files * Update arango conftests + update initial tests * Update manual annotations tests * Update neo4j api tests * Update database annotations tests * Use camel_to_snake_dict instead of recent change * Update remaining visualizer tests * Add comment to redis queue tests * Fix appserver linting checks * Fix client lint checks * Update enrichment queries to loop over inputs We noticed that when using an `IN` clause, the results were being sorted in seemingly alphabetical order. To avoid this, we changed the queries to iterate over the inputs to return the results in input order. * Add perf. improvement to stats-enrichment query * Add perf. improvement to anno fallback queries * Fix typo in genes to organism query * Add another date conversion case for arango data * Fix bad error handling in global creation * Generalize arango date format checks * Remove debug comments * Fix linter issues * Fix appserver issues * Fix incorrect property name in go term query * Update deployment submodule (add AQL vars to qa) * Update deployment submodule (rm bad pip installs) * Update deployment submodule (demo vars) * Increase ansible log verbosity for debugging * Fix typo * Update deployment submodule (rm apm vars) * Update deployment submodule (switch to gpt branch) * Update deployment submodule (add gpt key to demo) * Fix pycodestyle errors * Fix pytest * Add auto lint changes for pytest update * Fix prettier & black warnings * Fix additional black/prettier errors * Fix code style issues with Black * Fix code style issues with Prettier * Remove old `util.py` in favor of new files * Rename `neo4j_test.py` to `arango_test.py` * Fix flake8 issue * Fix silent bugs in visualizer search * Fix typo in associated type snippet count query * Fix merge conflict in visualizer search records * Change deployment submodule ref * Remove unnecessary secret from az workflows * Update deployment submodule (fix bad value) * Update deployment submodule (add docker-az role) * Update deployment submodule (fix bad file location) * Update deployment submodule (re-add JWKS vars) * Update deployment submodule (+ openai vars to env) * Update deployment submodule (add networks) * Update deployment submodule (edit JWKS vars) * Update deployment submodule (remove vals from JWKS) * Add empty string defaults for JWKS flask config * Fix badly merged changes for LL-5300 * Add synonym field to organism query result * Update deployment to latest lifelike-public-temp-fix * Update deployment submodule (update frontend host) * Update deployment submodule (update stg app version) * Update deployment submodule to latest * Update deployment submodule (rm var from env) * Update deployment submodule (update flask env) * Fix code style issues with Prettier --------- Co-authored-by: Ethan Sanchez Co-authored-by: Lint Action --- .github/workflows/deployment-az-public.yml | 1 - .github/workflows/deployment-az.yml | 2 - .github/workflows/deployment-gcp.yml | 2 +- appserver/Dockerfile | 1 + appserver/bin/startup.sh | 2 +- appserver/bin/wait-for-arango | 16 + appserver/config.py | 8 +- appserver/migrations/utils.py | 69 +- appserver/neo4japp/blueprints/annotations.py | 39 +- .../neo4japp/blueprints/enrichment_table.py | 39 +- .../neo4japp/blueprints/entity_resources.py | 11 +- appserver/neo4japp/blueprints/kg.py | 51 - appserver/neo4japp/blueprints/playground.py | 2 +- appserver/neo4japp/blueprints/search.py | 55 +- appserver/neo4japp/blueprints/visualizer.py | 122 +- appserver/neo4japp/constants.py | 69 +- .../data_transfer_objects/visualization.py | 56 +- appserver/neo4japp/database.py | 91 +- appserver/neo4japp/factory.py | 4 - appserver/neo4japp/models/common.py | 10 +- .../neo4japp/request_schemas/visualizer.py | 8 +- appserver/neo4japp/schemas/annotations.py | 6 +- appserver/neo4japp/services/__init__.py | 3 - .../neo4japp/services/annotations/README.md | 1 - .../neo4japp/services/annotations/__init__.py | 1 - .../annotations/annotation_graph_service.py | 490 +- .../annotations/annotation_service.py | 33 +- .../enrichment_annotation_service.py | 22 +- .../services/annotations/initializer.py | 18 +- .../services/annotations/lmdb_service.py | 3 +- .../annotations/manual_annotation_service.py | 435 +- .../neo4japp/services/annotations/pipeline.py | 20 +- .../profilers/annotations_profiler.py | 2 - .../annotations/utils/graph_queries.py | 950 +- appserver/neo4japp/services/arangodb.py | 25 +- appserver/neo4japp/services/common.py | 95 - .../services/elastic/elastic_service.py | 10 +- .../services/enrichment/enrichment_table.py | 383 +- appserver/neo4japp/services/kg_service.py | 849 - appserver/neo4japp/services/search.py | 1015 +- .../ale_mutation_data/42C.json | 18937 - .../ale_mutation_data/acetate.json | 4332 - .../ale_mutation_data/glycerol.json | 7507 - .../ale_mutation_data/hexanoic.json | 5611 - .../ale_mutation_data/isobutyric.json | 21559 - .../ale_mutation_data/nagA.json | 467786 --------------- .../ale_mutation_data/nagAC.json | 714 - .../nagAC_shortestpaths.json | 3670 - .../ale_mutation_data/nagC.json | 3003 - .../ale_mutation_data/putrescine.json | 8952 - .../ale_mutation_data/serine.json | 3700 - .../ale_mutation_data/tpiA.json | 3861 - .../ale_mutation_data/xylose.json | 28230 - .../Auxilin recruits HSPA8.json | 20536 - .../CSNK1D phosphorylates SEC23.json | 14166 - ...AK1 and dephosphorylation of AP-2 mu2.json | 20276 - .../Expression of PERIOD-1.json | 11886 - .../cytoscape_data/F_BAR proteins_ARP.json | 20306 - .../cytoscape_data/FosB to PER1_vis_js.json | 1056 - ...hydrolysis promotes vesicle uncoating.json | 20276 - .../Interleukin-1 family are secreted.json | 13406 - .../cytoscape_data/PER1 [cytosol].json | 11886 - .../PTHLH2Ca2metab_shortPage_graphml.json | 886 - .../PTHLH2metab_shortPage_graphml.json | 2016 - .../PTHLH2metab_short_graphml.json | 7626 - ...he Ligand_GPCR_Gs complex dissociates.json | 16436 - .../cytoscape_data/Vesicle budding.json | 19246 - .../cytoscape_data/aak1_graphml.json | 2576 - .../aak1_to_metab_noOct_graphml.json | 8066 - .../metab2PTHLH_shortPage_graphml.json | 2966 - .../metab2PTHLH_short_graphml.json | 7436 - .../metab2PTHLH_short_graphml_truncated.json | 7436 - .../minMeanShort_metabs_Acetate_graphml.json | 6526 - .../minMeanShort_metabs_Butyrate_graphml.json | 6526 - ...inMeanShort_metabs_Propionate_graphml.json | 6526 - ...minMeanShort_metabs_Serotonin_graphml.json | 5086 - .../minMeanShort_metabs_top10_graphml.json | 13876 - .../minMeanShort_updown_Acetate_graphml.json | 14956 - .../minMeanShort_updown_Butyrate_graphml.json | 14956 - ...minMeanShort_updown_Serotonin_graphml.json | 15466 - ...on_genes_and_top20_metabolites_vis_js.json | 16867 - ...racterized_iModulon_genes_only_vis_js.json | 2576 - ...d_iModulon_genes_to_methionine_vis_js.json | 3065 - ...Modulon_genes_yjdI_metabolites_vis_js.json | 4827 - .../zink-imodulon-metals_vis_js.json | 1401 - .../zink-imodulon-test2_vis_js.json | 1783 - .../shortest_path_data/serine-to-malZp.json | 5026 - .../services/shortest_path_data/serine.json | 3796 - appserver/neo4japp/services/visualizer.py | 1359 +- appserver/neo4japp/util.py | 368 - appserver/neo4japp/utils/flask.py | 2 +- appserver/neo4japp/utils/jsonify.py | 2 +- appserver/neo4japp/utils/labels.py | 27 +- appserver/neo4japp/utils/string.py | 11 +- appserver/tests/api/account_test.py | 41 +- appserver/tests/api/annotations_test.py | 38 +- .../api/{neo4j_test.py => arango_test.py} | 63 +- appserver/tests/api/entity_resources_test.py | 2 +- appserver/tests/api/filesystem/object_test.py | 9 +- appserver/tests/conftest.py | 1294 +- appserver/tests/constants.py | 72 + .../services/annotations/annotations_test.py | 85 +- .../database/services/annotations/conftest.py | 49 +- .../manual_annotations_test.py | 5 + .../database/services/annotations/util.py | 2 +- .../redis_queue/test_redis_queue_service.py | 4 + .../database/services/visualizer/conftest.py | 661 + .../visualizer.py} | 66 +- appserver/tests/unit/util_test.py | 2 +- cache-invalidator/Dockerfile | 12 +- cache-invalidator/Pipfile | 2 +- cache-invalidator/Pipfile.lock | 74 +- cache-invalidator/bin/startup.sh | 13 + cache-invalidator/bin/wait-for-arango.sh | 14 + cache-invalidator/main.py | 448 +- client/nginx.conf | 2 +- client/src/app/app-routing.module.ts | 6 - client/src/app/app.module.ts | 2 - .../clustergram/clustergram.component.html | 4 +- .../enrichment/models/enrichment-document.ts | 78 +- .../services/enrichment-table.service.ts | 14 +- client/src/app/interfaces/neo4j.interface.ts | 23 +- .../app/interfaces/visualization.interface.ts | 68 +- .../search-record-node.component.html | 4 +- .../search-record-node.component.ts | 8 +- ...search-record-relationships.component.html | 2 +- .../search/services/graph-search.service.ts | 2 +- client/src/app/search/utils/records.ts | 2 +- .../components/route-builder.component.html | 56 - .../components/route-builder.component.scss | 27 - .../route-builder.component.spec.ts | 30 - .../components/route-builder.component.ts | 75 - .../components/route-display.component.html | 18 - .../components/route-display.component.scss | 0 .../route-display.component.spec.ts | 33 - .../components/route-display.component.ts | 189 - .../containers/route-search.component.html | 1 - .../containers/route-search.component.scss | 0 .../containers/route-search.component.spec.ts | 29 - .../containers/route-search.component.ts | 12 - .../containers/shortest-path.component.html | 23 - .../containers/shortest-path.component.scss | 0 .../shortest-path.component.spec.ts | 36 - .../containers/shortest-path.component.ts | 50 - .../services/shortest-path.service.ts | 26 - .../app/shortest-path/shortest-path.module.ts | 22 - .../sidenav-type-view.component.ts | 4 +- .../visualization-canvas.component.spec.ts | 26 +- .../visualization-canvas.component.ts | 572 +- .../visualization.component.html | 4 - .../visualization.component.spec.ts | 114 +- .../visualization/visualization.component.ts | 217 +- .../services/visualization.service.ts | 98 +- deployment | 2 +- docker-compose.override.yml | 44 +- docs/wiki/appserver/logging-guide.md | 2 +- statistical-enrichment/Pipfile | 2 +- statistical-enrichment/Pipfile.lock | 613 +- .../statistical_enrichment/config.py | 19 +- .../statistical_enrichment/database.py | 24 + .../services/__init__.py | 1 - .../services/arangodb.py | 22 + .../services/enrichment/__init__.py | 10 - .../enrichment/enrichment_visualisation.py | 246 +- .../services/graphdb.py | 17 - .../statistical_enrichment/views.py | 11 +- 166 files changed, 5808 insertions(+), 916431 deletions(-) create mode 100755 appserver/bin/wait-for-arango delete mode 100644 appserver/neo4japp/blueprints/kg.py delete mode 100644 appserver/neo4japp/services/kg_service.py delete mode 100644 appserver/neo4japp/services/shortest_path_data/ale_mutation_data/42C.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/ale_mutation_data/acetate.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/ale_mutation_data/glycerol.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/ale_mutation_data/hexanoic.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/ale_mutation_data/isobutyric.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/ale_mutation_data/nagA.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/ale_mutation_data/nagAC.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/ale_mutation_data/nagAC_shortestpaths.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/ale_mutation_data/nagC.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/ale_mutation_data/putrescine.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/ale_mutation_data/serine.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/ale_mutation_data/tpiA.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/ale_mutation_data/xylose.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/Auxilin recruits HSPA8.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/CSNK1D phosphorylates SEC23.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/Dissociation of AAK1 and dephosphorylation of AP-2 mu2.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/Expression of PERIOD-1.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/F_BAR proteins_ARP.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/FosB to PER1_vis_js.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/HSPA8-mediated ATP hydrolysis promotes vesicle uncoating.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/Interleukin-1 family are secreted.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/PER1 [cytosol].json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/PTHLH2Ca2metab_shortPage_graphml.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/PTHLH2metab_shortPage_graphml.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/PTHLH2metab_short_graphml.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/The Ligand_GPCR_Gs complex dissociates.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/Vesicle budding.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/aak1_graphml.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/aak1_to_metab_noOct_graphml.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/metab2PTHLH_shortPage_graphml.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/metab2PTHLH_short_graphml.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/metab2PTHLH_short_graphml_truncated.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/minMeanShort_metabs_Acetate_graphml.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/minMeanShort_metabs_Butyrate_graphml.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/minMeanShort_metabs_Propionate_graphml.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/minMeanShort_metabs_Serotonin_graphml.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/minMeanShort_metabs_top10_graphml.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/minMeanShort_updown_Acetate_graphml.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/minMeanShort_updown_Butyrate_graphml.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/cytoscape_data/minMeanShort_updown_Serotonin_graphml.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/marina_sankey_data/uncharacterized_iModulon_genes_and_top20_metabolites_vis_js.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/marina_sankey_data/uncharacterized_iModulon_genes_only_vis_js.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/marina_sankey_data/uncharacterized_iModulon_genes_to_methionine_vis_js.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/marina_sankey_data/uncharacterized_iModulon_genes_yjdI_metabolites_vis_js.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/marina_sankey_data/zink-imodulon-metals_vis_js.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/marina_sankey_data/zink-imodulon-test2_vis_js.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/serine-to-malZp.json delete mode 100644 appserver/neo4japp/services/shortest_path_data/serine.json delete mode 100644 appserver/neo4japp/util.py rename appserver/tests/api/{neo4j_test.py => arango_test.py} (59%) create mode 100644 appserver/tests/constants.py create mode 100644 appserver/tests/database/services/visualizer/conftest.py rename appserver/tests/database/services/{neo4j_test.py => visualizer/visualizer.py} (81%) create mode 100755 cache-invalidator/bin/startup.sh create mode 100755 cache-invalidator/bin/wait-for-arango.sh delete mode 100644 client/src/app/shortest-path/components/route-builder.component.html delete mode 100644 client/src/app/shortest-path/components/route-builder.component.scss delete mode 100644 client/src/app/shortest-path/components/route-builder.component.spec.ts delete mode 100644 client/src/app/shortest-path/components/route-builder.component.ts delete mode 100644 client/src/app/shortest-path/components/route-display.component.html delete mode 100644 client/src/app/shortest-path/components/route-display.component.scss delete mode 100644 client/src/app/shortest-path/components/route-display.component.spec.ts delete mode 100644 client/src/app/shortest-path/components/route-display.component.ts delete mode 100644 client/src/app/shortest-path/containers/route-search.component.html delete mode 100644 client/src/app/shortest-path/containers/route-search.component.scss delete mode 100644 client/src/app/shortest-path/containers/route-search.component.spec.ts delete mode 100644 client/src/app/shortest-path/containers/route-search.component.ts delete mode 100644 client/src/app/shortest-path/containers/shortest-path.component.html delete mode 100644 client/src/app/shortest-path/containers/shortest-path.component.scss delete mode 100644 client/src/app/shortest-path/containers/shortest-path.component.spec.ts delete mode 100644 client/src/app/shortest-path/containers/shortest-path.component.ts delete mode 100644 client/src/app/shortest-path/services/shortest-path.service.ts delete mode 100644 client/src/app/shortest-path/shortest-path.module.ts create mode 100644 statistical-enrichment/statistical_enrichment/database.py create mode 100644 statistical-enrichment/statistical_enrichment/services/arangodb.py delete mode 100644 statistical-enrichment/statistical_enrichment/services/graphdb.py diff --git a/.github/workflows/deployment-az-public.yml b/.github/workflows/deployment-az-public.yml index f874707ea5..0347495991 100644 --- a/.github/workflows/deployment-az-public.yml +++ b/.github/workflows/deployment-az-public.yml @@ -18,5 +18,4 @@ jobs: SSH_KEY: ${{ secrets.ANSIBLE_PRIVATE_SSH_KEY }} CONTAINER_REGISTRY_USERNAME: ${{ secrets.AZURE_CR_USERNAME }} CONTAINER_REGISTRY_PASSWORD: ${{ secrets.AZURE_CR_PASSWORD }} - GCP_CREDENTIALS: ${{ secrets.GCE_SA_KEY }} INFRA_PAT: ${{ secrets.INFRA_PAT }} diff --git a/.github/workflows/deployment-az.yml b/.github/workflows/deployment-az.yml index 906a06b11b..f2cb12a9bd 100644 --- a/.github/workflows/deployment-az.yml +++ b/.github/workflows/deployment-az.yml @@ -26,8 +26,6 @@ on: required: true SSH_KEY: required: true - GCP_CREDENTIALS: - required: true INFRA_PAT: required: true diff --git a/.github/workflows/deployment-gcp.yml b/.github/workflows/deployment-gcp.yml index 3739638461..a5ab0c6ce9 100644 --- a/.github/workflows/deployment-gcp.yml +++ b/.github/workflows/deployment-gcp.yml @@ -156,4 +156,4 @@ jobs: --extra-vars github_run_id=${{ github.run_id }} --extra-vars postgres_host=${{ steps.database-host.outputs.ip_address }} --user ansible - --verbose + -vvvv diff --git a/appserver/Dockerfile b/appserver/Dockerfile index 1cde0b3fd4..d2e572feb9 100644 --- a/appserver/Dockerfile +++ b/appserver/Dockerfile @@ -33,6 +33,7 @@ COPY --chown=1000:1000 . . ENV PYTHONUNBUFFERED 1 ENV PYTHONPATH $N4J_HOME +# Set Python3 as the default when running "python" RUN echo 'alias python=python3' >> ~/.bashrc && source ~/.bashrc USER $N4J_USER diff --git a/appserver/bin/startup.sh b/appserver/bin/startup.sh index 765323c874..87179382d4 100755 --- a/appserver/bin/startup.sh +++ b/appserver/bin/startup.sh @@ -9,7 +9,7 @@ if [ "${FLASK_ENV}" = "development" ] && [ "${FLASK_APP_CONFIG}" = "Development" # wait for postgres timeout 300 ${__dir__}/wait-for-postgres # wait for neo4j - timeout 300 ${__dir__}/wait-for-neo4j + timeout 300 ${__dir__}/wait-for-arango #wait for elastic timeout 300 ${__dir__}/wait-for-elastic # setup db diff --git a/appserver/bin/wait-for-arango b/appserver/bin/wait-for-arango new file mode 100755 index 0000000000..3084fe3a03 --- /dev/null +++ b/appserver/bin/wait-for-arango @@ -0,0 +1,16 @@ +#!/bin/bash + +echo "Waiting for Arango" + +ARANGO_STATUS="000" + +until [ "$ARANGO_STATUS" = "200" ] +do + ARANGO_STATUS=`curl -s -o /dev/null -I -w "%{http_code}" --basic --user "${ARANGO_USERNAME}:${ARANGO_PASSWORD}" -X GET ${ARANGO_HOST}/_api/endpoint` + echo "Status of Arango: $ARANGO_STATUS" + sleep 2 +done + +# Run command | https://docs.docker.com/compose/startup-order/ +>&2 echo "Arango started - executing command" +exec $@ \ No newline at end of file diff --git a/appserver/config.py b/appserver/config.py index a4e4259440..3f01a758f0 100644 --- a/appserver/config.py +++ b/appserver/config.py @@ -18,10 +18,10 @@ class Base: APP_VERSION = os.environ.get('APP_VERSION', 'undefined') LOGGING_LEVEL = os.environ.get('LOGGING_LEVEL', logging.INFO) - JWKS_URL = os.environ.get('JWKS_URL', None) - JWT_SECRET = os.environ.get('JWT_SECRET', 'secrets') - JWT_AUDIENCE = os.environ.get('JWT_AUDIENCE', None) - JWT_ALGORITHM = os.environ.get('JWT_ALGORITHM', 'HS256') + JWKS_URL = os.environ.get('JWKS_URL', None) or None + JWT_SECRET = os.environ.get('JWT_SECRET', 'secrets') or 'secrets' + JWT_AUDIENCE = os.environ.get('JWT_AUDIENCE', None) or None + JWT_ALGORITHM = os.environ.get('JWT_ALGORITHM', 'HS256') or 'HS256' POSTGRES_HOST = os.environ.get('POSTGRES_HOST') POSTGRES_PORT = os.environ.get('POSTGRES_PORT') diff --git a/appserver/migrations/utils.py b/appserver/migrations/utils.py index 1627469c75..19661d550d 100644 --- a/appserver/migrations/utils.py +++ b/appserver/migrations/utils.py @@ -1,9 +1,14 @@ +from arango.client import ArangoClient import multiprocessing as mp +from typing import Dict, List + +from neo4japp.database import get_or_create_arango_client # flake8: noqa: OIG001 # It is legacy file with imports from appserver which we decided to not fix from neo4japp.models import Files -from neo4japp.services.annotations.initializer import get_annotation_graph_service from neo4japp.services.annotations.constants import EntityType +from neo4japp.services.annotations.utils.graph_queries import get_docs_by_ids_query +from neo4japp.services.arangodb import execute_arango_query, get_db def window_chunk(q, windowsize=100): @@ -20,6 +25,34 @@ def window_chunk(q, windowsize=100): yield chunk +# NOTE DEPRECATED: just used in old migration +def _get_mesh_by_ids_query(): + return """ + FOR doc IN mesh + FILTER 'TopicalDescriptor' IN doc.labels + FILTER doc.eid IN @ids + RETURN {'mesh_id': doc.eid, 'mesh_name': doc.name} + """ + + +def _get_mesh_from_mesh_ids( + arango_client: ArangoClient, mesh_ids: List[str] +) -> Dict[str, str]: + result = execute_arango_query( + db=get_db(arango_client), query=_get_mesh_by_ids_query(), ids=mesh_ids + ) + return {row['mesh_id']: row['mesh_name'] for row in result} + + +def _get_nodes_from_node_ids( + arango_client: ArangoClient, entity_type: str, node_ids: List[str] +) -> Dict[str, str]: + result = execute_arango_query( + db=get_db(arango_client), query=get_docs_by_ids_query(entity_type), ids=node_ids + ) + return {row['entity_id']: row['entity_name'] for row in result} + + def get_primary_names(annotations): """Copied from AnnotationService.add_primary_name""" chemical_ids = set() @@ -30,7 +63,7 @@ def get_primary_names(annotations): organism_ids = set() mesh_ids = set() - neo4j = get_annotation_graph_service() + arango_client = get_or_create_arango_client() updated_annotations = [] # Note: We need to split the ids by colon because @@ -77,25 +110,25 @@ def get_primary_names(annotations): organism_ids.add(meta_id) try: - chemical_names = neo4j.get_nodes_from_node_ids( - EntityType.CHEMICAL.value, list(chemical_ids) - ) # noqa - compound_names = neo4j.get_nodes_from_node_ids( - EntityType.COMPOUND.value, list(compound_ids) - ) # noqa - disease_names = neo4j.get_nodes_from_node_ids( - EntityType.DISEASE.value, list(disease_ids) + chemical_names = _get_nodes_from_node_ids( + arango_client, EntityType.CHEMICAL.value, list(chemical_ids) + ) + compound_names = _get_nodes_from_node_ids( + arango_client, EntityType.COMPOUND.value, list(compound_ids) + ) + disease_names = _get_nodes_from_node_ids( + arango_client, EntityType.DISEASE.value, list(disease_ids) + ) + gene_names = _get_nodes_from_node_ids( + arango_client, EntityType.GENE.value, list(gene_ids) ) - gene_names = neo4j.get_nodes_from_node_ids( - EntityType.GENE.value, list(gene_ids) + protein_names = _get_nodes_from_node_ids( + arango_client, EntityType.PROTEIN.value, list(protein_ids) ) - protein_names = neo4j.get_nodes_from_node_ids( - EntityType.PROTEIN.value, list(protein_ids) + organism_names = _get_nodes_from_node_ids( + arango_client, EntityType.SPECIES.value, list(organism_ids) ) - organism_names = neo4j.get_nodes_from_node_ids( - EntityType.SPECIES.value, list(organism_ids) - ) # noqa - mesh_names = neo4j.get_mesh_from_mesh_ids(list(mesh_ids)) + mesh_names = _get_mesh_from_mesh_ids(arango_client, list(mesh_ids)) except Exception: raise diff --git a/appserver/neo4japp/blueprints/annotations.py b/appserver/neo4japp/blueprints/annotations.py index ded0f04cfb..059fdd37ff 100644 --- a/appserver/neo4japp/blueprints/annotations.py +++ b/appserver/neo4japp/blueprints/annotations.py @@ -73,7 +73,6 @@ from ..services.annotations.initializer import ( get_annotation_service, get_annotation_db_service, - get_annotation_graph_service, get_annotation_tokenizer, get_bioc_document_service, get_enrichment_annotation_service, @@ -91,6 +90,7 @@ get_global_inclusions_query, get_global_inclusions_count_query, ) +from ..services.arangodb import convert_datetime, execute_arango_query, get_db from ..services.enrichment.data_transfer_objects import EnrichmentCellTextMapping from ..services.filesystem import Filesystem from ..utils.globals import get_current_user @@ -656,7 +656,6 @@ def _annotate( pipeline = Pipeline( { 'adbs': get_annotation_db_service, - 'ags': get_annotation_graph_service, 'aers': get_recognition_service, 'tkner': get_annotation_tokenizer, 'as': get_annotation_service, @@ -700,7 +699,6 @@ def _annotate_enrichment_table( pipeline = Pipeline( { 'adbs': get_annotation_db_service, - 'ags': get_annotation_graph_service, 'aers': get_recognition_service, 'tkner': get_annotation_tokenizer, 'as': get_enrichment_annotation_service, @@ -881,8 +879,11 @@ class GlobalAnnotationExportInclusions(MethodView): def get(self): yield g.current_user - graph = get_annotation_graph_service() - inclusions = graph.exec_read_query(get_global_inclusions_query()) + arango_client = get_or_create_arango_client() + inclusions = execute_arango_query( + db=get_db(arango_client), + query=get_global_inclusions_query(), + ) file_uuids = {inclusion['file_reference'] for inclusion in inclusions} file_data_query = db.session.query( @@ -891,7 +892,7 @@ def get(self): file_uuids_map = {d.file_uuid: d.file_deleted_by for d in file_data_query} - def get_inclusion_for_review(inclusion, file_uuids_map, graph): + def get_inclusion_for_review(inclusion, file_uuids_map): user = AppUser.query.filter_by( id=file_uuids_map[inclusion['file_reference']] ).one_or_none() @@ -905,9 +906,7 @@ def get_inclusion_for_review(inclusion, file_uuids_map, graph): 'file_uuid': inclusion['file_reference'], 'file_deleted': deleter, 'type': ManualAnnotationType.INCLUSION.value, - 'creation_date': str( - graph.convert_datetime(inclusion['creation_date']) - ), + 'creation_date': convert_datetime(inclusion['creation_date']), 'text': inclusion['synonym'], 'case_insensitive': True, 'entity_type': inclusion['entity_type'], @@ -917,7 +916,7 @@ def get_inclusion_for_review(inclusion, file_uuids_map, graph): } data = [ - get_inclusion_for_review(inclusion, file_uuids_map, graph) + get_inclusion_for_review(inclusion, file_uuids_map) for inclusion in inclusions if inclusion['file_reference'] in file_uuids_map ] @@ -1036,10 +1035,12 @@ def get(self, params, global_type): ] query_total = exclusions.total else: - graph = get_annotation_graph_service() - global_inclusions = graph.exec_read_query_with_params( - get_global_inclusions_paginated_query(), - {'skip': 0 if page == 1 else (page - 1) * limit, 'limit': limit}, + arango_client = get_or_create_arango_client() + global_inclusions = execute_arango_query( + db=get_db(arango_client), + query=get_global_inclusions_paginated_query(), + skip=0 if page == 1 else (page - 1) * limit, + limit=limit, ) file_uuids = { @@ -1065,7 +1066,7 @@ def get(self, params, global_type): if file_uuids_map.get(i['file_reference'], True) else False, 'type': ManualAnnotationType.INCLUSION.value, - 'creation_date': graph.convert_datetime(i['creation_date']), + 'creation_date': convert_datetime(i['creation_date']), 'text': i['synonym'], 'case_insensitive': True, 'entity_type': i['entity_type'], @@ -1075,9 +1076,11 @@ def get(self, params, global_type): } for i in global_inclusions ] - query_total = graph.exec_read_query(get_global_inclusions_count_query())[0][ - 'total' - ] + + query_total = execute_arango_query( + db=get_db(arango_client), + query=get_global_inclusions_count_query(), + )[0]['total'] results = {'total': query_total, 'results': data} yield jsonify(GlobalAnnotationListSchema().dump(results)) diff --git a/appserver/neo4japp/blueprints/enrichment_table.py b/appserver/neo4japp/blueprints/enrichment_table.py index 5736fe8ac9..502f330f92 100644 --- a/appserver/neo4japp/blueprints/enrichment_table.py +++ b/appserver/neo4japp/blueprints/enrichment_table.py @@ -1,8 +1,12 @@ from http import HTTPStatus from flask import Blueprint, request, jsonify +import numpy as np +from pandas import DataFrame -from neo4japp.database import get_enrichment_table_service +from neo4japp.constants import KGDomain +from neo4japp.database import get_or_create_arango_client +from neo4japp.services.enrichment.enrichment_table import get_genes, match_ncbi_genes bp = Blueprint('enrichment-table-api', __name__, url_prefix='/enrichment-table') @@ -17,10 +21,37 @@ def match_ncbi_nodes(): nodes = [] if organism is not None and gene_names is not None: - enrichment_table = get_enrichment_table_service() + arango_client = get_or_create_arango_client() # list(dict...) is to drop duplicates, but want to keep order - nodes = enrichment_table.match_ncbi_genes( - list(dict.fromkeys(gene_names)), organism + nodes = match_ncbi_genes( + arango_client, list(dict.fromkeys(gene_names)), organism ) + return jsonify({'result': nodes}), 200 + + +@bp.route('/get-ncbi-nodes/enrichment-domains', methods=['POST']) +def get_ncbi_enrichment_domains(): + """Find all domains matched to given node id, then return dictionary with all domains as + result. All domains should have matching indices e.g. regulon[1] should be data from + matching same node as uniprot[1]. + """ + # TODO: Validate incoming data using webargs + Marshmallow + data = request.get_json() + doc_ids = data.get('docIds') + tax_id = data.get('taxID') + domains = data.get('domains') + + if doc_ids is not None and tax_id is not None: + arango_client = get_or_create_arango_client() + domain_nodes = { + domain.lower(): get_genes(arango_client, KGDomain(domain), doc_ids, tax_id) + for domain in domains + } + df = DataFrame(domain_nodes).replace({np.nan: None}).transpose() + # Redundant but just following old implementation + nodes = df.append(df.columns.to_series(name='doc_id')).to_dict() + else: + nodes = {} + return jsonify({'result': nodes}), HTTPStatus.OK diff --git a/appserver/neo4japp/blueprints/entity_resources.py b/appserver/neo4japp/blueprints/entity_resources.py index 3bc00225dc..34ca3750b2 100644 --- a/appserver/neo4japp/blueprints/entity_resources.py +++ b/appserver/neo4japp/blueprints/entity_resources.py @@ -1,6 +1,7 @@ from flask import Blueprint, request -from neo4japp.models import AnnotationStyle, DomainURLsMap +from neo4japp.constants import DOMAIN_URLS_MAP +from neo4japp.models import AnnotationStyle bp = Blueprint('entity-resources', __name__, url_prefix='/entity-resources') @@ -31,8 +32,8 @@ def get_uri(): """ payload = request.json - uri = DomainURLsMap.query.filter_by(domain=payload['domain'])[0] - return {'uri': uri.base_URL.format(payload['term'])} + uri = DOMAIN_URLS_MAP[payload['domain']] + return {'uri': uri.format(payload['term'])} @bp.route('/uri/batch', methods=['POST']) @@ -60,7 +61,7 @@ def get_uri_batch(): uris = [] payload = request.json for entry in payload['batch']: - uri = DomainURLsMap.query.filter_by(domain=entry['domain'])[0] - uris.append({'uri': uri.base_URL.format(entry['term'])}) + uri = DOMAIN_URLS_MAP[entry['domain']] + uris.append({'uri': uri.format(entry['term'])}) return {'batch': uris} diff --git a/appserver/neo4japp/blueprints/kg.py b/appserver/neo4japp/blueprints/kg.py deleted file mode 100644 index 5d549e5074..0000000000 --- a/appserver/neo4japp/blueprints/kg.py +++ /dev/null @@ -1,51 +0,0 @@ -from http import HTTPStatus - -from flask import Blueprint, request, jsonify -from pandas import DataFrame - -from neo4japp.constants import KGDomain -from neo4japp.database import get_kg_service -import numpy as np - -bp = Blueprint('kg-api', __name__, url_prefix='/knowledge-graph') - - -@bp.route('/get-ncbi-nodes/enrichment-domains', methods=['POST']) -def get_ncbi_enrichment_domains(): - """Find all domains matched to given node id, then return dictionary with all domains as - result. All domains should have matching indices e.g. regulon[1] should be data from - matching same node as uniprot[1]. - """ - # TODO: Validate incoming data using webargs + Marshmallow - data = request.get_json() - node_ids = data.get('nodeIds') - tax_id = data.get('taxID') - domains = data.get('domains') - - if node_ids is not None and tax_id is not None: - kg = get_kg_service() - domain_nodes = { - domain.lower(): kg.get_genes(KGDomain(domain), node_ids, tax_id) - for domain in domains - } - df = DataFrame(domain_nodes).replace({np.nan: None}).transpose() - # Redundant but just following old implementation - nodes = df.append(df.columns.to_series(name='node_id')).to_dict() - else: - nodes = {} - - return jsonify({'result': nodes}), HTTPStatus.OK - - -@bp.route('/shortest-path-query/', methods=['GET']) -def get_shortest_path_query_result(query_id): - kg = get_kg_service() - result = kg.get_shortest_path_data(query_id) - return jsonify({'result': result}), HTTPStatus.OK - - -@bp.route('/shortest-path-query-list', methods=['GET']) -def get_shortest_path_query_list(): - kg = get_kg_service() - result = kg.get_shortest_path_query_list() - return jsonify({'result': result}), HTTPStatus.OK diff --git a/appserver/neo4japp/blueprints/playground.py b/appserver/neo4japp/blueprints/playground.py index ce0c5138c6..3bafcd7514 100644 --- a/appserver/neo4japp/blueprints/playground.py +++ b/appserver/neo4japp/blueprints/playground.py @@ -5,8 +5,8 @@ from neo4japp.schemas.playground.chat_completions import ChatCompletionsRequestSchema from neo4japp.schemas.playground.completions import CompletionsRequestSchema from neo4japp.services.chat_gpt import ChatGPT -from neo4japp.util import stream_to_json_lines from neo4japp.utils.globals import config, get_current_username +from neo4japp.utils.string import stream_to_json_lines bp = Blueprint('playground', __name__, url_prefix='/playground') diff --git a/appserver/neo4japp/blueprints/search.py b/appserver/neo4japp/blueprints/search.py index 5ba3c9ae26..cb98c4b156 100644 --- a/appserver/neo4japp/blueprints/search.py +++ b/appserver/neo4japp/blueprints/search.py @@ -9,11 +9,12 @@ from neo4japp.blueprints.filesystem import FilesystemBaseView from neo4japp.blueprints.projects import ProjectBaseView from neo4japp.constants import FRAGMENT_SIZE, LogEventType +from neo4japp.data_transfer_objects import FTSResult from neo4japp.data_transfer_objects.common import ResultQuery from neo4japp.database import ( - get_search_service_dao, get_elastic_service, get_file_type_service, + get_or_create_arango_client, ) from neo4japp.exceptions import ServerException from neo4japp.models import Files, Projects @@ -27,6 +28,13 @@ VizSearchSchema, ) from neo4japp.services.file_types.providers import DirectoryTypeProvider +from neo4japp.services.search import ( + get_organisms, + get_organism_with_tax_id, + get_synonyms, + get_synonyms_count, + visualizer_search, +) from neo4japp.services.filesystem import Filesystem from neo4japp.utils.globals import config from neo4japp.utils.jsonify import jsonify_with_class @@ -36,10 +44,9 @@ bp = Blueprint('search', __name__, url_prefix='/search') -@bp.route('/viz-search', methods=['POST']) +@bp.route('/visualizer', methods=['POST']) @use_kwargs(VizSearchSchema) -def visualizer_search(query, page, limit, domains, entities, organism): - search_dao = get_search_service_dao() +def viz_search(query, page, limit, domains, entities, organism): current_app.logger.info( f'Term: {query}, Organism: {organism}, Entities: {entities}, Domains: {domains}', extra=UserEventLog( @@ -48,7 +55,16 @@ def visualizer_search(query, page, limit, domains, entities, organism): ).to_dict(), ) - results = search_dao.visualizer_search( + if not query: + return jsonify( + { + 'result': FTSResult(query, [], 0, page, limit).to_dict(), + } + ) + + arango_client = get_or_create_arango_client() + results = visualizer_search( + arango_client, term=query, organism=organism, page=page, @@ -58,7 +74,9 @@ def visualizer_search(query, page, limit, domains, entities, organism): ) return jsonify( { - 'result': results.to_dict(), + 'result': FTSResult( + query, results['rows'], results['count'], page, limit + ).to_dict(), } ) @@ -331,14 +349,15 @@ def get(self, params, pagination: Pagination): page = pagination.page limit = pagination.limit - offset = (page - 1) * limit + skip = (page - 1) * limit + + arango_client = get_or_create_arango_client() try: - search_dao = get_search_service_dao() - results = search_dao.get_synonyms( - search_term, organisms, types, offset, limit + results = get_synonyms( + arango_client, search_term, organisms, types, skip, limit ) - count = search_dao.get_synonyms_count(search_term, organisms, types) + count = get_synonyms_count(arango_client, search_term, organisms, types) except Exception as e: current_app.logger.error( f'Failed to get synonym data for term: {search_term}', @@ -363,14 +382,14 @@ def get(self, params, pagination: Pagination): @bp.route('/organism/', methods=['GET']) @jsonify_with_class() def get_organism(organism_tax_id: str): - search_dao = get_search_service_dao() - result = search_dao.get_organism_with_tax_id(organism_tax_id) - return SuccessResponse(result=result, status_code=200) + arango_client = get_or_create_arango_client() + return SuccessResponse( + result=get_organism_with_tax_id(arango_client, organism_tax_id), status_code=200 + ) @bp.route('/organisms', methods=['POST']) @use_kwargs(OrganismSearchSchema) -def get_organisms(query, limit): - search_dao = get_search_service_dao() - results = search_dao.get_organisms(query, limit) - return jsonify({'result': results}) +def search_organisms(query, limit): + arango_client = get_or_create_arango_client() + return jsonify({'result': get_organisms(arango_client, query, limit)}) diff --git a/appserver/neo4japp/blueprints/visualizer.py b/appserver/neo4japp/blueprints/visualizer.py index 7b42bfe766..6d7559567a 100644 --- a/appserver/neo4japp/blueprints/visualizer.py +++ b/appserver/neo4japp/blueprints/visualizer.py @@ -1,61 +1,59 @@ -from http import HTTPStatus - -from flask import Blueprint, request, jsonify +from flask import Blueprint, jsonify +from flask.views import MethodView from flask_apispec import use_kwargs +from http import HTTPStatus from neo4japp.blueprints.auth import login_optional from neo4japp.constants import ANNOTATION_STYLES_DICT +from neo4japp.database import get_or_create_arango_client from neo4japp.data_transfer_objects.visualization import ( ExpandNodeRequest, GetSnippetsForEdgeRequest, GetSnippetsForClusterRequest, ReferenceTableDataRequest, ) -from neo4japp.database import get_visualizer_service from neo4japp.exceptions import InvalidArgument from neo4japp.request_schemas.visualizer import ( GetSnippetsForNodePairRequest, AssociatedTypeSnippetCountRequest, ) +from neo4japp.services.visualizer import ( + expand_node_as_clusters, + get_associated_type_snippet_count, + get_document_for_visualizer, + get_reference_table_data, + get_snippets_for_edge, + get_snippets_for_cluster, + get_snippets_for_node_pair, +) from neo4japp.schemas.common import SuccessResponse from neo4japp.utils.jsonify import jsonify_with_class +from neo4japp.utils.string import camel_to_snake_dict bp = Blueprint('visualizer-api', __name__, url_prefix='/visualizer') -@bp.route('/batch', methods=['GET']) +@bp.route('/get-annotation-legend', methods=['GET']) @jsonify_with_class() -def get_batch(): - """Uses a home-brew query language - to get a batch of nodes and their - relationship - TODO: Document query language - """ - visualizer_service = get_visualizer_service() - data_query = request.args.get('data', '') - try: - decoded_query = bytearray.fromhex(data_query).decode() - except ValueError: - return SuccessResponse(result='No results found', status_code=HTTPStatus.OK) - result = visualizer_service.query_batch(decoded_query) - # This response might contain warnings to avoid breaking changes the status code remains 200 - return SuccessResponse(result=result, status_code=HTTPStatus.OK) +def get_annotation_legend(): + return SuccessResponse(result=ANNOTATION_STYLES_DICT, status_code=200) @bp.route('/expand', methods=['POST']) @jsonify_with_class(ExpandNodeRequest) -def expand_graph_node(req: ExpandNodeRequest): - visualizer = get_visualizer_service() - node = visualizer.expand_graph(req.node_id, req.filter_labels) - return SuccessResponse(result=node, status_code=HTTPStatus.OK) +def expand_graph_node_as_clusters(req: ExpandNodeRequest): + arango_client = get_or_create_arango_client() + clusters = expand_node_as_clusters(arango_client, req.node_id, req.filter_labels) + return SuccessResponse(result=clusters, status_code=200) -@bp.route('/get-reference-table-data', methods=['POST']) +@bp.route('/get-reference-table', methods=['POST']) @jsonify_with_class(ReferenceTableDataRequest) -def get_reference_table_data(req: ReferenceTableDataRequest): - visualizer = get_visualizer_service() - reference_table_data = visualizer.get_reference_table_data( - req.node_edge_pairs, +def get_ref_table(req: ReferenceTableDataRequest): + arango_client = get_or_create_arango_client() + reference_table_data = get_reference_table_data( + arango_client, + [camel_to_snake_dict(pair.to_dict()) for pair in req.node_edge_pairs], ) return SuccessResponse(reference_table_data, status_code=HTTPStatus.OK) @@ -63,8 +61,6 @@ def get_reference_table_data(req: ReferenceTableDataRequest): @bp.route('/get-snippets-for-edge', methods=['POST']) @jsonify_with_class(GetSnippetsForEdgeRequest) def get_edge_snippet_data(req: GetSnippetsForEdgeRequest): - visualizer = get_visualizer_service() - # TODO: In the future would be better to refactor this request to use Marshmallow and handle # the validation in the schema, but in the interest of time favoring this approach for now. if not (0 <= req.limit and req.limit <= 1000): @@ -74,19 +70,14 @@ def get_edge_snippet_data(req: GetSnippetsForEdgeRequest): code=HTTPStatus.BAD_REQUEST, ) - edge_snippets_result = visualizer.get_snippets_for_edge( - page=req.page, - limit=req.limit, - edge=req.edge, - ) - return SuccessResponse(edge_snippets_result, status_code=HTTPStatus.OK) + arango_client = get_or_create_arango_client() + result = get_snippets_for_edge(arango_client, req.edge, req.page, req.limit) + return SuccessResponse(result, status_code=200) @bp.route('/get-snippets-for-cluster', methods=['POST']) @jsonify_with_class(GetSnippetsForClusterRequest) def get_cluster_snippet_data(req: GetSnippetsForClusterRequest): - visualizer = get_visualizer_service() - # TODO: In the future would be better to refactor this request to use Marshmallow and handle # the validation in the schema, but in the interest of time favoring this approach for now. if not (0 <= req.limit and req.limit <= 1000): @@ -96,44 +87,45 @@ def get_cluster_snippet_data(req: GetSnippetsForClusterRequest): code=HTTPStatus.BAD_REQUEST, ) - cluster_snippets_result = visualizer.get_snippets_for_cluster( - page=req.page, - limit=req.limit, - edges=req.edges, - ) - return SuccessResponse(cluster_snippets_result, status_code=HTTPStatus.OK) - - -@bp.route('/get-annotation-legend', methods=['GET']) -@login_optional -@jsonify_with_class() -def get_annotation_legend(): - return SuccessResponse(result=ANNOTATION_STYLES_DICT, status_code=HTTPStatus.OK) + arango_client = get_or_create_arango_client() + result = get_snippets_for_cluster(arango_client, req.edges, req.page, req.limit) + return SuccessResponse(result, status_code=HTTPStatus.OK) @bp.route('/get-associated-type-snippet-count', methods=['POST']) @use_kwargs(AssociatedTypeSnippetCountRequest) -def get_associated_type_snippet_count(source_node, associated_nodes): - visualizer = get_visualizer_service() - - associated_types_result = visualizer.get_associated_type_snippet_count( - source_node, - associated_nodes, +def get_assoc_type_snippet_count(source_node, associated_nodes): + arango_client = get_or_create_arango_client() + result = get_associated_type_snippet_count( + arango_client, source_node, associated_nodes ) return jsonify( { - 'result': associated_types_result.to_dict(), + 'result': result.to_dict(), } ) @bp.route('/get-snippets-for-node-pair', methods=['POST']) @use_kwargs(GetSnippetsForNodePairRequest) -def get_snippets_for_node_pair(node_1_id, node_2_id, page, limit): - visualizer = get_visualizer_service() - - node_pair_snippet_result = visualizer.get_snippets_for_node_pair( - node_1_id, node_2_id, page, limit +def get_snippets_for_pair(node_1_id, node_2_id, page, limit): + arango_client = get_or_create_arango_client() + result = get_snippets_for_node_pair( + arango_client, node_1_id, node_2_id, page, limit ) - return jsonify({'result': node_pair_snippet_result.to_dict()}) + return jsonify({'result': result.to_dict()}) + + +class GetDocumentView(MethodView): + def get(self, collection: str, key: str): + arango_client = get_or_create_arango_client() + doc_id = f'{collection}/{key}' + result = get_document_for_visualizer(arango_client, doc_id) + return jsonify({'nodes': [result], 'edges': []}) + + +bp.add_url_rule( + '/document//', + view_func=GetDocumentView.as_view('fetch_document'), +) diff --git a/appserver/neo4japp/constants.py b/appserver/neo4japp/constants.py index 58152fa699..1952651df5 100644 --- a/appserver/neo4japp/constants.py +++ b/appserver/neo4japp/constants.py @@ -101,17 +101,70 @@ class LogEventType(Enum): UNHANDLED = 'unhandled_exception' -DOMAIN_LABELS = [ - 'db_CHEBI', - 'db_GO', - 'db_Literature', - 'db_MESH', - 'db_NCBI', - 'db_UniProt', -] +DATA_SOURCES = { + 'NCBI Gene': 'NCBI', + 'NCBI Taxonomy': 'NCBI', + 'ChEBI': 'CHEBI', + 'GO': 'GO', + 'MeSH': 'MESH', + 'UniProt': 'UniProt', +} BIOCYC_ORG_ID_DICT = {'9606': 'HUMAN', '511145': 'ECOLI', '559292': 'YEAST'} +# Note that this data used to be stored in Postgres +DOMAIN_URLS_MAP = { + 'CHEBI': 'https://www.ebi.ac.uk/chebi/searchId.do?chebiId={}', + 'MESH': 'https://www.ncbi.nlm.nih.gov/mesh/?term={}', + 'Literature': 'https://pubmed.ncbi.nlm.nih.gov/{}', + 'NCBI_Gene': 'https://www.ncbi.nlm.nih.gov/gene/{}', + 'NCBI_Taxonomy': 'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id={}', + 'asap': 'http://identifiers.org/asap/{}', + 'bigg.compartment': 'http://identifiers.org/bigg.compartment/{}', + 'bigg.metabolite': 'http://identifiers.org/bigg.metabolite/{}', + 'bigg.reaction': 'http://identifiers.org/bigg.reaction/{}', + 'ccds': 'http://identifiers.org/ccds/{}', + 'cco': 'http://identifiers.org/cco/{}', + 'chebi': 'http://identifiers.org/chebi/CHEBI:{}', + 'ecogene': 'http://identifiers.org/ecogene/{}', + 'envipath': 'http://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/{}', + 'go': 'http://identifiers.org/go/{}', + 'goa': 'http://identifiers.org/goa/{}', + 'hgnc': 'http://identifiers.org/hgnc/{}', + 'hmdb': 'http://identifiers.org/hmdb/{}', + 'hprd': 'http://identifiers.org/hprd/{}', + 'hssp': 'http://identifiers.org/hssp/{}', + 'interpro': 'http://identifiers.org/interpro/{}', + 'kegg.compound': 'http://identifiers.org/kegg.compound/{}', + 'kegg.drug': 'http://identifiers.org/kegg.drug/{}', + 'kegg.reaction': 'http://identifiers.org/kegg.reaction/{}', + 'lipidmaps': 'http://identifiers.org/lipidmaps/{}', + 'mgd': 'http://identifiers.org/mgd/{}', + 'mnx.chemical': 'http://identifiers.org/metanetx.chemical/{}', + 'mnx.equation': 'http://identifiers.org/metanetx.reaction/{}', + 'myco.tuber': 'http://identifiers.org/myco.tuber/{}', + 'metacyc.compound': 'http://identifiers.org/metacyc.compound/{}', + 'metacyc.reaction': 'http://identifiers.org/metacyc.reaction/{}', + 'ncbigene': 'http://identifiers.org/ncbigene/{}', + 'ncbigi': 'http://identifiers.org/ncbigi/gi:{}', + 'omim': 'http://identifiers.org/omim/{}', + 'pdb': 'http://identifiers.org/pdb/{}', + 'pubchem.compound': 'http://identifiers.org/pubchem.compound/{}', + 'reactome': 'http://www.reactome.org/content/detail/R-ALL-{}', + 'rhea': 'http://identifiers.org/rhea/{}', + 'sabiork': 'http://identifiers.org/sabiork.compound/{}', + 'sabiork.reaction': 'http://identifiers.org/sabiork.reaction/{}', + 'seed': 'http://identifiers.org/seed.reaction/{}', + 'seed.compound': 'http://identifiers.org/seed.compound/{}', + 'sgd': 'http://identifiers.org/sgd/{}', + 'slm': 'http://www.swisslipids.org/#/entity/SLM:{}', + 'subtilist': 'http://identifiers.org/subtilist/{}', + 'umbbd.compound': 'http://identifiers.org/umbbd.compound/{}', + 'unipathway.compound': 'http://identifiers.org/unipathway.compound/{}', + 'unipathway.reaction': 'http://identifiers.org/unipathway.reaction/{}', + 'uniprot': 'http://identifiers.org/uniprot/{}', + 'ec': 'http://identifiers.org/ec-code/{}: ', +} # End BioCyc, Regulon, Ecocyc Dataset diff --git a/appserver/neo4japp/data_transfer_objects/visualization.py b/appserver/neo4japp/data_transfer_objects/visualization.py index c1885cbf73..9b10b6c4a5 100644 --- a/appserver/neo4japp/data_transfer_objects/visualization.py +++ b/appserver/neo4japp/data_transfer_objects/visualization.py @@ -1,5 +1,5 @@ from enum import Enum -from typing import List, Optional +from typing import Dict, List, Optional import attr @@ -21,7 +21,7 @@ class Direction(Enum): @attr.s(frozen=True) class VisNode(CamelDictMixin): - id: int = attr.ib() + id: str = attr.ib() label: str = attr.ib() data: dict = attr.ib() sub_labels: List[str] = attr.ib() @@ -34,16 +34,16 @@ class VisNode(CamelDictMixin): @attr.s(frozen=True) class DuplicateVisNode(VisNode): id: str = attr.ib() # type: ignore - duplicate_of: int = attr.ib() + duplicate_of: str = attr.ib() @attr.s(frozen=True) class VisEdge(CamelDictMixin): - id: int = attr.ib() + id: str = attr.ib() label: str = attr.ib() data: dict = attr.ib() - to: int = attr.ib() - from_: int = attr.ib() + to: str = attr.ib() + from_: str = attr.ib() to_label: str = attr.ib() from_label: str = attr.ib() arrows: Optional[str] = attr.ib() @@ -78,9 +78,9 @@ def to_dict_formatter(self, vis_edge_output_dict: dict): @attr.s(frozen=True) class DuplicateVisEdge(VisEdge): id: str = attr.ib() # type: ignore - duplicate_of: int = attr.ib() - original_from: int = attr.ib() - original_to: int = attr.ib() + duplicate_of: str = attr.ib() + original_from: str = attr.ib() + original_to: str = attr.ib() @attr.s(frozen=True) @@ -93,8 +93,8 @@ class NodeData(CamelDictMixin): @attr.s(frozen=True) class EdgeData(CamelDictMixin): - original_from: int = attr.ib() - original_to: int = attr.ib() + original_from: str = attr.ib() + original_to: str = attr.ib() label: str = attr.ib() node: NodeData = attr.ib() @@ -119,8 +119,8 @@ class Snippet(CamelDictMixin): class EdgeConnectionData(CamelDictMixin): from_label: str = attr.ib() to_label: str = attr.ib() - from_: int = attr.ib() - to: int = attr.ib() + from_: str = attr.ib() + to: str = attr.ib() label: str = attr.ib() # 'from_' will be formatted as 'from' because it is coming from the client. @@ -135,10 +135,10 @@ def build_from_dict_formatter(self, edge_data_input_dict: dict): class DuplicateEdgeConnectionData(CamelDictMixin): from_label: str = attr.ib() to_label: str = attr.ib() - from_: int = attr.ib() - to: int = attr.ib() - original_from: int = attr.ib() - original_to: int = attr.ib() + from_: str = attr.ib() + to: str = attr.ib() + original_from: str = attr.ib() + original_to: str = attr.ib() label: str = attr.ib() def build_from_dict_formatter(self, edge_data_input_dict: dict): @@ -152,13 +152,20 @@ def build_from_dict_formatter(self, edge_data_input_dict: dict): @attr.s(frozen=True) class ExpandNodeRequest(CamelDictMixin): - node_id: int = attr.ib() + node_id: str = attr.ib() filter_labels: List[str] = attr.ib() @attr.s(frozen=True) class ReferenceTableDataRequest(CamelDictMixin): node_edge_pairs: List[ReferenceTablePair] = attr.ib() + description: Optional[str] = attr.ib() + direction: Optional[str] = attr.ib() + + +@attr.s(frozen=True) +class BulkReferenceTableDataRequest(CamelDictMixin): + associations: List[ReferenceTableDataRequest] = attr.ib() @attr.s(frozen=True) @@ -182,8 +189,8 @@ class GetSnippetsForClusterRequest(CamelDictMixin): @attr.s(frozen=True) class GetSnippetsFromEdgeResult(CamelDictMixin): - from_node_id: int = attr.ib() - to_node_id: int = attr.ib() + from_node_id: str = attr.ib() + to_node_id: str = attr.ib() association: str = attr.ib() snippets: List[Snippet] = attr.ib() @@ -225,13 +232,20 @@ class GetNodePairSnippetsResult(CamelDictMixin): @attr.s(frozen=True) class GetReferenceTableDataResult(CamelDictMixin): direction: str = attr.ib() + description: str = attr.ib() reference_table_rows: List[ReferenceTableRow] = attr.ib() + duplicate_node_edge_pairs: List[Dict] = attr.ib() + + +@attr.s(frozen=True) +class GetBulkReferenceTableDataResult(CamelDictMixin): + reference_tables: List[GetReferenceTableDataResult] = attr.ib() @attr.s(frozen=True) class AssociatedTypesResult(CamelDictMixin): name: str = attr.ib() - node_id: int = attr.ib() + node_id: str = attr.ib() snippet_count: int = attr.ib() diff --git a/appserver/neo4japp/database.py b/appserver/neo4japp/database.py index 3b328800f8..fd5b886cde 100644 --- a/appserver/neo4japp/database.py +++ b/appserver/neo4japp/database.py @@ -3,12 +3,11 @@ from arango import ArangoClient from arango.http import DefaultHTTPClient from elasticsearch import Elasticsearch -from flask import g +from flask import g, current_app from flask_marshmallow import Marshmallow from flask_migrate import Migrate from flask_sqlalchemy import SQLAlchemy from jwt import PyJWKClient -from neo4j import Driver, GraphDatabase, basic_auth from redis import Redis from sqlalchemy import MetaData, Table, UniqueConstraint from typing import Union @@ -62,37 +61,6 @@ def get_jwt_client(): return _jwt_client -_neo4j_driver: Driver = None - - -def get_neo4j_driver(): - global _neo4j_driver - if _neo4j_driver is None: - host = config.get('NEO4J_HOST') - scheme = config.get('NEO4J_SCHEME') - port = config.get('NEO4J_PORT') - url = f'{scheme}://{host}:{port}' - username, password = config.get('NEO4J_AUTH').split('/') - _neo4j_driver = GraphDatabase.driver(url, auth=basic_auth(username, password)) - return _neo4j_driver - - -# TODO: with the DatabaseConnection class -# these functions that save to `g` are no longer needed -# remove them when possible -def get_neo4j_db(): - if not hasattr(g, 'neo4j_db'): - graph = get_neo4j_driver() - g.neo4j_db = graph.session() - return g.neo4j_db - - -def close_neo4j_db(e=None): - neo4j_db = g.pop('neo4j_db', None) - if neo4j_db: - neo4j_db.close() - - def get_redis_connection() -> Redis: if not hasattr(g, 'redis_conn'): g.redis_conn = Redis.from_url(config.get('RQ_REDIS_URL')) @@ -116,8 +84,13 @@ def create_arango_client(hosts=None) -> ArangoClient: class CustomHTTPClient(DefaultHTTPClient): REQUEST_TIMEOUT = 1000 - hosts = hosts or config.get('ARANGO_HOST') - return ArangoClient(hosts=hosts, http_client=CustomHTTPClient()) + hosts = hosts or current_app.config.get('ARANGO_HOST') + return ArangoClient( + hosts=hosts, + # Without this setting any requests to Arango will fail because we don't have a valid cert + verify_override=False, + http_client=CustomHTTPClient(), + ) def close_arango_client(error): @@ -134,12 +107,6 @@ def __init__(self): self.session = db.session -class GraphConnection: - def __init__(self): - super().__init__() - self.graph = get_neo4j_db() - - class ElasticConnection: def __init__(self): super().__init__() @@ -148,7 +115,7 @@ def __init__(self): """ TODO: Update all of these functions to use -DBConnection or GraphConnection above. +DBConnection above. Separation of concerns/Single responsibility. @@ -162,30 +129,6 @@ def __init__(self): """ -def get_kg_service(): - if 'kg_service' not in g: - from neo4japp.services import KgService - - graph = get_neo4j_db() - g.kg_service = KgService( - graph=graph, - session=db.session, - ) - return g.kg_service - - -def get_visualizer_service(): - if 'visualizer_service' not in g: - from neo4japp.services import VisualizerService - - graph = get_neo4j_db() - g.visualizer_service = VisualizerService( - graph=graph, - session=db.session, - ) - return g.visualizer_service - - @scope_flask_app_ctx('file_type_service') def get_file_type_service(): """ @@ -225,23 +168,10 @@ def get_enrichment_table_service(): if 'enrichment_table_service' not in g: from neo4japp.services import EnrichmentTableService - graph = get_neo4j_db() - g.enrichment_table_service = EnrichmentTableService( - graph=graph, - session=db.session, - ) + g.enrichment_table_service = EnrichmentTableService(session=db.session) return g.enrichment_table_service -def get_search_service_dao(): - if 'search_dao' not in g: - from neo4japp.services import SearchService - - graph = get_neo4j_db() - g.search_service_dao = SearchService(graph=graph) - return g.search_service_dao - - def get_authorization_service(): if 'authorization_service' not in g: from neo4japp.services import AuthService @@ -293,7 +223,6 @@ def reset_dao(): handy for production later. """ for dao in [ - 'kg_service', 'user_file_import_service', 'search_dao', 'authorization_service', diff --git a/appserver/neo4japp/factory.py b/appserver/neo4japp/factory.py index b849d3d12f..9f510361dd 100644 --- a/appserver/neo4japp/factory.py +++ b/appserver/neo4japp/factory.py @@ -3,7 +3,6 @@ from http import HTTPStatus from elasticapm.contrib.flask import ElasticAPM -from neo4j.exceptions import ServiceUnavailable from functools import partial from flask import current_app, Flask, jsonify, has_request_context, request from flask.logging import wsgi_errors_stream @@ -18,7 +17,6 @@ from neo4japp.constants import LogEventType from neo4japp.database import ( - close_neo4j_db, close_redis_conn, close_arango_client, db, @@ -118,7 +116,6 @@ def create_app(name='neo4japp', config_package='config.Development'): app = Flask(name) app.config.from_object(config_package) app.teardown_appcontext_funcs = [ - close_neo4j_db, close_redis_conn, close_arango_client, ] @@ -158,7 +155,6 @@ def create_app(name='neo4japp', config_package='config.Development'): ) app.register_error_handler(ServerException, handle_error) app.register_error_handler(BrokenPipeError, handle_error) - app.register_error_handler(ServiceUnavailable, handle_error) app.register_error_handler(ServerWarning, handle_warning) app.register_error_handler(Warning, partial(handle_generic_warning, 199)) app.register_error_handler(Exception, partial(handle_generic_error, 500)) diff --git a/appserver/neo4japp/models/common.py b/appserver/neo4japp/models/common.py index 1fbdcfe204..ff337a67dc 100644 --- a/appserver/neo4japp/models/common.py +++ b/appserver/neo4japp/models/common.py @@ -1,18 +1,18 @@ -from datetime import datetime -from decimal import Decimal -from typing import Iterable, Callable, TypeVar - import sqlalchemy as sa import timeflake + +from datetime import datetime +from decimal import Decimal from flask import g from marshmallow import fields from marshmallow_sqlalchemy.convert import ModelConverter as BaseModelConverter from sqlalchemy.ext.declarative import declared_attr from sqlalchemy.types import TIMESTAMP from sqlalchemy_utils.types import TSVectorType +from typing import Iterable, Callable, TypeVar from neo4japp.database import db -from neo4japp.utils import snake_to_camel, camel_to_snake +from neo4japp.utils.string import snake_to_camel, camel_to_snake def generate_hash_id(): diff --git a/appserver/neo4japp/request_schemas/visualizer.py b/appserver/neo4japp/request_schemas/visualizer.py index a96ebe5b8f..6e11159883 100644 --- a/appserver/neo4japp/request_schemas/visualizer.py +++ b/appserver/neo4japp/request_schemas/visualizer.py @@ -2,14 +2,14 @@ class AssociatedTypeSnippetCountRequest(ma.Schema): - source_node = ma.Integer(required=True) - associated_nodes = ma.List(ma.Integer(required=True)) + source_node = ma.String(required=True) + associated_nodes = ma.List(ma.String(required=True)) class GetSnippetsForNodePairRequest(ma.Schema): # Note that we avoid using "from" and "to" terminology here since we can't be sure there aren't # bidirectional relationships between these two nodes - node_1_id = ma.Integer(required=True) - node_2_id = ma.Integer(required=True) + node_1_id = ma.String(required=True) + node_2_id = ma.String(required=True) page = ma.Integer(required=True) limit = ma.Integer(required=True) diff --git a/appserver/neo4japp/schemas/annotations.py b/appserver/neo4japp/schemas/annotations.py index 4447291f6b..f73fdaab33 100644 --- a/appserver/neo4japp/schemas/annotations.py +++ b/appserver/neo4japp/schemas/annotations.py @@ -136,8 +136,8 @@ class AnnotationUUIDListSchema(ResultListSchema): class GlobalAnnotationListItemSchema(CamelCaseSchema): - global_id = fields.Integer() - synonym_id = fields.Integer(required=False, missing=lambda: None) + global_id = fields.String() + synonym_id = fields.String(required=False, missing=lambda: None) file_uuid = fields.String() creator = fields.String() file_deleted = fields.Boolean() @@ -303,4 +303,4 @@ class FileAnnotationHistoryResponseSchema(ResultListSchema): class GlobalAnnotationsDeleteSchema(Schema): - pids = fields.List(fields.Tuple((fields.Integer(), fields.Integer()))) + pids = fields.List(fields.Tuple((fields.String(), fields.String()))) diff --git a/appserver/neo4japp/services/__init__.py b/appserver/neo4japp/services/__init__.py index 0ca1d92e5e..1d2dcb8a09 100644 --- a/appserver/neo4japp/services/__init__.py +++ b/appserver/neo4japp/services/__init__.py @@ -1,7 +1,4 @@ -from .kg_service import KgService -from .search import SearchService from .auth import AuthService from .account import AccountService from .projects import ProjectsService -from .visualizer import VisualizerService from neo4japp.services.enrichment.enrichment_table import EnrichmentTableService diff --git a/appserver/neo4japp/services/annotations/README.md b/appserver/neo4japp/services/annotations/README.md index f4b6498012..71ab2d16d1 100644 --- a/appserver/neo4japp/services/annotations/README.md +++ b/appserver/neo4japp/services/annotations/README.md @@ -59,7 +59,6 @@ text, parsed = Pipeline.parse(file.mime_type, file_id=file.id, exclude_reference pipeline = Pipeline( { 'adbs': get_annotation_db_service, - 'ags': get_annotation_graph_service, 'aers': get_recognition_service, 'tkner': get_annotation_tokenizer, 'as': get_annotation_service, diff --git a/appserver/neo4japp/services/annotations/__init__.py b/appserver/neo4japp/services/annotations/__init__.py index d3da764dce..00e4c6b010 100644 --- a/appserver/neo4japp/services/annotations/__init__.py +++ b/appserver/neo4japp/services/annotations/__init__.py @@ -1,6 +1,5 @@ from .annotation_interval_tree import AnnotationInterval, AnnotationIntervalTree from .annotation_db_service import AnnotationDBService -from .annotation_graph_service import AnnotationGraphService from .annotation_service import AnnotationService from .bioc_service import BiocDocumentService from .entity_recognition import EntityRecognitionService diff --git a/appserver/neo4japp/services/annotations/annotation_graph_service.py b/appserver/neo4japp/services/annotations/annotation_graph_service.py index b8c4dd3f8e..658824e482 100644 --- a/appserver/neo4japp/services/annotations/annotation_graph_service.py +++ b/appserver/neo4japp/services/annotations/annotation_graph_service.py @@ -1,19 +1,22 @@ +from arango.client import ArangoClient from collections import defaultdict from typing import Any, Dict, List from flask import current_app from neo4japp.constants import LogEventType +from neo4japp.exceptions import InvalidArgument from neo4japp.services.arangodb import execute_arango_query, get_db -from neo4japp.utils import EventLog, normalize_str +from neo4japp.utils.logger import EventLog +from neo4japp.utils.string import normalize_str + from .constants import EntityType from .data_transfer_objects import GlobalInclusions, GeneOrProteinToOrganism from .utils.graph_queries import ( + collection_labels, get_gene_to_organism_query, get_global_inclusions_by_type_query, get_lifelike_global_inclusions_by_type_query, - get_mesh_by_ids, - get_nodes_by_ids, get_organisms_from_gene_ids_query, get_protein_to_organism_query, ) @@ -34,264 +37,259 @@ create_ner_type_lab_strain, EntityIdStr, ) -from ..common import GraphConnection -from ...exceptions import ServerWarning -from ...utils.globals import warn - -class AnnotationGraphService(GraphConnection): - def __init__(self, conn): - super().__init__(conn) - def get_nodes_from_node_ids( - self, entity_type: str, node_ids: List[str] - ) -> Dict[str, str]: - result = self.exec_read_query_with_params( - get_nodes_by_ids(entity_type), {'ids': node_ids} - ) - return {row['entity_id']: row['entity_name'] for row in result} - - # NOTE DEPRECATED: just used in old migration - def get_mesh_from_mesh_ids(self, mesh_ids: List[str]) -> Dict[str, str]: - result = self.exec_read_query_with_params(get_mesh_by_ids(), {'ids': mesh_ids}) - return {row['mesh_id']: row['mesh_name'] for row in result} - - def _create_entity_inclusion(self, entity_type: str, inclusion_dict: dict) -> None: - createfuncs = { - EntityType.ANATOMY.value: create_ner_type_anatomy, - EntityType.CHEMICAL.value: create_ner_type_chemical, - EntityType.COMPOUND.value: create_ner_type_compound, - EntityType.DISEASE.value: create_ner_type_disease, - EntityType.FOOD.value: create_ner_type_food, - EntityType.GENE.value: create_ner_type_gene, - EntityType.PHENOMENA.value: create_ner_type_phenomena, - EntityType.PHENOTYPE.value: create_ner_type_phenotype, - EntityType.PROTEIN.value: create_ner_type_protein, - EntityType.SPECIES.value: create_ner_type_species, - EntityType.COMPANY.value: create_ner_type_company, - EntityType.ENTITY.value: create_ner_type_entity, - EntityType.LAB_SAMPLE.value: create_ner_type_lab_sample, - EntityType.LAB_STRAIN.value: create_ner_type_lab_strain, - } - - # TODO: can we just do get_global_inclusions_by_type_query once? - # get all nodes that a Synonym points to and filter on labels in python? - # or would that be too much data to retrieve all at once? - global_inclusions = self.exec_read_query( - get_global_inclusions_by_type_query(entity_type) +def _create_entity_inclusion( + arango_client: ArangoClient, entity_type: str, inclusion_dict: dict +) -> None: + createfuncs = { + EntityType.ANATOMY.value: create_ner_type_anatomy, + EntityType.CHEMICAL.value: create_ner_type_chemical, + EntityType.COMPOUND.value: create_ner_type_compound, + EntityType.DISEASE.value: create_ner_type_disease, + EntityType.FOOD.value: create_ner_type_food, + EntityType.GENE.value: create_ner_type_gene, + EntityType.PHENOMENA.value: create_ner_type_phenomena, + EntityType.PHENOTYPE.value: create_ner_type_phenotype, + EntityType.PROTEIN.value: create_ner_type_protein, + EntityType.SPECIES.value: create_ner_type_species, + EntityType.COMPANY.value: create_ner_type_company, + EntityType.ENTITY.value: create_ner_type_entity, + EntityType.LAB_SAMPLE.value: create_ner_type_lab_sample, + EntityType.LAB_STRAIN.value: create_ner_type_lab_strain, + } + + # TODO: can we just do get_global_inclusions_by_type_query once? + # get all nodes that a Synonym points to and filter on labels in python? + # or would that be too much data to retrieve all at once? + try: + global_inclusions = execute_arango_query( + db=get_db(arango_client), + query=get_global_inclusions_by_type_query(), + collection=collection_labels[entity_type], + entity_type=entity_type, ) - # need to append here because an inclusion - # might've not been matched to an existing entity - # so look for it in Lifelike - global_inclusions += self.exec_read_query( - get_lifelike_global_inclusions_by_type_query(entity_type) + except KeyError: + raise InvalidArgument( + f'Could not query for document with entity type: {entity_type}. No ' + 'collection exists for this type.' ) + # need to append here because an inclusion + # might've not been matched to an existing entity + # so look for it in Lifelike + global_inclusions += execute_arango_query( + db=get_db(arango_client), + query=get_lifelike_global_inclusions_by_type_query(), + entity_type=entity_type, + ) - for inclusion in global_inclusions: - normalized_synonym = normalize_str(inclusion['synonym']) - if ( - entity_type != EntityType.GENE.value - and entity_type != EntityType.PROTEIN.value - ): - entity = createfuncs[entity_type]( - id=inclusion['entity_id'], - name=inclusion['entity_name'], - synonym=inclusion['synonym'], - ) # type: ignore - else: - entity = createfuncs[entity_type]( - name=inclusion['entity_name'], synonym=inclusion['synonym'] - ) # type: ignore - - # for proteins, we use the name as the id in the LMDB data, but we don't - # want to do this if the user provided an id or left it blank - # so set it back to what it was - if entity_type == EntityType.PROTEIN.value: - entity[EntityIdStr.PROTEIN.value] = inclusion['entity_id'] - - # override the default data source - # e.g gene default is NCBI, but globals can be BioCyc - entity['id_type'] = inclusion['data_source'] - entity['id_hyperlinks'] = inclusion.get('hyperlinks') - inclusion_dict[normalized_synonym].append(entity) - - def get_entity_inclusions(self, inclusions: List[dict]) -> GlobalInclusions: - """Returns global inclusions for each entity type. - For species (taxonomy), also return the local inclusions. - - :param inclusions: custom annotations relative to file - - need to be filtered for local inclusions - """ - inclusion_dicts: Dict[str, dict] = { - EntityType.ANATOMY.value: defaultdict(list), - EntityType.CHEMICAL.value: defaultdict(list), - EntityType.COMPOUND.value: defaultdict(list), - EntityType.DISEASE.value: defaultdict(list), - EntityType.FOOD.value: defaultdict(list), - EntityType.GENE.value: defaultdict(list), - EntityType.PHENOMENA.value: defaultdict(list), - EntityType.PHENOTYPE.value: defaultdict(list), - EntityType.PROTEIN.value: defaultdict(list), - EntityType.SPECIES.value: defaultdict(list), - EntityType.COMPANY.value: defaultdict(list), - EntityType.ENTITY.value: defaultdict(list), - EntityType.LAB_SAMPLE.value: defaultdict(list), - EntityType.LAB_STRAIN.value: defaultdict(list), - } - - local_inclusion_dicts: Dict[str, dict] = { - EntityType.SPECIES.value: defaultdict(list) - } - - for k, v in inclusion_dicts.items(): - self._create_entity_inclusion(k, v) - - local_species_inclusions = [ - local - for local in inclusions - if local.get('meta', {}).get('type') == EntityType.SPECIES.value - and not local.get('meta', {}).get( - 'includeGlobally', False - ) # safe to default to False? - ] - - for local_inclusion in local_species_inclusions: - entity_type = EntityType.SPECIES.value - try: - entity_id = local_inclusion['meta']['id'] - entity_id_type = local_inclusion['meta']['idType'] - entity_id_hyperlinks = local_inclusion['meta']['idHyperlinks'] - synonym = local_inclusion['meta']['allText'] - except KeyError as e: - message = f'Error creating local inclusion {local_inclusion} for {entity_type}' - current_app.logger.error( - message, - extra=EventLog(event_type=LogEventType.ANNOTATION.value).to_dict(), + for inclusion in global_inclusions: + normalized_synonym = normalize_str(inclusion['synonym']) + if ( + entity_type != EntityType.GENE.value + and entity_type != EntityType.PROTEIN.value + ): + entity = createfuncs[entity_type]( + id=inclusion['entity_id'], + name=inclusion['entity_name'], + synonym=inclusion['synonym'], + ) # type: ignore + else: + entity = createfuncs[entity_type]( + name=inclusion['entity_name'], synonym=inclusion['synonym'] + ) # type: ignore + + # for proteins, we use the name as the id in the LMDB data, but we don't + # want to do this if the user provided an id or left it blank + # so set it back to what it was + if entity_type == EntityType.PROTEIN.value: + entity[EntityIdStr.PROTEIN.value] = inclusion['entity_id'] + + # override the default data source + # e.g gene default is NCBI, but globals can be BioCyc + entity['id_type'] = inclusion['data_source'] + entity['id_hyperlinks'] = inclusion.get('hyperlinks') + inclusion_dict[normalized_synonym].append(entity) + + +def get_entity_inclusions(arango_client, inclusions: List[dict]) -> GlobalInclusions: + """Returns global inclusions for each entity type. + For species (taxonomy), also return the local inclusions. + + :param inclusions: custom annotations relative to file + - need to be filtered for local inclusions + """ + inclusion_dicts: Dict[str, dict] = { + EntityType.ANATOMY.value: defaultdict(list), + EntityType.CHEMICAL.value: defaultdict(list), + EntityType.COMPOUND.value: defaultdict(list), + EntityType.DISEASE.value: defaultdict(list), + EntityType.FOOD.value: defaultdict(list), + EntityType.GENE.value: defaultdict(list), + EntityType.PHENOMENA.value: defaultdict(list), + EntityType.PHENOTYPE.value: defaultdict(list), + EntityType.PROTEIN.value: defaultdict(list), + EntityType.SPECIES.value: defaultdict(list), + EntityType.COMPANY.value: defaultdict(list), + EntityType.ENTITY.value: defaultdict(list), + EntityType.LAB_SAMPLE.value: defaultdict(list), + EntityType.LAB_STRAIN.value: defaultdict(list), + } + + local_inclusion_dicts: Dict[str, dict] = { + EntityType.SPECIES.value: defaultdict(list) + } + + for k, v in inclusion_dicts.items(): + _create_entity_inclusion(arango_client, k, v) + + local_species_inclusions = [ + local + for local in inclusions + if local.get('meta', {}).get('type') == EntityType.SPECIES.value + and not local.get('meta', {}).get( + 'includeGlobally', False + ) # safe to default to False? + ] + + for local_inclusion in local_species_inclusions: + entity_type = EntityType.SPECIES.value + try: + entity_id = local_inclusion['meta']['id'] + entity_id_type = local_inclusion['meta']['idType'] + entity_id_hyperlinks = local_inclusion['meta']['idHyperlinks'] + synonym = local_inclusion['meta']['allText'] + except KeyError: + current_app.logger.error( + f'Error creating local inclusion {local_inclusion} for {entity_type}', + extra=EventLog(event_type=LogEventType.ANNOTATION.value).to_dict(), + ) + else: + # entity_name could be empty strings + # probably a result of testing + # but will keep here just in case + if entity_id and synonym: + normalized_synonym = normalize_str(synonym) + + if not entity_id: + # ID is required for global inclusions + # but we also include local species inclusion + entity_id = synonym + + entity = create_ner_type_species( + id=entity_id, name=synonym, synonym=synonym ) - warn(ServerWarning(message=message), cause=e) - else: - # entity_name could be empty strings - # probably a result of testing - # but will keep here just in case - if entity_id and synonym: - normalized_synonym = normalize_str(synonym) - - if not entity_id: - # ID is required for global inclusions - # but we also include local species inclusion - entity_id = synonym - - entity = create_ner_type_species( - id=entity_id, name=synonym, synonym=synonym - ) - - # override the default data source - # e.g gene default is NCBI, but globals can be BioCyc - entity['id_type'] = entity_id_type - entity['id_hyperlinks'] = entity_id_hyperlinks - local_inclusion_dicts[entity_type][normalized_synonym].append( - entity - ) - - return GlobalInclusions( - included_anatomy=inclusion_dicts[EntityType.ANATOMY.value], - included_chemicals=inclusion_dicts[EntityType.CHEMICAL.value], - included_compounds=inclusion_dicts[EntityType.COMPOUND.value], - included_diseases=inclusion_dicts[EntityType.DISEASE.value], - included_foods=inclusion_dicts[EntityType.FOOD.value], - included_genes=inclusion_dicts[EntityType.GENE.value], - included_phenomenas=inclusion_dicts[EntityType.PHENOMENA.value], - included_phenotypes=inclusion_dicts[EntityType.PHENOTYPE.value], - included_proteins=inclusion_dicts[EntityType.PROTEIN.value], - included_species=inclusion_dicts[EntityType.SPECIES.value], - included_local_species=local_inclusion_dicts[EntityType.SPECIES.value], - included_companies=inclusion_dicts[EntityType.COMPANY.value], - included_entities=inclusion_dicts[EntityType.ENTITY.value], - included_lab_samples=inclusion_dicts[EntityType.LAB_SAMPLE.value], - included_lab_strains=inclusion_dicts[EntityType.LAB_STRAIN.value], - ) - def get_genes_to_organisms( - self, - genes: List[str], - organisms: List[str], - ) -> GeneOrProteinToOrganism: - gene_to_organism_map: Dict[str, Dict[str, Dict[str, str]]] = {} - data_sources: Dict[str, str] = {} - primary_names: Dict[str, str] = {} - - result = self.exec_read_query_with_params( - get_gene_to_organism_query(), {'genes': genes, 'organisms': organisms} - ) + # override the default data source + # e.g gene default is NCBI, but globals can be BioCyc + entity['id_type'] = entity_id_type + entity['id_hyperlinks'] = entity_id_hyperlinks + local_inclusion_dicts[entity_type][normalized_synonym].append(entity) + + return GlobalInclusions( + included_anatomy=inclusion_dicts[EntityType.ANATOMY.value], + included_chemicals=inclusion_dicts[EntityType.CHEMICAL.value], + included_compounds=inclusion_dicts[EntityType.COMPOUND.value], + included_diseases=inclusion_dicts[EntityType.DISEASE.value], + included_foods=inclusion_dicts[EntityType.FOOD.value], + included_genes=inclusion_dicts[EntityType.GENE.value], + included_phenomenas=inclusion_dicts[EntityType.PHENOMENA.value], + included_phenotypes=inclusion_dicts[EntityType.PHENOTYPE.value], + included_proteins=inclusion_dicts[EntityType.PROTEIN.value], + included_species=inclusion_dicts[EntityType.SPECIES.value], + included_local_species=local_inclusion_dicts[EntityType.SPECIES.value], + included_companies=inclusion_dicts[EntityType.COMPANY.value], + included_entities=inclusion_dicts[EntityType.ENTITY.value], + included_lab_samples=inclusion_dicts[EntityType.LAB_SAMPLE.value], + included_lab_strains=inclusion_dicts[EntityType.LAB_STRAIN.value], + ) - for row in result: - gene_name = row['gene_name'] - gene_synonym = row['gene_synonym'] - gene_id = row['gene_id'] - organism_id = row['organism_id'] - data_source = row['data_source'] - data_source_key = f'{gene_synonym}{organism_id}' - - primary_names[gene_id] = gene_name - data_sources[data_source_key] = data_source - - if gene_to_organism_map.get(gene_synonym, None) is not None: - if gene_to_organism_map[gene_synonym].get(gene_name, None): - gene_to_organism_map[gene_synonym][gene_name][organism_id] = gene_id - else: - gene_to_organism_map[gene_synonym][gene_name] = { - organism_id: gene_id - } - else: - gene_to_organism_map[gene_synonym] = {gene_name: {organism_id: gene_id}} - - # clean any gene/organism matches that have excess results - # we want to prioritize matches where the primary name and synonym are the same - for synonym, v in gene_to_organism_map.items(): - if synonym in v and len(v) > 1: - gene_to_organism_map[synonym] = {synonym: v[synonym]} - - return GeneOrProteinToOrganism( - matches=gene_to_organism_map, - data_sources=data_sources, - primary_names=primary_names, - ) - def get_proteins_to_organisms( - self, - proteins: List[str], - organisms: List[str], - ) -> GeneOrProteinToOrganism: - protein_to_organism_map: Dict[str, Dict[str, str]] = {} - primary_names: Dict[str, str] = {} - - result = self.exec_read_query_with_params( - get_protein_to_organism_query(), - {'proteins': proteins, 'organisms': organisms}, - ) +def get_organisms_from_gene_ids(arango_client: ArangoClient, gene_ids: Dict[Any, int]): + return execute_arango_query( + db=get_db(arango_client), + query=get_organisms_from_gene_ids_query(), + gene_ids=list(gene_ids.keys()), + ) + + +def get_genes_to_organisms( + arango_client: ArangoClient, + genes: List[str], + organisms: List[str], +) -> GeneOrProteinToOrganism: + gene_to_organism_map: Dict[str, Dict[str, Dict[str, str]]] = {} + data_sources: Dict[str, str] = {} + primary_names: Dict[str, str] = {} + + result = execute_arango_query( + db=get_db(arango_client), + query=get_gene_to_organism_query(), + genes=genes, + organisms=organisms, + ) - for row in result: - protein_name: str = row['protein'] - organism_id: str = row['organism_id'] - # For now just get the first protein in the list of matches, - # no way for us to infer which to use - protein_id: str = row['protein_ids'][0] + for row in result: + gene_name = row['gene_name'] + gene_synonym = row['gene_synonym'] + gene_id = row['gene_id'] + organism_id = row['organism_id'] + data_source = row['data_source'] + data_source_key = f'{gene_synonym}{organism_id}' - primary_names[protein_id] = protein_name + primary_names[gene_id] = gene_name + data_sources[data_source_key] = data_source - if protein_to_organism_map.get(protein_name, None) is not None: - protein_to_organism_map[protein_name][organism_id] = protein_id + if gene_to_organism_map.get(gene_synonym, None) is not None: + if gene_to_organism_map[gene_synonym].get(gene_name, None): + gene_to_organism_map[gene_synonym][gene_name][organism_id] = gene_id else: - protein_to_organism_map[protein_name] = {organism_id: protein_id} + gene_to_organism_map[gene_synonym][gene_name] = {organism_id: gene_id} + else: + gene_to_organism_map[gene_synonym] = {gene_name: {organism_id: gene_id}} + + # clean any gene/organism matches that have excess results + # we want to prioritize matches where the primary name and synonym are the same + for synonym, v in gene_to_organism_map.items(): + if synonym in v and len(v) > 1: + gene_to_organism_map[synonym] = {synonym: v[synonym]} + + return GeneOrProteinToOrganism( + matches=gene_to_organism_map, + data_sources=data_sources, + primary_names=primary_names, + ) - return GeneOrProteinToOrganism( - matches=protein_to_organism_map, primary_names=primary_names - ) +def get_proteins_to_organisms( + arango_client: ArangoClient, + proteins: List[str], + organisms: List[str], +) -> GeneOrProteinToOrganism: + protein_to_organism_map: Dict[str, Dict[str, str]] = {} + primary_names: Dict[str, str] = {} -def get_organisms_from_gene_ids(arango_client, gene_ids: Dict[Any, int]): - return execute_arango_query( + result = execute_arango_query( db=get_db(arango_client), - query=get_organisms_from_gene_ids_query(), - gene_ids=list(gene_ids.keys()), + query=get_protein_to_organism_query(), + proteins=proteins, + organisms=organisms, + ) + + for row in result: + protein_name: str = row['protein'] + organism_id: str = row['organism_id'] + # For now just get the first protein in the list of matches, + # no way for us to infer which to use + protein_id: str = row['protein_ids'][0] + + primary_names[protein_id] = protein_name + + if protein_to_organism_map.get(protein_name, None) is not None: + protein_to_organism_map[protein_name][organism_id] = protein_id + else: + protein_to_organism_map[protein_name] = {organism_id: protein_id} + + return GeneOrProteinToOrganism( + matches=protein_to_organism_map, primary_names=primary_names ) diff --git a/appserver/neo4japp/services/annotations/annotation_service.py b/appserver/neo4japp/services/annotations/annotation_service.py index be853a2c65..64e71c42c9 100644 --- a/appserver/neo4japp/services/annotations/annotation_service.py +++ b/appserver/neo4japp/services/annotations/annotation_service.py @@ -1,18 +1,21 @@ import json import time + +from arango.client import ArangoClient from bisect import bisect_left +from flask import current_app +from math import inf, isinf from typing import cast, Dict, List, Set, Tuple from urllib.parse import quote as uri_encode from uuid import uuid4 -from flask import current_app -from math import inf, isinf - from neo4japp.constants import LogEventType from neo4japp.exceptions import wrap_exceptions, AnnotationError, ServerException -from neo4japp.utils import EventLog, equal_number_of_words, normalize_str +from neo4japp.utils.logger import EventLog +from neo4japp.utils.string import equal_number_of_words, normalize_str + from .annotation_db_service import AnnotationDBService -from .annotation_graph_service import AnnotationGraphService +from .annotation_graph_service import get_genes_to_organisms, get_proteins_to_organisms from .annotation_interval_tree import AnnotationInterval, AnnotationIntervalTree from .constants import ( DatabaseType, @@ -43,10 +46,14 @@ class AnnotationService: def __init__( self, db: AnnotationDBService, - graph: AnnotationGraphService, + # TODO: I don't think this is the best way to handle the arango client connection, but the + # pattern is pretty deeply ingrained into the annotations pipeline. Keeping it this way for + # now, but I think we should slowly try to migrate away from the "service-as-an-object" + # pattern + arango_client: ArangoClient, ) -> None: self.db = db - self.graph = graph + self.arango_client = arango_client self.organism_frequency: Dict[str, int] = {} self.organism_locations: Dict[str, List[Tuple[int, int]]] = {} @@ -590,7 +597,8 @@ def _annotate_type_gene( organism_ids = list(self.organism_frequency) gene_match_time = time.time() - graph_results = self.graph.get_genes_to_organisms( + graph_results = get_genes_to_organisms( + arango_client=self.arango_client, genes=gene_names_list, organisms=organism_ids, ) @@ -608,7 +616,8 @@ def _annotate_type_gene( if self.specified_organism.synonym: gene_match_time = time.time() - fallback_graph_results = self.graph.get_genes_to_organisms( + fallback_graph_results = get_genes_to_organisms( + arango_client=self.arango_client, genes=gene_names_list, organisms=[self.specified_organism.organism_id], ) @@ -734,7 +743,8 @@ def _annotate_type_protein( protein_names_list = list(protein_names) protein_match_time = time.time() - graph_results = self.graph.get_proteins_to_organisms( + graph_results = get_proteins_to_organisms( + arango_client=self.arango_client, proteins=protein_names_list, organisms=list(self.organism_frequency), ) @@ -750,7 +760,8 @@ def _annotate_type_protein( if self.specified_organism.synonym: protein_match_time = time.time() - fallback_graph_results = self.graph.get_proteins_to_organisms( + fallback_graph_results = get_proteins_to_organisms( + arango_client=self.arango_client, proteins=protein_names_list, organisms=[self.specified_organism.organism_id], ) diff --git a/appserver/neo4japp/services/annotations/enrichment_annotation_service.py b/appserver/neo4japp/services/annotations/enrichment_annotation_service.py index c5dd74570f..66f5329898 100644 --- a/appserver/neo4japp/services/annotations/enrichment_annotation_service.py +++ b/appserver/neo4japp/services/annotations/enrichment_annotation_service.py @@ -1,15 +1,17 @@ import bisect import itertools import time -from collections import defaultdict -from typing import Dict, List, Set, Tuple +from arango.client import ArangoClient +from collections import defaultdict from flask import current_app +from typing import Dict, List, Set, Tuple from neo4japp.constants import LogEventType from neo4japp.utils import EventLog + from .annotation_db_service import AnnotationDBService -from .annotation_graph_service import AnnotationGraphService +from .annotation_graph_service import get_genes_to_organisms, get_proteins_to_organisms from .annotation_service import AnnotationService from .constants import EntityType from .data_transfer_objects import ( @@ -25,9 +27,13 @@ class EnrichmentAnnotationService(AnnotationService): def __init__( self, db: AnnotationDBService, - graph: AnnotationGraphService, + # TODO: I don't think this is the best way to handle the arango client connection, but the + # pattern is pretty deeply ingrained into the annotations pipeline. Keeping it this way for + # now, but I think we should slowly try to migrate away from the "service-as-an-object" + # pattern. + arango_client: ArangoClient, ) -> None: - super().__init__(db=db, graph=graph) + super().__init__(db=db, arango_client=arango_client) def _annotate_type_gene( self, recognized_entities: RecognizedEntities @@ -39,7 +45,8 @@ def _annotate_type_gene( gene_names_list, entity_token_pairs = self._parse_matches_list(matches_list) gene_match_time = time.time() - fallback_graph_results = self.graph.get_genes_to_organisms( + fallback_graph_results = get_genes_to_organisms( + arango_client=self.arango_client, genes=gene_names_list, organisms=[self.specified_organism.organism_id], ) @@ -132,7 +139,8 @@ def _annotate_type_protein( protein_match_time = time.time() organism = self.specified_organism organism_id = organism.organism_id - fallback_graph_results = self.graph.get_proteins_to_organisms( + fallback_graph_results = get_proteins_to_organisms( + arango_client=self.arango_client, proteins=protein_names_list, organisms=[organism_id], ) diff --git a/appserver/neo4japp/services/annotations/initializer.py b/appserver/neo4japp/services/annotations/initializer.py index 22ef994aea..c1487b8d9f 100644 --- a/appserver/neo4japp/services/annotations/initializer.py +++ b/appserver/neo4japp/services/annotations/initializer.py @@ -1,9 +1,9 @@ -from neo4japp.database import get_neo4j_driver +from neo4japp.database import get_or_create_arango_client from neo4japp.utils.globals import config + from .annotation_service import AnnotationService from .annotation_db_service import AnnotationDBService -from .annotation_graph_service import AnnotationGraphService from .bioc_service import BiocDocumentService from .enrichment_annotation_service import EnrichmentAnnotationService from .entity_recognition import EntityRecognitionService @@ -53,26 +53,24 @@ def get_annotation_db_service(): return AnnotationDBService() -def get_annotation_graph_service(): - driver = get_neo4j_driver() - return AnnotationGraphService(driver) - - def get_manual_annotation_service(): return ManualAnnotationService( - graph=get_annotation_graph_service(), tokenizer=get_annotation_tokenizer() + tokenizer=get_annotation_tokenizer(), + arango_client=get_or_create_arango_client(), ) def get_annotation_service(): return AnnotationService( - db=get_annotation_db_service(), graph=get_annotation_graph_service() + db=get_annotation_db_service(), + arango_client=get_or_create_arango_client(), ) def get_enrichment_annotation_service(): return EnrichmentAnnotationService( - db=get_annotation_db_service(), graph=get_annotation_graph_service() + db=get_annotation_db_service(), + arango_client=get_or_create_arango_client(), ) diff --git a/appserver/neo4japp/services/annotations/lmdb_service.py b/appserver/neo4japp/services/annotations/lmdb_service.py index a28b6eabd8..9e1c9ad57c 100644 --- a/appserver/neo4japp/services/annotations/lmdb_service.py +++ b/appserver/neo4japp/services/annotations/lmdb_service.py @@ -5,7 +5,8 @@ import lmdb -from neo4japp.utils import normalize_str +from neo4japp.utils.string import normalize_str + from .constants import ( CHEMICALS_LMDB, COMPOUNDS_LMDB, diff --git a/appserver/neo4japp/services/annotations/manual_annotation_service.py b/appserver/neo4japp/services/annotations/manual_annotation_service.py index 429b87600e..82f00d3670 100644 --- a/appserver/neo4japp/services/annotations/manual_annotation_service.py +++ b/appserver/neo4japp/services/annotations/manual_annotation_service.py @@ -1,11 +1,10 @@ import uuid -from datetime import datetime -from http import HTTPStatus -from typing import List, Tuple -from uuid import uuid4 +from arango.client import ArangoClient +from datetime import datetime from flask import current_app -from neo4j.exceptions import ServiceUnavailable +from http import HTTPStatus +from typing import Callable, Dict, List, Tuple from neo4japp.constants import TIMEZONE, LogEventType from neo4japp.database import db @@ -17,8 +16,11 @@ ) from neo4japp.models import Files, GlobalList, AppUser from neo4japp.models.files import FileAnnotationsVersion, AnnotationChangeCause -from neo4japp.utils import standardize_str, EventLog -from .annotation_graph_service import AnnotationGraphService +from neo4japp.services.arangodb import get_db, execute_arango_query +from neo4japp.utils.logger import EventLog +from neo4japp.utils.string import standardize_str + +from .exceptions import AnnotationLimitationError from .constants import ( ManualAnnotationType, MAX_ENTITY_WORD_LENGTH, @@ -29,18 +31,38 @@ MIN_ENTITY_LENGTH, ) from .data_transfer_objects.dto import PDFWord -from .exceptions import AnnotationLimitationError from .tokenizer import Tokenizer from .utils.common import has_center_point -from .utils.graph_queries import * +from .utils.graph_queries import ( + EntityType, + get_chemical_global_inclusion_exist_query, + get_compound_global_inclusion_exist_query, + get_create_chemical_global_inclusion_query, + get_create_compound_global_inclusion_query, + get_create_gene_global_inclusion_query, + get_create_lifelike_global_inclusion_query, + get_create_mesh_global_inclusion_query, + get_create_protein_global_inclusion_query, + get_create_species_global_inclusion_query, + get_delete_global_inclusion_query, + get_docs_by_ids_query, + get_gene_global_inclusion_exist_query, + get_lifelike_global_inclusion_exist_query, + get_mesh_global_inclusion_exist_query, + get_node_labels_and_relationship_query, + get_pathway_global_inclusion_exist_query, + get_protein_global_inclusion_exist_query, + get_species_global_inclusion_exist_query, + query_builder, +) from .utils.parsing import parse_content from ...utils.globals import warn class ManualAnnotationService: - def __init__(self, graph: AnnotationGraphService, tokenizer: Tokenizer) -> None: - self.graph = graph + def __init__(self, tokenizer: Tokenizer, arango_client: ArangoClient) -> None: self.tokenizer = tokenizer + self.arango_client = arango_client def _annotation_exists( self, term: str, new_annotation_metadata: dict, custom_annotations: List[dict] @@ -142,12 +164,17 @@ def add_inclusions( EntityType.PROTEIN.value, EntityType.SPECIES.value, ]: - primary_name = self.graph.get_nodes_from_node_ids( - entity_type, [entity_id] - )[entity_id] + result = execute_arango_query( + db=get_db(self.arango_client), + query=get_docs_by_ids_query(entity_type), + ids=[entity_id], + ) + primary_name = { + row['entity_id']: row['entity_name'] for row in result + }[entity_id] except KeyError: pass - except (BrokenPipeError, ServiceUnavailable): + except BrokenPipeError: raise except Exception as e: raise AnnotationError( @@ -299,21 +326,24 @@ def remove_inclusions(self, file: Files, user: AppUser, uuid, remove_all): @wrap_exceptions(AnnotationError, title='Failed to Remove Global Inclusion') def remove_global_inclusions(self, inclusion_ids: List[Tuple[int, int]]): try: - self.graph.exec_write_query_with_params( - get_delete_global_inclusion_query(), - {'node_ids': [[gid, sid] for gid, sid in inclusion_ids]}, + pairs = [[gid, sid] for gid, sid in inclusion_ids] + execute_arango_query( + db=get_db(self.arango_client), + query=get_delete_global_inclusion_query(), + pairs=pairs, ) - except (BrokenPipeError, ServiceUnavailable): + except BrokenPipeError: raise except Exception as e: current_app.logger.error( - f'Failed executing cypher: {get_delete_global_inclusion_query()}.\n' - + f'PARAMETERS: .', + f'Failed executing AQL: {get_delete_global_inclusion_query()}.\n' + + f'PARAMETERS: .', extra=EventLog(event_type=LogEventType.ANNOTATION.value).to_dict(), ) raise ServerException( - message='A system error occurred while creating the annotation, ' - 'we are working on a solution. Please try again later.' + title='Failed to Remove Global Inclusion', + message='A system error occurred while deleting the annotation, ' + 'we are working on a solution. Please try again later.', ) from e try: @@ -321,61 +351,82 @@ def remove_global_inclusions(self, inclusion_ids: List[Tuple[int, int]]): # a global could've been added with the wrong entity type # so we need to remove those bad labels to prevent # incorrect results coming back as synonyms - results = self.graph.exec_read_query_with_params( - get_node_labels_and_relationship_query(), - {'node_ids': [gid for gid, _ in inclusion_ids]}, + results = execute_arango_query( + db=get_db(self.arango_client), + query=get_node_labels_and_relationship_query(), + ids=[gid for gid, _ in inclusion_ids], ) - - for result in results: - mismatch = set(result['node_labels']) - set(result['rel_entity_types']) - # remove Taxonomy because there is inconsistency between graph and annotations - # annotation uses Species instead - if EntityType.SPECIES.value in result['rel_entity_types']: - mismatch.remove('Taxonomy') - - s = '' - for label in list(mismatch): - if label not in result['valid_entity_types']: - if label == 'Anatomy': - s += ':Anatomy' - elif label == 'Chemical': - s += ':Chemical' - elif label == 'Compound': - s += ':Compound' - elif label == 'Disease': - s += ':Disease' - elif label == 'Food': - s += ':Food' - elif label == 'Gene': - s += ':Gene' - elif label == 'Phenomena': - s += ':Phenomena' - elif label == 'Phenotype': - s += ':Phenotype' - elif label == 'Protein': - s += ':Protein' - elif label == 'Taxonomy': - s += ':Taxonomy' - if s: - self.graph.exec_write_query_with_params( - query_builder( - ['MATCH (n) WHERE id(n) = $node_id', f'REMOVE n{s}'] - ), - {'node_id': result['node_id']}, - ) - except (BrokenPipeError, ServiceUnavailable): - raise - except Exception as e: - query = query_builder(["MATCH (n) WHERE id(n) = $node_id", f"REMOVE n{s}"]) - current_app.logger.error( - f'Failed executing cypher: {query}.\n' - + f'PARAMETERS: .', + except Exception: + current_app.logger.info( + f'Failed During Cleanup of Global Inclusion Removal', extra=EventLog(event_type=LogEventType.ANNOTATION.value).to_dict(), ) - raise ServerException( - message='A system error occurred while creating the annotation, ' - 'we are working on a solution. Please try again later.' - ) from e + raise AnnotationError( + title='Global Inclusion Deleted, But Cleanup Failed', + message='A system error occurred after deleting the annotation, ' + 'we are working on a solution. Please try again later.', + ) + for result in results: + mismatch = set(result['node_labels']) - set(result['rel_entity_types']) + # remove Taxonomy because there is inconsistency between graph and annotations + # annotation uses Species instead + if EntityType.SPECIES.value in result['rel_entity_types']: + mismatch.remove('Taxonomy') + + s = [] + for label in list(mismatch): + if label not in result['valid_entity_types']: + if label == 'Anatomy': + s.append('Anatomy') + elif label == 'Chemical': + s.append('Chemical') + elif label == 'Compound': + s.append('Compound') + elif label == 'Disease': + s.append('Disease') + elif label == 'Food': + s.append('Food') + elif label == 'Gene': + s.append('Gene') + elif label == 'Phenomena': + s.append('Phenomena') + elif label == 'Phenotype': + s.append('Phenotype') + elif label == 'Protein': + s.append('Protein') + elif label == 'Taxonomy': + s.append('Taxonomy') + if len(s): + try: + query = """ + FOR doc IN synonym + FILTER doc._key == @node_id + FOR val IN @labels + UPDATE doc WITH {labels: REMOVE_VALUE(doc.labels, val)} IN synonym + """ + execute_arango_query( + db=get_db(self.arango_client), + query=query, + node_id=result['node_id'], + ) + except BrokenPipeError: + raise + except Exception: + query = query_builder( + ["MATCH (n) WHERE id(n) = $node_id", f"REMOVE n{s}"] + ) + current_app.logger.error( + f'Failed executing cypher: {query}.\n' + + f'PARAMETERS: .', + extra=EventLog( + event_type=LogEventType.ANNOTATION.value + ).to_dict(), + ) + raise ServerException( + title='Global Inclusion Deleted, But Cleanup Failed', + message='A system error occurred after deleting the annotation, ' + 'we are working on a solution. Please try again later.', + ) @wrap_exceptions(AnnotationError, title='Failed to Create Custom Annotation') def add_exclusion(self, file: Files, user: AppUser, exclusion): @@ -487,6 +538,11 @@ def isExcluded(exclusions, annotation): ] return filtered_annotations + file.custom_annotations + # TODO: Seems like there is some unexpected behavior in saving a new global: If both the + # entity and the synonym already exist, no global is created. This is probably "correct" in the + # sense that the term should get annotated without the existence of the global, but it's very + # confusing because the new annotation will not appear in the global list. A term annotated in + # this way is effectively the same as a local annotation. @wrap_exceptions(AnnotationError, title='Failed to Create Custom Annotation') def save_global( self, @@ -525,9 +581,9 @@ def save_global( ) from e if entity_id == '': - entity_id = f'NULL-{str(uuid4())}' + entity_id = f'NULL-{str(uuid.uuid4())}' - createval = { + all_params = { 'entity_type': entity_type, 'entity_id': entity_id, 'synonym': synonym, @@ -542,7 +598,7 @@ def save_global( # NOTE: # definition of `main node`: the node that contains the common/primary name # e. g `Homo sapiens` is the common/primary name, while `human` is the synonym - check = self._global_annotation_exists_in_kg(createval) + check = self._global_annotation_exists_in_kg(all_params) # several possible scenarios # 1. main node exists and synonym exists # 2. main node exists and synonym does not exist @@ -558,43 +614,88 @@ def save_global( if check['node_exist'] and ( not check['synonym_exist'] or check.get('node_has_entity_label', False) ): + mesh_params = { + 'entity_type': entity_type, + 'entity_id': entity_id, + 'synonym': synonym, + 'inclusion_date': inclusion_date, + 'user': username, + 'file_uuid': file_hash_id, + 'hyperlinks': hyperlinks, + } + others_params = { + 'entity_id': entity_id, + 'synonym': synonym, + 'inclusion_date': inclusion_date, + 'user': username, + 'file_uuid': file_hash_id, + 'hyperlinks': hyperlinks, + } + queries = { - EntityType.ANATOMY.value: get_create_mesh_global_inclusion_query( - entity_type + EntityType.ANATOMY.value: ( + get_create_mesh_global_inclusion_query, + mesh_params, + ), + EntityType.DISEASE.value: ( + get_create_mesh_global_inclusion_query, + mesh_params, ), - EntityType.DISEASE.value: get_create_mesh_global_inclusion_query( - entity_type + EntityType.FOOD.value: ( + get_create_mesh_global_inclusion_query, + mesh_params, ), - EntityType.FOOD.value: get_create_mesh_global_inclusion_query( - entity_type + EntityType.PHENOMENA.value: ( + get_create_mesh_global_inclusion_query, + mesh_params, ), - EntityType.PHENOMENA.value: get_create_mesh_global_inclusion_query( - entity_type + EntityType.PHENOTYPE.value: ( + get_create_mesh_global_inclusion_query, + mesh_params, ), - EntityType.PHENOTYPE.value: get_create_mesh_global_inclusion_query( - entity_type + EntityType.CHEMICAL.value: ( + get_create_chemical_global_inclusion_query, + others_params, + ), + EntityType.COMPOUND.value: ( + get_create_compound_global_inclusion_query, + others_params, + ), + EntityType.GENE.value: ( + get_create_gene_global_inclusion_query, + others_params, + ), + EntityType.PROTEIN.value: ( + get_create_protein_global_inclusion_query, + others_params, + ), + EntityType.SPECIES.value: ( + get_create_species_global_inclusion_query, + others_params, + ), + EntityType.PATHWAY.value: ( + get_pathway_global_inclusion_exist_query, + others_params, ), - EntityType.CHEMICAL.value: get_create_chemical_global_inclusion_query(), - EntityType.COMPOUND.value: get_create_compound_global_inclusion_query(), - EntityType.GENE.value: get_create_gene_global_inclusion_query(), - EntityType.PROTEIN.value: get_create_protein_global_inclusion_query(), - EntityType.SPECIES.value: get_create_species_global_inclusion_query(), - EntityType.PATHWAY.value: get_pathway_global_inclusion_exist_query(), } - query = queries.get(entity_type, '') + query_fn, params = queries.get( + entity_type, + (get_create_lifelike_global_inclusion_query, all_params), + ) + try: - if query: - self.graph.exec_write_query_with_params(query, createval) - else: - query = get_create_lifelike_global_inclusion_query(entity_type) - self.graph.exec_write_query_with_params(query, createval) - except (BrokenPipeError, ServiceUnavailable): + execute_arango_query( + db=get_db(self.arango_client), + query=query_fn(), + **params, + ) + except BrokenPipeError: raise except Exception as e: message = ( f'Failed to create global inclusion, ' - f'knowledge graph failed with query: {query}.' + f'knowledge graph failed with query: {query_fn()}.' ) current_app.logger.error( message, @@ -605,9 +706,13 @@ def save_global( warn(ServerWarning(message=message), cause=e) elif not check['node_exist']: try: - query = get_create_lifelike_global_inclusion_query(entity_type) - self.graph.exec_write_query_with_params(query, createval) - except (BrokenPipeError, ServiceUnavailable): + query = get_create_lifelike_global_inclusion_query() + execute_arango_query( + db=get_db(self.arango_client), + query=query, + **all_params, + ) + except BrokenPipeError: raise except Exception as e: message = ( @@ -643,62 +748,100 @@ def save_global( def _global_annotation_exists_in_kg(self, values: dict): entity_type = values['entity_type'] - queries = { - EntityType.ANATOMY.value: get_mesh_global_inclusion_exist_query( - entity_type + mesh_params = { + 'entity_type': entity_type, + 'entity_id': values['entity_id'], + 'synonym': values['synonym'], + } + lifelike_params = { + 'common_name': values['common_name'], + 'entity_type': entity_type, + 'synonym': values['synonym'], + } + other_params = { + 'entity_id': values['entity_id'], + 'synonym': values['synonym'], + } + queries: Dict[str, Tuple[Callable, dict]] = { + EntityType.ANATOMY.value: ( + get_mesh_global_inclusion_exist_query, + mesh_params, + ), + EntityType.DISEASE.value: ( + get_mesh_global_inclusion_exist_query, + mesh_params, + ), + EntityType.FOOD.value: (get_mesh_global_inclusion_exist_query, mesh_params), + EntityType.PHENOMENA.value: ( + get_mesh_global_inclusion_exist_query, + mesh_params, ), - EntityType.DISEASE.value: get_mesh_global_inclusion_exist_query( - entity_type + EntityType.PHENOTYPE.value: ( + get_mesh_global_inclusion_exist_query, + mesh_params, ), - EntityType.FOOD.value: get_mesh_global_inclusion_exist_query(entity_type), - EntityType.PHENOMENA.value: get_mesh_global_inclusion_exist_query( - entity_type + EntityType.CHEMICAL.value: ( + get_chemical_global_inclusion_exist_query, + other_params, ), - EntityType.PHENOTYPE.value: get_mesh_global_inclusion_exist_query( - entity_type + EntityType.COMPOUND.value: ( + get_compound_global_inclusion_exist_query, + other_params, + ), + EntityType.GENE.value: ( + get_gene_global_inclusion_exist_query, + other_params, + ), + EntityType.PROTEIN.value: ( + get_protein_global_inclusion_exist_query, + other_params, + ), + EntityType.SPECIES.value: ( + get_species_global_inclusion_exist_query, + other_params, + ), + EntityType.PATHWAY.value: ( + get_pathway_global_inclusion_exist_query, + other_params, ), - EntityType.CHEMICAL.value: get_chemical_global_inclusion_exist_query(), - EntityType.COMPOUND.value: get_compound_global_inclusion_exist_query(), - EntityType.GENE.value: get_gene_global_inclusion_exist_query(), - EntityType.PROTEIN.value: get_protein_global_inclusion_exist_query(), - EntityType.SPECIES.value: get_species_global_inclusion_exist_query(), - EntityType.PATHWAY.value: get_pathway_global_inclusion_exist_query(), } - # query can be empty string because some entity types - # do not exist in the normal domain/labels - query = queries.get(entity_type, '') - try: - check = ( - self.graph.exec_read_query_with_params(query, values)[0] - if query - else {'node_exist': False} - ) - except (BrokenPipeError, ServiceUnavailable): - raise - except Exception as e: - message = ( - f'Failed to create global inclusion, ' - f'knowledge graph failed with query: {query}.' - ) - current_app.logger.error( - message, - extra=EventLog(event_type=LogEventType.ANNOTATION.value).to_dict(), - ) - warn(ServerWarning(message=message), cause=e) + if entity_type in queries: + try: + query_fn, params = queries[entity_type] + check = execute_arango_query( + db=get_db(self.arango_client), query=query_fn(), **params + )[0] + except BrokenPipeError: + raise + except Exception as e: + message = ( + f'Failed to create global inclusion, ' + f'knowledge graph failed with query: {query_fn()}.' + ) + current_app.logger.error( + message, + extra=EventLog(event_type=LogEventType.ANNOTATION.value).to_dict(), + ) + warn(ServerWarning(message=message), cause=e) + else: + check = {'node_exist': False} if check['node_exist']: return check else: try: - query = get_lifelike_global_inclusion_exist_query(entity_type) - check = self.graph.exec_read_query_with_params(query, values)[0] - except (BrokenPipeError, ServiceUnavailable): + check = execute_arango_query( + db=get_db(self.arango_client), + query=get_lifelike_global_inclusion_exist_query(), + **lifelike_params, + )[0] + except BrokenPipeError: raise except Exception as e: message = ( f'Failed to create global inclusion, ' - f'knowledge graph failed with query: {query}.' + f'knowledge graph failed with query: {query_fn()}.' ) current_app.logger.error( message, diff --git a/appserver/neo4japp/services/annotations/pipeline.py b/appserver/neo4japp/services/annotations/pipeline.py index 4df7ea938a..c7a44b5066 100644 --- a/appserver/neo4japp/services/annotations/pipeline.py +++ b/appserver/neo4japp/services/annotations/pipeline.py @@ -1,14 +1,18 @@ import json import time -from typing import List, Tuple from flask import current_app +from typing import List, Optional, Tuple from neo4japp.constants import LogEventType, FILE_MIME_TYPE_PDF +from neo4japp.database import get_or_create_arango_client from neo4japp.exceptions import AnnotationError -from neo4japp.utils import normalize_str, EventLog +from neo4japp.utils.string import normalize_str +from neo4japp.utils.logger import EventLog + +from .annotation_graph_service import get_entity_inclusions from .constants import SPECIES_LMDB -from .data_transfer_objects import PDFWord, SpecifiedOrganismStrain +from .data_transfer_objects import GlobalInclusions, PDFWord, SpecifiedOrganismStrain from .utils.nlp import predict from .utils.parsing import parse_content @@ -30,7 +34,7 @@ class Pipeline: """ def __init__(self, steps: dict, **kwargs): - if not all(k in ['adbs', 'ags', 'aers', 'tkner', 'as', 'bs'] for k in steps): + if not all(k in ['adbs', 'aers', 'tkner', 'as', 'bs'] for k in steps): raise AnnotationError( 'Unable to Annotate', 'Configurations for the annotation pipeline is incorrect, please try again later.', @@ -40,7 +44,7 @@ def __init__(self, steps: dict, **kwargs): self.parsed = kwargs.get('parsed', []) self.entities = None self.global_exclusions = None - self.global_inclusions = None + self.global_inclusions: Optional[GlobalInclusions] = None @classmethod def parse(self, content_type: str, **kwargs) -> Tuple[str, List[PDFWord]]: @@ -74,12 +78,14 @@ def parse(self, content_type: str, **kwargs) -> Tuple[str, List[PDFWord]]: def get_globals( self, excluded_annotations: List[dict], custom_annotations: List[dict] ): + arango_client = get_or_create_arango_client() db_service = self.steps['adbs']() - graph_service = self.steps['ags']() start = time.time() self.global_exclusions = db_service.get_entity_exclusions(excluded_annotations) - self.global_inclusions = graph_service.get_entity_inclusions(custom_annotations) + self.global_inclusions = get_entity_inclusions( + arango_client, custom_annotations + ) current_app.logger.info( f'Time to process entity exclusions/inclusions {time.time() - start}', extra=EventLog(event_type=LogEventType.ANNOTATION.value).to_dict(), diff --git a/appserver/neo4japp/services/annotations/profilers/annotations_profiler.py b/appserver/neo4japp/services/annotations/profilers/annotations_profiler.py index b354d5feef..d4f5b5ee95 100644 --- a/appserver/neo4japp/services/annotations/profilers/annotations_profiler.py +++ b/appserver/neo4japp/services/annotations/profilers/annotations_profiler.py @@ -15,7 +15,6 @@ from neo4japp.services.annotations.pipeline import Pipeline from neo4japp.services.annotations.initializer import ( get_annotation_db_service, - get_annotation_graph_service, get_recognition_service, get_annotation_tokenizer, get_annotation_service, @@ -95,7 +94,6 @@ def main(): pipeline = Pipeline( { 'adbs': get_annotation_db_service, - 'ags': get_annotation_graph_service, 'aers': get_recognition_service, 'tkner': get_annotation_tokenizer, 'as': get_annotation_service, diff --git a/appserver/neo4japp/services/annotations/utils/graph_queries.py b/appserver/neo4japp/services/annotations/utils/graph_queries.py index 6af18927d1..7456069246 100644 --- a/appserver/neo4japp/services/annotations/utils/graph_queries.py +++ b/appserver/neo4japp/services/annotations/utils/graph_queries.py @@ -1,4 +1,6 @@ -from neo4japp.utils import compose_lines +from neo4japp.exceptions import InvalidArgument +from neo4japp.utils.string import compose_lines + from ..constants import EntityType @@ -20,13 +22,13 @@ EntityType.DISEASE.value: 'Disease', EntityType.FOOD.value: 'Food', EntityType.PHENOMENA.value: 'Phenomena', + EntityType.PHENOTYPE.value: 'Phenotype', EntityType.CHEMICAL.value: 'Chemical', EntityType.COMPOUND.value: 'Compound', EntityType.GENE.value: 'Gene', EntityType.SPECIES.value: 'Taxonomy', - EntityType.PATHWAY.value: 'Pathway', EntityType.PROTEIN.value: 'Protein', - EntityType.PHENOTYPE.value: 'Phenotype', + EntityType.PATHWAY.value: 'Pathway', EntityType.ENTITY.value: 'Entity', EntityType.COMPANY.value: 'Company', EntityType.LAB_SAMPLE.value: 'LabSample', @@ -34,411 +36,793 @@ } +collection_labels = { + EntityType.ANATOMY.value: 'mesh', + EntityType.DISEASE.value: 'mesh', + EntityType.FOOD.value: 'mesh', + EntityType.PHENOMENA.value: 'mesh', + EntityType.PHENOTYPE.value: 'mesh', + EntityType.CHEMICAL.value: 'chebi', + EntityType.COMPOUND.value: 'biocyc', + EntityType.GENE.value: 'ncbi', + EntityType.SPECIES.value: 'taxonomy', + EntityType.PROTEIN.value: 'uniprot', + EntityType.PATHWAY.value: 'kegg', + EntityType.ENTITY.value: 'lifelike', + EntityType.COMPANY.value: 'lifelike', + EntityType.LAB_SAMPLE.value: 'lifelike', + EntityType.LAB_STRAIN.value: 'lifelike', +} + + def query_builder(parts): return compose_lines(*parts) def get_organisms_from_gene_ids_query(): return """ - FOR doc IN ncbi - FILTER 'Gene' IN doc.labels - FILTER doc.eid IN @gene_ids - FOR v IN 1..1 OUTBOUND doc has_taxonomy - RETURN { - 'gene_id': doc.eid, - 'gene_name': doc.name, - 'taxonomy_id': v.eid, - 'species_name': v.name - } + FOR doc IN ncbi + FILTER 'Gene' IN doc.labels + FILTER doc.eid IN @gene_ids + FOR v IN 1..1 OUTBOUND doc has_taxonomy + RETURN { + 'gene_id': doc.eid, + 'gene_name': doc.name, + 'taxonomy_id': v.eid, + 'species_name': v.name + } """ def get_gene_to_organism_query(): return """ - MATCH (s:Synonym)-[]-(g:Gene) - WHERE s.name IN $genes - WITH s, g MATCH (g)-[:HAS_TAXONOMY]-(t:Taxonomy)-[:HAS_PARENT*0..2]->(p:Taxonomy) - WHERE p.eid IN $organisms - RETURN g.name AS gene_name, s.name AS gene_synonym, g.eid AS gene_id, - p.eid AS organism_id, g.data_source AS data_source + FOR s IN synonym + FILTER s.name IN @genes + FOR gene, synonym_rel IN INBOUND s has_synonym + FILTER 'Gene' IN gene.labels + LET t = FIRST( + FOR t IN OUTBOUND gene has_taxonomy + FILTER t.eid IN @organisms + RETURN t.eid + ) + LET t_parent = FIRST( + FOR temp_t IN OUTBOUND gene has_taxonomy + FOR parent IN OUTBOUND temp_t has_parent + FILTER parent.eid IN @organisms + RETURN parent.eid + ) + LET t_grandparent = FIRST( + FOR temp_t IN OUTBOUND gene has_taxonomy + FOR temp_parent IN OUTBOUND temp_t has_parent + FOR grand_parent IN OUTBOUND temp_parent has_parent + FILTER grand_parent.eid IN @organisms + RETURN grand_parent.eid + ) + LET organism_to_use = FIRST([t, t_parent, t_grandparent][* FILTER CURRENT != null]) + FILTER organism_to_use != null + RETURN DISTINCT { + 'gene_name': gene.name, + 'gene_synonym': s.name, + 'gene_id': gene.eid, + 'organism_id': organism_to_use, + 'data_source': gene.data_source + } """ def get_protein_to_organism_query(): return """ - MATCH (s:Synonym)-[]-(g:db_UniProt) - WHERE s.name IN $proteins - WITH s, g MATCH (g)-[:HAS_TAXONOMY]-(t:Taxonomy)-[:HAS_PARENT*0..2]->(p:Taxonomy) - WHERE p.eid IN $organisms - RETURN s.name AS protein, collect(g.eid) AS protein_ids, p.eid AS organism_id + FOR s IN synonym + FILTER s.name IN @proteins + FOR protein IN INBOUND s has_synonym OPTIONS {vertexCollections: 'uniprot'} + FILTER 'Protein' IN protein.labels + LET t = FIRST( + FOR t IN OUTBOUND protein has_taxonomy + FILTER t.eid IN @organisms + RETURN t.eid + ) + LET t_parent = FIRST( + FOR temp_t IN OUTBOUND protein has_taxonomy + FOR parent IN OUTBOUND temp_t has_parent + FILTER parent.eid IN @organisms + RETURN parent.eid + ) + LET t_grandparent = FIRST( + FOR temp_t IN OUTBOUND protein has_taxonomy + FOR temp_parent IN OUTBOUND temp_t has_parent + FOR grand_parent IN OUTBOUND temp_parent has_parent + FILTER grand_parent.eid IN @organisms + RETURN grand_parent.eid + ) + LET organism_to_use = FIRST([t, t_parent, t_grandparent][* FILTER CURRENT != null]) + FILTER organism_to_use != null + COLLECT organism = organism_to_use, protein_name = s.name INTO protein_ids + RETURN { + 'protein': protein_name, + 'protein_ids': protein_ids[*].protein.eid, + 'organism_id': organism, + } """ def get_global_inclusions_count_query(): return """ - MATCH (s:GlobalInclusion:Synonym)-[r:HAS_SYNONYM]-(n) - WHERE r.global_inclusion = true AND exists(r.inclusion_date) - RETURN count(s) AS total + RETURN { + 'total': COUNT( + FOR doc IN synonym + FILTER 'GlobalInclusion' in doc.labels + FOR v, e IN 1..1 INBOUND doc has_synonym + FILTER e.global_inclusion == true + FILTER e.inclusion_date != null + SORT e.inclusion_date DESC + RETURN e.inclusion_date + ) + } """ def get_global_inclusions_query(): return """ - MATCH (s:GlobalInclusion:Synonym)-[r:HAS_SYNONYM]-(n) - WHERE r.global_inclusion = true AND exists(r.inclusion_date) - RETURN - id(n) AS node_internal_id, - id(s) AS syn_node_internal_id, - n.eid AS entity_id, - s.name AS synonym, - n.data_source AS data_source, - r.entity_type AS entity_type, - r.file_reference AS file_reference, - r.user AS creator, - r.inclusion_date AS creation_date - ORDER BY toLower(synonym) + FOR doc IN synonym + FILTER 'GlobalInclusion' IN doc.labels + FOR v, e IN 1..1 INBOUND doc has_synonym + FILTER e.label == 'has_synonym' + FILTER e.global_inclusion == true + FILTER e.inclusion_date != null + SORT LOWER(doc.name) + RETURN { + 'node_internal_id': v._id, + 'syn_node_internal_id': doc._id, + 'entity_id': v.eid, + 'synonym': doc.name, + 'data_source': v.data_source, + 'entity_type': e.entity_type, + 'file_reference': e.file_reference, + 'creator': e.user, + 'creation_date': e.inclusion_date + } """ def get_global_inclusions_paginated_query(): return """ - MATCH (s:GlobalInclusion:Synonym)-[r:HAS_SYNONYM]-(n) - WHERE r.global_inclusion = true AND exists(r.inclusion_date) - RETURN - id(n) AS node_internal_id, - id(s) AS syn_node_internal_id, - n.eid AS entity_id, - s.name AS synonym, - n.data_source AS data_source, - r.entity_type AS entity_type, - r.file_reference AS file_reference, - r.user AS creator, - r.inclusion_date AS creation_date - ORDER BY toLower(synonym) - SKIP $skip - LIMIT $limit + FOR doc IN synonym + FILTER 'GlobalInclusion' IN doc.labels + FOR v, e IN 1..1 INBOUND doc has_synonym + FILTER e.label == 'has_synonym' + FILTER e.global_inclusion == true + FILTER e.inclusion_date != null + SORT LOWER(doc.name) ASC + LIMIT @skip, @limit + RETURN { + 'node_internal_id': v._id, + 'syn_node_internal_id': doc._id, + 'entity_id': v.eid, + 'synonym': doc.name, + 'data_source': v.data_source, + 'entity_type': e.entity_type, + 'file_reference': e.file_reference, + 'creator': e.user, + 'creation_date': e.inclusion_date + } """ -def get_nodes_by_ids(entity_type): - if entity_type not in node_labels: - return '' - - query_label = node_labels[entity_type] - if entity_type in source_labels: - query_label = f'{source_labels[entity_type]}:{query_label}' +def get_docs_by_ids_query(entity_type): + try: + collection = collection_labels[entity_type] + except KeyError: + raise InvalidArgument( + f'Could not query for document with entity type: {entity_type}. No ' + 'collection exists for this type.' + ) return f""" - MATCH (n:{query_label}) WHERE n.eid IN $ids - RETURN n.eid AS entity_id, n.name AS entity_name - """ - - -# NOTE DEPRECATED: just used in old migration -def get_mesh_by_ids(): - return """ - MATCH (n:db_MESH:TopicalDescriptor) WHERE n.eid IN $ids - RETURN n.eid AS mesh_id, n.name AS mesh_name + FOR doc IN {collection} + FILTER doc.eid IN @ids + RETURN {{'entity_id': doc.eid, 'entity_name': doc.name}} """ def get_node_labels_and_relationship_query(): return """ - MATCH (n)-[r:HAS_SYNONYM]-() - WHERE id(n) IN $node_ids AND exists(n.original_entity_types) - RETURN id(n) AS node_id, n.eid AS entity_id, - [l IN labels(n) WHERE NOT l starts WITH 'db_' AND - NOT l IN [ - 'TopicalDescriptor', - 'TreeNumber', - 'BioCycClass', - 'GlobalInclusion', - 'Complex'] - ] AS node_labels, - n.original_entity_types AS valid_entity_types, - collect(DISTINCT r.entity_type) AS rel_entity_types + // Review Note: The original cypher query was returning no results even without the ID filter, + // so the AQL is not easily testable. + FOR doc IN synonym + FILTER doc._id IN @ids + FILTER doc.original_entity_types != null + LET rel_types = ( + FOR v, e IN 1..1 INBOUND doc has_synonym + RETURN DISTINCT e.entity_type + ) + RETURN { + 'node_id': doc._id, + 'entity_id': doc.eid, + 'node_labels': doc.labels[ + * FILTER + CURRENT NOT IN [ + 'TopicalDescriptor', + 'TreeNumber', + 'BioCycClass', + 'GlobalInclusion', + 'Complex' + ] + ], + 'valid_entity_types': doc.original_entity_types, + 'rel_entity_types': rel_types + } """ def get_delete_global_inclusion_query(): return """ - UNWIND $node_ids AS node_ids - MATCH (s)-[r:HAS_SYNONYM]-(n) - WHERE id(n) = node_ids[0] AND id(s) = node_ids[1] - DELETE r - WITH s - MATCH (s)-[r:HAS_SYNONYM]-() - WHERE r.global_inclusion = true AND exists(r.inclusion_date) - WITH s, collect(r) AS synonym_rel - CALL apoc.do.when( - size(synonym_rel) = 0, - 'REMOVE s:GlobalInclusion', '', {synonym_rel: synonym_rel, s:s} - ) - YIELD value - RETURN COUNT(*) + FOR id_pair IN @pairs + LET entity_doc_id = id_pair[0] + LET synonym_doc_id = id_pair[1] + + // Note that in converting this query from cypher, we've reversed the query: you + // cannot read from a collection in Arango after deleting from it, so here we get the + // total count of global relationships first, then delete any between the entity node + // and the synonym. + + // Get the count of global relationships *before* removing any + LET prev_global_rels_for_synonym = LENGTH( + FOR doc IN has_synonym + FILTER doc._to == synonym_doc_id + FILTER doc.global_inclusion == true + FILTER doc.inclusion_date != null + RETURN doc + ) + + // Remove the provided relationships, and return how many were removed + LET num_removed = LENGTH( + FOR s IN has_synonym + FILTER s._from == entity_doc_id + FILTER s._to == synonym_doc_id + REMOVE s IN has_synonym + RETURN s + ) + + // Remove the 'GlobalInclusion' label from the synonym if the previous number of global + // relationships remaining equals the number we've just removed. + FILTER prev_global_rels_for_synonym == num_removed + // Review note: The original query returns the count of the results returned from an + // apoc call. However, it only does that because it needs to end in a 'RETURN' + // statement. We don't actually use those values. I'm opting to not return anything in + // this query, because we don't need to. + // Another note: shouldn't we delete the synonym if it has no more has_synonym edges? + // This should be possible if the synonym is purely a global inclusion, so if we don't + // delete it we could be generating orphaned synonyms. I guess in practice it doesn't + // really matter, but it's a little smelly. + FOR doc IN synonym + FILTER doc._id == synonym_doc_id + UPDATE doc WITH {labels: REMOVE_VALUE(doc.labels, 'GlobalInclusion')} IN synonym """ -def get_global_inclusions_by_type_query(entity_type): - if entity_type not in node_labels: - return '' - - query_label = node_labels[entity_type] - - if entity_type in source_labels: - query_label = f'{source_labels[entity_type]}:{query_label}' - - return f""" - MATCH (s:GlobalInclusion:Synonym)-[r:HAS_SYNONYM]-(n:{query_label}) - WHERE r.global_inclusion = true AND exists(r.inclusion_date) - RETURN - id(n) AS internal_id, - n.eid AS entity_id, - n.name AS entity_name, - n.data_source AS data_source, - s.name AS synonym, - r.hyperlinks AS hyperlinks +def get_global_inclusions_by_type_query(): + return """ + FOR doc IN synonym + FILTER 'GlobalInclusion' IN doc.labels + FOR v, e IN 1..1 INBOUND doc has_synonym OPTIONS { vertexCollections: @collection } + FILTER e.global_inclusion == true + FILTER e.inclusion_date != null + // Need the 'OR' clause here since documents in the 'taxonomy' collection don't have + // any entries in their labels. + FILTER @entity_type IN v.labels OR LENGTH(v.labels) == 0 + RETURN { + 'internal_id': v._id, + 'entity_id': v.eid, + 'entity_name': v.name, + 'data_source': v.data_source, + 'synonym': doc.name, + 'hyperlinks': e.hyperlinks + } """ -def get_lifelike_global_inclusions_by_type_query(entity_type): - if entity_type not in node_labels: - return '' - - query_label = node_labels[entity_type] - if entity_type == EntityType.SPECIES.value: - query_label = 'Organism' - - return f""" - MATCH (s:GlobalInclusion:Synonym)-[r:HAS_SYNONYM]-(n:db_Lifelike:{query_label}) - RETURN - id(n) AS internal_id, - n.eid AS entity_id, - n.name AS entity_name, - n.data_source AS data_source, - s.name AS synonym, - r.hyperlinks AS hyperlinks +def get_lifelike_global_inclusions_by_type_query(): + return """ + FOR doc IN synonym + FILTER 'GlobalInclusion' IN doc.labels + FOR v, e IN 1..1 INBOUND doc has_synonym OPTIONS { vertexCollections: 'lifelike' } + FILTER e.label == 'has_synonym' + FILTER @entity_type IN v.labels + SORT v._id ASC + RETURN { + 'internal_id': v._id, + 'entity_id': v.eid, + 'entity_name': v.name, + 'data_source': v.data_source, + 'synonym': doc.name, + 'hyperlinks': e.hyperlinks + } """ -def get_mesh_global_inclusion_exist_query(entity_type): - if entity_type not in node_labels: - return '' - - query_label = node_labels[entity_type] +def get_mesh_global_inclusion_exist_query(): return f""" - OPTIONAL MATCH (n:db_MESH)-[:HAS_SYNONYM]->(s) - WHERE n.eid = $entity_id - RETURN n IS NOT NULL AS node_exist, - '{query_label}' IN labels(n) AS node_has_entity_label, - $synonym IN collect(s.name) AS synonym_exist + LET meshGlobalInclusion = FIRST( + FOR doc IN mesh + FILTER doc.eid == @entity_id + RETURN doc + ) + LET synonymWithName = FIRST( + FOR doc IN synonym + FILTER doc.name == @synonym + RETURN doc + ) + LET inclusionToSynonymRel = FIRST( + FOR rel IN has_synonym + FILTER rel._from == meshGlobalInclusion._id + FILTER rel._to == synonymWithName._id + RETURN rel + ) + RETURN {{ + 'node_exist': meshGlobalInclusion != NULL, + 'synonym_exist': synonymWithName != NULL AND inclusionToSynonymRel != NULL, + 'node_has_entity_label': @entity_type IN meshGlobalInclusion.labels + }} """ def get_chemical_global_inclusion_exist_query(): return """ - OPTIONAL MATCH (n:db_CHEBI:Chemical)-[:HAS_SYNONYM]->(s) - WHERE n.eid = $entity_id - RETURN n IS NOT NULL AS node_exist, - $synonym IN collect(s.name) AS synonym_exist + LET chebiGlobalInclusion = FIRST( + FOR doc IN chebi + FILTER 'Chemical' IN doc.labels + FILTER doc.eid == @entity_id + RETURN doc + ) + LET synonymWithName = FIRST( + FOR doc IN synonym + FILTER doc.name == @synonym + RETURN doc + ) + LET inclusionToSynonymRel = FIRST( + FOR rel IN has_synonym + FILTER rel._from == chebiGlobalInclusion._id + FILTER rel._to == synonymWithName._id + RETURN rel + ) + RETURN { + 'node_exist': chebiGlobalInclusion != NULL, + 'synonym_exist': synonymWithName != NULL AND inclusionToSynonymRel != NULL + } """ def get_compound_global_inclusion_exist_query(): return """ - OPTIONAL MATCH (n:db_BioCyc:Compound)-[:HAS_SYNONYM]->(s) - WHERE n.eid = $entity_id - RETURN n IS NOT NULL AS node_exist, - $synonym IN collect(s.name) AS synonym_exist + LET biocycGlobalInclusion = FIRST( + FOR doc IN biocyc + FILTER 'Compound' IN doc.labels + FILTER doc.eid == @entity_id + RETURN doc + ) + LET synonymWithName = FIRST( + FOR doc IN synonym + FILTER doc.name == @synonym + RETURN doc + ) + LET inclusionToSynonymRel = FIRST( + FOR rel IN has_synonym + FILTER rel._from == biocycGlobalInclusion._id + FILTER rel._to == synonymWithName._id + RETURN rel + ) + RETURN { + 'node_exist': biocycGlobalInclusion != NULL, + 'synonym_exist': synonymWithName != NULL AND inclusionToSynonymRel != NULL + } """ def get_gene_global_inclusion_exist_query(): return """ - OPTIONAL MATCH (n:Gene)-[:HAS_SYNONYM]->(s) - WHERE n.eid = $entity_id - RETURN n IS NOT NULL AS node_exist, - $synonym IN collect(s.name) AS synonym_exist + LET res = ( + // Review note: This union may not be necessary if we're strictly expecting either ncbi or + // biocyc results from this query + FOR n IN union( + ( + FOR n1 IN ncbi + FILTER n1.eid == @entity_id + FILTER 'Master' IN n1.labels + RETURN n1 + ), + ( + FOR n2 IN biocyc + FILTER n2.eid == @entity_id + FILTER 'Master' IN n2.labels + RETURN n2 + ) + ) + FILTER 'Gene' IN n.labels + LET synList = ( + FOR v, e IN 1..1 OUTBOUND n has_synonym + FILTER v.name == @synonym + RETURN 1 + ) + RETURN {node_exist: true, synonym_exist: length(synList) > 0} + ) + RETURN length(res) == 0 ? { node_exist: false, synonym_exist: false } : res[0] """ def get_pathway_global_inclusion_exist_query(): return """ - OPTIONAL MATCH (n:Pathway)-[:HAS_SYNONYM]->(s) - WHERE n.eid = $entity_id - RETURN n IS NOT NULL AS node_exist, - $synonym IN collect(s.name) AS synonym_exist + LET res = ( + FOR n IN biocyc + FILTER n.eid == @entity_id + FILTER 'Pathway' IN n.labels + LET synList = ( + FOR v, e IN 1..1 OUTBOUND n has_synonym + FILTER v.name == @synonym + RETURN 1 + ) + RETURN {node_exist: true, synonym_exist: length(synList) > 0} + ) + RETURN length(res) == 0 ? { node_exist: false, synonym_exist: false } : res[0] """ def get_protein_global_inclusion_exist_query(): return """ - OPTIONAL MATCH (n:db_UniProt:Protein)-[:HAS_SYNONYM]->(s) - WHERE n.eid = $entity_id - RETURN n IS NOT NULL AS node_exist, - $synonym IN collect(s.name) AS synonym_exist + LET res = ( + FOR n IN uniprot + FILTER n.eid == @entity_id + FILTER 'Protein' IN n.labels + LET synList = ( + FOR v, e IN 1..1 OUTBOUND n has_synonym + FILTER v.name == @synonym + RETURN 1 + ) + RETURN {node_exist: true, synonym_exist: length(synList) > 0} + ) + RETURN length(res) == 0 ? { node_exist: false, synonym_exist: false } : res[0] """ def get_species_global_inclusion_exist_query(): return """ - OPTIONAL MATCH (n:db_NCBI:Taxonomy)-[:HAS_SYNONYM]->(s) - WHERE n.eid = $entity_id - RETURN n IS NOT NULL AS node_exist, - $synonym IN collect(s.name) AS synonym_exist + LET res = ( + FOR n IN taxonomy + FILTER n.eid == @entity_id + LET synList = ( + FOR v, e IN 1..1 OUTBOUND n has_synonym + FILTER v.name == @synonym + RETURN 1 + ) + RETURN {node_exist: true, synonym_exist: length(synList) > 0} + ) + RETURN length(res) == 0 ? { node_exist: false, synonym_exist: false } : res[0] """ -def get_lifelike_global_inclusion_exist_query(entity_type): - if entity_type not in node_labels: - return '' - - query_label = node_labels[entity_type] +def get_lifelike_global_inclusion_exist_query(): return f""" - OPTIONAL MATCH (n:db_Lifelike:{query_label})-[r:HAS_SYNONYM]->(s) - WHERE n.name = $common_name AND r.entity_type = $entity_type - RETURN n IS NOT NULL AS node_exist, - $synonym IN collect(s.name) OR - CASE WHEN - n IS NOT NULL THEN NOT 'NULL_' IN n.eid - ELSE false END AS synonym_exist + LET res = ( + FOR n IN lifelike + FILTER n.name == @common_name + FILTER @entity_type IN n.labels + LET synList = ( + FOR v, e IN 1..1 OUTBOUND n has_synonym + FILTER v.name == @synonym + FILTER e.entity_type == @entity_type + RETURN 1 + ) + RETURN {{node_exist: true, synonym_exist: length(synList) > 0}} + ) + RETURN length(res) == 0 ? {{ node_exist: false, synonym_exist: false }} : res[0] """ -def get_create_mesh_global_inclusion_query(entity_type): - if entity_type not in node_labels: - return '' - - query_label = node_labels[entity_type] +def get_create_mesh_global_inclusion_query(): return """ - MATCH (n:db_MESH) WHERE n.eid = $entity_id - SET n:replace_with_param - MERGE (s: Synonym {name: $synonym}) - SET s:GlobalInclusion, s.lowercase_name = toLower($synonym) - MERGE (n)-[r:HAS_SYNONYM]->(s) - ON CREATE - SET r.inclusion_date = apoc.date.parseAsZonedDateTime($inclusion_date), - r.global_inclusion = true, - r.user = $user, - r.file_reference = $file_uuid, - r.entity_type = $entity_type, - r.hyperlinks = $hyperlinks - """.replace( - 'replace_with_param', query_label - ) + FOR doc IN mesh + FILTER doc.eid == @entity_id + // First, update the mesh document with the new label (it won't be added if it already + // exists). Note that the subqueries are required because you cannot use the OLD/NEW + // special variables more than once in a single scope. + LET m = FIRST( + UPDATE doc WITH { + labels: PUSH(doc.labels, @entity_type, true) + } IN mesh + RETURN NEW + ) + // Then, create a synonym with the given name, if one doesn't exist. + LET s = FIRST( + UPSERT { name: @synonym } + INSERT { name: @synonym, lowercase_name: lower(@synonym), labels: ['GlobalInclusion'] } + UPDATE { + lowercase_name: lower(@synonym), + labels: PUSH(OLD.labels, 'GlobalInclusion', true) + } IN synonym + RETURN NEW + ) + // Finally, create a new 'has_synonym' relation if there is none between 'm' and 's'. Note + // that if 's' was just created, this always inserts a new document. Also, if *ANY* + // has_synonym exists between 'm' and 's', a new document is *NOT* created and the existing + // document is *NOT* updated. + UPSERT { + _from: m._id, + _to: s._id, + } + // TODO: Write comment regarding existing labels in mesh being used in favor of any new ones + INSERT { + _from: m._id, + _to: s._id, + label: 'has_synonym', + inclusion_date: date_format(@inclusion_date, '%z'), + global_inclusion: true, + user: @user, + file_reference: @file_uuid, + entity_type: @entity_type, + hyperlinks: @hyperlinks + } + UPDATE OLD IN has_synonym + """ def get_create_chemical_global_inclusion_query(): return """ - MATCH (n:db_CHEBI:Chemical) WHERE n.eid = $entity_id - MERGE (s:Synonym {name: $synonym}) - SET s:GlobalInclusion, s.lowercase_name = toLower($synonym) - MERGE (n)-[r:HAS_SYNONYM]->(s) - ON CREATE - SET r.inclusion_date = apoc.date.parseAsZonedDateTime($inclusion_date), - r.global_inclusion = true, - r.user = $user, - r.file_reference = $file_uuid, - r.entity_type = 'Chemical', - r.hyperlinks = $hyperlinks + FOR c IN chebi + FILTER c.eid == @entity_id + FILTER 'Chemical' IN c.labels + // First, create a synonym with the given name, if one doesn't exist. Note that the + // subquery is required because you cannot use the OLD/NEW special variables more than + // once in a single scope. + LET s = FIRST( + UPSERT { name: @synonym } + INSERT { name: @synonym, lowercase_name: lower(@synonym), labels: ['GlobalInclusion'] } + UPDATE { + lowercase_name: lower(@synonym), + labels: PUSH(OLD.labels, 'GlobalInclusion', true) + } IN synonym + RETURN NEW + ) + // Finally, create a new 'has_synonym' relation if there is none between 'm' and 's'. Note + // that if 's' was just created, this always inserts a new document. Also, if *ANY* + // has_synonym exists between 'm' and 's', a new document is *NOT* created and the existing + // document is *NOT* updated. + UPSERT { + _from: c._id, + _to: s._id, + } + INSERT { + _from: c._id, + _to: s._id, + label: 'has_synonym', + inclusion_date: date_format(@inclusion_date, '%z'), + global_inclusion: true, + user: @user, + file_reference: @file_uuid, + entity_type: 'Chemical', + hyperlinks: @hyperlinks + } + UPDATE OLD IN has_synonym """ def get_create_compound_global_inclusion_query(): return """ - MATCH (n:db_BioCyc:Compound) WHERE n.eid = $entity_id - MERGE (s:Synonym {name: $synonym}) - SET s:GlobalInclusion, s.lowercase_name = toLower($synonym) - MERGE (n)-[r:HAS_SYNONYM]->(s) - ON CREATE - SET r.inclusion_date = apoc.date.parseAsZonedDateTime($inclusion_date), - r.global_inclusion = true, - r.user = $user, - r.file_reference = $file_uuid, - r.entity_type = 'Compound', - r.hyperlinks = $hyperlinks + FOR b IN biocyc + FILTER b.eid == @entity_id + FILTER 'Compound' IN b.labels + // First, create a synonym with the given name, if one doesn't exist. Note that the + // subquery is required because you cannot use the OLD/NEW special variables more than + // once in a single scope. + LET s = FIRST( + UPSERT { name: @synonym } + INSERT { name: @synonym, lowercase_name: lower(@synonym), labels: ['GlobalInclusion'] } + UPDATE { + lowercase_name: lower(@synonym), + labels: PUSH(OLD.labels, 'GlobalInclusion', true) + } IN synonym + RETURN NEW + ) + // Finally, create a new 'has_synonym' relation if there is none between 'm' and 's'. Note + // that if 's' was just created, this always inserts a new document. Also, if *ANY* + // has_synonym exists between 'm' and 's', a new document is *NOT* created and the existing + // document is *NOT* updated. + UPSERT { + _from: b._id, + _to: s._id, + } + INSERT { + _from: b._id, + _to: s._id, + label: 'has_synonym', + inclusion_date: date_format(@inclusion_date, '%z'), + global_inclusion: true, + user: @user, + file_reference: @file_uuid, + entity_type: 'Compound', + hyperlinks: @hyperlinks + } + UPDATE OLD IN has_synonym """ def get_create_gene_global_inclusion_query(): return """ - MATCH (n:Gene) WHERE n.eid = $entity_id - MERGE (s:Synonym {name: $synonym}) - SET s:GlobalInclusion, s.lowercase_name = toLower($synonym) - MERGE (n)-[r:HAS_SYNONYM]->(s) - ON CREATE - SET r.inclusion_date = apoc.date.parseAsZonedDateTime($inclusion_date), - r.global_inclusion = true, - r.user = $user, - r.file_reference = $file_uuid, - r.entity_type = 'Gene', - r.hyperlinks = $hyperlinks + FOR g IN UNION ( + ( + FOR g1 IN ncbi + FILTER g1.eid == @entity_id + RETURN g1 + ), + ( + FOR g2 IN biocyc + FILTER g2.eid == @entity_id + RETURN g2 + ) + ) + FILTER 'Gene' IN g.labels + // First, create a synonym with the given name, if one doesn't exist. Note that the + // subquery is required because you cannot use the OLD/NEW special variables more than + // once in a single scope. + LET s = FIRST( + UPSERT { name: @synonym } + INSERT { name: @synonym, lowercase_name: lower(@synonym), labels: ['GlobalInclusion'] } + UPDATE { + lowercase_name: lower(@synonym), + labels: PUSH(OLD.labels, 'GlobalInclusion', true) + } IN synonym + RETURN NEW + ) + // Finally, create a new 'has_synonym' relation if there is none between 'm' and 's'. Note + // that if 's' was just created, this always inserts a new document. Also, if *ANY* + // has_synonym exists between 'm' and 's', a new document is *NOT* created and the existing + // document is *NOT* updated. + UPSERT { + _from: g._id, + _to: s._id, + } + INSERT { + _from: g._id, + _to: s._id, + label: 'has_synonym', + inclusion_date: date_format(@inclusion_date, '%z'), + global_inclusion: true, + user: @user, + file_reference: @file_uuid, + entity_type: 'Gene', + hyperlinks: @hyperlinks + } + UPDATE OLD IN has_synonym """ def get_create_species_global_inclusion_query(): return """ - MATCH (n:db_NCBI:Taxonomy) WHERE n.eid = $entity_id - MERGE (s:Synonym {name: $synonym}) - SET s:GlobalInclusion, s.lowercase_name = toLower($synonym) - MERGE (n)-[r:HAS_SYNONYM]->(s) - ON CREATE - SET r.inclusion_date = apoc.date.parseAsZonedDateTime($inclusion_date), - r.global_inclusion = true, - r.user = $user, - r.file_reference = $file_uuid, - r.entity_type = 'Species', - r.hyperlinks = $hyperlinks + FOR t IN taxonomy + FILTER t.eid == @entity_id + // First, create a synonym with the given name, if one doesn't exist. Note that the + // subquery is required because you cannot use the OLD/NEW special variables more than + // once in a single scope. + LET s = FIRST( + UPSERT { name: @synonym } + INSERT { name: @synonym, lowercase_name: lower(@synonym), labels: ['GlobalInclusion'] } + UPDATE { + lowercase_name: lower(@synonym), + labels: PUSH(OLD.labels, 'GlobalInclusion', true) + } IN synonym + RETURN NEW + ) + // Finally, create a new 'has_synonym' relation if there is none between 'm' and 's'. Note + // that if 's' was just created, this always inserts a new document. Also, if *ANY* + // has_synonym exists between 'm' and 's', a new document is *NOT* created and the existing + // document is *NOT* updated. + UPSERT { + _from: t._id, + _to: s._id, + } + INSERT { + _from: t._id, + _to: s._id, + label: 'has_synonym', + inclusion_date: date_format(@inclusion_date, '%z'), + global_inclusion: true, + user: @user, + file_reference: @file_uuid, + entity_type: 'Species', + hyperlinks: @hyperlinks + } + UPDATE OLD IN has_synonym """ def get_create_protein_global_inclusion_query(): return """ - MATCH (n:db_UniProt:Protein) WHERE n.eid = $entity_id - MERGE (s:Synonym {name: $synonym}) - SET s:GlobalInclusion, s.lowercase_name = toLower($synonym) - MERGE (n)-[r:HAS_SYNONYM]->(s) - ON CREATE - SET r.inclusion_date = apoc.date.parseAsZonedDateTime($inclusion_date), - r.global_inclusion = true, - r.user = $user, - r.file_reference = $file_uuid, - r.entity_type = 'Protein', - r.hyperlinks = $hyperlinks + FOR p IN uniprot + FILTER p.eid == @entity_id + FILTER 'Protein' IN p.labels + // First, create a synonym with the given name, if one doesn't exist. Note that the + // subquery is required because you cannot use the OLD/NEW special variables more than + // once in a single scope. + LET s = FIRST( + UPSERT { name: @synonym } + INSERT { name: @synonym, lowercase_name: lower(@synonym), labels: ['GlobalInclusion'] } + UPDATE { + lowercase_name: lower(@synonym), + labels: PUSH(OLD.labels, 'GlobalInclusion', true) + } IN synonym + RETURN NEW + ) + // Finally, create a new 'has_synonym' relation if there is none between 'm' and 's'. Note + // that if 's' was just created, this always inserts a new document. Also, if *ANY* + // has_synonym exists between 'm' and 's', a new document is *NOT* created and the existing + // document is *NOT* updated. + UPSERT { + _from: p._id, + _to: s._id, + } + INSERT { + _from: p._id, + _to: s._id, + label: 'has_synonym', + inclusion_date: date_format(@inclusion_date, '%z'), + global_inclusion: true, + user: @user, + file_reference: @file_uuid, + entity_type: 'Protein', + hyperlinks: @hyperlinks + } + UPDATE OLD IN has_synonym """ -def get_create_lifelike_global_inclusion_query(entity_type): - if entity_type not in node_labels: - return '' - - query_label = node_labels[entity_type] - if entity_type == EntityType.SPECIES.value: - query_label = 'Organism' - +def get_create_lifelike_global_inclusion_query(): # NOTE: a new gene should not be created, because # we have no option to specify an organism relationship # rather a new synonym of an existing gene can be created # so no need to add a :Master Gene label return """ - MERGE (n:db_Lifelike {name: $common_name}) - ON CREATE - SET n.eid = $entity_id, - n:GlobalInclusion:replace_with_param, - n.data_source = $data_source, - n.name = $common_name - WITH n - MERGE (s:Synonym {name: $synonym}) - SET s:GlobalInclusion, s.lowercase_name = toLower($synonym) - MERGE (n)-[r:HAS_SYNONYM]->(s) - ON CREATE - SET r.inclusion_date = apoc.date.parseAsZonedDateTime($inclusion_date), - r.global_inclusion = true, - r.user = $user, - r.file_reference = $file_uuid, - r.entity_type = $entity_type, - r.hyperlinks = $hyperlinks - """.replace( - 'replace_with_param', query_label + LET mergedLifelikeDoc = FIRST( + UPSERT { name: @common_name } + INSERT { + name: @common_name, + eid: @entity_id, + data_source: @data_source, + labels: ['GlobalInclusion', @entity_type] + } + UPDATE { + eid: @entity_id, + } IN lifelike + RETURN NEW ) + // First, create a synonym with the given name, if one doesn't exist. Note that the + // subquery is required because you cannot use the OLD/NEW special variables more than + // once in a single scope. + LET s = FIRST( + UPSERT { name: @synonym } + INSERT { name: @synonym, lowercase_name: lower(@synonym), labels: ['GlobalInclusion'] } + UPDATE { + lowercase_name: lower(@synonym), + labels: PUSH(OLD.labels, 'GlobalInclusion', true) + } IN synonym + RETURN NEW + ) + // Finally, create a new 'has_synonym' relation if there is none between 'mergedLifelikeDoc' + // and 's'. Note that if 's' was just created, this always inserts a new document. Also, if + // *ANY* has_synonym exists between 'mergedLifelikeDoc' and 's', a new document is *NOT* + // created and the existing document is *NOT* updated. + UPSERT { + _from: mergedLifelikeDoc._id, + _to: s._id, + } + INSERT { + _from: mergedLifelikeDoc._id, + _to: s._id, + label: 'has_synonym', + inclusion_date: date_format(@inclusion_date, '%z'), + global_inclusion: true, + user: @user, + file_reference: @file_uuid, + entity_type: @entity_type, + hyperlinks: @hyperlinks + } + UPDATE OLD IN has_synonym + """ diff --git a/appserver/neo4japp/services/arangodb.py b/appserver/neo4japp/services/arangodb.py index 7f2996ecb2..01579e74bc 100644 --- a/appserver/neo4japp/services/arangodb.py +++ b/appserver/neo4japp/services/arangodb.py @@ -1,11 +1,30 @@ from arango import ArangoClient from arango.database import StandardDatabase -from typing import Dict, List, Optional +from datetime import datetime +from typing import Any, Dict, List, Optional + from neo4japp.utils.globals import config # Helpers +def convert_datetime(date_val: str) -> datetime: + valid_formats = [ + '%Y-%m-%d %H:%M:%S', + '%Y-%m-%dT%H:%M:%S.%fZ', + '%Y-%m-%dT%H:%M:%SZ[UTC]', + '%Y-%m-%dT%H:%MZ[UTC]', + ] + for format in valid_formats: + try: + return datetime.strptime(date_val, format) + except ValueError: + continue + raise ValueError( + f'time data {date_val} does not match any of the accepted formats.' + ) + + def get_version(client: ArangoClient): return client.version @@ -23,7 +42,7 @@ def get_db( ) -def execute_arango_query(db: StandardDatabase, query: str, **bind_vars) -> List[Dict]: +def execute_arango_query(db: StandardDatabase, query: str, **bind_vars) -> List[Any]: cursor = db.aql.execute(query, ttl=600, max_runtime=600, bind_vars=bind_vars) return [row for row in cursor] @@ -40,7 +59,7 @@ def add_document_to_collection( overwrite: bool = False, ) -> Dict: collection = db.collection(colxn_name) - return collection.insert(doc, return_new=True, overwrite=overwrite) + return collection.insert(doc, return_new=True, overwrite=overwrite)['new'] def add_many_to_collection( diff --git a/appserver/neo4japp/services/common.py b/appserver/neo4japp/services/common.py index 06b4cf64af..9c3d1265c8 100644 --- a/appserver/neo4japp/services/common.py +++ b/appserver/neo4japp/services/common.py @@ -1,9 +1,5 @@ import abc -from datetime import datetime -from typing import Any, Callable -from neo4j import Session -from neo4j.exceptions import ServiceUnavailable from sqlalchemy.exc import SQLAlchemyError @@ -66,97 +62,6 @@ def begin(self, **kwargs): raise NotImplementedError -class GraphConnection(DatabaseConnection): - def __init__(self, conn): - self.conn = conn - - class _context(TransactionContext): - def __init__(self, conn): - self.conn = conn - - def __enter__(self): - self.session = self.conn.session() - return self.session - - def __exit__(self, exc_type, exc_val, exc_traceback): - self.session.close() - - def convert_datetime(self, graph_date): - """Convert a neo4j Datetime to python datetime""" - return datetime( - graph_date.year, - graph_date.month, - graph_date.day, - graph_date.hour, - graph_date.minute, - int(graph_date.second), - int(graph_date.second * 1000000 % 1000000), - tzinfo=graph_date.tzinfo, - ) - - def begin(self, **kwargs): - return self._context(self.conn) - - def exec_read_query(self, query: str): - try: - with self.begin() as session: - return session.read_transaction(lambda tx: list(tx.run(query))) - except BrokenPipeError as e: - raise BrokenPipeError( - 'The graph connection became stale while processing data. ' - 'Please refresh the browser and try again.' - ) from e - except ServiceUnavailable as e: - raise ServiceUnavailable( - 'Timed out trying to establish connection to the graph database. ' - 'Please try again at a later time.' - ) from e - - def exec_write_query(self, query: str): - try: - with self.begin() as session: - return session.write_transaction(lambda tx: list(tx.run(query))) - except BrokenPipeError as e: - raise BrokenPipeError( - 'The graph connection became stale while processing data, ' - 'Please refresh the browser and try again.' - ) from e - except ServiceUnavailable as e: - raise ServiceUnavailable( - 'Timed out trying to establish connection to the graph database. ' - 'Please try again at a later time.' - ) from e - - def _exec_with_wrapped_exceptions(self, exec: Callable[[Session], Any]): - try: - with self.begin() as session: - return exec(session) - except BrokenPipeError as e: - raise BrokenPipeError( - 'The graph connection became stale while processing data, ' - 'Please refresh the browser and try again.' - ) from e - except ServiceUnavailable as e: - raise ServiceUnavailable( - 'Timed out trying to establish connection to the graph database. ' - 'Please try again at a later time.' - ) from e - - def exec_read_query_with_params(self, query: str, values: dict): - return self._exec_with_wrapped_exceptions( - lambda session: session.read_transaction( - lambda tx: list(tx.run(query, **values)) - ) - ) - - def exec_write_query_with_params(self, query: str, values: dict): - return self._exec_with_wrapped_exceptions( - lambda session: session.write_transaction( - lambda tx: list(tx.run(query, **values)) - ) - ) - - class GraphBaseDao: def __init__(self, graph, **kwargs): # TODO LL-2916: Should rename this to neo4j_session or something similar. diff --git a/appserver/neo4japp/services/elastic/elastic_service.py b/appserver/neo4japp/services/elastic/elastic_service.py index 5859ccffe6..7372de7ce4 100644 --- a/appserver/neo4japp/services/elastic/elastic_service.py +++ b/appserver/neo4japp/services/elastic/elastic_service.py @@ -1,10 +1,5 @@ import base64 import json -from typing import ( - Any, - Dict, - List, -) from elasticsearch.exceptions import RequestError as ElasticRequestError from elasticsearch.helpers import parallel_bulk, streaming_bulk @@ -22,10 +17,11 @@ ) from sqlalchemy import and_ from sqlalchemy.orm import joinedload, raiseload +from typing import Any, Dict, List from app import app from neo4japp.constants import LogEventType -from neo4japp.database import get_file_type_service, ElasticConnection, GraphConnection +from neo4japp.database import get_file_type_service, ElasticConnection from neo4japp.exceptions import ServerException, wrap_exceptions from neo4japp.models import ( Files, @@ -49,7 +45,7 @@ ParserElement.enablePackrat() -class ElasticService(ElasticConnection, GraphConnection): +class ElasticService(ElasticConnection): # Begin indexing methods def update_or_create_index(self, index_id, index_mapping_file): """Creates an index with the given index id and mapping file. If the index already exists, diff --git a/appserver/neo4japp/services/enrichment/enrichment_table.py b/appserver/neo4japp/services/enrichment/enrichment_table.py index 2fd2e74c22..0f4961ee0d 100644 --- a/appserver/neo4japp/services/enrichment/enrichment_table.py +++ b/appserver/neo4japp/services/enrichment/enrichment_table.py @@ -1,22 +1,35 @@ +import time + +from arango.client import ArangoClient from flask import current_app -from neo4j import Session as Neo4jSession, Transaction as Neo4jTx from sqlalchemy.orm import Session as SQLAlchemySession from typing import List +from urllib.parse import urlencode -from neo4japp.constants import EnrichmentDomain, LogEventType -from neo4japp.exceptions import AnnotationError, ServerException, wrap_exceptions -from neo4japp.models import DomainURLsMap -from neo4japp.services import KgService +from neo4japp.constants import ( + BIOCYC_ORG_ID_DICT, + EnrichmentDomain, + KGDomain, + LogEventType, +) +from neo4japp.exceptions import ( + AnnotationError, + ServerException, + ServerWarning, + wrap_exceptions, +) +from neo4japp.services.arangodb import execute_arango_query, get_db +from neo4japp.services.common import RDBMSBaseDao from neo4japp.services.enrichment.data_transfer_objects import EnrichmentCellTextMapping from neo4japp.schemas.formats.enrichment_tables import validate_enrichment_table +from neo4japp.utils.dict import compact from neo4japp.utils.globals import warn -from neo4japp.utils import EventLog -from neo4japp.exceptions import ServerWarning +from neo4japp.utils.logger import EventLog -class EnrichmentTableService(KgService): - def __init__(self, graph: Neo4jSession, session: SQLAlchemySession): - super().__init__(graph=graph, session=session) +class EnrichmentTableService(RDBMSBaseDao): + def __init__(self, session: SQLAlchemySession): + super().__init__(session=session) @wrap_exceptions(AnnotationError, title='Could not annotate enrichment table') def create_annotation_mappings(self, enrichment: dict) -> EnrichmentCellTextMapping: @@ -133,55 +146,319 @@ def create_annotation_mappings(self, enrichment: dict) -> EnrichmentCellTextMapp text=combined_text, text_index_map=text_index_map, cell_texts=cell_texts ) - def match_ncbi_genes(self, gene_names: List[str], organism: str): - """Match list of gene names to list of NCBI gene nodes with same name and has taxonomy - ID of given organism. Input order is maintained in result. - """ - results = self.graph.read_transaction( - self.match_ncbi_genes_query, gene_names, organism - ) - domain = ( - self.session.query(DomainURLsMap) - .filter(DomainURLsMap.domain == 'NCBI_Gene') - .one_or_none() - ) +def match_ncbi_genes(arango_client: ArangoClient, gene_names: List[str], organism: str): + """Match list of gene names to list of NCBI gene nodes with same name and has taxonomy + ID of given organism. Input order is maintained in result. + """ + results = execute_arango_query( + db=get_db(arango_client), + query=match_ncbi_genes_query(), + gene_names=gene_names, + organism=organism, + ) - if domain is None: - raise ServerException( - message='There was a problem finding NCBI domain URLs.' - ) - - return [ + retval = [] + for result in results: + gene_id = result['gene_id'] if result['gene_id'] else '' + retval.append( { 'gene': { 'name': result['gene_name'], 'full_name': result['gene_full_name'], }, 'synonym': result['synonym'], - 'geneNeo4jId': result['gene_neo4j_id'], - 'synonymNeo4jId': result['syn_neo4j_id'], - 'link': domain.base_URL.format(result['gene_id']) - if result['gene_id'] - else '', + 'geneArangoId': result['gene_arango_id'], + 'synonymArangoId': result['syn_arango_id'], + 'link': f"https://www.ncbi.nlm.nih.gov/gene/{gene_id}", } - for result in results - ] - - def match_ncbi_genes_query( - self, tx: Neo4jTx, gene_names: List[str], organism: str - ) -> List[dict]: - """Need to collect synonyms because a gene node can have multiple - synonyms. So it is possible to send duplicate internal node ids to - a later query.""" - return tx.run( - """ - UNWIND $gene_names AS gene - MATCH(s:Synonym {name:gene})-[:HAS_SYNONYM]-(g:Gene)-\ - [:HAS_TAXONOMY]-(t:Taxonomy {eid:$organism}) - RETURN s.name AS synonym, id(s) AS syn_neo4j_id, id(g) AS gene_neo4j_id, - g.eid AS gene_id, g.name AS gene_name, g.full_name AS gene_full_name - """, - gene_names=gene_names, - organism=organism, - ).data() + ) + return retval + + +def get_uniprot_genes(arango_client: ArangoClient, ncbi_gene_ids: List[int]): + start = time.time() + results = execute_arango_query( + db=get_db(arango_client), + query=get_uniprot_genes_query(), + ncbi_gene_ids=ncbi_gene_ids, + ) + + current_app.logger.info( + f'Enrichment UniProt KG query time {time.time() - start}', + extra=EventLog(event_type=LogEventType.ENRICHMENT.value).to_dict(), + ) + + return { + result['doc_id']: { + 'result': {'id': result['uniprot_id'], 'function': result['function']}, + 'link': f'http://identifiers.org/uniprot/{result["uniprot_id"]}', + } + for result in results + } + + +def get_string_genes(arango_client: ArangoClient, ncbi_gene_ids: List[int]): + start = time.time() + results = execute_arango_query( + db=get_db(arango_client), + query=get_string_genes_query(), + ncbi_gene_ids=ncbi_gene_ids, + ) + + current_app.logger.info( + f'Enrichment String KG query time {time.time() - start}', + extra=EventLog(event_type=LogEventType.ENRICHMENT.value).to_dict(), + ) + + return { + result['doc_id']: { + 'result': {'id': result['string_id'], 'annotation': result['annotation']}, + 'link': f"https://string-db.org/cgi/network?identifiers={result['string_id']}", + } + for result in results + } + + +def get_biocyc_genes( + arango_client: ArangoClient, ncbi_gene_ids: List[int], tax_id: str +): + start = time.time() + results = execute_arango_query( + db=get_db(arango_client), + query=get_biocyc_genes_query(), + ncbi_gene_ids=ncbi_gene_ids, + ) + + current_app.logger.info( + f'Enrichment Biocyc KG query time {time.time() - start}', + extra=EventLog(event_type=LogEventType.ENRICHMENT.value).to_dict(), + ) + + return { + result['doc_id']: { + 'result': result['pathways'], + 'link': "https://biocyc.org/gene?" + + urlencode( + compact( + dict( + orgid=BIOCYC_ORG_ID_DICT.get(tax_id, None), + id=result['biocyc_id'], + ) + ) + ), + } + for result in results + } + + +def get_go_genes(arango_client: ArangoClient, ncbi_gene_ids: List[int]): + start = time.time() + results = execute_arango_query( + db=get_db(arango_client), + query=get_go_genes_query(), + ncbi_gene_ids=ncbi_gene_ids, + ) + + current_app.logger.info( + f'Enrichment GO KG query time {time.time() - start}', + extra=EventLog(event_type=LogEventType.ENRICHMENT.value).to_dict(), + ) + + return { + result['doc_id']: { + 'result': result['go_terms'], + 'link': 'https://www.ebi.ac.uk/QuickGO/annotations?geneProductId=', + } + for result in results + } + + +def get_regulon_genes(arango_client: ArangoClient, ncbi_gene_ids: List[int]): + start = time.time() + results = execute_arango_query( + db=get_db(arango_client), + query=get_regulon_genes_query(), + ncbi_gene_ids=ncbi_gene_ids, + ) + + current_app.logger.info( + f'Enrichment Regulon KG query time {time.time() - start}', + extra=EventLog(event_type=LogEventType.ENRICHMENT.value).to_dict(), + ) + + return { + result['doc_id']: { + 'result': result['node'], + 'link': "https://regulondb.ccg.unam.mx/gene?" + + urlencode( + compact( + dict( + term=result['regulondb_id'], + organism='ECK12', + format='jsp', + type='gene', + ) + ) + ), + } + for result in results + } + + +def get_kegg_genes(arango_client: ArangoClient, ncbi_gene_ids: List[int]): + start = time.time() + results = execute_arango_query( + db=get_db(arango_client), + query=get_kegg_genes_query(), + ncbi_gene_ids=ncbi_gene_ids, + ) + + current_app.logger.info( + f'Enrichment KEGG KG query time {time.time() - start}', + extra=EventLog(event_type=LogEventType.ENRICHMENT.value).to_dict(), + ) + + return { + result['doc_id']: { + 'result': result['pathway'], + 'link': f"https://www.genome.jp/entry/{result['kegg_id']}", + } + for result in results + } + + +def get_genes( + arango_client: ArangoClient, domain: KGDomain, gene_ids: List[int], tax_id: str +): + if domain == KGDomain.REGULON: + return get_regulon_genes(arango_client, gene_ids) + if domain == KGDomain.BIOCYC: + return get_biocyc_genes(arango_client, gene_ids, tax_id) + if domain == KGDomain.GO: + return get_go_genes(arango_client, gene_ids) + if domain == KGDomain.STRING: + return get_string_genes(arango_client, gene_ids) + if domain == KGDomain.UNIPROT: + return get_uniprot_genes(arango_client, gene_ids) + if domain == KGDomain.KEGG: + return get_kegg_genes(arango_client, gene_ids) + + +def match_ncbi_genes_query() -> str: + """Need to collect synonyms because a gene node can have multiple + synonyms. So it is possible to send duplicate internal node ids to + a later query.""" + return """ + FOR name IN @gene_names + FOR s IN synonym + FILTER s.name == name + FOR g IN INBOUND s has_synonym + FILTER 'Gene' IN g.labels + FOR t IN OUTBOUND g has_taxonomy + FILTER t.eid == @organism + RETURN { + synonym: s.name, + syn_arango_id: s._id, + gene_arango_id: g._id, + gene_id: g.eid, + gene_name: g.name, + gene_full_name: g.full_name + } + """ + + +def get_uniprot_genes_query() -> str: + return """ + FOR gene_id IN @ncbi_gene_ids + FOR n IN ncbi + FILTER n._id == gene_id + FOR x IN INBOUND n has_gene OPTIONS { vertexCollections:'uniprot' } + RETURN { + doc_id: n._id, + function: x.function, + uniprot_id: x.eid + } + """ + + +def get_string_genes_query() -> str: + return """ + FOR gene_id IN @ncbi_gene_ids + FOR n IN ncbi + FILTER n._id == gene_id + FILTER 'Gene' IN n.labels + FOR x IN INBOUND n has_gene OPTIONS { vertexCollections: ["string"] } + RETURN { + doc_id: n._id, + string_id: x.eid, + annotation: x.annotation, + } + """ + + +def get_go_genes_query() -> str: + return """ + FOR gene_id IN @ncbi_gene_ids + FOR n IN ncbi + FILTER n._id == gene_id + LET go_terms = ( + FOR g IN OUTBOUND n go_link OPTIONS { vertexCollections:'go' } + RETURN g.name + ) + FILTER length(go_terms) > 0 + RETURN { + doc_id: n._id, + go_terms: go_terms + } + """ + + +def get_biocyc_genes_query() -> str: + return """ + FOR gene_id IN @ncbi_gene_ids + FOR n IN ncbi + FILTER n._id == gene_id + FOR b IN INBOUND n is OPTIONS { vertexCollections:'biocyc' } + RETURN { + doc_id: n._id, + pathways: b.pathways, + biocyc_id: b.biocyc_id + } + """ + + +def get_regulon_genes_query() -> str: + return """ + FOR gene_id IN @ncbi_gene_ids + FOR n IN ncbi + FILTER n._id == gene_id + FILTER 'Gene' IN n.labels + FOR x IN INBOUND n is OPTIONS { vertexCollections: ["regulondb"] } + RETURN { + doc_id: n._id, + node: x, + regulondb_id: x.regulondb_id + } + """ + + +def get_kegg_genes_query() -> str: + return """ + FOR gene_id IN @ncbi_gene_ids + FOR n IN ncbi + FILTER n._id == gene_id + FILTER 'Gene' IN n.labels + FOR x IN INBOUND n is OPTIONS { vertexCollections: ["kegg"] } + FOR gnm IN OUTBOUND x has_ko + LET pathway = ( + FOR pth IN OUTBOUND gnm in_pathway + RETURN pth.name + ) + FILTER length(pathway) > 0 + RETURN { + doc_id: n._id, + kegg_id: x.eid, + pathway: pathway + } + """ diff --git a/appserver/neo4japp/services/kg_service.py b/appserver/neo4japp/services/kg_service.py deleted file mode 100644 index 3683894cd0..0000000000 --- a/appserver/neo4japp/services/kg_service.py +++ /dev/null @@ -1,849 +0,0 @@ -import json -import os -import time -from typing import List -from urllib.parse import urlencode - -from flask import current_app -from neo4j import Transaction as Neo4jTx -from neo4j.graph import Node as N4jDriverNode, Relationship as N4jDriverRelationship - -from neo4japp.constants import ( - ANNOTATION_STYLES_DICT, - DISPLAY_NAME_MAP, - LogEventType, -) -from neo4japp.constants import ( - BIOCYC_ORG_ID_DICT, - KGDomain, -) -from neo4japp.exceptions import ServerException -from neo4japp.exceptions import ServerWarning -from neo4japp.models import ( - DomainURLsMap, - GraphNode, - GraphRelationship, -) -from neo4japp.services.common import HybridDBDao -from neo4japp.utils import EventLog, snake_to_camel_dict -from neo4japp.utils.dict import compact -from neo4japp.utils.globals import warn -from neo4japp.utils.labels import ( - get_first_known_label_from_node, - get_first_known_label_from_list, -) - - -class KgService(HybridDBDao): - def __init__(self, graph, session): - super().__init__(graph=graph, session=session) - - def _neo4j_objs_to_graph_objs( - self, - nodes: List[N4jDriverNode], - relationships: List[N4jDriverRelationship], - ): - # TODO: Can possibly use a dispatch method/injection - # of sorts to use custom labeling methods for - # different type of nodes/edges being converted. - # The default does not always set an appropriate label - # name. - node_dict = {} - rel_dict = {} - - for node in nodes: - try: - label = get_first_known_label_from_node(node) - except ValueError as e: - label = 'Unknown' - message = ( - f"Node with ID {node.id}" - f" had an unexpected list of labels: {list(node.labels)}" - ) - current_app.logger.warning( - message, - extra=EventLog( - event_type=LogEventType.KNOWLEDGE_GRAPH.value - ).to_dict(), - ) - warn(ServerWarning(message=message), cause=e) - graph_node = GraphNode( - id=node.id, - label=get_first_known_label_from_node(node), - sub_labels=list(node.labels), - domain_labels=[], - display_name=node.get(DISPLAY_NAME_MAP[label], 'Unknown'), - data=snake_to_camel_dict(dict(node), {}), - url=None, - ) - node_dict[graph_node.id] = graph_node - - for rel in relationships: - graph_rel = GraphRelationship( - id=rel.id, - label=type(rel).__name__, - data=dict(rel), - to=rel.end_node.id, - _from=rel.start_node.id, - to_label=list(rel.end_node.labels)[0], - from_label=list(rel.start_node.labels)[0], - ) - rel_dict[graph_rel.id] = graph_rel - return { - 'nodes': [n.to_dict() for n in node_dict.values()], - 'edges': [r.to_dict() for r in rel_dict.values()], - } - - def query_batch(self, data_query: str): - """query batch uses a custom query language (one we make up here) - for returning a list of nodes and their relationships. - It also works on single nodes with no relationship. - - Example: - If we wanted all relationships between - the node pairs (node1, node2) and - (node3, node4), we will write the - query as follows: - - node1,node2&node3,node4 - """ - - # TODO: This no longer works as expected with the refactor of the visualizer - # search. May need to refactor this in the future, or just get rid of it. - split_data_query = data_query.split('&') - - if len(split_data_query) == 1 and split_data_query[0].find(',') == -1: - result = self.graph.read_transaction( - lambda tx: list( - tx.run( - 'MATCH (n) WHERE ID(n)=$node_id RETURN n AS node', - node_id=int(split_data_query.pop()), - ) - ) - ) - - node = [] - if len(result) > 0: - node = [result[0]['node']] - - return self._neo4j_objs_to_graph_objs(node, []) - else: - data = [x.split(',') for x in split_data_query] - result = self.graph.read_transaction( - lambda tx: list( - tx.run( - """ - UNWIND $data as node_pair - WITH node_pair[0] as from_id, node_pair[1] as to_id - MATCH (a)-[relationship]->(b) - WHERE ID(a)=from_id AND ID(b)=to_id - RETURN - apoc.convert.toSet(collect(a) + collect(b)) as nodes, - apoc.convert.toSet(collect(relationship)) as relationships - """, - data=data, - ) - ) - ) - - nodes = [] - relationships = [] - if len(result) > 0: - nodes = result[0]['nodes'] - relationships = result[0]['relationships'] - - return self._neo4j_objs_to_graph_objs(nodes, relationships) - - def get_uniprot_genes(self, ncbi_gene_ids: List[int]): - start = time.time() - results = self.graph.read_transaction( - self.get_uniprot_genes_query, ncbi_gene_ids - ) - - current_app.logger.info( - f'Enrichment UniProt KG query time {time.time() - start}', - extra=EventLog(event_type=LogEventType.ENRICHMENT.value).to_dict(), - ) - - domain = ( - self.session.query(DomainURLsMap) - .filter(DomainURLsMap.domain == 'uniprot') - .one_or_none() - ) - - if domain is None: - raise ServerException( - message='There was a problem finding UniProt domain URLs.' - ) - - return { - result['node_id']: { - 'result': {'id': result['uniprot_id'], 'function': result['function']}, - 'link': domain.base_URL.format(result['uniprot_id']), - } - for result in results - } - - def get_string_genes(self, ncbi_gene_ids: List[int]): - start = time.time() - results = self.graph.read_transaction( - self.get_string_genes_query, ncbi_gene_ids - ) - - current_app.logger.info( - f'Enrichment String KG query time {time.time() - start}', - extra=EventLog(event_type=LogEventType.ENRICHMENT.value).to_dict(), - ) - - return { - result['node_id']: { - 'result': { - 'id': result['string_id'], - 'annotation': result['annotation'], - }, - 'link': f"https://string-db.org/cgi/network?identifiers={result['string_id']}", - } - for result in results - } - - def get_biocyc_genes(self, ncbi_gene_ids: List[int], tax_id: str): - start = time.time() - results = self.graph.read_transaction( - self.get_biocyc_genes_query, ncbi_gene_ids - ) - - current_app.logger.info( - f'Enrichment Biocyc KG query time {time.time() - start}', - extra=EventLog(event_type=LogEventType.ENRICHMENT.value).to_dict(), - ) - - return { - result['node_id']: { - 'result': result['pathways'], - 'link': "https://biocyc.org/gene?" - + urlencode( - compact( - dict( - orgid=BIOCYC_ORG_ID_DICT.get(tax_id, None), - id=result['biocyc_id'], - ) - ) - ), - } - for result in results - } - - def get_go_genes(self, ncbi_gene_ids: List[int]): - start = time.time() - results = self.graph.read_transaction( - self.get_go_genes_query, - ncbi_gene_ids, - ) - - current_app.logger.info( - f'Enrichment GO KG query time {time.time() - start}', - extra=EventLog(event_type=LogEventType.ENRICHMENT.value).to_dict(), - ) - - return { - result['node_id']: { - 'result': result['go_terms'], - 'link': 'https://www.ebi.ac.uk/QuickGO/annotations?geneProductId=', - } - for result in results - } - - def get_regulon_genes(self, ncbi_gene_ids: List[int]): - start = time.time() - results = self.graph.read_transaction( - self.get_regulon_genes_query, ncbi_gene_ids - ) - - current_app.logger.info( - f'Enrichment Regulon KG query time {time.time() - start}', - extra=EventLog(event_type=LogEventType.ENRICHMENT.value).to_dict(), - ) - - return { - result['node_id']: { - 'result': result['node'], - 'link': "https://regulondb.ccg.unam.mx/gene?" - + urlencode( - compact( - dict( - term=result['regulondb_id'], - organism='ECK12', - format='jsp', - type='gene', - ) - ) - ), - } - for result in results - } - - def get_genes(self, domain: KGDomain, gene_ids: List[int], tax_id: str): - if domain == KGDomain.REGULON: - return self.get_regulon_genes(gene_ids) - if domain == KGDomain.BIOCYC: - return self.get_biocyc_genes(gene_ids, tax_id) - if domain == KGDomain.GO: - return self.get_go_genes(gene_ids) - if domain == KGDomain.STRING: - return self.get_string_genes(gene_ids) - if domain == KGDomain.UNIPROT: - return self.get_uniprot_genes(gene_ids) - if domain == KGDomain.KEGG: - return self.get_kegg_genes(gene_ids) - - def get_kegg_genes(self, ncbi_gene_ids: List[int]): - start = time.time() - results = self.graph.read_transaction(self.get_kegg_genes_query, ncbi_gene_ids) - - current_app.logger.info( - f'Enrichment KEGG KG query time {time.time() - start}', - extra=EventLog(event_type=LogEventType.ENRICHMENT.value).to_dict(), - ) - - return { - result['node_id']: { - 'result': result['pathway'], - 'link': f"https://www.genome.jp/entry/{result['kegg_id']}", - } - for result in results - } - - def get_nodes_and_edges_from_paths(self, paths): - nodes = [] - node_ids = set() - edges = [] - edge_ids = set() - for path in paths: - if path.get('nodes', None) is not None: - for node in path['nodes']: - if node['id'] not in node_ids: - node_display_name = 'Node Display Name Unknown' - if node.get('display_name', None) is not None: - node_display_name = node['display_name'] - elif node.get('name', None) is not None: - node_display_name = node['name'] - - try: - node_label = get_first_known_label_from_list(node['labels']) - node_color = ANNOTATION_STYLES_DICT[node_label.lower()][ - 'color' - ] - except ValueError as e: - # If label is unknown, then use fallbacks - node_label = 'Unknown' - node_color = '#000000' - message = f"Node had an unexpected list of labels: {node['labels']}" - current_app.logger.warning( - message, - extra=EventLog( - event_type=LogEventType.KNOWLEDGE_GRAPH.value - ).to_dict(), - ) - warn(ServerWarning(message=message), cause=e) - except KeyError: - # If label does not exist in styles dict, then use fallbacks - node_label = 'Unknown' - node_color = '#000000' - - node_data = { - 'id': node['id'], - 'label': node_display_name, - 'databaseLabel': node_label, - 'font': { - 'color': node_color, - }, - 'color': { - 'background': '#FFFFFF', - 'border': node_color, - 'hover': { - 'background': '#FFFFFF', - 'border': node_color, - }, - 'highlight': { - 'background': '#FFFFFF', - 'border': node_color, - }, - }, - } - - nodes.append(node_data) - node_ids.add(node['id']) - - if path.get('edges', None) is not None: - for edge in path['edges']: - if edge['id'] not in edge_ids: - edge_data = { - 'id': edge['id'], - 'label': edge['type'], - 'from': edge['start_node'], - 'to': edge['end_node'], - 'color': { - 'color': '#0c8caa', - }, - 'arrows': 'to', - } - - edges.append(edge_data) - edge_ids.add(edge['id']) - return {'nodes': nodes, 'edges': edges} - - def get_shortest_path_query_list(self): - query_pathway_names = [ - '3-hydroxyisobutyric Acid to pykF Using ChEBI', - '3-hydroxyisobutyric Acid to pykF using BioCyc', - 'icd to rhsE', - 'Two pathways using BioCyc', - # 'Glycolisis Regulon', - # 'SIRT5 to NFE2L2 Using Literature Data', - # 'CTNNB1 to Diarrhea Using Literature Data', - ] - file_pathway_names = [ - 'Serine SP Pathway', - 'Serine to malZp', - 'Acetate (ALE Mutation Data)', - 'Glycerol (ALE Mutation Data)', - 'Hexanoic (ALE Mutation Data)', - 'Isobutyric (ALE Mutation Data)', - 'Putrescine (ALE Mutation Data)', - 'Serine (ALE Mutation Data)', - 'tpiA (ALE Mutation Data)', - 'Xylose (ALE Mutation Data)', - '42C Temperature (ALE Mutation Data)', - 'nagC (ALE Mutation Data)', - 'nagA/nagC (ALE Mutation Data)', - 'nagA/nagC Shortest Paths (ALE Mutation Data)', - 'metab2PTHLH Short', - 'PTHLH2metab Short', - 'metab2PTHLH Short Page', - 'PTHLH2metab Short Page', - 'PTHLH2Ca2metab Short Page', - 'AAK1', - 'Auxilin Recruits HSPA8', - 'CSNK1D Phosphorylates SEC23', - 'Dissociation of AAK1 and Dephosphorylation of AP-2 mu2', - 'Expression of PERIOD-1', - 'F_BAR proteins_ARP', - 'HSPA8-mediated ATP Hydrolysis Promotes Vesicle Uncoating', - 'Interleukin-1 Family are Secreted', - 'PER1 [cytosol]', - 'The Ligand_GPCR_Gs Complex Dissociates', - 'Vesicle Budding', - 'Min Mean Short Updown Serotonin', - 'Min Mean Short Metabs Acetate', - 'Min Mean Short Metabs Butyrate', - 'Min Mean Short Metabs Propionate', - 'Min Mean Short Metabs Serotonin', - 'Min Mean Short Metabs top10', - 'Min Mean Short Updown Acetate', - 'Min Mean Short Updown Butyrate', - 'AAK1 to Metab noOct', - 'FosB to PER1', - 'Uncharacterized iModulon Genes and Top 20 Metabolites', - 'Uncharacterized iModulon Genes Only', - 'Uncharacterized iModulon Genes to Methionine', - 'Uncharacterized iModulon Genes yjdI Metabolites', - 'Zink iModulon Metals', - 'Zink iModulon Test2' - # 'nagA (ALE Mutation Data)', - ] - return { - num: name - for num, name in enumerate(query_pathway_names + file_pathway_names) - } - - def get_query_id_to_func_map(self): - query_pathways = [ - self.get_three_hydroxisobuteric_acid_to_pykf_chebi_query, - self.get_three_hydroxisobuteric_acid_to_pykf_biocyc_query, - self.get_icd_to_rhse_query, - self.get_two_pathways_biocyc_query - # self.get_glycolisis_regulon_query, - # self.get_sirt5_to_nfe2l2_literature_query, - # self.get_ctnnb1_to_diarrhea_literature_query, - ] - file_pathways = [ - 'serine.json', - 'serine-to-malZp.json', - 'ale_mutation_data/acetate.json', - 'ale_mutation_data/glycerol.json', - 'ale_mutation_data/hexanoic.json', - 'ale_mutation_data/isobutyric.json', - 'ale_mutation_data/putrescine.json', - 'ale_mutation_data/serine.json', - 'ale_mutation_data/tpiA.json', - 'ale_mutation_data/xylose.json', - 'ale_mutation_data/42C.json', - 'ale_mutation_data/nagC.json', - 'ale_mutation_data/nagAC.json', - 'ale_mutation_data/nagAC_shortestpaths.json', - 'cytoscape_data/metab2PTHLH_short_graphml.json', - 'cytoscape_data/PTHLH2metab_short_graphml.json', - 'cytoscape_data/metab2PTHLH_shortPage_graphml.json', - 'cytoscape_data/PTHLH2metab_shortPage_graphml.json', - 'cytoscape_data/PTHLH2Ca2metab_shortPage_graphml.json', - 'cytoscape_data/aak1_graphml.json', - 'cytoscape_data/Auxilin recruits HSPA8.json', - 'cytoscape_data/CSNK1D phosphorylates SEC23.json', - 'cytoscape_data/Dissociation of AAK1 and dephosphorylation of AP-2 mu2.json', - 'cytoscape_data/Expression of PERIOD-1.json', - 'cytoscape_data/F_BAR proteins_ARP.json', - 'cytoscape_data/HSPA8-mediated ATP hydrolysis promotes vesicle uncoating.json', - 'cytoscape_data/Interleukin-1 family are secreted.json', - 'cytoscape_data/PER1 [cytosol].json', - 'cytoscape_data/The Ligand_GPCR_Gs complex dissociates.json', - 'cytoscape_data/Vesicle budding.json', - 'cytoscape_data/minMeanShort_updown_Serotonin_graphml.json', - 'cytoscape_data/minMeanShort_metabs_Acetate_graphml.json', - 'cytoscape_data/minMeanShort_metabs_Butyrate_graphml.json', - 'cytoscape_data/minMeanShort_metabs_Propionate_graphml.json', - 'cytoscape_data/minMeanShort_metabs_Serotonin_graphml.json', - 'cytoscape_data/minMeanShort_metabs_top10_graphml.json', - 'cytoscape_data/minMeanShort_updown_Acetate_graphml.json', - 'cytoscape_data/minMeanShort_updown_Butyrate_graphml.json', - 'cytoscape_data/aak1_to_metab_noOct_graphml.json', - 'cytoscape_data/FosB to PER1_vis_js.json', - 'marina_sankey_data/uncharacterized_iModulon_genes_and_top20_metabolites_vis_js.json', - 'marina_sankey_data/uncharacterized_iModulon_genes_only_vis_js.json', - 'marina_sankey_data/uncharacterized_iModulon_genes_to_methionine_vis_js.json', - 'marina_sankey_data/uncharacterized_iModulon_genes_yjdI_metabolites_vis_js.json', - 'marina_sankey_data/zink-imodulon-metals_vis_js.json', - 'marina_sankey_data/zink-imodulon-test2_vis_js.json' - # 'ale_mutation_data/nagA.json', - ] - - pathway_num = 0 - pathways = dict() - for query_pathway in query_pathways: - pathways[pathway_num] = [self.get_data_from_query, query_pathway] - pathway_num += 1 - - for file_pathway in file_pathways: - pathways[pathway_num] = [self.get_data_from_file, file_pathway] - pathway_num += 1 - - return pathways - - def get_shortest_path_data(self, query_id): - func, arg = self.get_query_id_to_func_map()[query_id] - return func(arg) - - def get_data_from_query(self, query_func): - result = self.graph.read_transaction(query_func) - return self.get_nodes_and_edges_from_paths(result) - - def get_data_from_file(self, filename): - directory = os.path.realpath(os.path.dirname(__file__)) - with open( - os.path.join(directory, f'./shortest_path_data/{filename}'), 'r' - ) as data_file: - return json.load(data_file) - - def get_uniprot_genes_query( - self, tx: Neo4jTx, ncbi_gene_ids: List[int] - ) -> List[dict]: - return tx.run( - """ - UNWIND $ncbi_gene_ids AS node_id - MATCH (g)-[:HAS_GENE]-(x:db_UniProt) - WHERE id(g)=node_id - RETURN node_id, x.function AS function, x.eid AS uniprot_id - """, - ncbi_gene_ids=ncbi_gene_ids, - ).data() - - def get_string_genes_query( - self, tx: Neo4jTx, ncbi_gene_ids: List[int] - ) -> List[dict]: - return tx.run( - """ - UNWIND $ncbi_gene_ids AS node_id - MATCH (g)-[:HAS_GENE]-(x:db_STRING) - WHERE id(g)=node_id - RETURN node_id, x.eid AS string_id, x.annotation AS annotation - """, - ncbi_gene_ids=ncbi_gene_ids, - ).data() - - def get_go_genes_query(self, tx: Neo4jTx, ncbi_gene_ids: List[int]) -> List[dict]: - return tx.run( - """ - UNWIND $ncbi_gene_ids AS node_id - MATCH(g) WHERE id(g) = node_id - OPTIONAL MATCH (g)-[:GO_LINK]-(go1:db_GO) - OPTIONAL MATCH (g)-[:IS]-(:db_BioCyc)-[:ENCODES]-()-[:GO_LINK]-(go2) - RETURN - id(g) as node_id, - apoc.convert.toSet(collect(go1.name) + collect(go2.name)) AS go_terms - """, - ncbi_gene_ids=ncbi_gene_ids, - ).data() - - def get_biocyc_genes_query( - self, tx: Neo4jTx, ncbi_gene_ids: List[int] - ) -> List[dict]: - return tx.run( - """ - UNWIND $ncbi_gene_ids AS node_id - MATCH (g)-[:IS]-(x:db_BioCyc) - WHERE id(g)=node_id - RETURN node_id, x.pathways AS pathways, x.biocyc_id AS biocyc_id - """, - ncbi_gene_ids=ncbi_gene_ids, - ).data() - - def get_regulon_genes_query( - self, tx: Neo4jTx, ncbi_gene_ids: List[int] - ) -> List[dict]: - return tx.run( - """ - UNWIND $ncbi_gene_ids AS node_id - MATCH (g)-[:IS]-(x:db_RegulonDB) - WHERE id(g)=node_id - RETURN node_id, x AS node, x.regulondb_id AS regulondb_id - """, - ncbi_gene_ids=ncbi_gene_ids, - ).data() - - def get_kegg_genes_query(self, tx: Neo4jTx, ncbi_gene_ids: List[int]) -> List[dict]: - return tx.run( - """ - UNWIND $ncbi_gene_ids AS node_id - MATCH (g)-[:IS]-(x:db_KEGG) - WHERE id(g)=node_id - WITH node_id, x - MATCH (x)-[:HAS_KO]-()-[:IN_PATHWAY]-(p:Pathway)-[:HAS_PATHWAY]-(gen:Genome) - WHERE gen.eid = x.genome - RETURN node_id, x.eid AS kegg_id, collect(p.name) AS pathway - """, - ncbi_gene_ids=ncbi_gene_ids, - ).data() - - def get_three_hydroxisobuteric_acid_to_pykf_chebi_query(self, tx: Neo4jTx): - return list( - tx.run( - """ - MATCH (chem:db_CHEBI:Chemical) WHERE chem.eid IN ['18064'] - WITH chem - MATCH p=allShortestPaths((gene:db_EcoCyc:Gene {name:'pykF'})-[*..9]-(chem)) - WHERE none(r IN relationships(p) WHERE type(r) IN [ - 'FUNCTION', - 'COMPONENT', - 'PROCESS', - 'HAS_TAXONOMY', - 'HAS_SYNONYM', - 'HAS_ROLE', - 'GO_LINK' - ]) - RETURN [ - node IN nodes(p) | - { - id: id(node), - name: node.name, - display_name: node.displayName, - labels: labels(node) - } - ] as nodes, [ - rel IN relationships(p) | - { - id: id(rel), - type: type(rel), - start_node: id(startNode(rel)), - end_node: id(endNode(rel)) - } - ] AS edges - """ - ) - ) - - def get_three_hydroxisobuteric_acid_to_pykf_biocyc_query(self, tx: Neo4jTx): - return list( - tx.run( - """ - MATCH (c:Compound {biocyc_id: 'CPD-12176'}), (g:Gene:db_BioCyc {name:'pykF'}) - MATCH p=allShortestPaths((c)-[*]-(g)) - WHERE none(r IN relationships(p) - WHERE type(r) IN [ - 'GO_LINK', - 'HAS_TAXONOMY', - 'HAS_SYNONYM', - 'REGULATES', - 'HAS_ROLE', - 'TYPE_OF' - ]) - RETURN [ - node IN nodes(p) | - { - id: id(node), - name: node.name, - display_name: node.displayName, - labels: labels(node) - } - ] as nodes, [ - rel IN relationships(p) | - { - id: id(rel), - type: type(rel), - start_node: id(startNode(rel)), - end_node: id(endNode(rel)) - } - ] AS edges - """ - ) - ) - - def get_icd_to_rhse_query(self, tx: Neo4jTx): - return list( - tx.run( - """ - MATCH p=allShortestPaths( - (gene:db_EcoCyc:Gene {name:'icd'})-[*..13]-(gene2:db_EcoCyc:Gene {name:'rhsE'}) - ) - WHERE none(r IN relationships(p) WHERE type(r) IN ['HAS_TAXONOMY']) - RETURN [ - node IN nodes(p) | - { - id: id(node), - name: node.name, - display_name: node.displayName, - labels: labels(node) - } - ] as nodes, [ - rel IN relationships(p) | - { - id: id(rel), - type: type(rel), - start_node: id(startNode(rel)), - end_node: id(endNode(rel)) - } - ] AS edges - """ - ) - ) - - def get_sirt5_to_nfe2l2_literature_query(self, tx: Neo4jTx): - return list( - tx.run( - """ - MATCH (g:db_Literature:Gene {name:'SIRT5'})-[:HAS_TAXONOMY]->(t:Taxonomy {eid:'9606'}), - (t)<-[:HAS_TAXONOMY]-(g2:db_Literature:Gene {name:'NFE2L2'}) - MATCH p=allShortestPaths((g)-[*]-(g2)) - WHERE all(rel IN relationships(p) WHERE type(rel) = 'ASSOCIATED') - RETURN [ - node IN nodes(p) | - { - id: id(node), - name: node.name, - display_name: node.displayName, - labels: labels(node) - } - ] as nodes, [ - rel IN relationships(p) | - { - id: id(rel), - type: type(rel), - start_node: id(startNode(rel)), - end_node: id(endNode(rel)) - } - ] AS edges - """ - ) - ) - - def get_ctnnb1_to_diarrhea_literature_query(self, tx: Neo4jTx): - return list( - tx.run( - """ - MATCH (g:db_Literature:Gene {name:'CTNNB1'})-[:HAS_TAXONOMY]->(t:Taxonomy {eid:'9606'}) - MATCH (d:Disease {name:'Diarrhea'}) - MATCH p=allShortestPaths((g)-[*]-(d)) - RETURN [ - node IN nodes(p) | - { - id: id(node), - name: node.name, - display_name: node.displayName, - labels: labels(node) - } - ] as nodes, [ - rel IN relationships(p) | - { - id: id(rel), - type: type(rel), - start_node: id(startNode(rel)), - end_node: id(endNode(rel)) - } - ] AS edges - """ - ) - ) - - def get_two_pathways_biocyc_query(self, tx: Neo4jTx): - return list( - tx.run( - """ - MATCH (p1:Pathway {biocyc_id:'PWY-6151'}), (p2:Pathway {biocyc_id: 'PWY-6123'}) - WITH p1, p2 - MATCH p=allShortestPaths((p1)-[*]-(p2)) - WHERE NONE (r IN relationships(p) WHERE type(r) IN ['TYPE_OF']) - AND NONE (n IN nodes(p) WHERE n.biocyc_id IN ['WATER','PROTON','Pi','ATP', 'ADP']) - RETURN [ - node IN nodes(p) | - { - id: id(node), - name: node.name, - display_name: node.displayName, - labels: labels(node) - } - ] as nodes, [ - rel IN relationships(p) | - { - id: id(rel), - type: type(rel), - start_node: id(startNode(rel)), - end_node: id(endNode(rel)) - } - ] AS edges - """ - ) - ) - - def get_glycolisis_regulon_query(self, tx: Neo4jTx): - return list( - tx.run( - """ - MATCH path= - (:Pathway {biocyc_id: 'GLYCOLYSIS'})--(r:Reaction)-- - (e:EnzReaction:db_EcoCyc)-[:CATALYZES]- - (:Protein)<-[:COMPONENT_OF*0..]- - (:Protein)-[:ENCODES]- - (:Gene:db_EcoCyc)-[:IS]- - (:db_NCBI)-[:IS]- - (g:db_RegulonDB) - WITH path, g, r - MATCH p1=(left)-[:CONSUMED_BY]->(r)-[:PRODUCES]->(right) - OPTIONAL MATCH p2=(g)--(:TranscriptionUnit)--(:Promoter)-[:REGULATES]-(rg:Regulon) - RETURN [ - node IN nodes(path) + nodes(p1) + nodes(p2) | - { - id: id(node), - name: node.name, - display_name: node.displayName, - labels: labels(node) - } - ] as nodes, [ - rel IN relationships(path) + relationships(p1) + relationships(p2) | - { - id: id(rel), - type: type(rel), - start_node: id(startNode(rel)), - end_node: id(endNode(rel)) - } - ] AS edges - """ - ) - ) diff --git a/appserver/neo4japp/services/search.py b/appserver/neo4japp/services/search.py index 8e5eca05cd..ca3d64a978 100644 --- a/appserver/neo4japp/services/search.py +++ b/appserver/neo4japp/services/search.py @@ -1,484 +1,605 @@ -import re +from arango.client import ArangoClient from typing import Any, Dict, List from flask import current_app -from neo4j import Record as N4jRecord, Transaction as Neo4jTx from neo4japp.constants import LogEventType -from neo4japp.data_transfer_objects import FTSQueryRecord, FTSResult, FTSTaxonomyRecord -from neo4japp.exceptions import ServerWarning +from neo4japp.data_transfer_objects import FTSQueryRecord, FTSTaxonomyRecord from neo4japp.models import GraphNode -from neo4japp.services.common import GraphBaseDao -from neo4japp.utils import snake_to_camel_dict, normalize_str, EventLog -from neo4japp.utils.globals import warn +from neo4japp.services.arangodb import execute_arango_query, get_db +from neo4japp.utils.string import snake_to_camel_dict, normalize_str from neo4japp.utils.labels import ( get_first_known_label_from_list, - get_known_domain_labels_from_list, + get_known_domain_labels_from_data_source, ) +from neo4japp.utils.logger import EventLog + + +def _get_collection_filters(domains: List[str]): + domains_list = [ + 'chebi', + 'go', + 'mesh', + 'ncbi', + # Include "taxonomy" here in case no domains were selected by the user. It has no use in + # the for loop below. + 'taxonomy', + 'uniprot', + ] + + result_domains = [] + + # NOTE: If the user supplies an domain that *isn't* in these maps, + # they may get unexpected results! We essentially silently ignore any + # unexpected values in favor of getting *some* results back. + + for domain in domains: + normalized_domain = normalize_str(domain) + if normalized_domain in domains_list: + result_domains.append(normalized_domain) + + # Add taxonomy if ncbi is included, since in the neo4j schema taxonomy nodes were part + # of ncbi. + if normalized_domain == 'ncbi': + result_domains.append('taxonomy') + else: + current_app.logger.info( + f'Found an unexpected value in `domains` list: {domain}', + extra=EventLog( + event_type=LogEventType.VISUALIZER_SEARCH.value + ).to_dict(), + ) + # If the domain list provided by the user is empty, then assume ALL domains/entities should be + # used. + result_domains = result_domains if len(result_domains) > 0 else domains_list + + return 'FILTER ' + ' OR '.join( + [f'IS_SAME_COLLECTION("{domain}", entity._id)' for domain in result_domains] + ) + + +def _get_labels_filter(entities: List[str]): + entities_map = { + 'biologicalprocess': 'BiologicalProcess', + 'cellularcomponent': 'CellularComponent', + 'chemical': 'Chemical', + 'disease': 'Disease', + 'gene': 'Gene', + 'molecularfunction': 'MolecularFunction', + 'protein': 'Protein', + 'taxonomy': 'Taxonomy', + } + result_entities = [] + + # NOTE: If the user supplies an entity that *isn't* in these maps, + # they may get unexpected results! We essentially silently ignore any + # unexpected values in favor of getting *some* results back. + + for entity in entities: + normalized_entity = normalize_str(entity) + if normalized_entity in entities_map: + result_entities.append(entities_map[normalized_entity]) + else: + current_app.logger.info( + f'Found an unexpected value in `entities` list: {entity}', + extra=EventLog( + event_type=LogEventType.VISUALIZER_SEARCH.value + ).to_dict(), + ) -class SearchService(GraphBaseDao): - def __init__(self, graph): - super().__init__(graph) + # If the entity list provided by the user is empty, then assume ALL domains/entities should be + # used. + return result_entities if len(result_entities) > 0 else list(entities_map.values()) - def _fulltext_query_sanitizer(self, query): - """Ensures the query is syntactically correct - and safe from cypher injections for Neo4j full - text search. - Special characters in Lucene - + - && || ! ( ) { } [ ] ^ " ~ * ? : \\ / - See docs: http://lucene.apache.org/ for more information - We will escape these characters with a forward ( \\ ) slash - """ - lucene_chars = re.compile(r'([\+\-\&\|!\(\)\{\}\[\]\^"~\*\?:\/])') +def _get_organism_match_string(organism: str): + return f""" + LET t = FIRST( + FOR tax IN OUTBOUND entity has_taxonomy + OPTIONS {{ vertexCollections: ["taxonomy"]}} + {'FILTER tax.eid == @organism' if organism else ''} + RETURN tax + ) + {'FILTER t != null' if organism else ''} + """ - def escape(m): - """Adds an escape '\' to reserved Lucene characters""" - char = m.group(1) - return r'\{c}'.format(c=char) - query = re.sub(lucene_chars, escape, query).strip() - if not query: - return query +def _get_organisms_match_string(organisms: List[str]): + return f""" + LET t = FIRST( + FOR tax IN OUTBOUND entity has_taxonomy + OPTIONS {{ vertexCollections: ["taxonomy"]}} + {'FILTER tax.eid IN @organisms' if organisms else ''} + RETURN tax + ) + {'FILTER t != null' if organisms else ''} + """ - # Wrap the query in backticks, doubling existing backticks. This effectively escapes the - # query input. - return f"`{query.replace('`', '``')}`" - def predictive_search(self, term: str, limit: int = 5): - """Performs a predictive search; not necessarily a prefix based autocomplete. - # TODO: FIX the search algorithm to perform a proper prefix based autocomplete - """ - raise NotImplementedError - - def _visualizer_search_result_formatter( - self, result: List[N4jRecord] - ) -> List[FTSQueryRecord]: - formatted_results: List[FTSQueryRecord] = [] - for record in result: - entity = record['entity'] - literature_id = record['literature_id'] - taxonomy_id = record.get('taxonomy_id', '') - taxonomy_name = record.get('taxonomy_name', '') - go_class = record.get('go_class', '') - - try: - entity_label = get_first_known_label_from_list(entity["labels"]) - except ValueError as e: - message = ( - f'Node with ID {entity["id"]} had an unexpected list of labels: ' - + f'{entity["labels"]}' - ) - current_app.logger.warning( - message, - extra=EventLog( - event_type=LogEventType.KNOWLEDGE_GRAPH.value - ).to_dict(), - ) - warn(ServerWarning(message=message), cause=e) - entity_label = 'Unknown' - - graph_node = GraphNode( - # When it exists, we use the literature node ID instead so the node can be expanded - # in the visualizer - id=literature_id or entity['id'], - label=entity_label, - sub_labels=entity['labels'], - domain_labels=( - get_known_domain_labels_from_list(entity['labels']) - + (['Literature'] if literature_id is not None else []) - ), - display_name=entity['name'], - data=snake_to_camel_dict(entity['data'], {}), - url=None, - ) - formatted_results.append( - FTSTaxonomyRecord( - node=graph_node, - taxonomy_id=taxonomy_id if taxonomy_id is not None else 'N/A', - taxonomy_name=taxonomy_name if taxonomy_name is not None else 'N/A', - go_class=go_class if go_class is not None else 'N/A', - ) - ) - return formatted_results - - def sanitize_filter( - self, - domains: List[str], - entities: List[str], - ): - domains_map = { - 'chebi': 'n:db_CHEBI', - 'go': 'n:db_GO', - 'mesh': 'n:db_MESH', - 'ncbi': 'n:db_NCBI', - 'uniprot': 'n:db_UniProt', - } - entities_map = { - 'biologicalprocess': 'n:BiologicalProcess', - 'cellularcomponent': 'n:CellularComponent', - 'chemical': 'n:Chemical', - 'disease': 'n:Disease', - 'gene': 'n:Gene', - 'molecularfunction': 'n:MolecularFunction', - 'protein': 'n:Protein', - 'taxonomy': 'n:Taxonomy', - } - result_domains = [] - result_entities = [] - - # NOTE: If the user supplies an entity/domain that *isn't* in these maps, - # they may get unexpected results! We essentially silently ignore any - # unexpected values in favor of getting *some* results back. - - for domain in domains: - normalized_domain = normalize_str(domain) - if normalized_domain in domains_map: - result_domains.append(domains_map[normalized_domain]) - else: - current_app.logger.info( - f'Found an unexpected value in `domains` list: {domain}', - extra=EventLog( - event_type=LogEventType.VISUALIZER_SEARCH.value - ).to_dict(), - ) +def _get_labels_match_string(types: List[str]): + return 'FILTER LENGTH(INTERSECTION(@types, entity.labels)) > 0' if types else '' - for entity in entities: - normalized_entity = normalize_str(entity) - if normalized_entity in entities_map: - result_entities.append(entities_map[normalized_entity]) - else: - current_app.logger.info( - f'Found an unexpected value in `entities` list: {entity}', - extra=EventLog( - event_type=LogEventType.VISUALIZER_SEARCH.value - ).to_dict(), - ) - # If the domain list or entity list provided by the user is empty, then assume ALL - # domains/entities should be used. - result_domains = ( - result_domains if len(result_domains) > 0 else list(domains_map.values()) +def _get_literature_match_string(domains: List[str]): + literature_in_selected_domains = any( + [normalize_str(domain) == 'literature' for domain in domains] + ) + + base_search_string = """ + LET literature_id = FIRST( + FOR lit_doc IN INBOUND entity mapped_to + RETURN lit_doc._id ) - result_entities = ( - result_entities if len(result_entities) > 0 else list(entities_map.values()) + """ + + # Return nodes in one or more domains, with mapped Literature data (if it exists) + if domains == [] or (len(domains) > 1 and literature_in_selected_domains): + return base_search_string + # Return nodes in one or more domains, and *exclude* Literature data from the result + elif not literature_in_selected_domains: + return "LET literature_id = null" + # Return only nodes mapped to Literature nodes + else: + return ( + base_search_string + + """ + \nFILTER literature_id != null + """ ) - return f'({" OR ".join(result_domains)}) AND ({" OR ".join(result_entities)})' - - def visualizer_search( - self, - term: str, - organism: str, - domains: List[str], - entities: List[str], - page: int = 1, - limit: int = 10, - ) -> FTSResult: - if not term: - return FTSResult(term, [], 0, page, limit) - - if organism: - organism_match_string = ( - 'MATCH (n)-[:HAS_TAXONOMY]-(t:Taxonomy {eid: $organism})' - ) - else: - organism_match_string = 'OPTIONAL MATCH (n)-[:HAS_TAXONOMY]-(t:Taxonomy)' - - result_filters = self.sanitize_filter(domains, entities) - literature_in_selected_domains = any( - [normalize_str(domain) == 'literature' for domain in domains] +def _visualizer_search_result_formatter(result: dict) -> dict: + formatted_results: List[FTSQueryRecord] = [] + for record in result['rows']: + entity = record['entity'] + literature_id = record['literature_id'] + taxonomy_id = record.get('taxonomy_id', '') + taxonomy_name = record.get('taxonomy_name', '') + go_class = record.get('go_class', '') + + try: + entity_label = get_first_known_label_from_list(entity["labels"]) + except ValueError: + current_app.logger.warning( + f'Node with ID {entity["id"]} had an unexpected list of labels: ' + + f'{entity["labels"]}', + extra=EventLog(event_type=LogEventType.KNOWLEDGE_GRAPH.value).to_dict(), + ) + entity_label = 'Unknown' + + graph_node = GraphNode( + # When it exists, we use the literature node ID instead so the node can be expanded + # in the visualizer + id=literature_id or entity['id'], + label=entity_label, + sub_labels=entity['labels'], + domain_labels=( + get_known_domain_labels_from_data_source(entity['data']['data_source']) + + (['Literature'] if literature_id is not None else []) + ), + display_name=entity['name'], + data=snake_to_camel_dict(entity['data'], {}), + url=None, ) - # Return nodes in one or more domains, with mapped Literature data (if it exists) - if domains == [] or (len(domains) > 1 and literature_in_selected_domains): - literature_match_string = """ - WITH n, t, n.namespace as go_class - OPTIONAL MATCH (n)<-[:MAPPED_TO]-(m:LiteratureEntity) - """ - # Return nodes in one or more domains, and *exclude* Literature data from the result - elif not literature_in_selected_domains: - literature_match_string = """ - WITH n, t, n.namespace as go_class, NULL as m - """ - # Return only nodes mapped to Literature nodes - else: - literature_match_string = """ - WITH n, t, n.namespace as go_class - MATCH (n)<-[:MAPPED_TO]-(m:LiteratureEntity) - """ - - result = self.graph.read_transaction( - self.visualizer_search_query, - term, - organism, - (page - 1) * limit, - limit, - result_filters, - organism_match_string, - literature_match_string, + formatted_results.append( + FTSTaxonomyRecord( + node=graph_node, + taxonomy_id=taxonomy_id if taxonomy_id is not None else 'N/A', + taxonomy_name=taxonomy_name if taxonomy_name is not None else 'N/A', + go_class=go_class if go_class is not None else 'N/A', + ) ) - - records = self._visualizer_search_result_formatter(result) - - # Wow, this seems barbarian. Fetch 1000 results just to count them? - # TODO: Counting should not fetch nor pre-process results! - total_results = len( - self.graph.read_transaction( - self.visualizer_search_query, - term, - organism, - 0, - 1001, - result_filters, - organism_match_string, - literature_match_string, + return {'rows': formatted_results, 'count': result['count']} + + +def get_organisms(arango_client: ArangoClient, term: str, limit: int) -> Dict[str, Any]: + nodes = execute_arango_query( + db=get_db(arango_client), query=get_organisms_query(), term=term, limit=limit + ) + return { + 'limit': limit, + 'nodes': nodes, + 'query': term, + 'total': len(nodes), + } + + +def get_organism_with_tax_id(arango_client: ArangoClient, tax_id: str): + result = execute_arango_query( + db=get_db(arango_client), query=get_organism_with_tax_id_query(), tax_id=tax_id + ) + return result[0] if len(result) else None + + +def visualizer_search( + arango_client: ArangoClient, + term: str, + organism: str, + domains: List[str], + entities: List[str], + page: int = 1, + limit: int = 10, +) -> dict: + collection_filters = _get_collection_filters(domains) + types = _get_labels_filter(entities) + literature_match_string = _get_literature_match_string(domains) + organism_match_string = _get_organism_match_string(organism) + query = visualizer_search_query( + collection_filters, + organism_match_string, + literature_match_string, + organism_required=True if organism else False, + literature_required=( + len(domains) == 1 + and any([normalize_str(domain) == 'literature' for domain in domains]) + ), + ) + query_args = { + 'term': term, + 'types': types, + 'skip': (page - 1) * limit, + 'limit': limit, + } + + # The call to arango needs to exclude the "organism" parameter if it isn't present in the query. + if organism: + query_args['organism'] = organism + + result = execute_arango_query(db=get_db(arango_client), query=query, **query_args)[ + 0 + ] + + return _visualizer_search_result_formatter(result) + + +def get_synonyms( + arango_client: ArangoClient, + search_term: str, + organisms: List[str], + types: List[str], + skip: int, + limit: int, +) -> List[dict]: + labels_match_str = _get_labels_match_string(types) + organism_match_string = _get_organisms_match_string(organisms) + + query_args = { + 'search_term': search_term, + 'types': types, + 'skip': skip, + 'limit': limit, + } + + # The call to arango needs to exclude the "organism" parameter if it isn't present in the query. + if organisms: + query_args['organisms'] = organisms + + results = execute_arango_query( + db=get_db(arango_client), + query=get_synonyms_query(labels_match_str, organism_match_string), + **query_args, + ) + + synonym_data = [] + for row in results: + try: + type = get_first_known_label_from_list(row['entity_labels']) + except ValueError: + type = 'Unknown' + current_app.logger.warning( + f"Node had an unexpected list of labels: {row['entity_labels']}", + extra=EventLog(event_type=LogEventType.KNOWLEDGE_GRAPH.value).to_dict(), ) + + synonym_data.append( + { + 'type': type, + 'name': row['entity_name'], + 'organism': row['taxonomy_name'], + 'synonyms': row['synonyms'], + } ) + return synonym_data + + +def get_synonyms_count( + arango_client: ArangoClient, + search_term: str, + organisms: List[str], + types: List[str], +) -> int: + labels_match_str = _get_labels_match_string(types) + organism_match_string = _get_organisms_match_string(organisms) + + query_args = { + 'search_term': search_term, + 'types': types, + } + + # The call to arango needs to exclude the "organism" parameter if it isn't present in the query. + if organisms: + query_args['organisms'] = organisms + + return execute_arango_query( + db=get_db(arango_client), + query=get_synonyms_count_query(labels_match_str, organism_match_string), + **query_args, + )[0] + + +def get_organisms_query() -> str: + return """ + FOR n IN synonym_ft + SEARCH PHRASE(n.name, @term, 'text_ll') + SORT BM25(n) DESC + FOR t IN INBOUND n has_synonym OPTIONS { vertexCollections: ["taxonomy" ] } + LIMIT @limit + RETURN { + tax_id: t.eid, + organism_name: t.name, + synonym: n.name + } + """ - return FTSResult(term, records, total_results, page, limit) - def get_organism_with_tax_id(self, tax_id: str): - result = self.graph.read_transaction( - self.get_organism_with_tax_id_query, tax_id - ) - return result[0] if len(result) else None - - def get_organisms(self, term: str, limit: int) -> Dict[str, Any]: - query_term = self._fulltext_query_sanitizer(term) - if not query_term: - return { - 'limit': limit, - 'nodes': [], - 'query': query_term, - 'total': 0, +def get_organism_with_tax_id_query() -> str: + return """ + FOR t IN taxonomy + FILTER t.eid == @tax_id + RETURN { + tax_id: t.eid, + organism_name: t.name, + synonym: t.name } + """ + + +def visualizer_search_query( + arango_col_filters: str, + organism_match_string: str, + literature_match_filter: str, + organism_required: bool, + literature_required: bool, +) -> str: + """Need to collect synonyms because a gene node can have multiple + synonyms. So it is possible to send duplicate internal node ids to + a later query.""" + + # The purpose of these dynamically chosen query strings is to prevent extra traversals from + # being calculated. If organism or literature matching is not strictly required for a match, + # we wait to do the matching until the last, paginated slice of data is acquired. This can mean + # the difference between performing a traversal on potentially hundreds or thousands of + # relationships, to instead just a handful. + + # It is especially useful when we need to find neither a literature nor an organism match. This + # also has the benefit of allowing us to return the total count of results as well, rather than + # do so in a separate query. + both_required_str = f""" + LET filtered_results = ( + FOR result IN unfiltered_results + LET entity = result.entity.id + {organism_match_string} + {literature_match_filter} + RETURN {{ + 'entity': result.entity, + 'literature_id': literature_id, + 'taxonomy_id': t.eid, + 'taxonomy_name': t.name, + 'go_class': result.go_class + }} + ) + LET final_count = LENGTH(filtered_results) + LET final_result = ( + FOR result in filtered_results + LIMIT @skip, @limit + RETURN {{ + 'entity': result.entity, + 'literature_id': result.literature_id, + 'taxonomy_id': result.taxonomy_id, + 'taxonomy_name': result.taxonomy_name, + 'go_class': result.go_class + }} + ) + """ - terms = query_term.split(' ') - query_term = ' AND '.join(terms) - nodes = self.graph.read_transaction(self.get_organisms_query, query_term, limit) - - return { - 'limit': limit, - 'nodes': nodes, - 'query': query_term, - 'total': len(nodes), - } - - def get_synonyms( - self, - search_term: str, - organisms: List[str], - types: List[str], - page: int, - limit: int, - ) -> List[dict]: - results = self.graph.read_transaction( - self.get_synonyms_query, search_term, organisms, types, page, limit + literature_required_str = f""" + LET filtered_results = ( + FOR result IN unfiltered_results + LET entity = result.entity.id + {literature_match_filter} + RETURN {{ + 'entity': result.entity, + 'literature_id': literature_id, + 'go_class': result.go_class + }} ) - synonym_data = [] - - for row in results: - try: - type = get_first_known_label_from_list(row['entity_labels']) - except ValueError as e: - type = 'Unknown' - message = ( - f"Node had an unexpected list of labels: {row['entity_labels']}" - ) - current_app.logger.warning( - message, - extra=EventLog( - event_type=LogEventType.KNOWLEDGE_GRAPH.value - ).to_dict(), - ) - warn(ServerWarning(message=message), cause=e) - - synonym_data.append( - { - 'type': type, - 'name': row['entity_name'], - 'organism': row['taxonomy_name'], - 'synonyms': row['synonyms'], - } - ) - return synonym_data + LET final_count = LENGTH(filtered_results) + LET final_result = ( + FOR result IN filtered_results + // Limit BEFORE the organism matching to prevent unnecessary traversals + LIMIT @skip, @limit + LET entity = result.entity.id + {organism_match_string} + RETURN {{ + 'entity': result.entity, + 'literature_id': result.literature_id, + 'taxonomy_id': t.eid, + 'taxonomy_name': t.name, + 'go_class': result.go_class + }} + ) + """ - def get_synonyms_count( - self, search_term: str, organisms: List[str], types: List[str] - ) -> List[dict]: - results = self.graph.read_transaction( - self.get_synonyms_count_query, search_term, organisms, types + organism_required_str = f""" + LET filtered_results = ( + FOR result IN unfiltered_results + LET entity = result.entity.id + {organism_match_string} + RETURN {{ + 'entity': result.entity, + 'taxonomy_id': t.eid, + 'taxonomy_name': t.name, + 'go_class': result.go_class + }} ) - return results[0]['count'] - - def visualizer_search_query( - self, - tx: Neo4jTx, - search_term: str, - organism: str, - amount: int, - limit: int, - result_filters: str, - organism_match_string: str, - literature_match_string: str, - ) -> List[N4jRecord]: - """Need to collect synonyms because a gene node can have multiple - synonyms. So it is possible to send duplicate internal node ids to - a later query.""" - return [ - record - for record in tx.run( - f""" - CALL db.index.fulltext.queryNodes("synonymIdx", $search_term) - YIELD node - MATCH (node)-[]-(n) - WHERE {result_filters} - WITH n + LET final_count = LENGTH(filtered_results) + LET final_result = ( + FOR result IN filtered_results + // Limit BEFORE the literature matching to prevent unnecessary traversals + LIMIT @skip, @limit + LET entity = result.entity.id + {literature_match_filter} + RETURN {{ + 'entity': result.entity, + 'literature_id': literature_id, + 'taxonomy_id': result.taxonomy_id, + 'taxonomy_name': result.taxonomy_name, + 'go_class': result.go_class + }} + ) + """ + + neither_required_str = f""" + LET final_count = LENGTH(unfiltered_results) + LET final_result = ( + FOR result IN unfiltered_results + // Limit BEFORE matching to prevent unnecessary traversals + LIMIT @skip, @limit + LET entity = result.entity.id {organism_match_string} - {literature_match_string} - WITH - {{ - id: id(n), - name: n.name, - labels: labels(n), - data: {{ - eid: n.eid, - data_source: n.data_source + {literature_match_filter} + RETURN {{ + 'entity': result.entity, + 'literature_id': literature_id, + 'taxonomy_id': t.eid, + 'taxonomy_name': t.name, + 'go_class': result.go_class + }} + ) + """ + + if organism_required and literature_required: + pagination_query_str = both_required_str + elif organism_required: + pagination_query_str = organism_required_str + elif literature_required: + pagination_query_str = literature_required_str + else: + pagination_query_str = neither_required_str + + return f""" + LET unfiltered_results = ( + FOR s IN synonym_ft + SEARCH + PHRASE(s.name, @term, 'text_ll') OR + PHRASE(s.name, {{STARTS_WITH: TOKENS(@term, "text_ll")[0]}}, 'text_ll') + FOR entity IN INBOUND s has_synonym + LET go_class = entity.namespace + // Need to manually add "Taxonomy" to the label list since taxonomy docs don't + // have labels as they would be redundant. + LET labels = UNION( + entity.labels, + IS_SAME_COLLECTION("taxonomy", entity._id) ? ["Taxonomy"] : [] + ) + {arango_col_filters} + FILTER LENGTH(INTERSECTION(@types, labels)) > 0 OR LENGTH(@types) == 0 + COLLECT + score = BM25(s), + id = entity._id, + name = entity.name, + entity_labels = labels, + eid = entity.eid, + data_source = entity.data_source, + entity_go_class = go_class + SORT score DESC, name ASC + RETURN DISTINCT {{ + 'entity': {{ + 'id': id, + 'name': name, + 'labels': entity_labels, + 'data': {{ + 'eid': eid, + 'data_source': data_source + }} + }}, + 'go_class': entity_go_class }} - }} as entity, id(m) as literature_id, t, go_class - RETURN DISTINCT entity, literature_id, t.eid AS taxonomy_id, - t.name AS taxonomy_name, go_class AS go_class - SKIP $amount - LIMIT $limit - """, - search_term=f'{search_term} OR {search_term}*', - organism=organism, - amount=amount, - limit=limit, - ) - # IMPORTANT: We do NOT use `data` here, because if we did we would lose some metadata - # attached to the `node` return value. We need this metadata to deterimine node labels. - # TODO: Should create a helper function that produces key-value pair records for all - # Neo4j driver data types, so we don't have to selectively use `data`. - ] - - def get_organism_with_tax_id_query(self, tx: Neo4jTx, tax_id: str) -> List[Dict]: - return [ - record - for record in tx.run( - """ - MATCH (t:Taxonomy {eid: $tax_id}) - RETURN t.eid AS tax_id, t.name AS organism_name, t.name AS synonym - """, - tax_id=tax_id, - ).data() - ] - - def get_organisms_query(self, tx: Neo4jTx, term: str, limit: int) -> List[Dict]: - return [ - record - for record in tx.run( - """ - CALL db.index.fulltext.queryNodes("synonymIdx", $term) - YIELD node, score - MATCH (node)-[]-(t:Taxonomy) - with t, collect(node.name) as synonyms LIMIT $limit - RETURN t.eid AS tax_id, t.name AS organism_name, synonyms[0] AS synonym - """, - term=term, - limit=limit, - ).data() - ] - - def get_synonyms_query( - self, - tx: Neo4jTx, - search_term: str, - organisms: List[str], - types: List[str], - page: int, - limit: int, - ) -> List[N4jRecord]: - """ - Gets a list of synoynm data for a given search term. Data includes any matched entities, as - well as any linked organism, if there is one. - """ - type_match_str = '' - if len(types): - type_match_str = ' AND any(x IN $types WHERE x IN labels(entity))' - - tax_match_str = 'OPTIONAL MATCH (entity)-[:HAS_TAXONOMY]-(t:Taxonomy)' - if len(organisms): - tax_match_str = ( - 'MATCH (entity)-[:HAS_TAXONOMY]-(t:Taxonomy) WHERE t.eid IN $organisms' - ) - - return list( - tx.run( - f""" - MATCH (synonym:Synonym {{lowercase_name: toLower($search_term)}}) - <-[:HAS_SYNONYM]-(entity) - WHERE NOT 'Protein' IN labels(entity){type_match_str} - MATCH (entity)-[:HAS_SYNONYM]->(synonyms) - WHERE - size(synonyms.name) > 2 OR - any(x IN ['Chemical', 'Compound'] WHERE x IN labels(entity)) - WITH - entity, - synonyms.name AS synonyms, - toLower(entity.name) = toLower($search_term) AS matches_term - ORDER BY size(synonyms) DESC - {tax_match_str} - RETURN - entity.name as entity_name, - t.name as taxonomy_name, - labels(entity) as entity_labels, - collect(DISTINCT synonyms) AS synonyms, - COUNT(DISTINCT synonyms) AS synonym_count, - matches_term - ORDER BY matches_term DESC - SKIP $page - LIMIT $limit - """, - search_term=search_term, - organisms=organisms, - types=types, - page=page, - limit=limit, - ) ) - - def get_synonyms_count_query( - self, tx: Neo4jTx, search_term: str, organisms: List[str], types: List[str] - ) -> List[N4jRecord]: - """ - Gets the count of synoynm data for a given search term. - """ - type_match_str = '' - if len(types): - type_match_str = ' AND all(x IN $types WHERE x IN labels(entity))' - - tax_match_str = '' - if len(organisms): - tax_match_str = ( - 'MATCH (entity)-[:HAS_TAXONOMY]-(t:Taxonomy) WHERE t.eid IN $organisms' - ) - - return tx.run( - f""" - MATCH (synonym:Synonym {{lowercase_name: toLower($search_term)}}) - <-[:HAS_SYNONYM]-(entity) - WHERE NOT 'Protein' IN labels(entity){type_match_str} - MATCH (entity)-[:HAS_SYNONYM]->(synonyms) - WHERE - size(synonyms.name) > 2 OR - any(x IN labels(entity) WHERE x IN ['Chemical', 'Compound']) - {tax_match_str} - RETURN count(DISTINCT entity) AS count - """, - search_term=search_term, - organisms=organisms, - types=types, - ).data() + {pagination_query_str} + RETURN {{ + 'count': final_count, + 'rows': final_result + }} + """ + + +def get_synonyms_query(labels_match_str: str, organism_match_string: str) -> str: + """ + Gets a list of synoynm data for a given search term. Data includes any matched entities, as + well as any linked organism, if there is one. + """ + return f""" + FOR syn IN synonym + FILTER syn.lowercase_name == @search_term + FOR entity IN INBOUND syn has_synonym + FILTER "Protein" NOT IN entity.labels + {labels_match_str} + LET synonyms = ( + FOR syn2 IN OUTBOUND entity has_synonym + // Could use INTERSECTION here? + FILTER + length(syn2.name) > 2 OR + "Chemical" IN entity.labels OR + "Compound" IN entity.labels + RETURN syn2.name + ) + LET matches_term = @search_term == LOWER(entity.name) + LET syn_len = length(synonyms) + {organism_match_string} + SORT matches_term DESC, syn_len DESC + LIMIT @skip, @limit + RETURN DISTINCT {{ + entity_name: entity.name, + taxonomy_name: t.name, + entity_labels: entity.labels, + synonyms: synonyms, + synonym_count: syn_len, + matches_term: matches_term + }} + """ + + +def get_synonyms_count_query(labels_match_str: str, organism_match_string: str) -> str: + """ + Gets the count of synoynm data for a given search term. + """ + return f""" + RETURN LENGTH( + FOR syn IN synonym + FILTER syn.lowercase_name == @search_term + FOR entity IN INBOUND syn has_synonym + FILTER "Protein" NOT IN entity.labels + {labels_match_str} + LET synonyms = ( + FOR syn2 IN OUTBOUND entity has_synonym + // Could use INTERSECTION here? + FILTER + length(syn2.name) > 2 OR + "Chemical" IN entity.labels OR + "Compound" IN entity.labels + RETURN syn2.name + ) + LET matches_term = @search_term == LOWER(entity.name) + LET syn_len = length(synonyms) + {organism_match_string} + RETURN DISTINCT {{ + entity_name: entity.name, + taxonomy_name: t.name, + entity_labels: entity.labels, + synonyms: synonyms, + synonym_count: syn_len, + matches_term: matches_term + }} + ) + """ diff --git a/appserver/neo4japp/services/shortest_path_data/ale_mutation_data/42C.json b/appserver/neo4japp/services/shortest_path_data/ale_mutation_data/42C.json deleted file mode 100644 index 857abbff3c..0000000000 --- a/appserver/neo4japp/services/shortest_path_data/ale_mutation_data/42C.json +++ /dev/null @@ -1,18937 +0,0 @@ -{ - 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"color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1217", - "label": "ENCODES", - "from": "1396", - "to": "3011", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1218", - "label": "PRODUCES", - "from": "2165", - "to": "2765", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1249", - "label": "CONSUMED_BY", - "from": "1678", - "to": "2155", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1254", - "label": "PRODUCES", - "from": "2155", - "to": "2822", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1260", - "label": "PRODUCES", - "from": "1175", - "to": "2788", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1279", - "label": "PRODUCES", - "from": "1178", - "to": "1398", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1352", - "label": "CONSUMED_BY", - "from": "3055", - "to": "2075", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1358", - "label": "PRODUCES", - "from": "2075", - "to": "1941", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1376", - "label": "CONSUMED_BY", - "from": "1305", - "to": "1227", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1379", - "label": "PRODUCES", - "from": "1227", - "to": "1675", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1512", - "label": "PRODUCES", - "from": "2003", - "to": "1309", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1548", - "label": "CATALYZES", - "from": "2858", - "to": "2668", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1549", - "label": "CATALYZES", - "from": "2668", - "to": "1607", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1551", - "label": "CONSUMED_BY", - "from": "1303", - "to": "2003", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1565", - "label": "CATALYZES", - "from": "1308", - "to": "1389", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1569", - "label": "CATALYZES", - "from": "1389", - "to": "1198", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1574", - "label": "CATALYZES", - "from": "2707", - "to": "3347", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1575", - "label": "CATALYZES", - "from": "1542", - "to": "2707", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1585", - "label": "PRODUCES", - "from": "2228", - "to": "2877", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1586", - "label": "CONSUMED_BY", - "from": "2868", - "to": "2228", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1588", - "label": "CATALYZES", - "from": "1443", - "to": "1397", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1591", - "label": "CATALYZES", - "from": "3011", - "to": "1443", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1594", - "label": "CONSUMED_BY", - "from": "1398", - "to": "2231", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1601", - "label": "PRODUCES", - "from": "2231", - "to": "1262", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1605", - "label": "CATALYZES", - "from": "1437", - "to": "1175", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1608", - "label": "CATALYZES", - "from": "1572", - "to": "1437", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1616", - "label": "CATALYZES", - "from": "3011", - "to": "2237", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1619", - "label": "CATALYZES", - "from": "2237", - "to": "1652", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1722", - "label": "PRODUCES", - "from": "2193", - "to": "2752", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1724", - "label": "CONSUMED_BY", - "from": "2765", - "to": "2193", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1733", - "label": "CONSUMED_BY", - "from": "1309", - "to": "3387", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1737", - "label": "PRODUCES", - "from": "3387", - "to": "1680", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1776", - "label": "PRODUCES", - "from": "2562", - "to": "3168", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1777", - "label": "CONSUMED_BY", - "from": "1784", - "to": "2562", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1778", - "label": "CONSUMED_BY", - "from": "2856", - "to": "2562", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1802", - "label": "PRODUCES", - "from": "1254", - "to": "3102", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1845", - "label": "COMPONENT_OF", - "from": "1108", - "to": "1572", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1848", - "label": "CONSUMED_BY", - "from": "2887", - "to": "2323", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1849", - "label": "PRODUCES", - "from": "2323", - "to": "2856", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1897", - "label": "CATALYZES", - "from": "3011", - "to": "2461", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1898", - "label": "CATALYZES", - "from": "2461", - "to": "1746", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1925", - "label": "PRODUCES", - "from": "2999", - "to": "2849", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1934", - "label": "PRODUCES", - "from": "2227", - "to": "1678", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1935", - "label": "CONSUMED_BY", - "from": "2849", - "to": "2227", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1942", - "label": "PRODUCES", - "from": "1241", - "to": "2887", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1969", - "label": "COMPONENT_OF", - "from": "1102", - "to": "3388", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1983", - "label": "CONSUMED_BY", - "from": "3161", - "to": "1606", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1985", - "label": "PRODUCES", - "from": "1606", - "to": "1675", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1987", - "label": "PRODUCES", - "from": "1240", - "to": "1303", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1988", - "label": "CONSUMED_BY", - "from": "1262", - "to": "1240", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "1993", - "label": "PRODUCES", - "from": "1607", - "to": "2885", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "2022", - "label": "PRODUCES", - "from": "3178", - "to": "2877", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "2026", - "label": "CONSUMED_BY", - "from": "2752", - "to": "3178", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "2055", - "label": "CONSUMED_BY", - "from": "2856", - "to": "1998", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "2058", - "label": "PRODUCES", - "from": "1998", - "to": "2945", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "2179", - "label": "CONSUMED_BY", - "from": "3102", - "to": "2252", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "2186", - "label": "PRODUCES", - "from": "2252", - "to": "2856", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "2251", - "label": "PRODUCES", - "from": "1415", - "to": "2676", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "2312", - "label": "CONSUMED_BY", - "from": "2849", - "to": "2373", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "2314", - "label": "PRODUCES", - "from": "2373", - "to": "1675", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "2346", - "label": "PRODUCES", - "from": "3347", - "to": "1894", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "2592", - "label": "CATALYZES", - "from": "3388", - "to": "2631", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - }, - { - "id": "2593", - "label": "CATALYZES", - "from": "2631", - "to": "2354", - "color": { - "color": "#0c8caa" - }, - "arrows": "to" - } - ] -} diff --git a/appserver/neo4japp/services/visualizer.py b/appserver/neo4japp/services/visualizer.py index 406733997c..34fb68bcea 100644 --- a/appserver/neo4japp/services/visualizer.py +++ b/appserver/neo4japp/services/visualizer.py @@ -1,10 +1,12 @@ -from typing import List - +from arango.client import ArangoClient from flask.globals import current_app -from neo4j import Record as Neo4jRecord, Transaction as Neo4jTx +from typing import Dict, List +from uuid import uuid4 from neo4japp.constants import ( LogEventType, + DISPLAY_NAME_MAP, + DOMAIN_URLS_MAP, TYPE_CHEMICAL, TYPE_DISEASE, TYPE_GENE, @@ -16,695 +18,728 @@ Direction, DuplicateEdgeConnectionData, EdgeConnectionData, + GetBulkReferenceTableDataResult, GetClusterSnippetsResult, GetEdgeSnippetsResult, GetNodePairSnippetsResult, GetReferenceTableDataResult, GetSnippetsFromEdgeResult, - ReferenceTablePair, ReferenceTableRow, Snippet, GetAssociatedTypesResult, ) -from neo4japp.exceptions import ServerWarning from neo4japp.models import GraphNode -from neo4japp.models.entity_resources import DomainURLsMap -from neo4japp.services import KgService -from neo4japp.utils import snake_to_camel_dict, EventLog -from neo4japp.utils.globals import warn +from neo4japp.services.arangodb import execute_arango_query, get_db from neo4japp.utils.labels import get_first_known_label_from_list - - -class VisualizerService(KgService): - def __init__(self, graph, session): - super().__init__(graph=graph, session=session) - - def _get_uri_of_node_data(self, id: int, label: str, entity_id: str): - """Given node meta data returns the appropriate - URL formatted with the node entity identifier. - """ - url_map = { - domain: base_url - for domain, base_url in self.session.query( - DomainURLsMap.domain, - DomainURLsMap.base_URL, - ) - } - - # Can't get the URI of the node if there is no 'eid' property, so return None - if entity_id is None: - current_app.logger.warning( - f'Node with EID {entity_id} does not have a URI.', - extra=EventLog(event_type=LogEventType.KNOWLEDGE_GRAPH.value).to_dict(), - ) - return None - - url = None - try: - if label == TYPE_CHEMICAL: - db_prefix, uid = entity_id.split(':') - if db_prefix == 'CHEBI': - url = url_map['chebi'].format(uid) - else: - url = url_map['MESH'].format(uid) - elif label == TYPE_DISEASE: - db_prefix, uid = entity_id.split(':') - if db_prefix == 'MESH': - url = url_map['MESH'].format(uid) - else: - url = url_map['omim'].format(uid) - elif label == TYPE_GENE: - url = url_map['NCBI_Gene'].format(entity_id) - elif label == TYPE_LITERATURE_CHEMICAL: - db_prefix, uid = entity_id.split(':') - if db_prefix == 'CHEBI': - url = url_map['chebi'].format(uid) - else: - url = url_map['MESH'].format(uid) - elif label == TYPE_LITERATURE_DISEASE: - db_prefix, uid = entity_id.split(':') - if db_prefix == 'MESH': - url = url_map['MESH'].format(uid) - else: - url = url_map['omim'].format(uid) - elif label == TYPE_LITERATURE_GENE: - url = url_map['NCBI_Gene'].format(entity_id) - except KeyError as e: - message = ( - f'url_map did not contain the expected key value for node with:\n' - f'\tID: {id}\n' - f'\tLabel: {label}\n' - f'\tURI: {entity_id}\n' - 'There may be something wrong in the database.' - ) - current_app.logger.warning( - message, - extra=EventLog(event_type=LogEventType.KNOWLEDGE_GRAPH.value).to_dict(), - ) - warn(ServerWarning(message=message), cause=e) - finally: - return url - - def expand_graph(self, node_id: str, filter_labels: List[str]): - result = self.graph.read_transaction( - self.get_expand_query, node_id, filter_labels +from neo4japp.utils.logger import EventLog +from neo4japp.utils.string import snake_to_camel_dict + + +def _get_uri_of_node_data(id: str, label: str, entity_id: str): + """Given node meta data returns the appropriate + URL formatted with the node entity identifier. + """ + # Can't get the URI of the node if there is no 'eid' property, so return None + if entity_id is None: + current_app.logger.warning( + f'Node with EID {entity_id} does not have a URI.', + extra=EventLog(event_type=LogEventType.KNOWLEDGE_GRAPH.value).to_dict(), ) - - node_data = [] - edge_data = [] - if len(result) > 0: - node_data = result[0]['nodes'] - edge_data = result[0]['relationships'] - - nodes = [] - for data in node_data: - try: - label = get_first_known_label_from_list(data['labels']) - except ValueError: - label = 'Unknown' - nodes.append( - { - 'id': data['id'], - 'label': label, - 'domainLabels': [], - 'data': { - 'name': data['name'], - 'id': data['entity_id'], - }, - 'subLabels': data['labels'], - 'displayName': data['name'], - 'entityUrl': self._get_uri_of_node_data( - data['id'], label, data['entity_id'] - ), - } + return None + + url = None + try: + if label == TYPE_CHEMICAL: + db_prefix, uid = entity_id.split(':') + if db_prefix == 'CHEBI': + url = DOMAIN_URLS_MAP['chebi'].format(uid) + else: + url = DOMAIN_URLS_MAP['MESH'].format(uid) + elif label == TYPE_DISEASE: + db_prefix, uid = entity_id.split(':') + if db_prefix == 'MESH': + url = DOMAIN_URLS_MAP['MESH'].format(uid) + else: + url = DOMAIN_URLS_MAP['omim'].format(uid) + elif label == TYPE_GENE: + url = DOMAIN_URLS_MAP['NCBI_Gene'].format(entity_id) + elif label == TYPE_LITERATURE_CHEMICAL: + db_prefix, uid = entity_id.split(':') + if db_prefix == 'CHEBI': + url = DOMAIN_URLS_MAP['chebi'].format(uid) + else: + url = DOMAIN_URLS_MAP['MESH'].format(uid) + elif label == TYPE_LITERATURE_DISEASE: + db_prefix, uid = entity_id.split(':') + if db_prefix == 'MESH': + url = DOMAIN_URLS_MAP['MESH'].format(uid) + else: + url = DOMAIN_URLS_MAP['omim'].format(uid) + elif label == TYPE_LITERATURE_GENE: + url = DOMAIN_URLS_MAP['NCBI_Gene'].format(entity_id) + except KeyError: + current_app.logger.warning( + f'url_map did not contain the expected key value for node with:\n' + + f'\tID: {id}\n' + + f'\tLabel: {label}\n' + + f'\tURI: {entity_id}\n' + + 'There may be something wrong in the database.', + extra=EventLog(event_type=LogEventType.KNOWLEDGE_GRAPH.value).to_dict(), + ) + finally: + return url + + +def get_document_for_visualizer(arango_client: ArangoClient, doc_id: str): + doc = execute_arango_query( + get_db(arango_client), query='RETURN DOCUMENT(@id)', id=doc_id + )[0] + label = get_first_known_label_from_list(doc['labels']) + return GraphNode( + id=doc['_id'], + label=label, + sub_labels=doc['labels'], + domain_labels=[], + display_name=doc.get(DISPLAY_NAME_MAP[label], 'Unknown'), + data=snake_to_camel_dict(doc, {}), + url=_get_uri_of_node_data(doc['_id'], label, doc['eid']), + ).to_dict() + + +def expand_node_as_clusters( + arango_client: ArangoClient, node_id: str, filter_labels: List[str] +): + expansion_results = execute_arango_query( + get_db(arango_client), + query=get_expand_query(), + node_id=node_id, + labels=filter_labels, + ) + + associations = dict() + for row in expansion_results: + description = row['description'] + direction = row['direction'] + pairs = row['pairs'] + association_key = f'{description}${direction}' + + duplicate_node_edge_pairs = [] + for pair in pairs: + node = pair['node'] + edge = pair['edge'] + node_label = get_first_known_label_from_list(node['labels']) + node_as_duplicate = { + **node, + 'id': f'duplicateNode:{uuid4()}', + 'duplicate_of': node['id'], + 'label': node_label, + 'entity_url': _get_uri_of_node_data( + node['id'], node_label, node['data']['id'] + ), + } + + edge_as_duplicate = { + **edge, + 'to_label': get_first_known_label_from_list(edge['to_labels']), + 'from_label': get_first_known_label_from_list(edge['from_labels']), + 'id': f'duplicateNode:{uuid4()}', + 'duplicate_of': edge['id'], + 'from': node_id if edge['from'] == node_id else node_as_duplicate['id'], + 'to': node_id if edge['to'] == node_id else node_as_duplicate['id'], + 'original_from': edge['from'], + 'original_to': edge['to'], + } + + duplicate_node_edge_pairs.append( + {'node': node_as_duplicate, 'edge': edge_as_duplicate} ) - - edges = [] - for data in edge_data: - try: - from_label = get_first_known_label_from_list(data['from_labels']) - except ValueError: - from_label = 'Unknown' - - try: - to_label = get_first_known_label_from_list(data['to_labels']) - except ValueError: - to_label = 'Unknown' - - edges.append( - { - 'id': data['id'], - 'label': data['label'], - 'data': { - 'description': data['relationship'].get('description'), - 'association_id': data['relationship'].get('association_id'), - 'type': data['relationship'].get('type'), - }, - 'to': data['relationship'].end_node.id, - 'from': data['relationship'].start_node.id, - 'toLabel': to_label, - 'fromLabel': from_label, - } + associations[association_key] = duplicate_node_edge_pairs + + reference_tables = [] + for association, node_edge_pairs in associations.items(): + description, direction = association.split('$') + reference_tables.append( + get_reference_table_data( + arango_client, node_edge_pairs, description, direction ) - - return {'nodes': nodes, 'edges': edges} - - def get_snippets_from_edges( - self, - from_ids: List[int], - to_ids: List[int], - description: str, - page: int, - limit: int, - ): - return self.graph.read_transaction( - self.get_snippets_from_edges_query, - from_ids, - to_ids, - description, - (page - 1) * limit, - limit, ) - - def get_snippets_from_node_pair( - self, node_1_id: int, node_2_id: int, page: int, limit: int - ): - return self.graph.read_transaction( - self.get_snippets_from_node_pair_query, - node_1_id, - node_2_id, - (page - 1) * limit, - limit, + return GetBulkReferenceTableDataResult(reference_tables=reference_tables) + + +def get_associated_type_snippet_count( + arango_client: ArangoClient, + source_node: int, + associated_nodes: List[int], +): + results = execute_arango_query( + db=get_db(arango_client), + query=get_associated_type_snippet_count_query(), + source_node=source_node, + associated_nodes=associated_nodes, + ) + return GetAssociatedTypesResult(associated_data=results) + + +def get_snippets_for_node_pair( + arango_client: ArangoClient, + node_1_id: int, + node_2_id: int, + page: int, + limit: int, +): + data = get_snippets_from_node_pair(arango_client, node_1_id, node_2_id, page, limit) + total_results = get_snippet_count_from_node_pair( + arango_client, node_1_id, node_2_id + ) + + results = [ + GetSnippetsFromEdgeResult( + from_node_id=row['from_id'], + to_node_id=row['to_id'], + association=row['description'], + snippets=[ + Snippet( + reference=GraphNode( + reference['snippet']['id'], + 'Snippet', + [], + snake_to_camel_dict(reference['snippet']['data'], {}), + [], + None, + None, + ), + publication=GraphNode( + reference['publication']['id'], + 'Publication', + [], + snake_to_camel_dict(reference['publication']['data'], {}), + [], + None, + None, + ), + ) + for reference in row['references'] + ], ) - - def get_snippet_count_from_node_pair( - self, - node_1_id: int, - node_2_id: int, - ): - return self.graph.read_transaction( - self.get_snippet_count_from_node_pair_query, node_1_id, node_2_id - )['snippet_count'] - - def get_reference_table_data(self, node_edge_pairs: List[ReferenceTablePair]): - # For duplicate edges, We need to remember which true node ID pairs map to which - # duplicate node ID pairs, otherwise when we send the data back to the frontend - # we won't know which duplicate nodes we should match the snippet data with - ids_to_pairs = { - (pair.edge.original_from, pair.edge.original_to): pair - for pair in node_edge_pairs - } - - # One of these lists will have all duplicates (depends on the direction - # of the cluster edge). We remove the duplicates so we don't get weird query results. - from_ids = list({pair.edge.original_from for pair in node_edge_pairs}) - to_ids = list({pair.edge.original_to for pair in node_edge_pairs}) - description = node_edge_pairs[ - 0 - ].edge.label # Every edge should have the same label + for row in data + ] + + return GetNodePairSnippetsResult( + snippet_data=results, + total_results=total_results, + query_data={'node_1_id': node_1_id, 'node_2_id': node_2_id}, + ) + + +def get_snippets_from_node_pair( + arango_client: ArangoClient, node_1_id: int, node_2_id: int, page: int, limit: int +): + return execute_arango_query( + get_db(arango_client), + query=get_snippets_from_node_pair_query(), + node_1_id=node_1_id, + node_2_id=node_2_id, + skip=(page - 1) * limit, + limit=limit, + ) + + +def get_snippet_count_from_node_pair( + arango_client: ArangoClient, + node_1_id: int, + node_2_id: int, +): + return execute_arango_query( + db=get_db(arango_client), + query=get_snippet_count_from_node_pair_query(), + node_1_id=node_1_id, + node_2_id=node_2_id, + )[0] + + +def get_snippets_from_edges( + arango_client: ArangoClient, + from_ids: List[str], + to_ids: List[str], + description: str, + page: int, + limit: int, +): + return execute_arango_query( + get_db(arango_client), + query=get_snippets_from_edges_query(), + from_ids=from_ids, + to_ids=to_ids, + description=description, + skip=(page - 1) * limit, + limit=limit, + ) + + +def get_reference_table_data( + arango_client: ArangoClient, + node_edge_pairs: List[Dict], + description: str = None, + direction: str = None, +): + # For duplicate edges, We need to remember which true node ID pairs map to which + # duplicate node ID pairs, otherwise when we send the data back to the frontend + # we won't know which duplicate nodes we should match the snippet data with + ids_to_pairs = { + (pair['edge']['original_from'], pair['edge']['original_to']): pair + for pair in node_edge_pairs + } + + # One of these lists will have all duplicates (depends on the direction + # of the cluster edge). We remove the duplicates so we don't get weird query results. + from_ids = list({pair['edge']['original_from'] for pair in node_edge_pairs}) + to_ids = list({pair['edge']['original_to'] for pair in node_edge_pairs}) + if description is None: + description = node_edge_pairs[0]['edge'][ + 'label' + ] # Every edge should have the same label + if direction is None: direction = Direction.FROM.value if len(from_ids) == 1 else Direction.TO.value - counts = self.graph.read_transaction( - self.get_snippet_count_from_edges_query, from_ids, to_ids, description - ) - - reference_table_rows: List[ReferenceTableRow] = [] - for row in counts: - pair = ids_to_pairs[(row['from_id'], row['to_id'])] - reference_table_rows.append( - ReferenceTableRow( - node_id=pair.node.id, - node_display_name=pair.node.display_name, - node_label=pair.node.label, - snippet_count=row['count'], - ) + counts = execute_arango_query( + get_db(arango_client), + query=get_snippet_count_from_edges_query(), + from_ids=from_ids, + to_ids=to_ids, + description=description, + ) + + reference_table_rows: List[ReferenceTableRow] = [] + for row in counts: + pair = ids_to_pairs[(row['from_id'], row['to_id'])] + reference_table_rows.append( + ReferenceTableRow( + node_id=pair['node']['id'], + node_display_name=pair['node']['display_name'], + node_label=pair['node']['label'], + snippet_count=row['count'], ) - - return GetReferenceTableDataResult( - reference_table_rows=reference_table_rows, direction=direction ) - def get_snippets_for_edge( - self, - edge: EdgeConnectionData, - page: int, - limit: int, - ) -> GetEdgeSnippetsResult: - from_ids = [edge.from_] - to_ids = [edge.to] - description = edge.label # Every edge should have the same label - - data = self.get_snippets_from_edges(from_ids, to_ids, description, page, limit) - count_results = self.graph.read_transaction( - self.get_snippet_count_from_edges_query, from_ids, to_ids, description - ) - total_results = sum(row['count'] for row in count_results) - - # `data` is either length 0 or 1 - snippets = [] - for row in data: - for reference in row['references']: - snippets.append( - Snippet( - reference=GraphNode( - reference['snippet']['id'], - 'Snippet', - [], - snake_to_camel_dict(reference['snippet']['data'], {}), - [], - None, - None, - ), - publication=GraphNode( - reference['publication']['id'], - 'Publication', - [], - snake_to_camel_dict(reference['publication']['data'], {}), - [], - None, - None, - ), - ) + return GetReferenceTableDataResult( + reference_table_rows=reference_table_rows, + duplicate_node_edge_pairs=node_edge_pairs, + direction=direction, + description=description, + ) + + +def get_snippets_for_edge( + arango_client: ArangoClient, + edge: EdgeConnectionData, + page: int, + limit: int, +) -> GetEdgeSnippetsResult: + from_ids = [edge.from_] + to_ids = [edge.to] + description = edge.label # Every edge should have the same label + + data = get_snippets_from_edges( + arango_client, from_ids, to_ids, description, page, limit + ) + count_results = execute_arango_query( + get_db(arango_client), + query=get_snippet_count_from_edges_query(), + from_ids=from_ids, + to_ids=to_ids, + description=description, + ) + total_results = sum(row['count'] for row in count_results) + + # `data` is either length 0 or 1 + snippets = [] + for row in data: + for reference in row['references']: + snippets.append( + Snippet( + reference=GraphNode( + reference['snippet']['id'], + 'Snippet', + [], + snake_to_camel_dict(reference['snippet']['data'], {}), + [], + None, + None, + ), + publication=GraphNode( + reference['publication']['id'], + 'Publication', + [], + snake_to_camel_dict(reference['publication']['data'], {}), + [], + None, + None, + ), ) - - result = GetSnippetsFromEdgeResult( - from_node_id=edge.from_, - to_node_id=edge.to, - association=edge.label, - snippets=snippets, - ) - - return GetEdgeSnippetsResult( - snippet_data=result, - total_results=total_results, - query_data=edge, - ) - - @staticmethod - def _compose_snippet_from_reference(reference) -> Snippet: - return Snippet( - reference=GraphNode( - reference['snippet']['id'], - 'Snippet', - [], - snake_to_camel_dict(reference['snippet']['data'], {}), - [], - None, - None, - ), - publication=GraphNode( - reference['publication']['id'], - 'Publication', - [], - snake_to_camel_dict(reference['publication']['data'], {}), - [], - None, - None, - ), - ) - - def get_snippets_for_cluster( - self, - edges: List[DuplicateEdgeConnectionData], - page: int, - limit: int, - ) -> GetClusterSnippetsResult: - # For duplicate edges, We need to remember which true node ID pairs map to which - # duplicate node ID pairs, otherwise when we send the data back to the frontend - # we won't know which duplicate nodes we should match the snippet data with - id_pairs = { - (edge.original_from, edge.original_to): {'from': edge.from_, 'to': edge.to} - for edge in edges - } - - # One of these lists will have all duplicates (depends on the direction - # of the cluster edge). We remove the duplicates so we don't get weird query results. - from_ids = list({edge.original_from for edge in edges}) - to_ids = list({edge.original_to for edge in edges}) - description = edges[0].label # Every edge should have the same label - - data = self.get_snippets_from_edges(from_ids, to_ids, description, page, limit) - count_results = self.graph.read_transaction( - self.get_snippet_count_from_edges_query, from_ids, to_ids, description - ) - total_results = sum(row['count'] for row in count_results) - - results = [ - GetSnippetsFromEdgeResult( - from_node_id=id_pairs[(row['from_id'], row['to_id'])]['from'], - to_node_id=id_pairs[(row['from_id'], row['to_id'])]['to'], - association=row['description'], - snippets=[ - self._compose_snippet_from_reference(reference) - for reference in row['references'] - ], ) - for row in data - ] - - return GetClusterSnippetsResult( - snippet_data=results, - total_results=total_results, - query_data=edges, - ) - def get_associated_type_snippet_count( - self, - source_node: int, - associated_nodes: List[int], - ): - results = self.graph.read_transaction( - self.get_associated_type_snippet_count_query, source_node, associated_nodes + result = GetSnippetsFromEdgeResult( + from_node_id=edge.from_, + to_node_id=edge.to, + association=edge.label, + snippets=snippets, + ) + + return GetEdgeSnippetsResult( + snippet_data=result, + total_results=total_results, + query_data=edge, + ) + + +def get_snippets_for_cluster( + arango_client: ArangoClient, + edges: List[DuplicateEdgeConnectionData], + page: int, + limit: int, +) -> GetClusterSnippetsResult: + # For duplicate edges, We need to remember which true node ID pairs map to which + # duplicate node ID pairs, otherwise when we send the data back to the frontend + # we won't know which duplicate nodes we should match the snippet data with + id_pairs = { + (edge.original_from, edge.original_to): {'from': edge.from_, 'to': edge.to} + for edge in edges + } + + # One of these lists will have all duplicates (depends on the direction + # of the cluster edge). We remove the duplicates so we don't get weird query results. + from_ids = list({edge.original_from for edge in edges}) + to_ids = list({edge.original_to for edge in edges}) + description = edges[0].label # Every edge should have the same label + + data = get_snippets_from_edges( + arango_client, from_ids, to_ids, description, page, limit + ) + count_results = execute_arango_query( + get_db(arango_client), + query=get_snippet_count_from_edges_query(), + from_ids=from_ids, + to_ids=to_ids, + description=description, + ) + total_results = sum(row['count'] for row in count_results) + + results = [ + GetSnippetsFromEdgeResult( + from_node_id=id_pairs[(row['from_id'], row['to_id'])]['from'], + to_node_id=id_pairs[(row['from_id'], row['to_id'])]['to'], + association=row['description'], + snippets=[ + Snippet( + reference=GraphNode( + reference['snippet']['id'], + 'Snippet', + [], + snake_to_camel_dict(reference['snippet']['data'], {}), + [], + None, + None, + ), + publication=GraphNode( + reference['publication']['id'], + 'Publication', + [], + snake_to_camel_dict(reference['publication']['data'], {}), + [], + None, + None, + ), + ) + for reference in row['references'] + ], ) - - return GetAssociatedTypesResult(associated_data=results) - - def get_snippets_for_node_pair( - self, - node_1_id: int, - node_2_id: int, - page: int, - limit: int, - ): - data = self.get_snippets_from_node_pair(node_1_id, node_2_id, page, limit) - total_results = self.get_snippet_count_from_node_pair(node_1_id, node_2_id) - - results = [ - GetSnippetsFromEdgeResult( - from_node_id=row['from_id'], - to_node_id=row['to_id'], - association=row['description'], - snippets=[ - self._compose_snippet_from_reference(reference) - for reference in row['references'] - ], + for row in data + ] + + return GetClusterSnippetsResult( + snippet_data=results, + total_results=total_results, + query_data=edges, + ) + + +def get_expand_query() -> str: + return """ + FOR n IN literature + FILTER n._id == @node_id + FOR m, e IN ANY n associated + FILTER LENGTH(INTERSECTION(@labels, m.labels)) > 0 + COLLECT description = e.description, outgoing = e._from == n._id INTO pairs = { + "node": { + "id": m._id, + "display_name": m.name, + "data": { + "name": m.name, + "id": m.eid, + }, + "labels": m.labels, + "domain_labels": [], + }, + "edge": { + "id": e._id, + "from": e._from, + "to": e._to, + "from_labels": DOCUMENT(e._from).labels, + "to_labels": DOCUMENT(e._to).labels, + "data": { + "description": e.description, + "association_id": e.association_id, + "type": e.type, + }, + "label": "associated" + } + } + RETURN { + "description": description, + "direction": outgoing ? "Outgoing" : "Incoming", + "pairs": pairs + } + """ + + +def get_associated_type_snippet_count_query() -> str: + return """ + FOR associated_node IN @associated_nodes + LET association_paths = ( + FOR assoc_edge IN associated + FILTER + (assoc_edge._from == @source_node AND assoc_edge._to == associated_node) OR + (assoc_edge._from == associated_node AND assoc_edge._to == @source_node) + RETURN DISTINCT { + "association": assoc_edge.association_id, + "from_id": assoc_edge._from, + "to_id": assoc_edge._to + } ) - for row in data - ] - - return GetNodePairSnippetsResult( - snippet_data=results, - total_results=total_results, - query_data={'node_1_id': node_1_id, 'node_2_id': node_2_id}, - ) - - def get_expand_query( - self, tx: Neo4jTx, node_id: str, labels: List[str] - ) -> List[Neo4jRecord]: - return list( - tx.run( - """ - MATCH (n) - WHERE ID(n)=$node_id - MATCH (n)-[l:ASSOCIATED]-(m) - WHERE any(x IN $labels WHERE x IN labels(m)) - RETURN - apoc.convert.toSet([{ - id: ID(n), - labels: labels(n), - entity_id: n.eid, - name: n.name - }] + collect({ - id: ID(m), - labels: labels(m), - entity_id: m.eid, - name: m.name - })) AS nodes, - apoc.convert.toSet(collect({ - // We have to return the entire relationship as well, so we can get the - // start and end nodes. - relationship: l, - id: id(l), - label: type(l), - from_labels: labels(n), - to_labels: labels(m) - })) AS relationships - """, - node_id=node_id, - labels=labels, + LET snippet_count = COUNT( + FOR obj IN association_paths + FOR snippet, e IN INBOUND obj.association indicates + RETURN DISTINCT [ + obj.from_id, + obj.to_id, + obj.association, + snippet.eid + ] ) - ) - - def get_associated_type_snippet_count_query( - self, tx, source_node: int, associated_nodes: List[int] - ): - return list( - tx.run( - """ - UNWIND $associated_nodes as associated_node - MATCH (f)-[r:ASSOCIATED]-(t) - WHERE - ID(f)=$source_node AND - ID(t)=associated_node - WITH - ID(startNode(r)) as from_id, - ID(endNode(r)) as to_id, - t.name as name, - ID(t) as node_id - MATCH (f)-[:HAS_ASSOCIATION]->(a:Association)-[:HAS_ASSOCIATION]->(t) - WHERE ID(f)=from_id AND ID(t)=to_id - WITH from_id, to_id, a AS association, name, node_id - MATCH (association)<-[r:INDICATES]-(s:Snippet) - RETURN - name, - node_id, - count(DISTINCT { - from_id: from_id, - to_id: to_id, - description: association.description, - snippet_id: s.eid - }) AS snippet_count - ORDER BY snippet_count DESC, node_id - """, - source_node=source_node, - associated_nodes=associated_nodes, - ).data() - ) - - def get_snippets_from_edges_query( - self, - tx: Neo4jTx, - from_ids: List[int], - to_ids: List[int], - description: str, - skip: int, - limit: int, - ) -> List[Neo4jRecord]: - return list( - tx.run( - """ - MATCH (f)-[:HAS_ASSOCIATION]->(a:Association)-[:HAS_ASSOCIATION]->(t) - WHERE - ID(f) IN $from_ids AND - ID(t) IN $to_ids AND - a.description=$description - WITH - a AS association, - ID(f) AS from_id, - ID(t) AS to_id, - a.description AS description - MATCH (association)<-[r:INDICATES]-(s:Snippet)-[:IN_PUB]-(p:Publication) - WITH - s, - p, - head(collect(r)) as sample_path, - coalesce(association.entry1_type, 'Unknown') as entry1_type, - coalesce(association.entry2_type, 'Unknown') as entry2_type, - from_id, - to_id, - description - WITH - collect({snippet: s, publication: p, path: sample_path}) as references, - count({snippet: s, publication: p, path: sample_path}) as snippet_count, - entry1_type, - entry2_type, - from_id, - to_id, - description - UNWIND references as reference - WITH - entry1_type, - entry2_type, - { - snippet: { - id: reference.snippet.eid, - data: { - entry1_text: reference.path.entry1_text, - entry2_text: reference.path.entry2_text, - entry1_type: entry1_type, - entry2_type: entry2_type, - sentence: reference.snippet.sentence + SORT snippet_count DESC, associated_node ASC + RETURN { + "node_id": associated_node, + "name": DOCUMENT(associated_node).name, + "snippet_count": snippet_count + } + """ + + +def get_snippets_from_node_pair_query() -> str: + return """ + LET paginated_results = ( + FOR assoc_edge IN associated + FILTER + (assoc_edge._from == @node_1_id AND assoc_edge._to == @node_2_id) OR + (assoc_edge._from == @node_2_id AND assoc_edge._to == @node_1_id) + LET from_id = assoc_edge._from + LET to_id = assoc_edge._to + LET association = DOCUMENT(assoc_edge.association_id) + LET references = ( + FOR snippet, indicates_rel IN INBOUND association indicates + // If there are multiple "indicates" between the association + // and snippet, just get one of them to avoid extra rows + OPTIONS {order: "bfs", uniqueVertices: "global"} + FOR publication IN OUTBOUND snippet in_pub + SORT publication.pub_year DESC + RETURN DISTINCT { + "snippet": snippet, + "publication": publication, + "indicates_rel": indicates_rel, } - }, - publication: { - id: reference.publication.pmid, - data: { - journal: reference.publication.journal, - title: reference.publication.title, - pmid: reference.publication.pmid, - pub_year: reference.publication.pub_year + ) + LET snippet_count = LENGTH(references) + SORT snippet_count DESC, [from_id, to_id] ASC + FOR reference IN references + LIMIT @skip, @limit + RETURN DISTINCT { + "snippet_count": snippet_count, + "from_id": from_id, + "to_id": to_id, + "description": association.description, + "reference": { + "snippet": { + "id": reference.snippet.eid, + "data": { + "entry1_text": reference.indicates_rel.entry1_text, + "entry2_text": reference.indicates_rel.entry2_text, + "entry1_type": association.entry1_type, + "entry2_type": association.entry2_type, + "sentence": reference.snippet.sentence + } + }, + "publication": { + "id": reference.publication.pmid, + "data": { + "journal": reference.publication.journal, + "title": reference.publication.title, + "pmid": reference.publication.pmid, + "pub_year": reference.publication.pub_year + } } } - } AS reference, - snippet_count, - from_id, - to_id, - description - ORDER BY - snippet_count DESC, - [from_id, to_id], - coalesce(reference.publication.data.pub_year, -1) DESC - SKIP $skip LIMIT $limit - RETURN collect(DISTINCT reference) AS references, from_id, to_id, description - """, - from_ids=from_ids, - to_ids=to_ids, - description=description, - skip=skip, - limit=limit, - ) + } ) - - def get_snippets_from_node_pair_query( - self, tx: Neo4jTx, node_1_id: int, node_2_id: int, skip: int, limit: int - ) -> List[Neo4jRecord]: - return list( - tx.run( - """ - MATCH (f)-[r:ASSOCIATED]-(t) - WHERE - ID(f)=$node_1_id AND - ID(t)=$node_2_id - WITH ID(startNode(r)) as from_id, ID(endNode(r)) as to_id - MATCH (f)-[:HAS_ASSOCIATION]->(a:Association)-[:HAS_ASSOCIATION]->(t) - WHERE - ID(f)=from_id AND - ID(t)=to_id - WITH - a AS association, - from_id, - to_id, - a.description AS description - MATCH (association)<-[r:INDICATES]-(s:Snippet)-[:IN_PUB]-(p:Publication) - WITH - s, - p, - head(collect(r)) as sample_path, - coalesce(association.entry1_type, 'Unknown') as entry1_type, - coalesce(association.entry2_type, 'Unknown') as entry2_type, - from_id, - to_id, - description - WITH - collect({snippet: s, publication: p, path: sample_path}) as references, - count({snippet: s, publication: p, path: sample_path}) as snippet_count, - entry1_type, - entry2_type, - from_id, - to_id, - description - UNWIND references as reference - WITH - entry1_type, - entry2_type, - { - snippet: { - id: reference.snippet.eid, - data: { - entry1_text: reference.path.entry1_text, - entry2_text: reference.path.entry2_text, - entry1_type: entry1_type, - entry2_type: entry2_type, - sentence: reference.snippet.sentence - } - }, - publication: { - id: reference.publication.pmid, - data: { - journal: reference.publication.journal, - title: reference.publication.title, - pmid: reference.publication.pmid, - pub_year: reference.publication.pub_year - } - } - } AS reference, - snippet_count, - from_id, - to_id, - description - ORDER BY - snippet_count DESC, - [from_id, to_id], - coalesce(reference.publication.data.pub_year, -1) DESC - SKIP $skip LIMIT $limit - RETURN collect(DISTINCT reference) AS references, from_id, to_id, description - """, - node_1_id=node_1_id, - node_2_id=node_2_id, - skip=skip, - limit=limit, - ) + FOR result IN paginated_results + COLLECT + snippet_count = result.snippet_count, + from_id = result.from_id, + to_id = result.to_id, + description = result.description + INTO groups + SORT snippet_count DESC, [from_id, to_id] ASC + RETURN { + "snippet_count": snippet_count, + "from_id": from_id, + "to_id": to_id, + "description": description, + "references": ( + FOR obj IN groups + RETURN obj.result.reference + ) + } + """ + + +def get_snippet_count_from_node_pair_query() -> str: + return """ + LET association_paths = ( + FOR assoc_edge IN associated + FILTER + (assoc_edge._from == @node_1_id AND assoc_edge._to == @node_2_id) OR + (assoc_edge._from == @node_2_id AND assoc_edge._to == @node_1_id) + RETURN DISTINCT { + "association": DOCUMENT(assoc_edge.association_id), + "from_id": assoc_edge._from, + "to_id": assoc_edge._to + } ) - - def get_snippet_count_from_node_pair_query( - self, tx: Neo4jTx, node_1_id: int, node_2_id: int - ) -> Neo4jRecord: - return tx.run( - """ - MATCH (f)-[r:ASSOCIATED]-(t) - WHERE - ID(f)=$node_1_id AND - ID(t)=$node_2_id - WITH ID(startNode(r)) as from_id, ID(endNode(r)) as to_id - MATCH (f)-[:HAS_ASSOCIATION]-(a:Association)-[:HAS_ASSOCIATION]-(t) - WHERE ID(f)=from_id AND ID(t)=to_id - WITH from_id, to_id, a AS association - MATCH (association)<-[r:INDICATES]-(s:Snippet)-[:IN_PUB]-(p:Publication) - RETURN - count(DISTINCT { - from_id: from_id, - to_id: to_id, - description: association.description, - snippet_id: s.eid - }) AS snippet_count - """, - node_1_id=node_1_id, - node_2_id=node_2_id, - ).single() - - def get_snippet_count_from_edges_query( - self, tx: Neo4jTx, from_ids: List[int], to_ids: List[int], description: str - ) -> List[Neo4jRecord]: - return list( - tx.run( - """ - MATCH (f)-[:HAS_ASSOCIATION]->(a:Association)-[:HAS_ASSOCIATION]->(t) - WHERE - ID(f) IN $from_ids AND - ID(t) IN $to_ids AND - a.description=$description - WITH - a AS association, - ID(f) AS from_id, - ID(t) AS to_id, - labels(f) AS from_labels, - labels(t) AS to_labels - OPTIONAL MATCH (association)<-[r:INDICATES]-(s:Snippet)-[:IN_PUB]-(p:Publication) - WITH - count(DISTINCT { - description: association.description, - snippet_id: s.eid - }) AS snippet_count, - max(p.pub_year) AS max_pub_year, - from_id, - to_id, - from_labels, - to_labels - ORDER BY snippet_count DESC, [from_id, to_id], coalesce(max_pub_year, -1) DESC - RETURN from_id, to_id, from_labels, to_labels, snippet_count AS count - """, - from_ids=from_ids, - to_ids=to_ids, - description=description, - ) + LET snippet_count = COUNT( + FOR obj IN association_paths + FOR snippet, e IN INBOUND obj.association indicates + RETURN DISTINCT [ + obj.from_id, + obj.to_id, + obj.association.description, + snippet.eid + ] + ) + RETURN snippet_count + """ + + +def get_snippets_from_edges_query() -> str: + return """ + LET paginated_results = ( + FOR source_node IN @from_ids + FOR dest_node IN @to_ids + FOR assoc_edge IN associated + FILTER assoc_edge._to == dest_node + FILTER assoc_edge._from == source_node + FILTER assoc_edge.description == @description + LET from_id = assoc_edge._from + LET to_id = assoc_edge._to + LET association = DOCUMENT(assoc_edge.association_id) + LET references = ( + FOR snippet, indicates_rel IN INBOUND association indicates + // If there are multiple "indicates" between the association + // and snippet, just get one of them to avoid extra rows + OPTIONS {order: "bfs", uniqueVertices: "global"} + FOR publication IN OUTBOUND snippet in_pub + SORT publication.pub_year DESC + RETURN DISTINCT { + "snippet": snippet, + "publication": publication, + "indicates_rel": indicates_rel, + } + ) + LET snippet_count = LENGTH(references) + SORT snippet_count DESC, [from_id, to_id] ASC + FOR reference IN references + LIMIT @skip, @limit + RETURN DISTINCT { + "snippet_count": snippet_count, + "from_id": from_id, + "to_id": to_id, + "description": association.description, + "reference": { + "snippet": { + "id": reference.snippet.eid, + "data": { + "entry1_text": reference.indicates_rel.entry1_text, + "entry2_text": reference.indicates_rel.entry2_text, + "entry1_type": association.entry1_type, + "entry2_type": association.entry2_type, + "sentence": reference.snippet.sentence + } + }, + "publication": { + "id": reference.publication.pmid, + "data": { + "journal": reference.publication.journal, + "title": reference.publication.title, + "pmid": reference.publication.pmid, + "pub_year": reference.publication.pub_year + } + } + } + } ) + FOR result IN paginated_results + COLLECT + snippet_count = result.snippet_count, + from_id = result.from_id, + to_id = result.to_id, + description = result.description + INTO groups + SORT snippet_count DESC, [from_id, to_id] ASC + RETURN { + "snippet_count": snippet_count, + "from_id": from_id, + "to_id": to_id, + "description": description, + "references": ( + FOR obj IN groups + RETURN obj.result.reference + ) + } + """ + + +def get_snippet_count_from_edges_query() -> str: + return """ + FOR source_node IN @from_ids + FOR dest_node IN @to_ids + LET associations = ( + FOR doc IN associated + FILTER doc._from == source_node + FILTER doc._to == dest_node + FILTER doc.description == @description + RETURN DOCUMENT(doc.association_id) + ) + FILTER LENGTH(associations) > 0 + LET snippets_result = ( + FOR association IN associations + FOR snippet, e IN INBOUND association indicates + RETURN DISTINCT [association.description, snippet._id] + ) + LET snippet_count = LENGTH(snippets_result) + SORT snippet_count DESC, [source_node, dest_node] ASC + RETURN { + "from_id": source_node, + "to_id": dest_node, + "count": snippet_count, + "from_labels": DOCUMENT(source_node).labels, + "to_labels": DOCUMENT(dest_node).labels + } + """ diff --git a/appserver/neo4japp/util.py b/appserver/neo4japp/util.py deleted file mode 100644 index 3444a7a2f8..0000000000 --- a/appserver/neo4japp/util.py +++ /dev/null @@ -1,368 +0,0 @@ -import json - -import attr -import hashlib -import itertools -import flask - -from decimal import Decimal, InvalidOperation -from enum import EnumMeta, Enum -from json import JSONDecodeError -from string import punctuation, whitespace -from typing import Any, Optional, Type, Iterator, Dict - -# Do not import from app - - -def normalize_str(s) -> str: - normalized = s.lower() - normalized = normalized.translate(str.maketrans('', '', punctuation)) - return normalized.translate(str.maketrans('', '', whitespace)) - - -def standardize_str(s) -> str: - standardized = s.translate(str.maketrans('', '', punctuation)) - return " ".join(standardized.split()) - - -def encode_to_str(obj): - """Converts different types into a string representation.""" - if isinstance(obj, str): - return obj - elif isinstance(obj, Enum): - return obj.name - elif isinstance(obj, int) or isinstance(obj, Decimal): - return str(obj) - else: - raise TypeError(f'No conversion definition for {obj}') - - -def _snake_to_camel_update(k, v): - return {snake_to_camel(encode_to_str(k)): v} - - -def snake_to_camel_dict(d, new_dict: dict) -> dict: - """Converts a snake_case dict to camelCase while taking into - consideration a nested list or dict as a value. - """ - if type(d) is not dict: - return d - for k, v in d.items(): - if callable(getattr(v, 'to_dict', None)): - new_dict.update(_snake_to_camel_update(k, v.to_dict())) - elif type(v) is list: - new_dict.update( - _snake_to_camel_update(k, [snake_to_camel_dict(i, {}) for i in v]) - ) - elif type(v) is dict: - new_dict.update(_snake_to_camel_update(k, snake_to_camel_dict(v, {}))) - else: - new_dict.update(_snake_to_camel_update(k, v)) - return new_dict - - -def snake_to_camel(v): - if v is None: - return None - if callable(getattr(v, 'to_dict', None)): - return v.to_dict() - elif type(v) is list: - return [snake_to_camel(item) for item in v] - elif type(v) is dict: - return {snake_to_camel(k): snake_to_camel(v) for k, v in v.items()} - elif type(v) is str: - parts = v.split('_') - return parts[0] + ''.join(x.capitalize() or '_' for x in parts[1:]) - else: - return v - - -def camel_to_snake(s): - """Converts camelCase to snake_case. - - The SO (stackoverflow) answer has a simple function: - - import re - def convert(name): - s1 = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', name) - return re.sub('([a-z0-9])([A-Z])', r'\1_\2', s1).lower() - - But its performance can be improved by about 33% with this - function, a simple hand translation of the regex matching - algorithm. Measured with timeit, speed improves from 122 ms to 78 - ms after 10K invocation - - """ - if not s: - return s - if len(s) == 1: - return s.lower() - - buf = [s[0].lower()] - prev_is_uppercase = s[0].isupper() - - # scan from the second char, with one lookahead - normal, lookahead = itertools.tee(s[1:]) - next(lookahead) - - for c, ahead in itertools.zip_longest(normal, lookahead): - # only add an underscore in front of an uppercase if it is not - # preceded by an uppercase and is followed by a lowercase - if c.isupper(): - if not prev_is_uppercase or (ahead and ahead.islower()): - buf.append('_') - prev_is_uppercase = True - else: - prev_is_uppercase = False - buf.append(c.lower()) - - return ''.join(buf) - - -def camel_to_snake_dict(d, new_dict: dict) -> dict: - """Converts a camelCase dict to snake case while taking into - consideration a nested list or dict as a value. - """ - if type(d) is not dict: - return d - for k, v in d.items(): - if type(v) is list: - new_dict.update( - {camel_to_snake(k): [camel_to_snake_dict(i, {}) for i in v]} - ) - elif type(v) is dict: - new_dict.update({camel_to_snake(k): camel_to_snake_dict(v, {})}) - elif type(v) is str: - # check if a number then convert to Decimal - # otherwise check if a string representation of dictionary - try: - v = Decimal(v) - # convert back because this is just to avoid - # flask.json.loads() from converting to a float - v = str(v) - new_dict.update({camel_to_snake(k): v}) - continue - except InvalidOperation: - pass - try: - v = flask.json.loads(v) - if type(v) is not list: - new_dict.update({camel_to_snake(k): camel_to_snake_dict(v, {})}) - else: - obj_list = [camel_to_snake_dict(obj, {}) for obj in v] - new_dict.update({camel_to_snake(k): obj_list}) - - except JSONDecodeError: - # not a string representation of JSON or number type - new_dict.update({camel_to_snake(k): v}) - else: - # for booleans, etc - new_dict.update({camel_to_snake(k): v}) - return new_dict - - -class DictMixin: - def build_from_dict_formatter(self, d: dict): - """Returns a formatted version of the input dictionary. Default - function definition simply returns the input without formatting. - - Intended to be used by any attr.s classes that have attribute - names we want to format when we get them from the client, e.g. - 'from' to 'from_'. Used in build_from_dict. - """ - return d - - @classmethod - def build_from_dict(cls, json_dict): - """Returns an instance of the class based on a - snake_case dictionary. Takes into consideration - values of key in dictionary that are also instances of - attrs classes. Handle deep nesting by recursing - back into cls.build_from_dict() using the subclass typing. - - Argument: - json_dict is a snake_case dictionary used to instantiate - """ - cls_attrs = attr.fields(cls) - attributes = {} - - json_dict = cls.build_from_dict_formatter(cls, json_dict) - - for a in cls_attrs: - if a.name in json_dict: - # this is to check if a mypy typing - if hasattr(a.type, '__args__') and a.type.__args__: - # check for Unions[, None], etc - # and get the first type - attr_type = a.type.__args__[0] - else: - # for built in types or mypy typing - # that doesn't have __args__ - attr_type = a.type - - # if the value of key is also an attrs class - # create an instance of it - value = json_dict.get(a.name) - if value and issubclass(attr_type, CamelDictMixin): - # assumption is if attr_type is a subclass - # then value must be type dict - if isinstance(value, list): - cls_list = [] - for v in value: - cls_list.append(attr_type.build_from_dict(v)) - attributes[a.name] = cls_list - else: - attributes[a.name] = attr_type.build_from_dict(value) - elif value and isinstance(attr_type, EnumMeta): - try: - attributes[a.name] = attr_type[str.upper(value)] - except TypeError: - # probably already an enum - attributes[a.name] = value - else: - attributes[a.name] = value - try: - return cls(**attributes) - except TypeError as err: - error = err.args[0].replace('__init__()', 'Server request') - raise Exception(error) - - def to_dict_formatter(self, d: dict): - """Returns a formatted version of the input dictionary. Default - function definition simply returns the input without formatting. - - Intended to be used by any attr.s classes that have attribute - names we want to format before sending to the client, e.g. - 'from_' to 'from'. Used in to_dict. - """ - return d - - def to_dict(self): - """Convert an attr.s class into a dict with camel case key values for - JSON serialization. - - Converts Decimal to str and Enum to the Enum name. - - Recurse is set to true in `attr.asdict` to recurse into classes - that are also attrs classes. - """ - - return self.to_dict_formatter(attr.asdict(self)) - - -class CamelDictMixin(DictMixin): - def to_dict(self): - """Convert an attr.s class into a dict with camel case key values for - JSON serialization. - - Converts Decimal to str and Enum to the Enum name. - - Recurse is set to true in `attr.asdict` to recurse into classes - that are also attrs classes. - """ - - return snake_to_camel_dict(self.to_dict_formatter(attr.asdict(self)), {}) - - -class CasePreservedDict(DictMixin): - items: Dict = {} - - def __init__(self, items=None): - self.items = items or {} - - def __setitem__(self, k, v) -> None: - self.items.__setitem__(k, v) - - def __delitem__(self, v) -> None: - self.items.__delitem__(v) - - def __getitem__(self, k): - return self.items.__getitem__(k) - - def __len__(self) -> int: - return self.items.__len__() - - def __iter__(self) -> Iterator: - return self.items.__iter__() - - def to_dict(self): - """Convert an attr.s class into a dict with camel case key values for - JSON serialization. - - Converts Decimal to str and Enum to the Enum name. - - Recurse is set to true in `attr.asdict` to recurse into classes - that are also attrs classes. - """ - - return self.items - - -@attr.s(frozen=True) -class FileTransfer: - model_file: Any = attr.ib() # actually Response type - status_code: int = attr.ib(validator=attr.validators.instance_of(int)) - - -def compute_hash(data: dict, **kwargs) -> str: - """Returns the hash value of args""" - h = hashlib.new(kwargs.get('alg') or 'sha256') - to_json = flask.json.dumps(data, sort_keys=True) - h.update(bytearray(to_json, 'utf-8')) - hexdigest = h.hexdigest() - - if 'limit' in kwargs: - return hexdigest[: kwargs['limit']] - return hexdigest - - -class AttrDict(dict): - """Wrap a python dictionary into an object""" - - def __init__(self, *args, **kwargs): - super(AttrDict, self).__init__(*args, **kwargs) - self.__dict__ = self - - def to_dict(self, exclude=[], snake_to_camel_transform=False): - new_dict = {} - - if len(exclude): - new_dict = { - key: self.__dict__[key] for key in self.__dict__ if key not in exclude - } - else: - new_dict = self.__dict__ - - if snake_to_camel_transform: - return snake_to_camel_dict(new_dict, {}) - else: - return new_dict - - -def filter_dict_by_value(condition, d: dict): - return {k: v for k, v in d.items() if condition(v)} - - -def compact(d): - if isinstance(d, dict): - return filter_dict_by_value(lambda v: v, d) - raise NotImplementedError - - -def equal_number_of_words(term_a: str, term_b: str) -> bool: - return len(term_a.split(' ')) == len(term_b.split(' ')) - - -class Enumd(Enum): - @classmethod - def get(cls, key, default=None): - # Non-throwing value accessor modeled to behave like dict.get() - try: - return cls(key) - except ValueError: - return default - - -def stream_to_json_lines(stream): - for chunk in stream: - yield json.dumps(chunk) + '\n' diff --git a/appserver/neo4japp/utils/flask.py b/appserver/neo4japp/utils/flask.py index e37003437a..645ff7df9f 100644 --- a/appserver/neo4japp/utils/flask.py +++ b/appserver/neo4japp/utils/flask.py @@ -4,7 +4,7 @@ import attr from flask import g, jsonify, request -from neo4japp.utils import CamelDictMixin, camel_to_snake_dict +from neo4japp.utils.string import camel_to_snake_dict, CamelDictMixin def scope_flask_app_ctx(name): diff --git a/appserver/neo4japp/utils/jsonify.py b/appserver/neo4japp/utils/jsonify.py index 70a6843237..5e290aa599 100644 --- a/appserver/neo4japp/utils/jsonify.py +++ b/appserver/neo4japp/utils/jsonify.py @@ -4,7 +4,7 @@ from flask import jsonify, request from neo4japp.schemas.common import SuccessResponse -from neo4japp.utils import CamelDictMixin, camel_to_snake_dict +from neo4japp.utils.string import camel_to_snake_dict, CamelDictMixin def jsonify_with_class( diff --git a/appserver/neo4japp/utils/labels.py b/appserver/neo4japp/utils/labels.py index 6c9a49d52d..134b993fa8 100644 --- a/appserver/neo4japp/utils/labels.py +++ b/appserver/neo4japp/utils/labels.py @@ -1,15 +1,14 @@ from typing import List from flask import current_app -from neo4j.graph import Node as N4jDriverNode -from neo4japp.constants import LogEventType, DISPLAY_NAME_MAP, DOMAIN_LABELS +from neo4japp.constants import LogEventType, DATA_SOURCES, DISPLAY_NAME_MAP from neo4japp.exceptions import ServerWarning from neo4japp.utils import EventLog from neo4japp.utils.globals import warn -def get_first_known_label_from_node(node: N4jDriverNode): +def get_first_known_label_from_node(node): try: return get_first_known_label_from_list(node.labels) except ValueError as e: @@ -31,23 +30,5 @@ def get_first_known_label_from_list(labels: List[str]): raise ValueError('Detected node label of an unknown type!') -def get_known_domain_labels_from_node(node: N4jDriverNode): - return get_known_domain_labels_from_list(node.labels) - - -def get_known_domain_labels_from_list(labels: List[str]): - domain_labels = [] - - for label in labels: - if label in DOMAIN_LABELS: - domain_labels.append(label) - - return domain_labels - - -__all__ = [ - 'get_first_known_label_from_node', - 'get_first_known_label_from_list', - 'get_known_domain_labels_from_node', - 'get_known_domain_labels_from_list', -] +def get_known_domain_labels_from_data_source(data_source: str): + return [DATA_SOURCES[data_source]] if data_source in DATA_SOURCES else [] diff --git a/appserver/neo4japp/utils/string.py b/appserver/neo4japp/utils/string.py index ff082375e1..090238b1a3 100644 --- a/appserver/neo4japp/utils/string.py +++ b/appserver/neo4japp/utils/string.py @@ -171,10 +171,13 @@ def convert(name): return ''.join(buf) -def camel_to_snake_dict(d, new_dict: dict) -> dict: +def camel_to_snake_dict(d, new_dict: dict = None) -> dict: """Converts a camelCase dict to snake case while taking into consideration a nested list or dict as a value. """ + if new_dict is None: + new_dict = dict() + if type(d) is not dict: return d for k, v in d.items(): @@ -354,6 +357,11 @@ def equal_number_of_words(term_a: str, term_b: str) -> bool: return len(term_a.split(' ')) == len(term_b.split(' ')) +def stream_to_json_lines(stream): + for chunk in stream: + yield json.dumps(chunk) + '\n' + + __all__ = [ 'is_nice_word_boundary_char', 'is_nice_char', @@ -375,4 +383,5 @@ def equal_number_of_words(term_a: str, term_b: str) -> bool: 'CamelDictMixin', 'CasePreservedDict', 'equal_number_of_words', + 'stream_to_json_lines', ] diff --git a/appserver/tests/api/account_test.py b/appserver/tests/api/account_test.py index 4edf6a4a21..910a8b3975 100644 --- a/appserver/tests/api/account_test.py +++ b/appserver/tests/api/account_test.py @@ -1,8 +1,9 @@ import json -from http import HTTPStatus -from types import SimpleNamespace - import pytest +import re +import responses + +from types import SimpleNamespace from neo4japp.models import AppUser from tests.helpers.api import generate_jwt_headers @@ -56,10 +57,22 @@ def lmdb_open(*args, **kwargs): monkeypatch.setattr('lmdb.open', lmdb_open) -def test_admin_can_create_user(client, fix_admin_user): +@pytest.mark.skip('Skipping until pdfparser can be properly mocked') +def test_admin_can_create_user( + client, fix_admin_user, test_arango_db, mocked_responses, mocked_lmdb_open +): login_resp = client.login_as_user(fix_admin_user.email, 'password') headers = generate_jwt_headers(login_resp['accessToken']['token']) + # # Mocked responses from pdfparser + mocked_responses.add( + responses.POST, + re.compile('.+/token/rect/.+'), + status=201, + content_type='application/json', + json={'pages': []}, + ) + response = client.post( '/accounts/', headers=headers, @@ -77,7 +90,7 @@ def test_admin_can_create_user(client, fix_admin_user): content_type='application/json', ) - assert response.status_code == HTTPStatus.OK + assert response.status_code == 200 def test_nonadmin_cannot_create_user(client, test_user): @@ -100,7 +113,7 @@ def test_nonadmin_cannot_create_user(client, test_user): content_type='application/json', ) - assert response.status_code == HTTPStatus.FORBIDDEN + assert response.status_code == 403 def test_admin_can_get_all_users(client, mock_users, fix_admin_user): @@ -111,7 +124,7 @@ def test_admin_can_get_all_users(client, mock_users, fix_admin_user): '/accounts/', headers=headers, content_type='application/json' ) - assert response.status_code == HTTPStatus.OK + assert response.status_code == 200 result = response.get_json() # Add 2 to include the current user AND the assumed to be present lifelike superuser assert int(result['total']) == len(mock_users) + 2 @@ -125,7 +138,7 @@ def test_admin_can_get_any_user(client, mock_users, fix_admin_user): response = client.get( f'/accounts/{user.hash_id}', headers=headers, content_type='application/json' ) - assert response.status_code == HTTPStatus.OK + assert response.status_code == 200 result = response.get_json() assert int(result['total']) == 1 @@ -138,7 +151,7 @@ def test_nonadmin_can_only_get_self(client, mock_users, test_user): '/accounts/', headers=headers, content_type='application/json' ) - assert response.status_code == HTTPStatus.OK + assert response.status_code == 200 result = response.get_json() assert int(result['total']) == 1 assert result['results'][0]['email'] == test_user.email @@ -149,7 +162,7 @@ def test_nonadmin_can_only_get_self(client, mock_users, test_user): content_type='application/json', ) - assert response.status_code == HTTPStatus.OK + assert response.status_code == 200 result = response.get_json() assert int(result['total']) == 1 assert result['results'][0]['email'] == test_user.email @@ -160,7 +173,7 @@ def test_nonadmin_can_only_get_self(client, mock_users, test_user): content_type='application/json', ) - assert response.status_code == HTTPStatus.FORBIDDEN + assert response.status_code == 403 @pytest.mark.parametrize( @@ -184,7 +197,7 @@ def test_can_update_only_allowed_attributes( content_type='application/json', ) - assert response.status_code == HTTPStatus.NO_CONTENT + assert response.status_code == 204 response = client.get( f'/accounts/{test_user.hash_id}', @@ -210,7 +223,7 @@ def test_can_update_password(client, test_user): content_type='application/json', ) - assert response.status_code == HTTPStatus.NO_CONTENT + assert response.status_code == 204 login_resp = client.login_as_user(test_user.email, 'new_password') headers = generate_jwt_headers(login_resp['accessToken']['token']) assert headers @@ -224,7 +237,7 @@ def test_can_filter_users(client, mock_users, auth_token_header, username): headers=auth_token_header, content_type='application/json', ) - assert response.status_code == HTTPStatus.OK + assert response.status_code == 200 response = response.get_json() users = response['result'] assert len(users) == 1 diff --git a/appserver/tests/api/annotations_test.py b/appserver/tests/api/annotations_test.py index 3ab14ca11b..8ea94123ff 100644 --- a/appserver/tests/api/annotations_test.py +++ b/appserver/tests/api/annotations_test.py @@ -1,8 +1,6 @@ -from http import HTTPStatus - -from arango.database import StandardDatabase import json -import pytest + +from http import HTTPStatus from neo4japp.models import Files, AppUser @@ -15,14 +13,10 @@ def test_user_can_get_gene_annotations_from_pdf( client, test_user_with_pdf: Files, fix_admin_user: AppUser, - test_arango_db: StandardDatabase, + test_arango_db, mock_get_combined_annotations_result, mock_get_organisms_from_gene_ids_result, ): - # Create the necessary collections in arango before calling the API. These are empty of course. - test_arango_db.create_collection('ncbi') - test_arango_db.create_collection('has_taxonomy', edge=True) - login_resp = client.login_as_user(fix_admin_user.email, 'password') headers = generate_headers(login_resp['accessToken']['token']) file_id = test_user_with_pdf.hash_id @@ -43,6 +37,7 @@ def test_user_can_get_all_annotations_from_pdf( client, test_user_with_pdf: Files, fix_admin_user: AppUser, + test_arango_db, mock_get_combined_annotations_result, ): login_resp = client.login_as_user(fix_admin_user.email, 'password') @@ -67,6 +62,7 @@ def test_user_can_get_global_inclusions( client, fix_project, fix_admin_user, + test_arango_db, mock_global_compound_inclusion, ): login_resp = client.login_as_user(fix_admin_user.email, 'password') @@ -86,6 +82,7 @@ def test_user_can_get_global_exclusions( client, fix_project, fix_admin_user, + test_arango_db, mock_global_gene_exclusion, ): login_resp = client.login_as_user(fix_admin_user.email, 'password') @@ -101,11 +98,11 @@ def test_user_can_get_global_exclusions( assert response.get_data() is not None -@pytest.mark.skip('Skipping for now to get code merged') def test_user_can_get_global_list( client, fix_project, fix_admin_user, + test_arango_db, mock_global_list, ): login_resp = client.login_as_user(fix_admin_user.email, 'password') @@ -114,23 +111,18 @@ def test_user_can_get_global_list( response = client.get( f'/annotations/global-list', headers=headers, - content_type='application/json', + content_type='multipart/form-data', + data={ + 'globalAnnotationType': 'exclusion', + }, ) assert response.status_code == HTTPStatus.OK data = json.loads(response.get_data().decode('utf-8')) - assert data['total'] == 2 - assert len(data['results']) == 2 - - if data['results'][0]['type'] == 'inclusion': - inclusion = data['results'][0] - exclusion = data['results'][1] - else: - inclusion = data['results'][1] - exclusion = data['results'][0] - - assert inclusion['text'] == 'compound-(12345)' - assert inclusion['entityType'] == 'Compound' + assert data['total'] == 1 + assert len(data['results']) == 1 + + exclusion = data['results'][0] assert exclusion['text'] == 'fake-gene' assert exclusion['entityType'] == 'Gene' diff --git a/appserver/tests/api/neo4j_test.py b/appserver/tests/api/arango_test.py similarity index 59% rename from appserver/tests/api/neo4j_test.py rename to appserver/tests/api/arango_test.py index 5104370370..c030aa6d73 100644 --- a/appserver/tests/api/neo4j_test.py +++ b/appserver/tests/api/arango_test.py @@ -1,70 +1,35 @@ -from http import HTTPStatus - -import pytest import json - -@pytest.mark.skip( - reason='Does not work unless we upgrade the Neo4j docker image to 4.0+ because of apoc function' -) -def test_expand(client, gas_gangrene): - response = client.post( - '/visualizer/expand', - data=json.dumps( - { - 'node_id': 1, - 'filter_labels': ['Chemical', 'Disease', 'Gene'], - } - ), - content_type='application/json', - ) - - assert response.status_code == HTTPStatus.OK +from http import HTTPStatus def generate_headers(jwt_token): return {'Authorization': f'Bearer {jwt_token}'} -def test_get_reference_table_data( - client, - test_user, - gas_gangrene_treatment_cluster_node_edge_pairs, -): +def test_get_reference_table_data(client, test_user, test_arango_db): login_resp = client.login_as_user(test_user.email, 'password') headers = generate_headers(login_resp['accessToken']['token']) response = client.post( - '/visualizer/get-reference-table-data', + '/visualizer/get-reference-table', data=json.dumps( { - 'node_edge_pairs': [ + 'nodeEdgePairs': [ { 'node': { 'id': f'duplicateNode:1', 'label': 'Chemical', - 'data': {}, - 'sub_labels': [], - 'display_name': 'penicillins', - 'primary_label': 'Chemical', - 'color': {}, - 'expanded': False, - 'duplicate_of': 1, + 'displayName': 'penicillins', }, 'edge': { - 'id': 'duplicateEdge:1', 'label': 'ASSOCIATED', - 'data': {}, - 'to': 'duplicateNode:1', - 'from_': 'duplicateNode:2', - 'to_label': 'Disease', - 'from_label': 'Chemical', - 'arrows': 'to', - 'duplicate_of': 1, - 'original_from': 2, - 'original_to': 1, + 'originalFrom': '2', + 'originalTo': '1', }, }, ], + 'description': 'treatment/therapy', + 'direction': 'Outgoing', } ), headers=headers, @@ -74,10 +39,7 @@ def test_get_reference_table_data( assert response.status_code == HTTPStatus.OK -def test_get_snippets_for_edge( - client, - test_user, -): +def test_get_snippets_for_edge(client, test_user, test_arango_db): login_resp = client.login_as_user(test_user.email, 'password') headers = generate_headers(login_resp['accessToken']['token']) response = client.post( @@ -102,10 +64,7 @@ def test_get_snippets_for_edge( assert response.status_code == HTTPStatus.OK -def test_get_snippets_for_cluster( - client, - test_user, -): +def test_get_snippets_for_cluster(client, test_user, test_arango_db): login_resp = client.login_as_user(test_user.email, 'password') headers = generate_headers(login_resp['accessToken']['token']) response = client.post( diff --git a/appserver/tests/api/entity_resources_test.py b/appserver/tests/api/entity_resources_test.py index 25b45cfead..777778979b 100644 --- a/appserver/tests/api/entity_resources_test.py +++ b/appserver/tests/api/entity_resources_test.py @@ -48,7 +48,7 @@ def test_user_can_get_uri(client, test_user, uri_fixture): } # noqa -def test_user_can_get_many_uris(client, test_user, uri_fixture): +def test_user_can_get_many_uris(client, test_user): login_resp = client.login_as_user(test_user.email, 'password') headers = generate_headers(login_resp['accessToken']['token']) headers['content_type'] = 'application/json' diff --git a/appserver/tests/api/filesystem/object_test.py b/appserver/tests/api/filesystem/object_test.py index d5e15a08bb..91493987eb 100644 --- a/appserver/tests/api/filesystem/object_test.py +++ b/appserver/tests/api/filesystem/object_test.py @@ -1,16 +1,17 @@ import hashlib -from http import HTTPStatus -from io import BytesIO import json import pytest +import zipfile + +from http import HTTPStatus +from io import BytesIO from sqlalchemy.orm import make_transient from typing import Any, Dict from urllib.parse import quote -import zipfile from neo4japp.models import AppUser, Files, Projects from neo4japp.models.files import FileContent, StarredFile -from neo4japp.utils import snake_to_camel +from neo4japp.utils.string import snake_to_camel from tests.api.filesystem.conftest import ( ParameterizedFile as TestFile, diff --git a/appserver/tests/conftest.py b/appserver/tests/conftest.py index 0ddea1db10..f18effc6ed 100644 --- a/appserver/tests/conftest.py +++ b/appserver/tests/conftest.py @@ -1,41 +1,21 @@ -import pytest -import os - from arango import ArangoClient from arango.database import StandardDatabase +from arango.graph import Graph from flask import request as flask_request, g from flask.app import Flask -from neo4j import GraphDatabase, Session, Transaction, basic_auth -import responses -from neo4j.graph import Node, Relationship from pathlib import Path -from typing import Optional +import pytest +import os +import responses -import neo4japp.utils.transaction_id from neo4japp.blueprints.auth import auth -from neo4japp.constants import DISPLAY_NAME_MAP -from neo4japp.database import db, reset_dao, create_arango_client -from neo4japp.data_transfer_objects.visualization import ( - DuplicateEdgeConnectionData, - DuplicateVisEdge, - DuplicateVisNode, - EdgeConnectionData, - ReferenceTablePair, - VisEdge, - VisNode, -) +from neo4japp.database import create_arango_client, db, reset_dao from neo4japp.factory import create_app -from neo4japp.models.neo4j import GraphNode, GraphRelationship -from neo4japp.services import ( - AccountService, - AuthService, - KgService, - VisualizerService, -) +from neo4japp.services import AccountService, AuthService from neo4japp.services.arangodb import create_db, get_db from neo4japp.services.elastic import ElasticService -from neo4japp.utils import snake_to_camel_dict -from neo4japp.utils.labels import get_first_known_label_from_node + +from .constants import DOCUMENT_COLLECTIONS, EDGE_COLLECTIONS, GRAPHS def setup_before_request_callbacks(app: Flask): @@ -107,41 +87,7 @@ def teardown(): return session -@pytest.fixture(scope='function') -def graph(request, app) -> Session: - """Returns a graph connection to the Neo4J database. - IMPORTANT: Tests may not behave as expected if the - Neo4J database is not cleared before running tests! - """ - host = os.getenv('NEO4J_HOST', '0.0.0.0') - scheme = os.getenv('NEO4J_SCHEME', 'bolt') - port = os.getenv('NEO4J_PORT', '7687') - url = f'{scheme}://{host}:{port}' - username, password = os.getenv('NEO4J_AUTH', 'neo4j/password').split('/') - driver = GraphDatabase.driver(url, auth=basic_auth(username, password)) - - graph = driver.session() - - # Ensure a clean graph state before every test - graph.write_transaction(lambda tx: tx.run('MATCH(n) DETACH DELETE n')) - - def teardown(): - graph.close() - - request.addfinalizer(teardown) - return graph - - -@pytest.fixture(scope='function') -def graph_driver(request, app): - host = os.getenv('NEO4J_HOST', '0.0.0.0') - scheme = os.getenv('NEO4J_SCHEME', 'bolt') - port = os.getenv('NEO4J_PORT', '7687') - url = f'{scheme}://{host}:{port}' - username, password = os.getenv('NEO4J_AUTH', 'neo4j/password').split('/') - return GraphDatabase.driver(url, auth=basic_auth(username, password)) - - +# Arango fixtures @pytest.fixture(scope="function") def arango_client(app): arango_client = create_arango_client(hosts=app.config.get('ARANGO_HOST')) @@ -161,17 +107,45 @@ def system_db(app, arango_client: ArangoClient): ) +def _create_empty_document_collections(arango_db: StandardDatabase): + for collection in DOCUMENT_COLLECTIONS: + arango_db.create_collection(collection) + + +def _create_empty_edge_collections(arango_db: StandardDatabase): + for collection in EDGE_COLLECTIONS: + arango_db.create_collection(collection, edge=True) + + +def _create_empty_graphs(arango_db: StandardDatabase): + edge_definitions = [ + { + 'edge_collection': edge_collection, + 'from_vertex_collections': DOCUMENT_COLLECTIONS, + 'to_vertex_collections': DOCUMENT_COLLECTIONS, + } + for edge_collection in EDGE_COLLECTIONS + ] + for graph in GRAPHS: + arango_db.create_graph(graph, edge_definitions) + + @pytest.fixture(scope="function") def test_arango_db(app, arango_client: ArangoClient, system_db: StandardDatabase): - create_db(system_db, app.config.get('ARANGO_DB_NAME')) - test_db_name = app.config.get('ARANGO_DB_NAME') + create_db(system_db, test_db_name) + test_db = get_db( arango_client=arango_client, name=test_db_name, username=app.config.get('ARANGO_USERNAME'), password=app.config.get('ARANGO_PASSWORD'), ) + + _create_empty_document_collections(test_db) + _create_empty_edge_collections(test_db) + _create_empty_graphs(test_db) + yield test_db # Drop the test database after every test to make it clean before the next one @@ -179,1200 +153,54 @@ def test_arango_db(app, arango_client: ArangoClient, system_db: StandardDatabase @pytest.fixture(scope='function') -def account_service(app, session): - return AccountService(session) - - -@pytest.fixture(scope='function') -def auth_service(app, session): - return AuthService(session) - - -@pytest.fixture(scope='function') -def account_user(app, session): - return AccountService(session) - - -@pytest.fixture(scope='function') -def kg_service(graph, session): - return KgService(graph=graph, session=session) - - -@pytest.fixture(scope='function') -def visualizer_service(app, graph, session): - return VisualizerService(graph=graph, session=session) - - -@pytest.fixture(scope='function') -def elastic_service(app, session): - elastic_service = ElasticService() - - # Ensures that anytime the elastic service is requested for a test, that the environment is - # clean - elastic_service.recreate_indices_and_pipelines() - - return elastic_service - - -# Begin Graph Data Fixtures # - -# Begin Graph Data Helpers # - - -def create_chemical_node(tx: Transaction, chem_name: str, chem_id: str) -> Node: - """Creates a chemical node and adds it to the graph.""" - query = """ - CREATE (c:Chemical {name: $chem_name, eid: $chem_id}) RETURN c - """ - return tx.run(query, chem_name=chem_name, chem_id=chem_id).single()['c'] - - -def create_disease_node(tx: Transaction, disease_name: str, disease_id: str) -> Node: - """Creates a disease node and adds it to the graph.""" - query = """ - CREATE (d:Disease {name: $disease_name, eid: $disease_id}) RETURN d - """ - return tx.run(query, disease_name=disease_name, disease_id=disease_id).single()['d'] - - -def create_gene_node( - tx: Transaction, - gene_name: str, - gene_id: str, -) -> Node: - """Creates a gene node and adds it to the graph.""" - query = """ - CREATE (g:Gene {name: $gene_name, eid: $gene_id}) RETURN g - """ - return tx.run(query, gene_name=gene_name, gene_id=gene_id).single()['g'] - - -def create_taxonomy_node( - tx: Transaction, - name: str, - rank: str, - tax_id: str, -) -> Node: - """Creates a taxonomy node and adds it to the graph.""" - query = """ - CREATE (t:Taxonomy {tax_id: $tax_id, name: $name, rank: $rank}) RETURN t - """ - return tx.run(query, name=name, rank=rank, tax_id=tax_id).single()['t'] - - -def create_association_node( - tx: Transaction, assoc_type: str, description: str, assoc_id: int -) -> Node: - """Creates an association node and adds it to the graph.""" - query = """ - CREATE (a:Association {assoc_type: $assoc_type, description: $description, eid: $assoc_id}) - RETURN a - """ - return tx.run( - query, assoc_type=assoc_type, description=description, assoc_id=assoc_id - ).single()['a'] - - -def create_snippet_node(tx: Transaction, snippet_id: int, sentence: str) -> Node: - """Creates a snippet node and adds it to the graph.""" - query = """ - CREATE (s:Snippet { - eid: $snippet_id, - sentence: $sentence - }) RETURN s - """ - return tx.run(query, snippet_id=snippet_id, sentence=sentence).single()['s'] - - -def create_publication_node( - tx: Transaction, - pub_id: int, - pub_year: Optional[int] = None, -) -> Node: - """Creates a publication node and adds it to the graph.""" - query = """ - CREATE (p:Publication {pmid: $pub_id, pub_year: $pub_year}) RETURN p - """ - return tx.run(query, pub_id=pub_id, pub_year=pub_year).single()['p'] - - -def create_associated_relationship( - tx: Transaction, - source_id: int, - target_id: int, - assoc_type: str, - description: str, -) -> Relationship: - """ - Creates an association relationship between two nodes (these should already be in the - graph!) and adds it to the graph. - """ - query = """ - MATCH (source) WHERE ID(source)=$source_id - MATCH (target) WHERE ID(target)=$target_id - CREATE - (source)-[r:ASSOCIATED {assoc_type: $assoc_type, description: $description}]->(target) - RETURN r, source, target - """ - result = tx.run( - query, - source_id=source_id, - target_id=target_id, - assoc_type=assoc_type, - description=description, - ) - single = result.single() - return single['r'] - - -def create_has_association_relationship( - tx: Transaction, source_id: int, target_id: int -) -> Relationship: - """ - Creates a has_association relationship between two nodes (these should already be in the - graph!) and adds it to the graph. - """ - query = """ - MATCH (source) WHERE ID(source)=$source_id - MATCH (target) WHERE ID(target)=$target_id - CREATE (source)-[r:HAS_ASSOCIATION]->(target) - RETURN r, source, target - """ - return tx.run(query, source_id=source_id, target_id=target_id).single()['r'] - - -def create_predicts_relationship( - tx: Transaction, - source_id: int, - target_id: int, - entry1_text: str, - entry2_text: str, - raw_score: Optional[float] = None, - normalized_score: Optional[float] = None, -) -> Relationship: - """ - Creates a predicts relationship between two nodes (these should already be in the - graph!) and adds it to the graph. - """ - query = """ - MATCH (source) WHERE ID(source)=$source_id - MATCH (target) WHERE ID(target)=$target_id - CREATE (source)-[r:INDICATES { - entry1_text: $entry1_text, - entry2_text: $entry2_text, - raw_score: $raw_score, - normalized_score: $normalized_score - }]->(target) - RETURN r, source, target - """ - return tx.run( - query, - entry1_text=entry1_text, - entry2_text=entry2_text, - source_id=source_id, - target_id=target_id, - raw_score=raw_score, - normalized_score=normalized_score, - ).single()['r'] - - -def create_in_pub_relationship( - tx: Transaction, source_id: int, target_id: int -) -> Relationship: - """ - Creates an in_pub relationship between two nodes (these should already be in the - graph!) and adds it to the graph. - """ - query = """ - MATCH (source) WHERE ID(source)=$source_id - MATCH (target) WHERE ID(target)=$target_id - CREATE (source)-[r:IN_PUB]->(target) - RETURN r, source, target - """ - return tx.run(query, source_id=source_id, target_id=target_id).single()['r'] - - -def create_has_taxonomy_relationship( - tx: Transaction, source_id: int, target_id: int -) -> Relationship: - """ - Creates a has_taxonomy relationship between two nodes (these should already be in the - graph!) and adds it to the graph. - """ - query = """ - MATCH (source) WHERE ID(source)=$source_id - MATCH (target) WHERE ID(target)=$target_id - CREATE (source)-[r:HAS_TAXONOMY]->(target) - RETURN r, source, target - """ - return tx.run(query, source_id=source_id, target_id=target_id).single()['r'] - - -# End Graph Data Helpers # - - -# Begin Entity Node Fixtures # -@pytest.fixture(scope='function') -def gas_gangrene(graph: Session) -> Node: - with graph.begin_transaction() as tx: - gas_gangrene = create_disease_node(tx, 'gas gangrene', 'MESH:D005738') - return gas_gangrene - - -@pytest.fixture(scope='function') -def penicillins(graph: Session) -> Node: - with graph.begin_transaction() as tx: - penicillins = create_chemical_node(tx, 'Penicillins', 'MESH:D010406') - return penicillins +def test_arango_all_graph(test_arango_db: StandardDatabase): + return test_arango_db.graph('all') @pytest.fixture(scope='function') -def oxygen(graph: Session) -> Node: - with graph.begin_transaction() as tx: - oxygen = create_chemical_node(tx, 'Oxygen', 'MESH:D010100') - return oxygen +def associated_edge_collection(test_arango_all_graph: Graph): + return test_arango_all_graph.edge_collection('associated') @pytest.fixture(scope='function') -def pomc(graph: Session) -> Node: - with graph.begin_transaction() as tx: - pomc = create_gene_node(tx, 'POMC', '5443') - return pomc +def has_association_edge_collection(test_arango_all_graph: Graph): + return test_arango_all_graph.edge_collection('has_association') -# End Entity Nodes Fixtures # - -# Begin Entity -> Entity Relationship Fixtures # - - -@pytest.fixture(scope='function') -def pomc_to_gas_gangrene_pathogenesis_edge( - graph: Session, - gas_gangrene: Node, - pomc: Node, -) -> Relationship: - with graph.begin_transaction() as tx: - pomc_to_gas_gangrene_pathogenesis_edge = create_associated_relationship( - tx=tx, - source_id=pomc.id, - target_id=gas_gangrene.id, - assoc_type='J', - description='role in disease pathogenesis', - ) - return pomc_to_gas_gangrene_pathogenesis_edge - - -@pytest.fixture(scope='function') -def penicillins_to_gas_gangrene_alleviates_edge( - graph: Session, - gas_gangrene: Node, - penicillins: Node, -) -> Relationship: - with graph.begin_transaction() as tx: - penicillins_to_gas_gangrene_alleviates_edge = create_associated_relationship( - tx=tx, - source_id=penicillins.id, - target_id=gas_gangrene.id, - assoc_type='Pa', - description='alleviates, reduces', - ) - return penicillins_to_gas_gangrene_alleviates_edge - - -@pytest.fixture(scope='function') -def oxygen_to_gas_gangrene_treatment_edge( - graph: Session, - gas_gangrene: Node, - oxygen: Node, -) -> Relationship: - with graph.begin_transaction() as tx: - oxygen_to_gas_gangrene_treatment_edge = create_associated_relationship( - tx=tx, - source_id=oxygen.id, - target_id=gas_gangrene.id, - assoc_type='Pa', - description='treatment/therapy (including investigatory)', - ) - return oxygen_to_gas_gangrene_treatment_edge - - -@pytest.fixture(scope='function') -def penicillins_to_gas_gangrene_treatment_edge( - graph: Session, - gas_gangrene: Node, - penicillins: Node, -) -> Relationship: - with graph.begin_transaction() as tx: - penicillins_to_gas_gangrene_treatment_edge = create_associated_relationship( - tx=tx, - source_id=penicillins.id, - target_id=gas_gangrene.id, - assoc_type='Pa', - description='treatment/therapy (including investigatory)', - ) - return penicillins_to_gas_gangrene_treatment_edge - - -# End Entity -> Entity Relationship Fixtures # - - -# Start Misc. Fixtures # @pytest.fixture(scope='function') -def gas_gangrene_with_associations_and_references( - graph: Session, - gas_gangrene: Node, - oxygen: Node, - penicillins: Node, - pomc: Node, - oxygen_to_gas_gangrene_treatment_edge: Relationship, - pomc_to_gas_gangrene_pathogenesis_edge: Relationship, - penicillins_to_gas_gangrene_alleviates_edge: Relationship, - penicillins_to_gas_gangrene_treatment_edge: Relationship, -): - with graph.begin_transaction() as tx: - # Association Nodes - oxygen_to_gas_gangrene_association_node = create_association_node( - tx=tx, - assoc_type='J', - description='treatment/therapy (including investigatory)', - assoc_id=1089126, - ) - pomc_to_gas_gangrene_association_node = create_association_node( - tx=tx, - assoc_type='J', - description='role in disease pathogenesis', - assoc_id=1387448, - ) - penicillins_to_gas_gangrene_association_node1 = create_association_node( - tx=tx, - assoc_type='Pa', - description='alleviates, reduces', - assoc_id=2771500, - ) - penicillins_to_gas_gangrene_association_node2 = create_association_node( - tx=tx, - assoc_type='J', - description='treatment/therapy (including investigatory)', - assoc_id=2771501, - ) - - # Snippet Nodes - oxygen_to_gas_gangrene_snippet_node1 = create_snippet_node( - tx=tx, - snippet_id=7430189, - sentence='In this study , we aimed to investigate the effect of HBO2...', - ) - oxygen_to_gas_gangrene_snippet_node2 = create_snippet_node( - tx=tx, - snippet_id=1890743, - sentence='Hyperbaric oxygen therapy has an adjunctive role...', - ) - penicillins_to_gas_gangrene_snippet_node1 = create_snippet_node( - tx=tx, - snippet_id=9810347, - sentence='In a mouse model of gas_gangrene caused by...', - ) - penicillins_to_gas_gangrene_snippet_node2 = create_snippet_node( - tx=tx, - snippet_id=9810346, - sentence='Toxin suppression and rapid bacterial killing may...', - ) - penicillins_to_gas_gangrene_snippet_node3 = create_snippet_node( - tx=tx, - snippet_id=9810348, - sentence='...penicillin was found to reduce the affect of...', - ) - penicillins_to_gas_gangrene_snippet_node4 = create_snippet_node( - tx=tx, - snippet_id=9810349, - sentence='...suppresses toxins and rapidly kills bacteria...', - ) - - # Publication Nodes - oxygen_to_gas_gangrene_publication_node = create_publication_node( - tx=tx, - pub_id=3, - pub_year=2019, - ) - penicillins_to_gas_gangrene_publication_node1 = create_publication_node( - tx=tx, pub_id=1, pub_year=2014 - ) - penicillins_to_gas_gangrene_publication_node2 = create_publication_node( - tx=tx, - pub_id=2, - ) - - # Entity -> Association Relationships - entity_to_association_rels = [ - [oxygen, oxygen_to_gas_gangrene_association_node], - [pomc, pomc_to_gas_gangrene_association_node], - [penicillins, penicillins_to_gas_gangrene_association_node1], - [penicillins, penicillins_to_gas_gangrene_association_node2], - ] - for rel in entity_to_association_rels: - create_has_association_relationship( - tx=tx, source_id=rel[0].id, target_id=rel[1].id - ) - - # Association -> Entity Relationships - association_to_entity_rels = [ - [oxygen_to_gas_gangrene_association_node, gas_gangrene], - [pomc_to_gas_gangrene_association_node, gas_gangrene], - [penicillins_to_gas_gangrene_association_node1, gas_gangrene], - [penicillins_to_gas_gangrene_association_node2, gas_gangrene], - ] - for rel in association_to_entity_rels: - create_has_association_relationship( - tx=tx, - source_id=rel[0].id, - target_id=rel[1].id, - ) - - # Snippet -> Association Relationships - snippet_to_association_rels = [ - [ - oxygen_to_gas_gangrene_snippet_node1, - oxygen_to_gas_gangrene_association_node, - None, - None, - 'oxygen', - 'gas gangrene', - ], # noqa - [ - oxygen_to_gas_gangrene_snippet_node2, - oxygen_to_gas_gangrene_association_node, - None, - None, - 'oxygen', - 'gas gangrene', - ], # noqa - [ - penicillins_to_gas_gangrene_snippet_node1, - penicillins_to_gas_gangrene_association_node1, - 2, - 0.385, - 'penicillin', - 'gas gangrene', - ], - # noqa - [ - penicillins_to_gas_gangrene_snippet_node3, - penicillins_to_gas_gangrene_association_node1, - 5, - 0.693, - 'penicillin', - 'gas gangrene', - ], - # noqa - [ - penicillins_to_gas_gangrene_snippet_node2, - penicillins_to_gas_gangrene_association_node2, - 1, - 0.222, - 'penicillin', - 'gas gangrene', - ], - # noqa - [ - penicillins_to_gas_gangrene_snippet_node4, - penicillins_to_gas_gangrene_association_node2, - 3, - 0.456, - 'penicillin', - 'gas gangrene', - ], - # noqa - ] - for rel in snippet_to_association_rels: - create_predicts_relationship( - tx=tx, - source_id=rel[0].id, - target_id=rel[1].id, - raw_score=rel[2], - normalized_score=rel[3], - entry1_text=rel[4], - entry2_text=rel[5], - ) - - # Snippet -> Publication Relationships - snippet_to_pub_rels = [ - [ - oxygen_to_gas_gangrene_snippet_node1, - oxygen_to_gas_gangrene_publication_node, - ], - [ - oxygen_to_gas_gangrene_snippet_node2, - oxygen_to_gas_gangrene_publication_node, - ], - [ - penicillins_to_gas_gangrene_snippet_node1, - penicillins_to_gas_gangrene_publication_node1, - ], # noqa - [ - penicillins_to_gas_gangrene_snippet_node3, - penicillins_to_gas_gangrene_publication_node2, - ], # noqa - [ - penicillins_to_gas_gangrene_snippet_node2, - penicillins_to_gas_gangrene_publication_node2, - ], # noqa - [ - penicillins_to_gas_gangrene_snippet_node4, - penicillins_to_gas_gangrene_publication_node2, - ], # noqa - ] - for rel in snippet_to_pub_rels: - create_in_pub_relationship(tx=tx, source_id=rel[0].id, target_id=rel[1].id) - return gas_gangrene +def indicates_edge_collection(test_arango_all_graph: Graph): + return test_arango_all_graph.edge_collection('indicates') @pytest.fixture(scope='function') -def example4_pdf_gene_and_organism_network( - graph: Session, -): - with graph.begin_transaction() as tx: - cysB = create_gene_node( - tx=tx, - gene_name='cysB', - gene_id='945771', - ) - - mcrB = create_gene_node( - tx=tx, - gene_name='mcrB', - gene_id='949122', - ) - - oxyR_e_coli = create_gene_node( - tx=tx, - gene_name='oxyR', - gene_id='948462', - ) - - oxyR_salmonella = create_gene_node( - tx=tx, - gene_name='cysB', - gene_id='1255651', - ) - - e_coli = create_taxonomy_node( - tx=tx, name='Escherichia coli', rank='species', tax_id='562' - ) - - salmonella = create_taxonomy_node( - tx=tx, name='Salmonella enterica', rank='species', tax_id='28901' - ) - - gene_to_organism_rels = [ - [cysB, e_coli], - [mcrB, e_coli], - [oxyR_e_coli, e_coli], - [oxyR_salmonella, salmonella], - ] - for rel in gene_to_organism_rels: - create_has_taxonomy_relationship( - tx=tx, source_id=rel[0].id, target_id=rel[1].id - ) - return graph - - -# End Graph Data Fixtures # - -# Start DTO Fixtures # +def in_pub_edge_collection(test_arango_all_graph: Graph): + return test_arango_all_graph.edge_collection('in_pub') @pytest.fixture(scope='function') -def gas_gangrene_vis_node(gas_gangrene: Node): - """Creates a VisNode from gas gangrene""" - labels = list(gas_gangrene.labels) - node_as_graph_node = GraphNode( - id=gas_gangrene.id, - label=labels[0], - sub_labels=labels, - domain_labels=[], - display_name=gas_gangrene.get( - DISPLAY_NAME_MAP[get_first_known_label_from_node(gas_gangrene)] - ), # noqa - data=snake_to_camel_dict(dict(gas_gangrene), {}), - url=None, - ) - - gas_gangrene_vis_node = VisNode( - id=node_as_graph_node.id, - label=node_as_graph_node.label, - data=node_as_graph_node.data, - sub_labels=node_as_graph_node.sub_labels, - display_name=node_as_graph_node.display_name, - primary_label=node_as_graph_node.sub_labels[0], - color={}, - expanded=False, - ) - - return gas_gangrene_vis_node - - -@pytest.fixture(scope='function') -def gas_gangrene_duplicate_vis_node(gas_gangrene: Node): - """Creates a DuplicateVisNode from gas gangrene""" - labels = list(gas_gangrene.labels) - node_as_graph_node = GraphNode( - id=gas_gangrene.id, - label=labels[0], - sub_labels=labels, - domain_labels=[], - display_name=gas_gangrene.get( - DISPLAY_NAME_MAP[get_first_known_label_from_node(gas_gangrene)] - ), # noqa - data=snake_to_camel_dict(dict(gas_gangrene), {}), - url=None, - ) - - gas_gangrene_duplicate_vis_node = DuplicateVisNode( - id=f'duplicateNode:{node_as_graph_node.id}', - label=node_as_graph_node.label, - data=node_as_graph_node.data, - sub_labels=node_as_graph_node.sub_labels, - display_name=node_as_graph_node.display_name, - primary_label=node_as_graph_node.sub_labels[0], - color={}, - expanded=False, - duplicate_of=node_as_graph_node.id, - ) - - return gas_gangrene_duplicate_vis_node - - -@pytest.fixture(scope='function') -def oxygen_duplicate_vis_node(oxygen: Node): - """Creates a DuplicateVisNode from oxygen""" - labels = list(oxygen.labels) - node_as_graph_node = GraphNode( - id=oxygen.id, - label=labels[0], - sub_labels=labels, - domain_labels=[], - display_name=oxygen.get( - DISPLAY_NAME_MAP[get_first_known_label_from_node(oxygen)] - ), # noqa - data=snake_to_camel_dict(dict(oxygen), {}), - url=None, - ) - - oxygen_duplicate_vis_node = DuplicateVisNode( - id=f'duplicateNode:{node_as_graph_node.id}', - label=node_as_graph_node.label, - data=node_as_graph_node.data, - sub_labels=node_as_graph_node.sub_labels, - display_name=node_as_graph_node.display_name, - primary_label=node_as_graph_node.sub_labels[0], - color={}, - expanded=False, - duplicate_of=node_as_graph_node.id, - ) - - return oxygen_duplicate_vis_node - - -@pytest.fixture(scope='function') -def penicillins_vis_node(penicillins: Node): - """Creates a VisNode from penicillins""" - labels = list(penicillins.labels) - node_as_graph_node = GraphNode( - id=penicillins.id, - label=labels[0], - sub_labels=labels, - domain_labels=[], - display_name=penicillins.get( - DISPLAY_NAME_MAP[get_first_known_label_from_node(penicillins)] - ), # noqa - data=snake_to_camel_dict(dict(penicillins), {}), - url=None, - ) - - penicillins_vis_node = VisNode( - id=node_as_graph_node.id, - label=node_as_graph_node.label, - data=node_as_graph_node.data, - sub_labels=node_as_graph_node.sub_labels, - display_name=node_as_graph_node.display_name, - primary_label=node_as_graph_node.sub_labels[0], - color={}, - expanded=False, - ) - - return penicillins_vis_node - - -@pytest.fixture(scope='function') -def penicillins_duplicate_vis_node(penicillins: Node): - """Creates a DuplicateVisNode from penicillins""" - labels = list(penicillins.labels) - node_as_graph_node = GraphNode( - id=penicillins.id, - label=labels[0], - sub_labels=labels, - domain_labels=[], - display_name=penicillins.get( - DISPLAY_NAME_MAP[get_first_known_label_from_node(penicillins)] - ), # noqa - data=snake_to_camel_dict(dict(penicillins), {}), - url=None, - ) - - penicillins_duplicate_vis_node = DuplicateVisNode( - id=f'duplicateNode:{node_as_graph_node.id}', - label=node_as_graph_node.label, - data=node_as_graph_node.data, - sub_labels=node_as_graph_node.sub_labels, - display_name=node_as_graph_node.display_name, - primary_label=node_as_graph_node.sub_labels[0], - color={}, - expanded=False, - duplicate_of=node_as_graph_node.id, - ) - - return penicillins_duplicate_vis_node - - -@pytest.fixture(scope='function') -def pomc_vis_node(pomc: Node): - """Creates a VisNode from pomc""" - labels = list(pomc.labels) - node_as_graph_node = GraphNode( - id=pomc.id, - label=labels[0], - sub_labels=labels, - domain_labels=[], - display_name=pomc.get( - DISPLAY_NAME_MAP[get_first_known_label_from_node(pomc)] - ), # noqa - data=snake_to_camel_dict(dict(pomc), {}), - url=None, - ) - - pomc_vis_node = VisNode( - id=node_as_graph_node.id, - label=node_as_graph_node.label, - data=node_as_graph_node.data, - sub_labels=node_as_graph_node.sub_labels, - display_name=node_as_graph_node.display_name, - primary_label=node_as_graph_node.sub_labels[0], - color={}, - expanded=False, - ) - - return pomc_vis_node - - -@pytest.fixture(scope='function') -def pomc_duplicate_vis_node(pomc: Node): - """Creates a DuplicateVisNode from pomc""" - labels = list(pomc.labels) - node_as_graph_node = GraphNode( - id=pomc.id, - label=labels[0], - sub_labels=labels, - domain_labels=[], - display_name=pomc.get( - DISPLAY_NAME_MAP[get_first_known_label_from_node(pomc)] - ), # noqa - data=snake_to_camel_dict(dict(pomc), {}), - url=None, - ) - - pomc_duplicate_vis_node = DuplicateVisNode( - id=f'duplicateNode:{node_as_graph_node.id}', - label=node_as_graph_node.label, - data=node_as_graph_node.data, - sub_labels=node_as_graph_node.sub_labels, - display_name=node_as_graph_node.display_name, - primary_label=node_as_graph_node.sub_labels[0], - color={}, - expanded=False, - duplicate_of=node_as_graph_node.id, - ) - - return pomc_duplicate_vis_node - - -@pytest.fixture(scope='function') -def oxygen_to_gas_gangrene_treatment_as_duplicate_vis_edge( - oxygen_to_gas_gangrene_treatment_edge: Relationship, -): - """Creates a DuplicateVisEdge from the oxygen to gas_gangrene - alleviates/reduces relationship.""" - - edge_as_graph_relationship = GraphRelationship( - id=oxygen_to_gas_gangrene_treatment_edge.id, - label=type(oxygen_to_gas_gangrene_treatment_edge).__name__, - data=dict(oxygen_to_gas_gangrene_treatment_edge), - to=oxygen_to_gas_gangrene_treatment_edge.end_node.id, - _from=oxygen_to_gas_gangrene_treatment_edge.start_node.id, - to_label=list(oxygen_to_gas_gangrene_treatment_edge.end_node.labels)[0], - from_label=list(oxygen_to_gas_gangrene_treatment_edge.start_node.labels)[0], - ) - - oxygen_to_gas_gangrene_treatment_as_duplicate_vis_edge = DuplicateVisEdge( - id=edge_as_graph_relationship.id, - label=edge_as_graph_relationship.data['description'], - data=edge_as_graph_relationship.data, - to=f'duplicateNode:{edge_as_graph_relationship.to}', # type:ignore - from_=f'duplicateNode:{edge_as_graph_relationship._from}', # type:ignore - to_label='Disease', - from_label='Chemical', - arrows='to', - duplicate_of=edge_as_graph_relationship.id, - original_from=edge_as_graph_relationship._from, - original_to=edge_as_graph_relationship.to, - ) - - return oxygen_to_gas_gangrene_treatment_as_duplicate_vis_edge - - -@pytest.fixture(scope='function') -def pomc_to_gas_gangrene_pathogenesis_as_vis_edge( - pomc_to_gas_gangrene_pathogenesis_edge: Relationship, -): - """Creates a VisEdge from the pomc to gas gangrene - role in disease pathogenesis relationship.""" - edge_as_graph_relationship = GraphRelationship( - id=pomc_to_gas_gangrene_pathogenesis_edge.id, - label=type(pomc_to_gas_gangrene_pathogenesis_edge).__name__, - data=dict(pomc_to_gas_gangrene_pathogenesis_edge), - to=pomc_to_gas_gangrene_pathogenesis_edge.end_node.id, - _from=pomc_to_gas_gangrene_pathogenesis_edge.start_node.id, - to_label=list(pomc_to_gas_gangrene_pathogenesis_edge.end_node.labels)[0], - from_label=list(pomc_to_gas_gangrene_pathogenesis_edge.start_node.labels)[0], - ) - - pomc_to_gas_gangrene_pathogenesis_as_vis_edge = VisEdge( - id=edge_as_graph_relationship.id, - label=edge_as_graph_relationship.data['description'], - data=edge_as_graph_relationship.data, - to=edge_as_graph_relationship.to, - from_=edge_as_graph_relationship._from, - to_label='Disease', - from_label='Gene', - arrows='to', - ) - - return pomc_to_gas_gangrene_pathogenesis_as_vis_edge - - -@pytest.fixture(scope='function') -def pomc_to_gas_gangrene_pathogenesis_as_duplicate_vis_edge( - pomc_to_gas_gangrene_pathogenesis_edge: Relationship, -): - """Creates a DuplicateVisEdge from the pomc to gas_gangrene - role in disease pathogenesis relationship.""" - edge_as_graph_relationship = GraphRelationship( - id=pomc_to_gas_gangrene_pathogenesis_edge.id, - label=type(pomc_to_gas_gangrene_pathogenesis_edge).__name__, - data=dict(pomc_to_gas_gangrene_pathogenesis_edge), - to=pomc_to_gas_gangrene_pathogenesis_edge.end_node.id, - _from=pomc_to_gas_gangrene_pathogenesis_edge.start_node.id, - to_label=list(pomc_to_gas_gangrene_pathogenesis_edge.end_node.labels)[0], - from_label=list(pomc_to_gas_gangrene_pathogenesis_edge.start_node.labels)[0], - ) - - pomc_to_gas_gangrene_pathogenesis_as_duplicate_vis_edge = DuplicateVisEdge( - id=edge_as_graph_relationship.id, - label=edge_as_graph_relationship.data['description'], - data=edge_as_graph_relationship.data, - to=f'duplicateNode:{edge_as_graph_relationship.to}', # type:ignore - from_=f'duplicateNode:{edge_as_graph_relationship._from}', # type:ignore - to_label='Disease', - from_label='Gene', - arrows='to', - duplicate_of=edge_as_graph_relationship.id, - original_from=edge_as_graph_relationship._from, - original_to=edge_as_graph_relationship.to, - ) - - return pomc_to_gas_gangrene_pathogenesis_as_duplicate_vis_edge - - -@pytest.fixture(scope='function') -def penicillins_to_gas_gangrene_alleviates_as_vis_edge( - penicillins_to_gas_gangrene_alleviates_edge: Relationship, -): - """Creates a VisEdge from the penicillins to gas gangrene - alleviates/reduces relationship.""" - edge_as_graph_relationship = GraphRelationship( - id=penicillins_to_gas_gangrene_alleviates_edge.id, - label=type(penicillins_to_gas_gangrene_alleviates_edge).__name__, - data=dict(penicillins_to_gas_gangrene_alleviates_edge), - to=penicillins_to_gas_gangrene_alleviates_edge.end_node.id, - _from=penicillins_to_gas_gangrene_alleviates_edge.start_node.id, - to_label=list(penicillins_to_gas_gangrene_alleviates_edge.end_node.labels)[0], - from_label=list(penicillins_to_gas_gangrene_alleviates_edge.start_node.labels)[ - 0 - ], - ) - - penicillins_to_gas_gangrene_alleviates_as_vis_edge = VisEdge( - id=edge_as_graph_relationship.id, - label=edge_as_graph_relationship.data['description'], - data=edge_as_graph_relationship.data, - to=edge_as_graph_relationship.to, - from_=edge_as_graph_relationship._from, - to_label='Disease', - from_label='Chemical', - arrows='to', - ) - - return penicillins_to_gas_gangrene_alleviates_as_vis_edge - - -@pytest.fixture(scope='function') -def penicillins_to_gas_gangrene_alleviates_as_duplicate_vis_edge( - penicillins_to_gas_gangrene_alleviates_edge: Relationship, -): - """Creates a DuplicateVisEdge from the penicillins to gas_gangrene - alleviates/reduces relationship.""" - edge_as_graph_relationship = GraphRelationship( - id=penicillins_to_gas_gangrene_alleviates_edge.id, - label=type(penicillins_to_gas_gangrene_alleviates_edge).__name__, - data=dict(penicillins_to_gas_gangrene_alleviates_edge), - to=penicillins_to_gas_gangrene_alleviates_edge.end_node.id, - _from=penicillins_to_gas_gangrene_alleviates_edge.start_node.id, - to_label=list(penicillins_to_gas_gangrene_alleviates_edge.end_node.labels)[0], - from_label=list(penicillins_to_gas_gangrene_alleviates_edge.start_node.labels)[ - 0 - ], - ) - - penicillins_to_gas_gangrene_alleviates_as_duplicate_vis_edge = DuplicateVisEdge( - id=edge_as_graph_relationship.id, - label=edge_as_graph_relationship.data['description'], - data=edge_as_graph_relationship.data, - to=f'duplicateNode:{edge_as_graph_relationship.to}', # type:ignore - from_=f'duplicateNode:{edge_as_graph_relationship._from}', # type:ignore - to_label='Disease', - from_label='Chemical', - arrows='to', - duplicate_of=edge_as_graph_relationship.id, - original_from=edge_as_graph_relationship._from, - original_to=edge_as_graph_relationship.to, - ) - - return penicillins_to_gas_gangrene_alleviates_as_duplicate_vis_edge - - -@pytest.fixture(scope='function') -def penicillins_to_gas_gangrene_treatment_as_vis_edge( - penicillins_to_gas_gangrene_treatment_edge: Relationship, -): - """Creates a VisEdge from the penicillins to gas_gangrene - treatment/therapy relationship.""" - edge_as_graph_relationship = GraphRelationship( - id=penicillins_to_gas_gangrene_treatment_edge.id, - label=type(penicillins_to_gas_gangrene_treatment_edge).__name__, - data=dict(penicillins_to_gas_gangrene_treatment_edge), - to=penicillins_to_gas_gangrene_treatment_edge.end_node.id, - _from=penicillins_to_gas_gangrene_treatment_edge.start_node.id, - to_label=list(penicillins_to_gas_gangrene_treatment_edge.end_node.labels)[0], - from_label=list(penicillins_to_gas_gangrene_treatment_edge.start_node.labels)[ - 0 - ], - ) - - penicillins_to_gas_gangrene_treatment_as_vis_edge = VisEdge( - id=edge_as_graph_relationship.id, - label=edge_as_graph_relationship.data['description'], - data=edge_as_graph_relationship.data, - to=edge_as_graph_relationship.to, - from_=edge_as_graph_relationship._from, - to_label='Disease', - from_label='Chemical', - arrows='to', - ) - - return penicillins_to_gas_gangrene_treatment_as_vis_edge - - -@pytest.fixture(scope='function') -def penicillins_to_gas_gangrene_treatment_as_duplicate_vis_edge( - penicillins_to_gas_gangrene_treatment_edge: Relationship, -): - """Creates a DuplicateVisEdge from the penicillins to gas_gangrene - treatment/therapy relationship.""" - edge_as_graph_relationship = GraphRelationship( - id=penicillins_to_gas_gangrene_treatment_edge.id, - label=type(penicillins_to_gas_gangrene_treatment_edge).__name__, - data=dict(penicillins_to_gas_gangrene_treatment_edge), - to=penicillins_to_gas_gangrene_treatment_edge.end_node.id, - _from=penicillins_to_gas_gangrene_treatment_edge.start_node.id, - to_label=list(penicillins_to_gas_gangrene_treatment_edge.end_node.labels)[0], - from_label=list(penicillins_to_gas_gangrene_treatment_edge.start_node.labels)[ - 0 - ], - ) - - penicillins_to_gas_gangrene_treatment_as_duplicate_vis_edge = DuplicateVisEdge( - id=f'duplicateEdge:{edge_as_graph_relationship.id}', - label=edge_as_graph_relationship.data['description'], - data=edge_as_graph_relationship.data, - to=f'duplicateNode:{edge_as_graph_relationship.to}', # type:ignore - from_=f'duplicateNode:{edge_as_graph_relationship._from}', # type:ignore - to_label='Disease', - from_label='Chemical', - arrows='to', - duplicate_of=edge_as_graph_relationship.id, - original_from=edge_as_graph_relationship._from, - original_to=edge_as_graph_relationship.to, - ) - - return penicillins_to_gas_gangrene_treatment_as_duplicate_vis_edge - - -@pytest.fixture(scope='function') -def gas_gangrene_treatment_cluster_node_edge_pairs( - oxygen_duplicate_vis_node, - oxygen_to_gas_gangrene_treatment_as_duplicate_vis_edge, - penicillins_duplicate_vis_node, - penicillins_to_gas_gangrene_treatment_as_duplicate_vis_edge, -): - """Creates a list of DuplicateNodeEdgePairs. Used for testing the - reference table endpoints and services.""" - return [ - ReferenceTablePair( - node=ReferenceTablePair.NodeData( - id=oxygen_duplicate_vis_node.id, - display_name=oxygen_duplicate_vis_node.display_name, - label=oxygen_duplicate_vis_node.primary_label, - ), - edge=ReferenceTablePair.EdgeData( - original_from=oxygen_to_gas_gangrene_treatment_as_duplicate_vis_edge.original_from, - # noqa - original_to=oxygen_to_gas_gangrene_treatment_as_duplicate_vis_edge.original_to, - label=oxygen_to_gas_gangrene_treatment_as_duplicate_vis_edge.label, - ), - ), - ReferenceTablePair( - node=ReferenceTablePair.NodeData( - id=penicillins_duplicate_vis_node.id, - display_name=penicillins_duplicate_vis_node.display_name, - label=penicillins_duplicate_vis_node.primary_label, - ), - edge=ReferenceTablePair.EdgeData( - original_from=penicillins_to_gas_gangrene_treatment_as_duplicate_vis_edge.original_from, - original_to=penicillins_to_gas_gangrene_treatment_as_duplicate_vis_edge.original_to, - label=penicillins_to_gas_gangrene_treatment_as_duplicate_vis_edge.label, - ), - ), - ] - - -@pytest.fixture(scope='function') -def gas_gangrene_treatement_edge_data( - penicillins_to_gas_gangrene_treatment_edge: Relationship, -): - edge_as_graph_relationship = GraphRelationship( - id=penicillins_to_gas_gangrene_treatment_edge.id, - label=type(penicillins_to_gas_gangrene_treatment_edge).__name__, - data=dict(penicillins_to_gas_gangrene_treatment_edge), - to=penicillins_to_gas_gangrene_treatment_edge.end_node.id, - _from=penicillins_to_gas_gangrene_treatment_edge.start_node.id, - to_label=list(penicillins_to_gas_gangrene_treatment_edge.end_node.labels)[0], - from_label=list(penicillins_to_gas_gangrene_treatment_edge.start_node.labels)[ - 0 - ], - ) - - return EdgeConnectionData( - label=edge_as_graph_relationship.data['description'], - to=edge_as_graph_relationship.to, - from_=edge_as_graph_relationship._from, - to_label='Disease', - from_label='Chemical', - ) +def account_service(app, session): + return AccountService(session) @pytest.fixture(scope='function') -def gas_gangrene_alleviates_edge_data( - penicillins_to_gas_gangrene_alleviates_edge: Relationship, -): - edge_as_graph_relationship = GraphRelationship( - id=penicillins_to_gas_gangrene_alleviates_edge.id, - label=type(penicillins_to_gas_gangrene_alleviates_edge).__name__, - data=dict(penicillins_to_gas_gangrene_alleviates_edge), - to=penicillins_to_gas_gangrene_alleviates_edge.end_node.id, - _from=penicillins_to_gas_gangrene_alleviates_edge.start_node.id, - to_label=list(penicillins_to_gas_gangrene_alleviates_edge.end_node.labels)[0], - from_label=list(penicillins_to_gas_gangrene_alleviates_edge.start_node.labels)[ - 0 - ], - ) - - return EdgeConnectionData( - label=edge_as_graph_relationship.data['description'], - to=edge_as_graph_relationship.to, - from_=edge_as_graph_relationship._from, - to_label='Disease', - from_label='Chemical', - ) +def auth_service(app, session): + return AuthService(session) @pytest.fixture(scope='function') -def gas_gangrene_treatement_duplicate_edge_data( - penicillins_to_gas_gangrene_treatment_edge: Relationship, -): - edge_as_graph_relationship = GraphRelationship( - id=penicillins_to_gas_gangrene_treatment_edge.id, - label=type(penicillins_to_gas_gangrene_treatment_edge).__name__, - data=dict(penicillins_to_gas_gangrene_treatment_edge), - to=penicillins_to_gas_gangrene_treatment_edge.end_node.id, - _from=penicillins_to_gas_gangrene_treatment_edge.start_node.id, - to_label=list(penicillins_to_gas_gangrene_treatment_edge.end_node.labels)[0], - from_label=list(penicillins_to_gas_gangrene_treatment_edge.start_node.labels)[ - 0 - ], - ) - - return [ - DuplicateEdgeConnectionData( - label=edge_as_graph_relationship.data['description'], - to=f'duplicateNode:{edge_as_graph_relationship.to}', # type:ignore - from_=f'duplicateNode:{edge_as_graph_relationship._from}', # type:ignore - to_label='Disease', - from_label='Chemical', - original_from=edge_as_graph_relationship._from, - original_to=edge_as_graph_relationship.to, - ) - ] +def account_user(app, session): + return AccountService(session) @pytest.fixture(scope='function') -def gas_gangrene_alleviates_duplicate_edge_data( - penicillins_to_gas_gangrene_alleviates_edge: Relationship, -): - edge_as_graph_relationship = GraphRelationship( - id=penicillins_to_gas_gangrene_alleviates_edge.id, - label=type(penicillins_to_gas_gangrene_alleviates_edge).__name__, - data=dict(penicillins_to_gas_gangrene_alleviates_edge), - to=penicillins_to_gas_gangrene_alleviates_edge.end_node.id, - _from=penicillins_to_gas_gangrene_alleviates_edge.start_node.id, - to_label=list(penicillins_to_gas_gangrene_alleviates_edge.end_node.labels)[0], - from_label=list(penicillins_to_gas_gangrene_alleviates_edge.start_node.labels)[ - 0 - ], - ) - - return [ - DuplicateEdgeConnectionData( - label=edge_as_graph_relationship.data['description'], - to=f'duplicateNode:{edge_as_graph_relationship.to}', # type:ignore - from_=f'duplicateNode:{edge_as_graph_relationship._from}', # type:ignore - to_label='Disease', - from_label='Chemical', - original_from=edge_as_graph_relationship._from, - original_to=edge_as_graph_relationship.to, - ) - ] +def elastic_service(app, session): + elastic_service = ElasticService() + # Ensures that anytime the elastic service is requested for a test, that the environment is + # clean + elastic_service.recreate_indices_and_pipelines() -# End DTO Fixtures # + return elastic_service @pytest.fixture(scope='session') diff --git a/appserver/tests/constants.py b/appserver/tests/constants.py new file mode 100644 index 0000000000..7989cfa82c --- /dev/null +++ b/appserver/tests/constants.py @@ -0,0 +1,72 @@ +# Arango vars + +DOCUMENT_COLLECTIONS = [ + 'biocyc', + 'chebi', + 'enzyme', + 'go', + 'kegg', + 'lifelike', + 'liquibasechangelog', + 'literature', + 'mesh', + 'ncbi', + 'other', + 'pubmed', + 'regulondb', + 'string', + 'synonym', + 'taxonomy', + 'uniprot', +] + +EDGE_COLLECTIONS = [ + 'associated', + 'binds', + 'catalyzes', + 'chebi_link', + 'component_of', + 'consumed_by', + 'element_of', + 'encodes', + 'ends_during', + 'enzyme_link', + 'go_link', + 'happens_during', + 'has_association', + 'has_author', + 'has_functional_parent', + 'has_gene', + 'has_ko', + 'has_ortholog', + 'has_parent', + 'has_parent_hydride', + 'has_part', + 'has_pathway', + 'has_role', + 'has_synonym', + 'has_taxonomy', + 'has_treenumber', + 'has_type', + 'in_changelog', + 'in_pathway', + 'in_pub', + 'indicates', + 'is', + 'is_a', + 'is_conjugate_acid_of', + 'is_conjugate_base_of', + 'is_enantiomer_of', + 'is_substituent_group_from', + 'is_tautomer_of', + 'mapped_to', + 'mapped_to_descriptor', + 'modified_to', + 'negatively_regulates', + 'produces', + 'regulates', + 'replaced_by', + 'type_of', +] + +GRAPHS = ['all'] diff --git a/appserver/tests/database/services/annotations/annotations_test.py b/appserver/tests/database/services/annotations/annotations_test.py index c09d0993a8..1b0145b4d2 100644 --- a/appserver/tests/database/services/annotations/annotations_test.py +++ b/appserver/tests/database/services/annotations/annotations_test.py @@ -8,8 +8,11 @@ GlobalInclusions, ) from neo4japp.services.annotations.utils.parsing import process_parsed_content +from neo4japp.services.annotations.annotation_graph_service import get_entity_inclusions +from neo4japp.services.annotations.constants import EntityType -from .util import * + +from .util import annotate_pdf_for_testing, create_mock_annotations # reference to this directory @@ -56,7 +59,7 @@ ], ) def test_fix_conflicting_annotations_same_types( - get_annotation_service, index, annotations + get_annotation_service, test_arango_db, index, annotations ): annotation_service = get_annotation_service fixed = annotation_service.fix_conflicting_annotations( @@ -153,7 +156,7 @@ def test_fix_conflicting_annotations_same_types( ], ) def test_fix_conflicting_annotations_different_types( - get_annotation_service, index, annotations + get_annotation_service, test_arango_db, index, annotations ): annotation_service = get_annotation_service fixed = annotation_service.fix_conflicting_annotations( @@ -210,6 +213,7 @@ def test_gene_organism_escherichia_coli_pdf( mock_graph_test_gene_organism_escherichia_coli_pdf, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join(directory, 'pdf_samples/annotations_test/ecoli_gene_test.json') @@ -249,6 +253,7 @@ def test_protein_organism_escherichia_coli_pdf( mock_graph_test_protein_organism_escherichia_coli_pdf, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join(directory, 'pdf_samples/annotations_test/ecoli_protein_test.json') @@ -273,7 +278,8 @@ def test_local_inclusion_affect_gene_organism_matching( mock_graph_test_local_inclusion_affect_gene_organism_matching, get_lmdb_service, get_annotation_service, - get_graph_service, + arango_client, + test_arango_db, ): pdf = path.join( directory, @@ -316,7 +322,7 @@ def test_local_inclusion_affect_gene_organism_matching( annotation_service=get_annotation_service, lmdb_service=get_lmdb_service, parsed=parsed, - inclusions=get_graph_service.get_entity_inclusions(inclusions), + inclusions=get_entity_inclusions(arango_client, inclusions), custom_annotations=inclusions, ) @@ -329,6 +335,7 @@ def test_local_exclusion_affect_gene_organism_matching( get_lmdb_service, get_annotation_service, get_db_service, + test_arango_db, ): pdf = path.join( directory, @@ -371,6 +378,7 @@ def test_assume_human_gene_after_finding_virus( mock_graph_test_assume_human_gene_after_finding_virus, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -400,7 +408,10 @@ def test_assume_human_gene_after_finding_virus( def test_can_find_food_entities( - lmdb_setup_test_can_find_food_entities, get_lmdb_service, get_annotation_service + lmdb_setup_test_can_find_food_entities, + get_lmdb_service, + get_annotation_service, + test_arango_db, ): pdf = path.join( directory, 'pdf_samples/annotations_test/test_can_find_food_entities.json' @@ -426,7 +437,10 @@ def test_can_find_food_entities( def test_can_find_anatomy_entities( - lmdb_setup_test_can_find_anatomy_entities, get_lmdb_service, get_annotation_service + lmdb_setup_test_can_find_anatomy_entities, + get_lmdb_service, + get_annotation_service, + test_arango_db, ): pdf = path.join( directory, 'pdf_samples/annotations_test/test_can_find_anatomy_entities.json' @@ -463,6 +477,7 @@ def test_genes_vs_proteins( mock_graph_test_genes_vs_proteins, get_lmdb_service, get_annotation_service, + test_arango_db, index, fpath, ): @@ -527,7 +542,7 @@ def test_genes_vs_proteins( ], ) def test_fix_false_positive_gene_annotations( - get_annotation_service, index, annotations + get_annotation_service, test_arango_db, index, annotations ): annotation_service = get_annotation_service fixed = annotation_service._get_fixed_false_positive_unified_annotations( @@ -572,7 +587,7 @@ def test_fix_false_positive_gene_annotations( ], ) def test_fix_false_positive_protein_annotations( - get_annotation_service, index, annotations + get_annotation_service, test_arango_db, index, annotations ): annotation_service = get_annotation_service fixed = annotation_service._get_fixed_false_positive_unified_annotations( @@ -596,6 +611,7 @@ def test_gene_id_changes_to_result_from_kg_if_matched_with_organism( mock_graph_test_gene_id_changes_to_result_from_kg_if_matched_with_organism, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -621,6 +637,7 @@ def test_human_is_prioritized_if_equal_distance_in_gene_organism_matching( mock_graph_test_human_is_prioritized_if_equal_distance_in_gene_organism_matching, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -646,6 +663,7 @@ def test_global_excluded_chemical_annotations( get_db_service, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -679,6 +697,7 @@ def test_global_excluded_compound_annotations( get_db_service, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -712,6 +731,7 @@ def test_global_excluded_disease_annotations( get_db_service, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -746,6 +766,7 @@ def test_global_excluded_gene_annotations( get_db_service, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -779,6 +800,7 @@ def test_global_excluded_phenotype_annotations( get_db_service, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -812,6 +834,7 @@ def test_global_excluded_protein_annotations( get_db_service, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -845,6 +868,7 @@ def test_global_excluded_species_annotations( get_db_service, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -878,6 +902,7 @@ def test_global_exclusions_does_not_interfere_with_other_entities( get_db_service, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -908,7 +933,10 @@ def test_global_exclusions_does_not_interfere_with_other_entities( def test_global_chemical_inclusion_annotation( - mock_global_chemical_inclusion_annotation, get_lmdb_service, get_annotation_service + mock_global_chemical_inclusion_annotation, + get_lmdb_service, + get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -934,7 +962,10 @@ def test_global_chemical_inclusion_annotation( def test_global_compound_inclusion_annotation( - mock_global_compound_inclusion_annotation, get_lmdb_service, get_annotation_service + mock_global_compound_inclusion_annotation, + get_lmdb_service, + get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -965,6 +996,7 @@ def test_global_gene_inclusion_annotation( mock_global_gene_inclusion_annotation, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -990,7 +1022,10 @@ def test_global_gene_inclusion_annotation( def test_global_disease_inclusion_annotation( - mock_global_disease_inclusion_annotation, get_lmdb_service, get_annotation_service + mock_global_disease_inclusion_annotation, + get_lmdb_service, + get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -1016,7 +1051,10 @@ def test_global_disease_inclusion_annotation( def test_global_phenomena_inclusion_annotation( - mock_global_phenomena_inclusion_annotation, get_lmdb_service, get_annotation_service + mock_global_phenomena_inclusion_annotation, + get_lmdb_service, + get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -1042,7 +1080,10 @@ def test_global_phenomena_inclusion_annotation( def test_global_phenotype_inclusion_annotation( - mock_global_phenotype_inclusion_annotation, get_lmdb_service, get_annotation_service + mock_global_phenotype_inclusion_annotation, + get_lmdb_service, + get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -1068,7 +1109,10 @@ def test_global_phenotype_inclusion_annotation( def test_global_protein_inclusion_annotation( - mock_global_protein_inclusion_annotation, get_lmdb_service, get_annotation_service + mock_global_protein_inclusion_annotation, + get_lmdb_service, + get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -1094,7 +1138,10 @@ def test_global_protein_inclusion_annotation( def test_global_species_inclusion_annotation( - mock_global_species_inclusion_annotation, get_lmdb_service, get_annotation_service + mock_global_species_inclusion_annotation, + get_lmdb_service, + get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -1124,6 +1171,7 @@ def test_no_annotation_for_abbreviation( mock_graph_test_no_annotation_for_abbreviation, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -1156,6 +1204,7 @@ def test_delta_gene_deletion_detected( mock_graph_test_gene_organism_escherichia_coli_pdf, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join( directory, 'pdf_samples/annotations_test/test_delta_gene_deletion_detected.json' @@ -1228,6 +1277,7 @@ def test_global_inclusion_normalized_already_in_lmdb( mock_global_inclusion_normalized_already_in_lmdb, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -1255,6 +1305,7 @@ def test_gene_matched_to_organism_before_if_closest_is_too_far( mock_graph_test_new_gene_organism_matching_algorithm, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -1284,6 +1335,7 @@ def test_gene_matched_to_most_freq_organism_if_closest_is_too_far_and_no_before_ mock_graph_test_new_gene_organism_matching_algorithm, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join( directory, @@ -1312,6 +1364,7 @@ def test_prioritize_primary_name_that_equals_synonym( lmdb_setup_test_prioritize_primary_name_that_equals_synonym, get_lmdb_service, get_annotation_service, + test_arango_db, ): pdf = path.join( directory, diff --git a/appserver/tests/database/services/annotations/conftest.py b/appserver/tests/database/services/annotations/conftest.py index 2c3908a7bd..8b3b140b5d 100644 --- a/appserver/tests/database/services/annotations/conftest.py +++ b/appserver/tests/database/services/annotations/conftest.py @@ -7,7 +7,6 @@ from neo4japp.services.annotations import ( AnnotationService, AnnotationDBService, - AnnotationGraphService, LMDBService, ManualAnnotationService, Tokenizer, @@ -38,7 +37,7 @@ create_ner_type_protein, create_ner_type_species, ) -from neo4japp.utils import normalize_str +from neo4japp.utils.string import normalize_str # reference to this directory @@ -71,26 +70,21 @@ def create_entity_lmdb(path_to_folder: str, db_name: str, entity_objs=[]): ) -@pytest.fixture(scope='function') -def get_graph_service(graph_driver): - return AnnotationGraphService(graph_driver) - - @pytest.fixture(scope='function') def get_db_service(session): return AnnotationDBService() @pytest.fixture(scope='function') -def get_annotation_service(get_db_service, get_graph_service, request): +def get_annotation_service(get_db_service, arango_client, request): request.addfinalizer(teardown) - return AnnotationService(db=get_db_service, graph=get_graph_service) + return AnnotationService(db=get_db_service, arango_client=arango_client) @pytest.fixture(scope='function') -def get_manual_annotation_service(get_graph_service): - return ManualAnnotationService(graph=get_graph_service, tokenizer=Tokenizer()) +def get_manual_annotation_service(arango_client): + return ManualAnnotationService(arango_client=arango_client, tokenizer=Tokenizer()) @pytest.fixture(scope='function') @@ -845,8 +839,7 @@ def get_match_result(*args, **kwargs): ) monkeypatch.setattr( - AnnotationGraphService, - 'get_genes_to_organisms', + 'neo4japp.services.annotations.annotation_service.get_genes_to_organisms', get_match_result, ) @@ -864,8 +857,7 @@ def get_match_result(*args, **kwargs): ) monkeypatch.setattr( - AnnotationGraphService, - 'get_genes_to_organisms', + 'neo4japp.services.annotations.annotation_service.get_genes_to_organisms', get_match_result, ) @@ -882,8 +874,7 @@ def get_match_result(*args, **kwargs): ) monkeypatch.setattr( - AnnotationGraphService, - 'get_genes_to_organisms', + 'neo4japp.services.annotations.annotation_service.get_genes_to_organisms', get_match_result, ) @@ -901,8 +892,7 @@ def get_match_result(*args, **kwargs): ) monkeypatch.setattr( - AnnotationGraphService, - 'get_genes_to_organisms', + 'neo4japp.services.annotations.annotation_service.get_genes_to_organisms', get_match_result, ) @@ -917,8 +907,7 @@ def get_match_result(*args, **kwargs): ) monkeypatch.setattr( - AnnotationGraphService, - 'get_genes_to_organisms', + 'neo4japp.services.annotations.annotation_service.get_genes_to_organisms', get_match_result, ) @@ -936,8 +925,7 @@ def get_match_result(*args, **kwargs): ) monkeypatch.setattr( - AnnotationGraphService, - 'get_genes_to_organisms', + 'neo4japp.services.annotations.annotation_service.get_genes_to_organisms', get_match_result, ) @@ -954,8 +942,7 @@ def get_match_result(*args, **kwargs): ) monkeypatch.setattr( - AnnotationGraphService, - 'get_genes_to_organisms', + 'neo4japp.services.annotations.annotation_service.get_genes_to_organisms', get_match_result, ) @@ -988,8 +975,7 @@ def get_match_result(*args, **kwargs): ) monkeypatch.setattr( - AnnotationGraphService, - 'get_genes_to_organisms', + 'neo4japp.services.annotations.annotation_service.get_genes_to_organisms', get_match_result, ) @@ -1007,8 +993,7 @@ def get_match_result(*args, **kwargs): ) monkeypatch.setattr( - AnnotationGraphService, - 'get_genes_to_organisms', + 'neo4japp.services.annotations.annotation_service.get_genes_to_organisms', get_match_result, ) @@ -1026,8 +1011,7 @@ def get_match_result(*args, **kwargs): ) monkeypatch.setattr( - AnnotationGraphService, - 'get_proteins_to_organisms', + 'neo4japp.services.annotations.annotation_service.get_proteins_to_organisms', get_match_result, ) @@ -1060,8 +1044,7 @@ def get_match_result(*args, **kwargs): ) monkeypatch.setattr( - AnnotationGraphService, - 'get_genes_to_organisms', + 'neo4japp.services.annotations.annotation_service.get_genes_to_organisms', get_match_result, ) diff --git a/appserver/tests/database/services/annotations/manual_annotations/manual_annotations_test.py b/appserver/tests/database/services/annotations/manual_annotations/manual_annotations_test.py index ab456724e3..d37d0f161d 100644 --- a/appserver/tests/database/services/annotations/manual_annotations/manual_annotations_test.py +++ b/appserver/tests/database/services/annotations/manual_annotations/manual_annotations_test.py @@ -13,6 +13,7 @@ def test_add_custom_annotation_inclusion_annotate_all( get_manual_annotation_service, mock_add_custom_annotation_inclusion, + test_arango_db, file_in_project, project_owner, ): @@ -42,6 +43,7 @@ def test_add_custom_annotation_inclusion_annotate_all( def test_add_custom_annotation_inclusion_multi_word( get_manual_annotation_service, mock_add_custom_annotation_inclusion, + test_arango_db, file_in_project, project_owner, ): @@ -72,6 +74,7 @@ def test_add_custom_annotation_inclusion_multi_word( def test_add_custom_annotation_inclusion( get_manual_annotation_service, mock_add_custom_annotation_inclusion, + test_arango_db, file_in_project, project_owner, ): @@ -101,6 +104,7 @@ def test_add_custom_annotation_inclusion( def test_add_custom_annotation_inclusion_multi_word_gene_limit( get_manual_annotation_service, mock_add_custom_annotation_inclusion, + test_arango_db, file_in_project, project_owner, ): @@ -130,6 +134,7 @@ def test_add_custom_annotation_inclusion_multi_word_gene_limit( def test_add_custom_annotation_inclusion_multi_word_food_limit( get_manual_annotation_service, mock_add_custom_annotation_inclusion, + test_arango_db, file_in_project, project_owner, ): diff --git a/appserver/tests/database/services/annotations/util.py b/appserver/tests/database/services/annotations/util.py index abef94760e..197b86eb00 100644 --- a/appserver/tests/database/services/annotations/util.py +++ b/appserver/tests/database/services/annotations/util.py @@ -1,4 +1,4 @@ -from typing import List, Tuple +from typing import Tuple from neo4japp.services.annotations import ( EntityRecognitionService, diff --git a/appserver/tests/database/services/redis_queue/test_redis_queue_service.py b/appserver/tests/database/services/redis_queue/test_redis_queue_service.py index c9efc6ef38..3b8adea7a8 100644 --- a/appserver/tests/database/services/redis_queue/test_redis_queue_service.py +++ b/appserver/tests/database/services/redis_queue/test_redis_queue_service.py @@ -9,6 +9,10 @@ from neo4japp.jobs import bad_job, bad_then_good_job +# Note that some of these tests assume the 'worker' container is running, or at least that there is +# a rq worker running somewhere in the Lifelike docker environment. + + def test_can_create_rq_service(rq_service: RedisQueueService): assert rq_service is not None diff --git a/appserver/tests/database/services/visualizer/conftest.py b/appserver/tests/database/services/visualizer/conftest.py new file mode 100644 index 0000000000..05b7bc3a76 --- /dev/null +++ b/appserver/tests/database/services/visualizer/conftest.py @@ -0,0 +1,661 @@ +from arango.database import StandardDatabase +from arango.collection import EdgeCollection +import pytest + +from neo4japp.constants import DISPLAY_NAME_MAP +from neo4japp.data_transfer_objects.visualization import ( + DuplicateEdgeConnectionData, + DuplicateVisEdge, + DuplicateVisNode, + EdgeConnectionData, + ReferenceTablePair, +) +from neo4japp.models.neo4j import GraphNode, GraphRelationship +from neo4japp.services.arangodb import add_document_to_collection +from neo4japp.utils.string import snake_to_camel_dict +from neo4japp.utils.labels import get_first_known_label_from_list + + +def _create_document(arango_db: StandardDatabase, colxn_name: str, **kwargs) -> dict: + return add_document_to_collection(db=arango_db, colxn_name=colxn_name, doc=kwargs) + + +def _create_relationship_document(edge_collection: EdgeCollection, **kwargs): + return edge_collection.insert(kwargs, return_new=True)['new'] + + +@pytest.fixture(scope='function') +def gas_gangrene(test_arango_db): + gas_gangrene = _create_document( + test_arango_db, + 'mesh', + name='gas gangrene', + eid='MESH:D005738', + labels=['Disease'], + ) + return gas_gangrene + + +@pytest.fixture(scope='function') +def penicillins(test_arango_db): + penicillins = _create_document( + test_arango_db, + 'mesh', + name='Penicillins', + eid='MESH:D010406', + labels=['Chemical'], + ) + return penicillins + + +@pytest.fixture(scope='function') +def oxygen(test_arango_db): + oxygen = _create_document( + test_arango_db, 'mesh', name='Oxygen', eid='MESH:D010100', labels=['Chemical'] + ) + return oxygen + + +@pytest.fixture(scope='function') +def pomc(test_arango_db): + pomc = _create_document( + test_arango_db, 'ncbi', name='POMC', eid='5443', labels=['Gene'] + ) + return pomc + + +@pytest.fixture(scope='function') +def oxygen_to_gas_gangrene_association(test_arango_db): + return _create_document( + test_arango_db, + 'literature', + assoc_type='J', + description='treatment/therapy (including investigatory)', + eid=1089126, + ) + + +@pytest.fixture(scope='function') +def pomc_to_gas_gangrene_association(test_arango_db): + return _create_document( + test_arango_db, + 'literature', + assoc_type='J', + description='role in disease pathogenesis', + eid=1387448, + ) + + +@pytest.fixture(scope='function') +def penicillins_to_gas_gangrene_association_1(test_arango_db): + return _create_document( + test_arango_db, + 'literature', + assoc_type='Pa', + description='alleviates, reduces', + eid=2771500, + ) + + +@pytest.fixture(scope='function') +def penicillins_to_gas_gangrene_association_2(test_arango_db): + return _create_document( + test_arango_db, + 'literature', + assoc_type='J', + description='treatment/therapy (including investigatory)', + eid=2771501, + ) + + +@pytest.fixture(scope='function') +def pomc_to_gas_gangrene_pathogenesis_edge( + associated_edge_collection: EdgeCollection, + gas_gangrene: dict, + pomc: dict, + pomc_to_gas_gangrene_association: dict, +): + return _create_relationship_document( + associated_edge_collection, + _from=pomc['_id'], + _to=gas_gangrene['_id'], + assoc_type='J', + description='role in disease pathogenesis', + association_id=pomc_to_gas_gangrene_association['_id'], + ) + + +@pytest.fixture(scope='function') +def penicillins_to_gas_gangrene_alleviates_edge( + associated_edge_collection: EdgeCollection, + gas_gangrene: dict, + penicillins: dict, + penicillins_to_gas_gangrene_association_1: dict, +): + return _create_relationship_document( + associated_edge_collection, + _from=penicillins['_id'], + _to=gas_gangrene['_id'], + assoc_type='Pa', + description='alleviates, reduces', + association_id=penicillins_to_gas_gangrene_association_1['_id'], + ) + + +@pytest.fixture(scope='function') +def oxygen_to_gas_gangrene_treatment_edge( + associated_edge_collection: EdgeCollection, + gas_gangrene: dict, + oxygen: dict, + oxygen_to_gas_gangrene_association: dict, +): + return _create_relationship_document( + associated_edge_collection, + _from=oxygen['_id'], + _to=gas_gangrene['_id'], + assoc_type='Pa', + description='treatment/therapy (including investigatory)', + association_id=oxygen_to_gas_gangrene_association['_id'], + ) + + +@pytest.fixture(scope='function') +def penicillins_to_gas_gangrene_treatment_edge( + associated_edge_collection: EdgeCollection, + gas_gangrene: dict, + penicillins: dict, + penicillins_to_gas_gangrene_association_2: dict, +): + return _create_relationship_document( + associated_edge_collection, + _from=penicillins['_id'], + _to=gas_gangrene['_id'], + assoc_type='Pa', + description='treatment/therapy (including investigatory)', + association_id=penicillins_to_gas_gangrene_association_2['_id'], + ) + + +@pytest.fixture(scope='function') +def gas_gangrene_with_associations_and_references( + test_arango_db, + has_association_edge_collection, + indicates_edge_collection, + in_pub_edge_collection, + gas_gangrene, + oxygen, + penicillins, + pomc, + oxygen_to_gas_gangrene_association, + pomc_to_gas_gangrene_association, + penicillins_to_gas_gangrene_association_1, + penicillins_to_gas_gangrene_association_2, + oxygen_to_gas_gangrene_treatment_edge, + pomc_to_gas_gangrene_pathogenesis_edge, + penicillins_to_gas_gangrene_alleviates_edge, + penicillins_to_gas_gangrene_treatment_edge, +): + # Snippet Nodes + oxygen_to_gas_gangrene_snippet_node1 = _create_document( + test_arango_db, + 'literature', + snippet_id=7430189, + sentence='In this study , we aimed to investigate the effect of HBO2...', + ) + oxygen_to_gas_gangrene_snippet_node2 = _create_document( + test_arango_db, + 'literature', + snippet_id=1890743, + sentence='Hyperbaric oxygen therapy has an adjunctive role...', + ) + penicillins_to_gas_gangrene_snippet_node1 = _create_document( + test_arango_db, + 'literature', + snippet_id=9810347, + sentence='In a mouse model of gas_gangrene caused by...', + ) + penicillins_to_gas_gangrene_snippet_node2 = _create_document( + test_arango_db, + 'literature', + snippet_id=9810346, + sentence='Toxin suppression and rapid bacterial killing may...', + ) + penicillins_to_gas_gangrene_snippet_node3 = _create_document( + test_arango_db, + 'literature', + snippet_id=9810348, + sentence='...penicillin was found to reduce the affect of...', + ) + penicillins_to_gas_gangrene_snippet_node4 = _create_document( + test_arango_db, + 'literature', + snippet_id=9810349, + sentence='...suppresses toxins and rapidly kills bacteria...', + ) + + # Publication Nodes + oxygen_to_gas_gangrene_publication_node = _create_document( + test_arango_db, + 'literature', + pub_id=3, + pub_year=2019, + ) + penicillins_to_gas_gangrene_publication_node1 = _create_document( + test_arango_db, 'literature', pub_id=1, pub_year=2014 + ) + penicillins_to_gas_gangrene_publication_node2 = _create_document( + test_arango_db, + 'literature', + pub_id=2, + ) + + # Entity -> Association Relationships + entity_to_association_rels = [ + [oxygen, oxygen_to_gas_gangrene_association], + [pomc, pomc_to_gas_gangrene_association], + [penicillins, penicillins_to_gas_gangrene_association_1], + [penicillins, penicillins_to_gas_gangrene_association_2], + ] + for rel in entity_to_association_rels: + _create_relationship_document( + has_association_edge_collection, _from=rel[0]['_id'], _to=rel[1]['_id'] + ) + + # Association -> Entity Relationships + association_to_entity_rels = [ + [oxygen_to_gas_gangrene_association, gas_gangrene], + [pomc_to_gas_gangrene_association, gas_gangrene], + [penicillins_to_gas_gangrene_association_1, gas_gangrene], + [penicillins_to_gas_gangrene_association_2, gas_gangrene], + ] + for rel in association_to_entity_rels: + _create_relationship_document( + has_association_edge_collection, + _from=rel[0]['_id'], + _to=rel[1]['_id'], + ) + + # Snippet -> Association Relationships + snippet_to_association_rels = [ + [ + oxygen_to_gas_gangrene_snippet_node1, + oxygen_to_gas_gangrene_association, + None, + None, + 'oxygen', + 'gas gangrene', + ], # noqa + [ + oxygen_to_gas_gangrene_snippet_node2, + oxygen_to_gas_gangrene_association, + None, + None, + 'oxygen', + 'gas gangrene', + ], # noqa + [ + penicillins_to_gas_gangrene_snippet_node1, + penicillins_to_gas_gangrene_association_1, + 2, + 0.385, + 'penicillin', + 'gas gangrene', + ], # noqa + [ + penicillins_to_gas_gangrene_snippet_node3, + penicillins_to_gas_gangrene_association_1, + 5, + 0.693, + 'penicillin', + 'gas gangrene', + ], # noqa + [ + penicillins_to_gas_gangrene_snippet_node2, + penicillins_to_gas_gangrene_association_2, + 1, + 0.222, + 'penicillin', + 'gas gangrene', + ], # noqa + [ + penicillins_to_gas_gangrene_snippet_node4, + penicillins_to_gas_gangrene_association_2, + 3, + 0.456, + 'penicillin', + 'gas gangrene', + ], # noqa + ] + for rel in snippet_to_association_rels: + _create_relationship_document( + indicates_edge_collection, + _from=rel[0]['_id'], + _to=rel[1]['_id'], + raw_score=rel[2], + normalized_score=rel[3], + entry1_text=rel[4], + entry2_text=rel[5], + ) + + # Snippet -> Publication Relationships + snippet_to_pub_rels = [ + [oxygen_to_gas_gangrene_snippet_node1, oxygen_to_gas_gangrene_publication_node], + [oxygen_to_gas_gangrene_snippet_node2, oxygen_to_gas_gangrene_publication_node], + [ + penicillins_to_gas_gangrene_snippet_node1, + penicillins_to_gas_gangrene_publication_node1, + ], # noqa + [ + penicillins_to_gas_gangrene_snippet_node3, + penicillins_to_gas_gangrene_publication_node2, + ], # noqa + [ + penicillins_to_gas_gangrene_snippet_node2, + penicillins_to_gas_gangrene_publication_node2, + ], # noqa + [ + penicillins_to_gas_gangrene_snippet_node4, + penicillins_to_gas_gangrene_publication_node2, + ], # noqa + ] + for rel in snippet_to_pub_rels: + _create_relationship_document( + in_pub_edge_collection, _from=rel[0]['_id'], _to=rel[1]['_id'] + ) + return gas_gangrene + + +@pytest.fixture(scope='function') +def oxygen_duplicate_vis_node(oxygen): + """Creates a DuplicateVisNode from oxygen""" + labels = list(oxygen['labels']) + node_as_graph_node = GraphNode( + id=oxygen['_id'], + label=labels[0], + sub_labels=labels, + domain_labels=[], + display_name=oxygen.get( + DISPLAY_NAME_MAP[get_first_known_label_from_list(oxygen['labels'])] + ), # noqa + data=snake_to_camel_dict(dict(oxygen), {}), + url=None, + ) + + oxygen_duplicate_vis_node = DuplicateVisNode( + id=f'duplicateNode:{node_as_graph_node.id}', + label=node_as_graph_node.label, + data=node_as_graph_node.data, + sub_labels=node_as_graph_node.sub_labels, + display_name=node_as_graph_node.display_name, + primary_label=node_as_graph_node.sub_labels[0], + color={}, + expanded=False, + duplicate_of=node_as_graph_node.id, + ) + + return oxygen_duplicate_vis_node + + +@pytest.fixture(scope='function') +def penicillins_duplicate_vis_node(penicillins): + """Creates a DuplicateVisNode from penicillins""" + labels = list(penicillins['labels']) + node_as_graph_node = GraphNode( + id=penicillins['_id'], + label=labels[0], + sub_labels=labels, + domain_labels=[], + display_name=penicillins.get( + DISPLAY_NAME_MAP[get_first_known_label_from_list(penicillins['labels'])] + ), # noqa + data=snake_to_camel_dict(dict(penicillins), {}), + url=None, + ) + + penicillins_duplicate_vis_node = DuplicateVisNode( + id=f'duplicateNode:{node_as_graph_node.id}', + label=node_as_graph_node.label, + data=node_as_graph_node.data, + sub_labels=node_as_graph_node.sub_labels, + display_name=node_as_graph_node.display_name, + primary_label=node_as_graph_node.sub_labels[0], + color={}, + expanded=False, + duplicate_of=node_as_graph_node.id, + ) + + return penicillins_duplicate_vis_node + + +@pytest.fixture(scope='function') +def oxygen_to_gas_gangrene_treatment_as_duplicate_vis_edge( + oxygen, + gas_gangrene, + oxygen_to_gas_gangrene_treatment_edge, +): + """Creates a DuplicateVisEdge from the oxygen to gas_gangrene + alleviates/reduces relationship.""" + + edge_as_graph_relationship = GraphRelationship( + id=oxygen_to_gas_gangrene_treatment_edge['_id'], + label='associated', + data=dict( + assoc_type=oxygen_to_gas_gangrene_treatment_edge['assoc_type'], + description=oxygen_to_gas_gangrene_treatment_edge['description'], + ), + to=oxygen_to_gas_gangrene_treatment_edge['_to'], + _from=oxygen_to_gas_gangrene_treatment_edge['_from'], + to_label=gas_gangrene['labels'][0], + from_label=oxygen['labels'][0], + ) + + oxygen_to_gas_gangrene_treatment_as_duplicate_vis_edge = DuplicateVisEdge( + id=edge_as_graph_relationship.id, + label=edge_as_graph_relationship.data['description'], + data=edge_as_graph_relationship.data, + to=f'duplicateNode:{edge_as_graph_relationship.to}', # type:ignore + from_=f'duplicateNode:{edge_as_graph_relationship._from}', # type:ignore + to_label='Disease', + from_label='Chemical', + arrows='to', + duplicate_of=edge_as_graph_relationship.id, + original_from=edge_as_graph_relationship._from, + original_to=edge_as_graph_relationship.to, + ) + + return oxygen_to_gas_gangrene_treatment_as_duplicate_vis_edge + + +@pytest.fixture(scope='function') +def penicillins_to_gas_gangrene_treatment_as_duplicate_vis_edge( + penicillins, + gas_gangrene, + penicillins_to_gas_gangrene_treatment_edge, +): + """Creates a DuplicateVisEdge from the penicillins to gas_gangrene + treatment/therapy relationship.""" + edge_as_graph_relationship = GraphRelationship( + id=penicillins_to_gas_gangrene_treatment_edge['_id'], + label='associated', + data=dict( + assoc_type=penicillins_to_gas_gangrene_treatment_edge['assoc_type'], + description=penicillins_to_gas_gangrene_treatment_edge['description'], + ), + to=penicillins_to_gas_gangrene_treatment_edge['_to'], + _from=penicillins_to_gas_gangrene_treatment_edge['_from'], + to_label=gas_gangrene['labels'][0], + from_label=penicillins['labels'][0], + ) + + penicillins_to_gas_gangrene_treatment_as_duplicate_vis_edge = DuplicateVisEdge( + id=f'duplicateEdge:{edge_as_graph_relationship.id}', + label=edge_as_graph_relationship.data['description'], + data=edge_as_graph_relationship.data, + to=f'duplicateNode:{edge_as_graph_relationship.to}', # type:ignore + from_=f'duplicateNode:{edge_as_graph_relationship._from}', # type:ignore + to_label='Disease', + from_label='Chemical', + arrows='to', + duplicate_of=edge_as_graph_relationship.id, + original_from=edge_as_graph_relationship._from, + original_to=edge_as_graph_relationship.to, + ) + + return penicillins_to_gas_gangrene_treatment_as_duplicate_vis_edge + + +@pytest.fixture(scope='function') +def gas_gangrene_treatment_cluster_node_edge_pairs( + oxygen_duplicate_vis_node, + oxygen_to_gas_gangrene_treatment_as_duplicate_vis_edge, + penicillins_duplicate_vis_node, + penicillins_to_gas_gangrene_treatment_as_duplicate_vis_edge, +): + """Creates a list of DuplicateNodeEdgePairs. Used for testing the + reference table endpoints and services.""" + return [ + ReferenceTablePair( + node=ReferenceTablePair.NodeData( + id=oxygen_duplicate_vis_node.id, + display_name=oxygen_duplicate_vis_node.display_name, + label=oxygen_duplicate_vis_node.primary_label, + ), + edge=ReferenceTablePair.EdgeData( + original_from=oxygen_to_gas_gangrene_treatment_as_duplicate_vis_edge.original_from, # noqa + original_to=oxygen_to_gas_gangrene_treatment_as_duplicate_vis_edge.original_to, + label=oxygen_to_gas_gangrene_treatment_as_duplicate_vis_edge.label, + ), + ), + ReferenceTablePair( + node=ReferenceTablePair.NodeData( + id=penicillins_duplicate_vis_node.id, + display_name=penicillins_duplicate_vis_node.display_name, + label=penicillins_duplicate_vis_node.primary_label, + ), + edge=ReferenceTablePair.EdgeData( + original_from=penicillins_to_gas_gangrene_treatment_as_duplicate_vis_edge.original_from, # noqa + original_to=penicillins_to_gas_gangrene_treatment_as_duplicate_vis_edge.original_to, + label=penicillins_to_gas_gangrene_treatment_as_duplicate_vis_edge.label, + ), + ), + ] + + +@pytest.fixture(scope='function') +def gas_gangrene_treatement_edge_data( + penicillins, + gas_gangrene, + penicillins_to_gas_gangrene_treatment_edge, +): + edge_as_graph_relationship = GraphRelationship( + id=penicillins_to_gas_gangrene_treatment_edge['_id'], + label='associated', + data=dict( + assoc_type=penicillins_to_gas_gangrene_treatment_edge['assoc_type'], + description=penicillins_to_gas_gangrene_treatment_edge['description'], + ), + to=penicillins_to_gas_gangrene_treatment_edge['_to'], + _from=penicillins_to_gas_gangrene_treatment_edge['_from'], + to_label=gas_gangrene['labels'][0], + from_label=penicillins['labels'][0], + ) + + return EdgeConnectionData( + label=edge_as_graph_relationship.data['description'], + to=edge_as_graph_relationship.to, + from_=edge_as_graph_relationship._from, + to_label='Disease', + from_label='Chemical', + ) + + +@pytest.fixture(scope='function') +def gas_gangrene_alleviates_edge_data( + penicillins, + gas_gangrene, + penicillins_to_gas_gangrene_alleviates_edge, +): + edge_as_graph_relationship = GraphRelationship( + id=penicillins_to_gas_gangrene_alleviates_edge['_id'], + label='associated', + data=dict( + assoc_type=penicillins_to_gas_gangrene_alleviates_edge['assoc_type'], + description=penicillins_to_gas_gangrene_alleviates_edge['description'], + ), + to=penicillins_to_gas_gangrene_alleviates_edge['_to'], + _from=penicillins_to_gas_gangrene_alleviates_edge['_from'], + to_label=gas_gangrene['labels'][0], + from_label=penicillins['labels'][0], + ) + + return EdgeConnectionData( + label=edge_as_graph_relationship.data['description'], + to=edge_as_graph_relationship.to, + from_=edge_as_graph_relationship._from, + to_label='Disease', + from_label='Chemical', + ) + + +@pytest.fixture(scope='function') +def gas_gangrene_treatement_duplicate_edge_data( + penicillins, + gas_gangrene, + penicillins_to_gas_gangrene_treatment_edge, +): + edge_as_graph_relationship = GraphRelationship( + id=penicillins_to_gas_gangrene_treatment_edge['_id'], + label='associated', + data=dict( + assoc_type=penicillins_to_gas_gangrene_treatment_edge['assoc_type'], + description=penicillins_to_gas_gangrene_treatment_edge['description'], + ), + to=penicillins_to_gas_gangrene_treatment_edge['_to'], + _from=penicillins_to_gas_gangrene_treatment_edge['_from'], + to_label=gas_gangrene['labels'][0], + from_label=penicillins['labels'][0], + ) + + return [ + DuplicateEdgeConnectionData( + label=edge_as_graph_relationship.data['description'], + to=f'duplicateNode:{edge_as_graph_relationship.to}', # type:ignore + from_=f'duplicateNode:{edge_as_graph_relationship._from}', # type:ignore + to_label='Disease', + from_label='Chemical', + original_from=edge_as_graph_relationship._from, + original_to=edge_as_graph_relationship.to, + ) + ] + + +@pytest.fixture(scope='function') +def gas_gangrene_alleviates_duplicate_edge_data( + penicillins, + gas_gangrene, + penicillins_to_gas_gangrene_alleviates_edge, +): + edge_as_graph_relationship = GraphRelationship( + id=penicillins_to_gas_gangrene_alleviates_edge['_id'], + label='associated', + data=dict( + assoc_type=penicillins_to_gas_gangrene_alleviates_edge['assoc_type'], + description=penicillins_to_gas_gangrene_alleviates_edge['description'], + ), + to=penicillins_to_gas_gangrene_alleviates_edge['_to'], + _from=penicillins_to_gas_gangrene_alleviates_edge['_from'], + to_label=gas_gangrene['labels'][0], + from_label=penicillins['labels'][0], + ) + + return [ + DuplicateEdgeConnectionData( + label=edge_as_graph_relationship.data['description'], + to=f'duplicateNode:{edge_as_graph_relationship.to}', # type:ignore + from_=f'duplicateNode:{edge_as_graph_relationship._from}', # type:ignore + to_label='Disease', + from_label='Chemical', + original_from=edge_as_graph_relationship._from, + original_to=edge_as_graph_relationship.to, + ) + ] diff --git a/appserver/tests/database/services/neo4j_test.py b/appserver/tests/database/services/visualizer/visualizer.py similarity index 81% rename from appserver/tests/database/services/neo4j_test.py rename to appserver/tests/database/services/visualizer/visualizer.py index ef9a5a94f5..7614bc2e1e 100644 --- a/appserver/tests/database/services/neo4j_test.py +++ b/appserver/tests/database/services/visualizer/visualizer.py @@ -1,31 +1,25 @@ -import pytest - - -@pytest.mark.skip( - reason='Does not work unless we upgrade the Neo4j docker image to 4.0+ because of apoc function' +from neo4japp.data_transfer_objects.visualization import Direction +from neo4japp.services.visualizer import ( + get_reference_table_data, + get_snippets_for_cluster, + get_snippets_for_edge, ) -def test_expand_node_gets_no_results_for_node_with_no_relationships( - visualizer_service, gas_gangrene -): - expand_query_result = visualizer_service.expand_graph( - node_id=gas_gangrene.identity, - filter_labels=['Chemical', 'Disease', 'Gene'], - ) - - assert expand_query_result.get('nodes', None) is not None - assert expand_query_result.get('nodes', None) is not None - - assert expand_query_result['nodes'] == [] - assert expand_query_result['edges'] == [] +from neo4japp.utils.string import camel_to_snake_dict def test_get_reference_table_data( - visualizer_service, + arango_client, gas_gangrene_treatment_cluster_node_edge_pairs, gas_gangrene_with_associations_and_references, ): - get_reference_table_data_result = visualizer_service.get_reference_table_data( - gas_gangrene_treatment_cluster_node_edge_pairs, + get_reference_table_data_result = get_reference_table_data( + arango_client=arango_client, + node_edge_pairs=[ + camel_to_snake_dict(pair.to_dict()) + for pair in gas_gangrene_treatment_cluster_node_edge_pairs + ], + description='treatment/therapy (including investigatory)', + direction=Direction.TO.value, ) assert get_reference_table_data_result.reference_table_rows is not None @@ -40,11 +34,12 @@ def test_get_reference_table_data( def test_get_snippets_for_edge( - visualizer_service, + arango_client, gas_gangrene_treatement_edge_data, gas_gangrene_with_associations_and_references, ): - get_edge_data_result = visualizer_service.get_snippets_for_edge( + get_edge_data_result = get_snippets_for_edge( + arango_client=arango_client, edge=gas_gangrene_treatement_edge_data, page=1, limit=25, @@ -80,11 +75,12 @@ def test_get_snippets_for_edge( def test_get_snippets_for_edge_low_limit( - visualizer_service, + arango_client, gas_gangrene_treatement_edge_data, gas_gangrene_with_associations_and_references, ): - get_edge_data_result = visualizer_service.get_snippets_for_edge( + get_edge_data_result = get_snippets_for_edge( + arango_client=arango_client, edge=gas_gangrene_treatement_edge_data, page=1, limit=1, @@ -105,11 +101,12 @@ def test_get_snippets_for_edge_low_limit( def test_get_snippets_for_edge_orders_by_pub_year( - visualizer_service, + arango_client, gas_gangrene_alleviates_edge_data, gas_gangrene_with_associations_and_references, ): - get_edge_data_result = visualizer_service.get_snippets_for_edge( + get_edge_data_result = get_snippets_for_edge( + arango_client=arango_client, edge=gas_gangrene_alleviates_edge_data, page=1, limit=25, @@ -129,11 +126,12 @@ def test_get_snippets_for_edge_orders_by_pub_year( def test_get_snippets_for_cluster( - visualizer_service, + arango_client, gas_gangrene_treatement_duplicate_edge_data, gas_gangrene_with_associations_and_references, ): - get_cluster_data_result = visualizer_service.get_snippets_for_cluster( + get_cluster_data_result = get_snippets_for_cluster( + arango_client=arango_client, edges=gas_gangrene_treatement_duplicate_edge_data, page=1, limit=25, @@ -173,11 +171,12 @@ def test_get_snippets_for_cluster( def test_get_snippets_for_cluster_low_limit( - visualizer_service, + arango_client, gas_gangrene_treatement_duplicate_edge_data, gas_gangrene_with_associations_and_references, ): - get_cluster_data_result = visualizer_service.get_snippets_for_cluster( + get_cluster_data_result = get_snippets_for_cluster( + arango_client=arango_client, edges=gas_gangrene_treatement_duplicate_edge_data, page=1, limit=1, @@ -202,11 +201,12 @@ def test_get_snippets_for_cluster_low_limit( def test_get_snippets_for_cluster_orders_by_pub_year( - visualizer_service, + arango_client, gas_gangrene_alleviates_duplicate_edge_data, gas_gangrene_with_associations_and_references, ): - get_cluster_data_result = visualizer_service.get_snippets_for_cluster( + get_cluster_data_result = get_snippets_for_cluster( + arango_client=arango_client, edges=gas_gangrene_alleviates_duplicate_edge_data, page=1, limit=25, diff --git a/appserver/tests/unit/util_test.py b/appserver/tests/unit/util_test.py index 8bda83adf8..7b4f063de6 100644 --- a/appserver/tests/unit/util_test.py +++ b/appserver/tests/unit/util_test.py @@ -3,7 +3,7 @@ from decimal import Decimal from enum import Enum -from neo4japp.utils import ( +from neo4japp.utils.string import ( camel_to_snake, camel_to_snake_dict, encode_to_str, diff --git a/cache-invalidator/Dockerfile b/cache-invalidator/Dockerfile index b94d985e1b..7a94eac270 100644 --- a/cache-invalidator/Dockerfile +++ b/cache-invalidator/Dockerfile @@ -1,23 +1,27 @@ FROM python:3.10-slim as base LABEL app=kg-prototypes +# Install dependencies +RUN apt-get update && apt-get install -y curl && apt-get clean +RUN pip install pipenv + ENV APP_USER lifelike ENV APP_HOME /home/$APP_USER ENV UID 1000 ENV GID 1000 +# User and group creation RUN groupadd -g $GID $APP_USER && \ useradd -u $UID -g $GID -G sudo --create-home --home-dir $APP_HOME --shell /bin/bash $APP_USER WORKDIR $APP_HOME -RUN pip install pipenv - +# Copy Pipfiles and install dependencies FIRST to better apply Docker layer cache COPY --chown=1000:1000 Pipfile . COPY --chown=1000:1000 Pipfile.lock . - RUN pipenv install --deploy --dev --system +# ...then copy everything else COPY --chown=1000:1000 . . # Don't lose stdin, stdout and stderr output due to buffering @@ -26,4 +30,4 @@ ENV PYTHONPATH $APP_HOME USER $APP_USER -CMD ["python", "main.py"] +CMD [ "bin/startup.sh" ] diff --git a/cache-invalidator/Pipfile b/cache-invalidator/Pipfile index ce2e9ae240..36401abcda 100644 --- a/cache-invalidator/Pipfile +++ b/cache-invalidator/Pipfile @@ -9,7 +9,7 @@ pycodestyle = "==2.7.0" [packages] redis = "==3.5.2" -neo4j = "==4.2.1" +python-arango = "==7.5.2" [requires] python_version = "3.11" diff --git a/cache-invalidator/Pipfile.lock b/cache-invalidator/Pipfile.lock index 195581e77b..e95b37a95e 100644 --- a/cache-invalidator/Pipfile.lock +++ b/cache-invalidator/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "a4531eea4788fac2ba636e22b252325438d5839787c999c478f13574694e6d09" + "sha256": "994e50c08cfebfc1cb190a9e6a6cc425ee8f061add7ca2e837f54c6e0e47dd9d" }, "pipfile-spec": 6, "requires": { @@ -16,6 +16,30 @@ ] }, "default": { + "certifi": { + "hashes": [ + "sha256:35824b4c3a97115964b408844d64aa14db1cc518f6562e8d7261699d1350a9e3", + "sha256:4ad3232f5e926d6718ec31cfc1fcadfde020920e278684144551c91769c7bc18" + ], + "markers": "python_version >= '3.6'", + "version": "==2022.12.7" + }, + "charset-normalizer": { + "hashes": [ + "sha256:5a3d016c7c547f69d6f81fb0db9449ce888b418b5b9952cc5e6e66843e9dd845", + "sha256:83e9a75d1911279afd89352c68b45348559d1fc0506b054b346651b5e7fee29f" + ], + "markers": "python_version >= '3.6'", + "version": "==2.1.1" + }, + "idna": { + "hashes": [ + "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4", + "sha256:90b77e79eaa3eba6de819a0c442c0b4ceefc341a7a2ab77d7562bf49f425c5c2" + ], + "markers": "python_version >= '3.5'", + "version": "==3.4" + }, "neo4j": { "hashes": [ "sha256:b6c49fbd60426e268ed4afbd414766444fe70aee1ac0376a0c871d75526b8251" @@ -23,6 +47,22 @@ "index": "pypi", "version": "==4.2.1" }, + "pyjwt": { + "hashes": [ + "sha256:69285c7e31fc44f68a1feb309e948e0df53259d579295e6cfe2b1792329f05fd", + "sha256:d83c3d892a77bbb74d3e1a2cfa90afaadb60945205d1095d9221f04466f64c14" + ], + "markers": "python_version >= '3.7'", + "version": "==2.6.0" + }, + "python-arango": { + "hashes": [ + "sha256:4554b7349348a05000128e42c77c4fe6a11461669463f3cd4fbf7a0ec0bc36d9", + "sha256:bb7cdd55776f5cf613e4bb9f0f0aba70b60408b964ec7c13b37f69b215acbbe8" + ], + "index": "pypi", + "version": "==7.5.2" + }, "pytz": { "hashes": [ "sha256:1e760e2fe6a8163bc0b3d9a19c4f84342afa0a2affebfaa84b01b978a02ecaa7", @@ -37,6 +77,38 @@ ], "index": "pypi", "version": "==3.5.2" + }, + "requests": { + "hashes": [ + "sha256:7c5599b102feddaa661c826c56ab4fee28bfd17f5abca1ebbe3e7f19d7c97983", + "sha256:8fefa2a1a1365bf5520aac41836fbee479da67864514bdb821f31ce07ce65349" + ], + "markers": "python_version >= '3.7' and python_version < '4'", + "version": "==2.28.1" + }, + "requests-toolbelt": { + "hashes": [ + "sha256:18565aa58116d9951ac39baa288d3adb5b3ff975c4f25eee78555d89e8f247f7", + "sha256:62e09f7ff5ccbda92772a29f394a49c3ad6cb181d568b1337626b2abb628a63d" + ], + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'", + "version": "==0.10.1" + }, + "setuptools": { + "hashes": [ + "sha256:57f6f22bde4e042978bcd50176fdb381d7c21a9efa4041202288d3737a0c6a54", + "sha256:a7620757bf984b58deaf32fc8a4577a9bbc0850cf92c20e1ce41c38c19e5fb75" + ], + "markers": "python_version >= '3.7'", + "version": "==65.6.3" + }, + "urllib3": { + "hashes": [ + "sha256:47cc05d99aaa09c9e72ed5809b60e7ba354e64b59c9c173ac3018642d8bb41fc", + "sha256:c083dd0dce68dbfbe1129d5271cb90f9447dea7d52097c6e0126120c521ddea8" + ], + "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'", + "version": "==1.26.13" } }, "develop": { diff --git a/cache-invalidator/bin/startup.sh b/cache-invalidator/bin/startup.sh new file mode 100755 index 0000000000..fdddf3f42c --- /dev/null +++ b/cache-invalidator/bin/startup.sh @@ -0,0 +1,13 @@ +#!/usr/bin/env bash + +set -o errexit # exit on command failure; use || true to allow for exception +set -o nounset # exit when script tries to use undeclared variables + +echo "### Starting up cache-invalidator ###" +__dir__="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" +# wait for arango +timeout 300 ${__dir__}/wait-for-arango.sh + +echo "### All DBs ready, starting statistics calculation ###" + +python ${__dir__}/../main.py diff --git a/cache-invalidator/bin/wait-for-arango.sh b/cache-invalidator/bin/wait-for-arango.sh new file mode 100755 index 0000000000..431c951cfe --- /dev/null +++ b/cache-invalidator/bin/wait-for-arango.sh @@ -0,0 +1,14 @@ +#!/bin/bash + +echo "Waiting for Arango" + +ARANGO_STATUS="000" + +until [ "$ARANGO_STATUS" = "200" ] +do + ARANGO_STATUS=`curl -s -o /dev/null -I -w "%{http_code}" --basic --user "${ARANGO_USERNAME}:${ARANGO_PASSWORD}" -X GET ${ARANGO_HOST}/_api/endpoint` + echo "Status of Arango: $ARANGO_STATUS" + sleep 2 +done + +echo "Arango started" diff --git a/cache-invalidator/main.py b/cache-invalidator/main.py index 5b9e17e911..f3f8c5a239 100644 --- a/cache-invalidator/main.py +++ b/cache-invalidator/main.py @@ -1,23 +1,14 @@ +from arango import ArangoClient +from arango.database import StandardDatabase +from arango.http import DefaultHTTPClient +from collections import defaultdict import json import logging import os import redis import time +from typing import Any, List, Optional -from collections import defaultdict -from neo4j import GraphDatabase, basic_auth - - -logger = logging.getLogger(__name__) -log_level = os.environ.get("LOG_LEVEL") -if log_level: - log_level = getattr(logging, log_level.upper()) -else: - log_level = logging.WARNING - -logger.setLevel(log_level) -print(f"Set log level to {log_level}") -logging.debug("Debug Logs") SUCCESSFUL_SLEEP_TIME = 3600 * 24 # refresh cached data this often ERROR_INITIAL_SLEEP_TIME = 60 # if error occurs, try again sooner @@ -25,133 +16,334 @@ ERROR_MAX_SLEEP_TIME = 3600 * 6 # but not longer than this CACHE_EXPIRATION_TIME = 3600 * 24 * 14 # expire cached data -REDIS_HOST = os.environ.get("REDIS_HOST") -REDIS_PORT = os.environ.get("REDIS_PORT") -REDIS_PASSWORD = os.environ.get("REDIS_PASSWORD") -REDIS_SSL = os.environ.get("REDIS_SSL", "false").lower() -connection_prefix = "rediss" if REDIS_SSL == "true" else "redis" -connection_url = f"{connection_prefix}://:{REDIS_PASSWORD}@{REDIS_HOST}:{REDIS_PORT}/0" +DEFAULT_LOG_LEVEL = logging.DEBUG + +logging.basicConfig() +logger = logging.getLogger('KG-Statistics') +try: + log_level = getattr(logging, os.environ.get('LOG_LEVEL').upper()) +except: + log_level = DEFAULT_LOG_LEVEL +logger.setLevel(log_level) +logger.info(f'Set log level to {log_level}') + + +def _get_redis_connection_url(): + host = os.environ.get('REDIS_HOST') + port = os.environ.get('REDIS_PORT') + password = os.environ.get('REDIS_PASSWORD') + ssl = os.environ.get('REDIS_SSL', 'false').lower() + connection_prefix = 'rediss' if ssl == 'true' else 'redis' + return f'{connection_prefix}://:{password}@{host}:{port}/0' + + +def _cache_data(key, value): + # Establish Redis Connection + redis_server = redis.Redis( + connection_pool=redis.BlockingConnectionPool.from_url( + _get_redis_connection_url() + ) + ) + try: + redis_server.set(key, json.dumps(value)) + redis_server.expire(key, CACHE_EXPIRATION_TIME) + except: + redis_server.connection_pool.disconnect() + raise + else: + redis_server.connection_pool.disconnect() + + +def _create_arango_client(hosts=None) -> ArangoClient: + # Need a custom HTTP client for Arango because the default timeout is only 60s + class CustomHTTPClient(DefaultHTTPClient): + REQUEST_TIMEOUT = 1000 + + hosts = hosts or os.getenv('ARANGO_HOST') + return ArangoClient( + hosts=hosts, + # Without this setting any requests to Arango will fail because we don't have a valid cert + verify_override=False, + http_client=CustomHTTPClient(), + ) + + +def _get_db( + arango_client: ArangoClient, + name: Optional[str] = None, + username: Optional[str] = None, + password: Optional[str] = None, +): + return arango_client.db( + name=name or os.getenv('ARANGO_DB_NAME'), + username=username or os.getenv('ARANGO_USERNAME'), + password=password or os.getenv('ARANGO_PASSWORD'), + ) + + +def _execute_arango_query( + db: StandardDatabase, query: str, batch_size=None, **bind_vars +) -> List[Any]: + cursor = db.aql.execute( + query, ttl=600, max_runtime=600, batch_size=batch_size, bind_vars=bind_vars + ) + return cursor -# Establish Redis Connection -redis_server = redis.Redis( - connection_pool=redis.BlockingConnectionPool.from_url(connection_url) -) -# Establish Neo4j Connection -host = os.getenv("NEO4J_HOST", "0.0.0.0") -scheme = os.getenv("NEO4J_SCHEME", "bolt") -port = os.getenv("NEO4J_PORT", "7687") -url = f"{scheme}://{host}:{port}" -username, password = os.getenv("NEO4J_AUTH", "neo4j/password").split("/") -neo4j_driver = GraphDatabase.driver(url, auth=basic_auth(username, password)) +def _entity_count_in_domain_query(domain: str) -> str: + return f''' + FOR doc IN {domain} + FOR label IN doc.labels + COLLECT entity = label WITH COUNT INTO length + RETURN {{ + 'entity' : entity, + 'count' : length + }} + ''' + + +def _entity_count_in_ncbi_query() -> str: + return ''' + FOR doc IN ncbi + FOR label IN doc.labels + COLLECT entity = label WITH COUNT INTO length + RETURN { + 'entity' : entity, + 'count' : length + } + ''' + + +def _taxonomy_count_query() -> str: + return ''' + RETURN LENGTH( + FOR doc IN taxonomy + FILTER doc.data_source == 'NCBI Taxonomy' + RETURN doc + ) + ''' + + +def _entity_count_in_biocyc_query() -> str: + return ''' + FOR doc IN biocyc + LET filtered_labels = REMOVE_VALUES(doc.labels, @biocyc_sub_domains) + FOR label IN filtered_labels + COLLECT entity = label WITH COUNT INTO length + RETURN { + 'entity' : entity, + 'count' : length + } + ''' + + +def _entity_count_in_biocyc_subdomain_query() -> str: + return ''' + FOR domain IN @biocyc_sub_domains + LET entity_counts_for_domain = ( + FOR doc IN biocyc + FILTER domain IN doc.labels + LET filtered_labels = REMOVE_VALUES(doc.labels, @biocyc_sub_domains) + FOR label IN filtered_labels + COLLECT entity = label WITH COUNT INTO length + RETURN { + 'entity' : entity, + 'count' : length + } + ) + RETURN { + 'domain': domain, + 'entities': entity_counts_for_domain + } + ''' + + +def _cache_kg_statistics(): + logger.info('Getting Kg Statistics') + arango_client = _create_arango_client() + statistics = defaultdict(lambda: defaultdict()) + try: + arango_db = _get_db(arango_client) + logger.info('Kg Statistics Query start...') + other_domains = { + 'literature': 'Literature', + 'go': 'GO', + 'pubmed': 'PubMed', + 'mesh': 'MESH', + 'uniprot': 'UniProt', + 'chebi': 'CHEBI', + 'enzyme': 'Enzyme', + 'regulondb': 'RegulonDB', + 'string': 'String', + 'kegg': 'KEGG', + 'lifelike': 'Lifelike', + } + + biocyc_sub_domains = [ + 'db_HumanCyc', + 'db_PseudomonasCyc', + 'db_YeastCyc', + 'db_BsubCyc', + 'db_EcoCyc', + ] + + logger.info('Getting stats for all domains aside from BioCyc and NCBI...') + for collection_name, display_name in other_domains.items(): + stats = _execute_arango_query( + arango_db, _entity_count_in_domain_query(collection_name) + ) + statistics[display_name] = defaultdict(lambda: defaultdict()) + for result in stats: + statistics[display_name][result.get('entity')] = result.get('count') + + logger.info('Getting stats for NCBI...') + statistics['NCBI'] = defaultdict(lambda: defaultdict()) + ncbi_stats = _execute_arango_query(arango_db, _entity_count_in_ncbi_query()) + for row in ncbi_stats: + statistics['NCBI'][row.get('entity')] = row.get('count') + + taxonomy_count = _execute_arango_query(arango_db, _taxonomy_count_query()) + for count in taxonomy_count: + # This should loop only once, the _execute_arango_query always returns a generator, + # but in this case it returns only one value + statistics['NCBI']['Taxonomy'] = count + + logger.info('Getting stats for all of BioCyc...') + statistics['BioCyc'] = defaultdict(lambda: defaultdict()) + biocyc_stats = _execute_arango_query( + arango_db, + _entity_count_in_biocyc_query(), + biocyc_sub_domains=biocyc_sub_domains, + ) + for entity_row in biocyc_stats: + statistics['BioCyc'][entity_row.get('entity')] = entity_row.get('count') + + logger.info('Getting stats for all BioCyc subdomains...') + entities_count_in_biocyc_subdomains = _execute_arango_query( + arango_db, + _entity_count_in_biocyc_subdomain_query(), + biocyc_sub_domains=biocyc_sub_domains, + ) + for domain_row in entities_count_in_biocyc_subdomains: + domain = domain_row.get('domain').split('_')[1] + statistics[domain] = defaultdict(lambda: defaultdict()) + for entity_row in domain_row.get('entities'): + statistics[domain][entity_row.get('entity')] = entity_row.get('count') + except: + arango_client.close() + raise + else: + arango_client.close() + logger.info('Kg Statistics Query finished with data:') + logger.info(json.dumps(statistics, indent=4)) + _cache_data('kg_statistics', statistics) + + +def _get_organism_genes_go_terms_query() -> str: + return ''' + LET go_links_grouped_by_organism = ( + FOR link IN go_link + FILTER link.tax_id != null + COLLECT organism = link.tax_id INTO links + RETURN { + 'organism': organism, + 'links': links + } + ) + FOR row IN go_links_grouped_by_organism + LET organism_name = FIRST( + FOR doc IN taxonomy + FILTER doc.eid == row.organism + RETURN doc.name + ) + LET gene_names_grouped_by_go_term = ( + FOR go_link IN row.links + COLLECT go = go_link.link._to INTO groups + LET go_doc = DOCUMENT(go) + RETURN { + 'goId': go_doc.eid, + 'goTerm': go_doc.name, + 'goLabel': go_doc.labels, + 'geneNames': DOCUMENT(groups[*].go_link.link._from)[*].name + } + ) + RETURN { + 'organism': { + 'id': row.organism, + 'name': organism_name + }, + 'go_terms': gene_names_grouped_by_go_term + } + ''' + + +def _precalculate_go(): + logger.info('Precalculating GO...') + arango_client = _create_arango_client() + + try: + arango_db = _get_db(arango_client) + results = _execute_arango_query( + arango_db, + query=_get_organism_genes_go_terms_query(), + # Normally would make a global for this but it's very unlikely we'll ever re-use this + # value. + batch_size=5, + ) + + for row in results: + organism = row['organism'] + go_terms = row['go_terms'] + logger.info(f'Caching GO for {organism["name"]} ({organism["id"]})') + _cache_data(f'GO_for_{organism["id"]}', go_terms) + except: + arango_client.close() + raise + arango_client.close() def main(): next_error_sleep_time = ERROR_INITIAL_SLEEP_TIME + kg_statistics_successful = False + precalculate_go_successful = False + time_slept_since_reset = 0 while True: + if time_slept_since_reset >= SUCCESSFUL_SLEEP_TIME: + kg_statistics_successful = False + precalculate_go_successful = False try: - statistics = get_kg_statistics() - cache_data("kg_statistics", statistics) - next_error_sleep_time = ERROR_INITIAL_SLEEP_TIME - logger.debug(f"Going to sleep for {SUCCESSFUL_SLEEP_TIME} seconds...") + if not kg_statistics_successful: + _cache_kg_statistics() + kg_statistics_successful = True except Exception as err: - logger.debug( - f"Error occured, will try again in {next_error_sleep_time} seconds: {err}" - ) - time.sleep(next_error_sleep_time) - next_error_sleep_time = min( - ERROR_MAX_SLEEP_TIME, - next_error_sleep_time * ERROR_SLEEP_TIME_MULTIPLIER, - ) + logger.error(err) + kg_statistics_successful = False finally: try: - precalculateGO() - next_error_sleep_time = ERROR_INITIAL_SLEEP_TIME - logger.debug(f"Going to sleep for {SUCCESSFUL_SLEEP_TIME} seconds...") + if not precalculate_go_successful: + _precalculate_go() + precalculate_go_successful = True except Exception as err: - logger.debug( - f"Error occured, will try again in {next_error_sleep_time} seconds: {err}" - ) - time.sleep(next_error_sleep_time) - next_error_sleep_time = min( - ERROR_MAX_SLEEP_TIME, - next_error_sleep_time * ERROR_SLEEP_TIME_MULTIPLIER, - ) + logger.error(err) + precalculate_go_successful = False else: - time.sleep(SUCCESSFUL_SLEEP_TIME) - - -def get_kg_statistics(): - logger.debug("Getting Kg Statistics") - graph = neo4j_driver.session() - logger.debug("Kg Statistics Query start...") - results = graph.read_transaction(lambda tx: tx.run("call db.labels()").data()) - logger.debug("Kg Statistics Query finished") - domain_labels = [] - entity_labels = [] - for row in results: - label = row["label"] - if label.startswith("db_"): - domain_labels.append(label) - elif label != "Synonym": - entity_labels.append(label) - statistics = defaultdict(lambda: defaultdict()) - for domain in domain_labels: - for entity in entity_labels: - query = f"MATCH (:`{domain}`:`{entity}`) RETURN count(*) as count" - logger.debug(f"NEO4J QUERY: {query}") - result = graph.read_transaction(lambda tx: tx.run(query).data()) - count = result[0]["count"] - if count != 0: - statistics[domain.replace("db_", "", 1)][entity] = count - graph.close() - return statistics - - -def precalculateGO(): - logger.debug("Precalculating GO...") - graph = neo4j_driver.session() - - def fetch_organism_go_query(tx, organism): - logger.debug(f"Precomputing GO for {organism['name']} ({organism['id']})") - return tx.run( - """ - MATCH (g:Gene)-[:GO_LINK {tax_id:$id}]-(go:db_GO) - WITH go, collect(distinct g) as genes - RETURN go.eid as goId, - go.name as goTerm, - [lbl in labels(go) where lbl <> 'db_GO'] as goLabel, - [g in genes |g.name] as geneNames - """, - id=organism["id"], - ).data() - - organisms = graph.read_transaction( - lambda tx: tx.run( - """ - MATCH (t:Taxonomy)-[:HAS_TAXONOMY]-(:Gene)-[:GO_LINK]-(go:db_GO) - with t, count(go) as c - where c > 0 - RETURN t.eid as id, t.name as name - """ - ).data() - ) - - for organism in organisms: - logging.debug(f"Catching data for organism: {organism}") - cache_data( - f"GO_for_{organism['id']}", - graph.read_transaction(fetch_organism_go_query, organism), - ) - graph.close() - - -def cache_data(key, value): - try: - redis_server.set(key, json.dumps(value)) - redis_server.expire(key, CACHE_EXPIRATION_TIME) - finally: - redis_server.connection_pool.disconnect() + if kg_statistics_successful and precalculate_go_successful: + next_error_sleep_time = ERROR_INITIAL_SLEEP_TIME + logger.info( + f'Going to sleep for {SUCCESSFUL_SLEEP_TIME} seconds...' + ) + time.sleep(SUCCESSFUL_SLEEP_TIME) + time_slept_since_reset += SUCCESSFUL_SLEEP_TIME + else: + logger.info( + f'Error occured, will try again in {next_error_sleep_time} seconds' + ) + time.sleep(next_error_sleep_time) + time_slept_since_reset += next_error_sleep_time + next_error_sleep_time = min( + ERROR_MAX_SLEEP_TIME, + next_error_sleep_time * ERROR_SLEEP_TIME_MULTIPLIER, + ) if __name__ == "__main__": diff --git a/client/nginx.conf b/client/nginx.conf index c873e07084..1a9f6579db 100644 --- a/client/nginx.conf +++ b/client/nginx.conf @@ -66,7 +66,7 @@ server { add_header X-Cache-Status "Non-cachable"; } - location ~ ^/api/(visualizer|search/viz-search)(.*)$ { + location ~ ^/api/(visualizer|search/visualizer)(.*)$ { access_log /dev/stdout upstream_logging; proxy_pass ${APPSERVER_UPSTREAM}/$1$2$is_args$args; diff --git a/client/src/app/app-routing.module.ts b/client/src/app/app-routing.module.ts index 19d7c14876..3e43ffe2af 100644 --- a/client/src/app/app-routing.module.ts +++ b/client/src/app/app-routing.module.ts @@ -24,7 +24,6 @@ import { CommunityBrowserComponent } from 'app/file-browser/components/community import { BrowserComponent } from 'app/file-browser/components/browser/browser.component'; import { ContentSearchComponent } from 'app/search/components/content-search.component'; import { ObjectNavigatorComponent } from 'app/file-navigator/components/object-navigator.component'; -import { ShortestPathComponent } from 'app/shortest-path/containers/shortest-path.component'; import { EnrichmentTableViewerComponent } from 'app/enrichment/components/table/enrichment-table-viewer.component'; import { EnrichmentVisualisationViewerComponent } from 'app/enrichment/components/visualisation/enrichment-visualisation-viewer.component'; import { BiocViewComponent } from 'app/bioc-viewer/components/bioc-view.component'; @@ -112,11 +111,6 @@ const routes: Routes = [ fontAwesomeIcon: 'search', }, }, - { - path: 'pathway-browser-prototype', - canActivate: [LifelikeAuthGuard], - component: ShortestPathComponent, - }, { path: 'projects/:project_name/enrichment-table/:file_id', canActivate: [], diff --git a/client/src/app/app.module.ts b/client/src/app/app.module.ts index c4611be1ca..7c932c3527 100644 --- a/client/src/app/app.module.ts +++ b/client/src/app/app.module.ts @@ -22,7 +22,6 @@ import { UnloadConfirmationGuard } from 'app/shared/guards/UnloadConfirmation.gu import { DashboardComponent } from 'app/dashboard.component'; import { AppVersionDialogComponent } from 'app/app-version-dialog.component'; import { FileNavigatorModule } from 'app/file-navigator/file-navigator.module'; -import { ShortestPathModule } from 'app/shortest-path/shortest-path.module'; import { PdfViewerLibModule } from 'app/pdf-viewer/pdf-viewer-lib.module'; import { GlobalErrorHandler } from 'app/global-error-handler'; import { EnrichmentTablesModule } from 'app/enrichment/enrichment-tables.module'; @@ -65,7 +64,6 @@ import { SankeyViewerLibModule } from 'app/sankey/sankey.module'; FileNavigatorModule, BiocViewerLibModule, EnrichmentVisualisationsModule, - ShortestPathModule, EnrichmentTablesModule, PoliciesModule, ReportsModule, diff --git a/client/src/app/enrichment/components/visualisation/group/clustergram/clustergram.component.html b/client/src/app/enrichment/components/visualisation/group/clustergram/clustergram.component.html index 6ed183d1ea..29bb70aa20 100644 --- a/client/src/app/enrichment/components/visualisation/group/clustergram/clustergram.component.html +++ b/client/src/app/enrichment/components/visualisation/group/clustergram/clustergram.component.html @@ -33,7 +33,9 @@ [ngClass]="{ match: value }" [style.backgroundColor]="value && geneColor" > - {{ entry.value.others || '' }} + + {{ entry.value.others || '' }} + others diff --git a/client/src/app/enrichment/models/enrichment-document.ts b/client/src/app/enrichment/models/enrichment-document.ts index 83621050fe..1eb1ce2734 100644 --- a/client/src/app/enrichment/models/enrichment-document.ts +++ b/client/src/app/enrichment/models/enrichment-document.ts @@ -269,64 +269,68 @@ export class EnrichmentDocument extends BaseEnrichmentDocument { ): Observable { return this.worksheetViewerService.matchNCBINodes(importGenes, taxID).pipe( mergeMap((ncbiNodesData: NCBIWrapper[]) => { - const neo4jIds = ncbiNodesData.map((wrapper) => wrapper.geneNeo4jId); - return this.worksheetViewerService.getNCBIEnrichmentDomains(neo4jIds, taxID, domains).pipe( + const arangoIds = ncbiNodesData.map((wrapper) => wrapper.geneArangoId); + return this.worksheetViewerService.getNCBIEnrichmentDomains(arangoIds, taxID, domains).pipe( map((domainResults: EnrichmentWrapper): EnrichmentResult => { // a gene can point to 2 different synonyms // and a synonym can point to 2 different genes - const neo4jIdSynonymMap: Map> = new Map(); - const neo4jIdNodeMap: Map> = new Map(); - const neo4jIdLinkMap: Map> = new Map(); - const geneSynonymNeo4jIdMap: Map> = new Map(); + const arangoIdSynonymMap: Map> = new Map(); + const arangoIdNodeMap: Map> = new Map(); + const arangoIdLinkMap: Map> = new Map(); + const geneSynonymArangoIdMap: Map> = new Map(); const geneMap: Set = new Set(); const genesList: EnrichedGene[] = []; const synonymsSet: Set = new Set(); // list of tuples - const synonymNeo4jIds: [number, number][] = []; + const synonymArangoIds: [string, string][] = []; ncbiNodesData.forEach((wrapper) => { - geneSynonymNeo4jIdMap.has(wrapper.synonymNeo4jId) - ? geneSynonymNeo4jIdMap - .get(wrapper.synonymNeo4jId) - .set(wrapper.geneNeo4jId, wrapper.geneNeo4jId) - : geneSynonymNeo4jIdMap.set( - wrapper.synonymNeo4jId, - new Map().set(wrapper.geneNeo4jId, wrapper.geneNeo4jId) + geneSynonymArangoIdMap.has(wrapper.synonymArangoId) + ? geneSynonymArangoIdMap + .get(wrapper.synonymArangoId) + .set(wrapper.geneArangoId, wrapper.geneArangoId) + : geneSynonymArangoIdMap.set( + wrapper.synonymArangoId, + new Map().set(wrapper.geneArangoId, wrapper.geneArangoId) ); - neo4jIdSynonymMap.has(wrapper.synonymNeo4jId) - ? neo4jIdSynonymMap - .get(wrapper.synonymNeo4jId) - .set(wrapper.geneNeo4jId, wrapper.synonym) - : neo4jIdSynonymMap.set( - wrapper.synonymNeo4jId, - new Map().set(wrapper.geneNeo4jId, wrapper.synonym) + arangoIdSynonymMap.has(wrapper.synonymArangoId) + ? arangoIdSynonymMap + .get(wrapper.synonymArangoId) + .set(wrapper.geneArangoId, wrapper.synonym) + : arangoIdSynonymMap.set( + wrapper.synonymArangoId, + new Map().set(wrapper.geneArangoId, wrapper.synonym) ); - neo4jIdNodeMap.has(wrapper.synonymNeo4jId) - ? neo4jIdNodeMap.get(wrapper.synonymNeo4jId).set(wrapper.geneNeo4jId, wrapper.gene) - : neo4jIdNodeMap.set( - wrapper.synonymNeo4jId, - new Map().set(wrapper.geneNeo4jId, wrapper.gene) + arangoIdNodeMap.has(wrapper.synonymArangoId) + ? arangoIdNodeMap + .get(wrapper.synonymArangoId) + .set(wrapper.geneArangoId, wrapper.gene) + : arangoIdNodeMap.set( + wrapper.synonymArangoId, + new Map().set(wrapper.geneArangoId, wrapper.gene) ); - neo4jIdLinkMap.has(wrapper.synonymNeo4jId) - ? neo4jIdLinkMap.get(wrapper.synonymNeo4jId).set(wrapper.geneNeo4jId, wrapper.link) - : neo4jIdLinkMap.set( - wrapper.synonymNeo4jId, - new Map().set(wrapper.geneNeo4jId, wrapper.link) + arangoIdLinkMap.has(wrapper.synonymArangoId) + ? arangoIdLinkMap + .get(wrapper.synonymArangoId) + .set(wrapper.geneArangoId, wrapper.link) + : arangoIdLinkMap.set( + wrapper.synonymArangoId, + new Map().set(wrapper.geneArangoId, wrapper.link) ); synonymsSet.add(wrapper.synonym); - synonymNeo4jIds.push([wrapper.synonymNeo4jId, wrapper.geneNeo4jId]); + synonymArangoIds.push([wrapper.synonymArangoId, wrapper.geneArangoId]); }); - for (const [synId, geneId] of synonymNeo4jIds) { - const synonym = neo4jIdSynonymMap.get(synId).get(geneId); - const node = neo4jIdNodeMap.get(synId).get(geneId); - const link = neo4jIdLinkMap.get(synId).get(geneId); + for (const [synId, geneId] of synonymArangoIds) { + const synonym = arangoIdSynonymMap.get(synId).get(geneId); + const node = arangoIdNodeMap.get(synId).get(geneId); + const link = arangoIdLinkMap.get(synId).get(geneId); const domainWrapper = - domainResults[geneSynonymNeo4jIdMap.get(synId).get(geneId)] || null; + domainResults[geneSynonymArangoIdMap.get(synId).get(geneId)] || null; if (domainWrapper !== null) { geneMap.add(synonym); diff --git a/client/src/app/enrichment/services/enrichment-table.service.ts b/client/src/app/enrichment/services/enrichment-table.service.ts index aac55db1f1..d7f472ce38 100644 --- a/client/src/app/enrichment/services/enrichment-table.service.ts +++ b/client/src/app/enrichment/services/enrichment-table.service.ts @@ -32,18 +32,18 @@ export class EnrichmentTableService { /** * Match enrichment domains to given node ids. - * @param nodeIds list of node ids to match to enrichment domains + * @param docIds list of document ids to match to enrichment domains * @param taxID tax id of organism */ getNCBIEnrichmentDomains( - nodeIds, + docIds: string[], taxID: string, domains: string[] ): Observable { return this.http .post<{ result: EnrichmentWrapper }>( - `/api/knowledge-graph/get-ncbi-nodes/enrichment-domains`, - { nodeIds, taxID, domains } + `/api/enrichment-table/get-ncbi-nodes/enrichment-domains`, + { docIds, taxID, domains } ) .pipe(map((resp) => resp.result)); } @@ -89,8 +89,8 @@ export interface NCBINode { } export interface NCBIWrapper { - geneNeo4jId: number; - synonymNeo4jId: number; + geneArangoId: string; + synonymArangoId: string; gene: NCBINode; link: string; synonym: string; @@ -154,7 +154,7 @@ export interface DomainWrapper { string: StringWrapper | null; uniprot: UniprotWrapper | null; kegg: KeggWrapper | null; - node_id: number; + doc_id: number; } export interface EnrichmentWrapper { diff --git a/client/src/app/interfaces/neo4j.interface.ts b/client/src/app/interfaces/neo4j.interface.ts index a1e74a742e..ef6c0e5085 100644 --- a/client/src/app/interfaces/neo4j.interface.ts +++ b/client/src/app/interfaces/neo4j.interface.ts @@ -1,3 +1,4 @@ +import { IdType } from 'vis-network'; import { ColorObject } from 'vis-network/dist/types/network/gephiParser'; export interface NodeLegend { @@ -10,7 +11,7 @@ export interface NodeLegend { export type DefaultNodeData = Record & { eid: any }; /** Node representation from the backend */ export interface GraphNode { - id: number; + id: IdType; label: string; data: Data; subLabels: Array; @@ -21,11 +22,11 @@ export interface GraphNode { /** Edge represenattion from the backend */ export interface GraphRelationship> { - id: number; + id: IdType; label: string; data: Data; - to: number; - from: number; + to: IdType; + from: IdType; toLabel: string; fromLabel: string; } @@ -39,8 +40,8 @@ export interface VisNode extends GraphNode { } export interface DuplicateVisNode extends VisNode { - id: any; - duplicateOf: number; + id: IdType; + duplicateOf: IdType; } /** VisJS Edge Representations for Client */ @@ -52,10 +53,10 @@ export interface VisEdge> extends GraphRelationship> extends VisEdge { - id: any; - duplicateOf: number | null; - originalFrom: number | null; - originalTo: number | null; + id: IdType; + duplicateOf: IdType | null; + originalFrom: IdType | null; + originalTo: IdType | null; } export interface Neo4jResults> { @@ -101,7 +102,7 @@ export interface FTSResult> { } export interface SearchRecord { - nodeId: number; + nodeId: IdType; label: string; subLabels: Array; data: string; diff --git a/client/src/app/interfaces/visualization.interface.ts b/client/src/app/interfaces/visualization.interface.ts index ea4ca20961..0acec7ceba 100644 --- a/client/src/app/interfaces/visualization.interface.ts +++ b/client/src/app/interfaces/visualization.interface.ts @@ -22,7 +22,7 @@ export enum AssociatedType { } export interface AssociatedTypeEntry { - id: number; + id: IdType; name: string; count: number; percentage: number; @@ -30,13 +30,13 @@ export interface AssociatedTypeEntry { export interface NodeAssociatedType { name: string; - nodeId: number; + nodeId: IdType; snippetCount: number; } export interface ClusterData { referenceTableRows: ReferenceTableRow[]; - relationship: string; + relationship: IdType; direction: Direction; } @@ -46,29 +46,29 @@ export enum Direction { } export interface DuplicateEdgeConnectionData { - from: number; - to: number; - originalFrom: number; - originalTo: number; + from: IdType; + to: IdType; + originalFrom: IdType; + originalTo: IdType; fromLabel: string; toLabel: string; label: string; } export interface NodePair { - // Note that it's inaccurate to use "from" and "to" terminology here, since the nodes *may* have bidirectional relationships. - node1Id: number; - node2Id: number; + // Note that it's inaccurate to use 'from' and 'to' terminology here, since the nodes *may* have bidirectional relationships. + node1Id: IdType; + node2Id: IdType; } -export interface DuplicateNodeEdgePair { - node: DuplicateVisNode; - edge: DuplicateVisEdge; +export interface DuplicateNodeEdgePair { + node: DuplicateVisNode; + edge: DuplicateVisEdge; } export interface EdgeConnectionData { - from: number; - to: number; + from: IdType; + to: IdType; fromLabel: string; toLabel: string; label: string; @@ -89,25 +89,25 @@ export interface Reference entry2Text: string; entry1Type: string; entry2Type: string; - id: string; + id: IdType; sentence: string; }> {} export interface ReferenceTablePair { node: { - id: string; + id: IdType; displayName: string; label: string; }; edge: { - originalFrom: number; - originalTo: number; + originalFrom: IdType; + originalTo: IdType; label: string; }; } export interface ReferenceTableRow { - nodeId: string; + nodeId: IdType; nodeDisplayName: string; nodeLabel: string; snippetCount: number; @@ -173,7 +173,7 @@ export interface SidenavSnippetData { // Begin Request Interfaces export interface ExpandNodeRequest { - nodeId: number; + nodeId: IdType; filterLabels: string[]; } @@ -203,23 +203,23 @@ export interface NewNodePairSnippetsPageRequest { export interface ReferenceTableDataRequest { nodeEdgePairs: ReferenceTablePair[]; + direction?: Direction; + description?: string; +} + +export interface BulkReferenceTableDataRequest { + associations: ReferenceTableDataRequest[]; } export interface AssociatedTypeSnippetCountRequest { - source_node: number; - associated_nodes: number[]; + source_node: IdType; + associated_nodes: IdType[]; } // End Request Interfaces // Begin Response Interfaces -export interface ExpandNodeResult { - expandedNode: number; - nodes: VisNode[]; - edges: VisEdge[]; -} - export interface GetEdgeSnippetsResult { queryData: EdgeConnectionData; snippetData: GetSnippetsResult; @@ -240,13 +240,19 @@ export interface GetNodePairSnippetsResult { export interface GetReferenceTableDataResult { referenceTableRows: ReferenceTableRow[]; + duplicateNodeEdgePairs: DuplicateNodeEdgePair[]; direction: Direction; + description: string; +} + +export interface GetBulkReferenceTableDataResult { + referenceTables: GetReferenceTableDataResult[]; } export interface GetSnippetsResult { snippets: AssociationSnippet[]; - fromNodeId: number; - toNodeId: number; + fromNodeId: IdType; + toNodeId: IdType; association: string; } diff --git a/client/src/app/search/components/search-record-node.component.html b/client/src/app/search/components/search-record-node.component.html index f33c2bfea4..330a837bcc 100644 --- a/client/src/app/search/components/search-record-node.component.html +++ b/client/src/app/search/components/search-record-node.component.html @@ -4,7 +4,7 @@
{{ node.node.displayName }} @@ -34,7 +34,7 @@
{{ domain }} - {{ domain.split('_')[1] }} + {{ domain }}
diff --git a/client/src/app/search/components/search-record-node.component.ts b/client/src/app/search/components/search-record-node.component.ts index caa57ce1ab..9681c30f28 100644 --- a/client/src/app/search/components/search-record-node.component.ts +++ b/client/src/app/search/components/search-record-node.component.ts @@ -1,5 +1,7 @@ import { Component, Input } from '@angular/core'; +import { isEmpty } from 'lodash-es'; + import { UniversalGraphNode } from 'app/drawing-tool/services/interfaces'; import { FTSQueryRecord } from 'app/interfaces'; import { DBHostname } from 'app/shared/constants'; @@ -28,8 +30,10 @@ export class SearchRecordNodeComponent { @Input() set node(value: FTSQueryRecord) { this.currentNode = value; - this.normalizedNodeLabel = value.node.label.toLowerCase(); - this.nodeURL = stringToHex(value.node.id.toString()); + if (!isEmpty(value.node)) { + this.normalizedNodeLabel = value.node.label.toLowerCase(); + this.nodeURL = stringToHex(value.node.id.toString()); + } } get node(): FTSQueryRecord { diff --git a/client/src/app/search/components/search-record-relationships.component.html b/client/src/app/search/components/search-record-relationships.component.html index 68c6171007..b5bb971af6 100644 --- a/client/src/app/search/components/search-record-relationships.component.html +++ b/client/src/app/search/components/search-record-relationships.component.html @@ -4,7 +4,7 @@
Snippet: {{ node.node.displayName }} diff --git a/client/src/app/search/services/graph-search.service.ts b/client/src/app/search/services/graph-search.service.ts index c10fc6bc7c..e9164d42e3 100644 --- a/client/src/app/search/services/graph-search.service.ts +++ b/client/src/app/search/services/graph-search.service.ts @@ -20,7 +20,7 @@ export class GraphSearchService { entities: string[] ) { return this.http - .post<{ result: FTSResult }>(`${this.searchApi}/viz-search`, { + .post<{ result: FTSResult }>(`${this.searchApi}/visualizer`, { query, organism, page, diff --git a/client/src/app/search/utils/records.ts b/client/src/app/search/utils/records.ts index 28bfd9846e..de69b35d28 100644 --- a/client/src/app/search/utils/records.ts +++ b/client/src/app/search/utils/records.ts @@ -10,7 +10,7 @@ const DOMAINS_URL = { }; export function getLink(data: FTSQueryRecord) { - const domain = data.node.domainLabels[0].split('_')[1]; + const domain = data.node.domainLabels[0]; const type = data.node.label; if (domain === 'NCBI' && type === 'Gene') { return DOMAINS_URL[domain + '_' + type] + data.node.data.eid; diff --git a/client/src/app/shortest-path/components/route-builder.component.html b/client/src/app/shortest-path/components/route-builder.component.html deleted file mode 100644 index 468542279e..0000000000 --- a/client/src/app/shortest-path/components/route-builder.component.html +++ /dev/null @@ -1,56 +0,0 @@ -
- -
-
-
- -
-
- -
-
-
-
-
- - -
-

- Could not load pre-defined shortest path queries! -

-
-
- - -
-
-
-
diff --git a/client/src/app/shortest-path/components/route-builder.component.scss b/client/src/app/shortest-path/components/route-builder.component.scss deleted file mode 100644 index 37dbb3a837..0000000000 --- a/client/src/app/shortest-path/components/route-builder.component.scss +++ /dev/null @@ -1,27 +0,0 @@ -.graph-type-btn-container { - height: 40px; - width: 40px; -} - -.route-builder-container-open { - position: absolute; - width: 400px; - right: 0; - z-index: 2; - transition: right 0.25s; -} - -.route-builder-container-closed { - position: absolute; - width: 400px; - right: -400px; - z-index: 2; - transition: right 0.25s; -} - -.toggle-route-builder-button { - height: 60px; - top: 28px; - right: 100%; - position: absolute; -} diff --git a/client/src/app/shortest-path/components/route-builder.component.spec.ts b/client/src/app/shortest-path/components/route-builder.component.spec.ts deleted file mode 100644 index a4affa36a5..0000000000 --- a/client/src/app/shortest-path/components/route-builder.component.spec.ts +++ /dev/null @@ -1,30 +0,0 @@ -import { ComponentFixture, TestBed } from '@angular/core/testing'; - -import { configureTestSuite } from 'ng-bullet'; - -import { RootStoreModule } from 'app/root-store'; -import { SharedModule } from 'app/shared/shared.module'; - -import { RouteBuilderComponent } from './route-builder.component'; - -describe('RouteBuilderComponent', () => { - let component: RouteBuilderComponent; - let fixture: ComponentFixture; - - configureTestSuite(() => { - TestBed.configureTestingModule({ - imports: [RootStoreModule, SharedModule], - declarations: [RouteBuilderComponent], - }); - }); - - beforeEach(() => { - fixture = TestBed.createComponent(RouteBuilderComponent); - component = fixture.componentInstance; - fixture.detectChanges(); - }); - - it('should create', () => { - expect(component).toBeTruthy(); - }); -}); diff --git a/client/src/app/shortest-path/components/route-builder.component.ts b/client/src/app/shortest-path/components/route-builder.component.ts deleted file mode 100644 index 0d31990a1b..0000000000 --- a/client/src/app/shortest-path/components/route-builder.component.ts +++ /dev/null @@ -1,75 +0,0 @@ -import { Component, EventEmitter, OnDestroy, OnInit, Output } from '@angular/core'; - -import { combineLatest, Subscription } from 'rxjs'; - -import { BackgroundTask } from 'app/shared/rxjs/background-task'; -import { loadingText, mockArrayOf } from 'app/shared/mocks/loading/utils'; - -import { ShortestPathService } from '../services/shortest-path.service'; -import { DisplayType } from './route-display.component'; - -@Component({ - selector: 'app-route-builder', - templateUrl: './route-builder.component.html', - styleUrls: ['./route-builder.component.scss'], -}) -export class RouteBuilderComponent implements OnInit, OnDestroy { - @Output() loadNewQuery: EventEmitter; - @Output() changeDisplayType: EventEmitter; - - loadShortestPathQueries: BackgroundTask<[], any>; - queriesLoadedsub: Subscription; - - routeBuilderContainerClass: string; - - routeBuilderOpen: boolean; - - queries: string[][] = mockArrayOf(() => mockArrayOf(loadingText)); - - constructor(public shortestPathService: ShortestPathService) { - this.queries = []; - - this.routeBuilderContainerClass = 'route-builder-container-open'; - this.routeBuilderOpen = true; - - this.loadNewQuery = new EventEmitter(); - this.changeDisplayType = new EventEmitter(); - - this.loadShortestPathQueries = new BackgroundTask(() => { - return combineLatest(this.shortestPathService.getShortestPathQueryList()); - }); - this.queriesLoadedsub = this.loadShortestPathQueries.results$.subscribe( - ({ result: [shortestPathQueries], value: [] }) => { - this.queries = Object.keys(shortestPathQueries).map((key) => [ - key, - shortestPathQueries[key], - ]); - } - ); - } - - ngOnInit() { - this.loadNewQuery.emit(0); - this.changeDisplayType.emit('NETWORK'); - this.loadShortestPathQueries.update([]); - } - - ngOnDestroy() { - this.queriesLoadedsub.unsubscribe(); - } - - toggleRouteBuilderOpen() { - this.routeBuilderOpen = !this.routeBuilderOpen; - this.routeBuilderContainerClass = this.routeBuilderOpen - ? 'route-builder-container-open' - : 'route-builder-container-closed'; - } - - requestQueryLoadFromParent(event: any) { - this.loadNewQuery.emit(Number.parseInt(event.target.value, 10)); - } - - requestChangeDisplayTypeFromParent(type: string) { - this.changeDisplayType.emit(type); - } -} diff --git a/client/src/app/shortest-path/components/route-display.component.html b/client/src/app/shortest-path/components/route-display.component.html deleted file mode 100644 index f0ba2043ec..0000000000 --- a/client/src/app/shortest-path/components/route-display.component.html +++ /dev/null @@ -1,18 +0,0 @@ -
-
-
- -
-
- -
-
-
diff --git a/client/src/app/shortest-path/components/route-display.component.scss b/client/src/app/shortest-path/components/route-display.component.scss deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/client/src/app/shortest-path/components/route-display.component.spec.ts b/client/src/app/shortest-path/components/route-display.component.spec.ts deleted file mode 100644 index b0d5db5415..0000000000 --- a/client/src/app/shortest-path/components/route-display.component.spec.ts +++ /dev/null @@ -1,33 +0,0 @@ -import { ComponentFixture, TestBed } from '@angular/core/testing'; - -import { configureTestSuite } from 'ng-bullet'; -import { MockComponents } from 'ng-mocks'; - -import { PlotlySankeyDiagramComponent } from 'app/shared/components/plotly-sankey-diagram/plotly-sankey-diagram.component'; -import { VisJsNetworkComponent } from 'app/shared/components/vis-js-network/vis-js-network.component'; - -import { RouteDisplayComponent } from './route-display.component'; - -describe('RouteDisplayComponent', () => { - let component: RouteDisplayComponent; - let fixture: ComponentFixture; - - configureTestSuite(() => { - TestBed.configureTestingModule({ - declarations: [ - RouteDisplayComponent, - MockComponents(PlotlySankeyDiagramComponent, VisJsNetworkComponent), - ], - }); - }); - - beforeEach(() => { - fixture = TestBed.createComponent(RouteDisplayComponent); - component = fixture.componentInstance; - fixture.detectChanges(); - }); - - it('should create', () => { - expect(component).toBeTruthy(); - }); -}); diff --git a/client/src/app/shortest-path/components/route-display.component.ts b/client/src/app/shortest-path/components/route-display.component.ts deleted file mode 100644 index f46884c379..0000000000 --- a/client/src/app/shortest-path/components/route-display.component.ts +++ /dev/null @@ -1,189 +0,0 @@ -import { Component, Input } from '@angular/core'; - -import { isNil } from 'lodash-es'; -import { Options } from 'vis-network'; - -import { GraphData } from 'app/interfaces/vis-js.interface'; - -export enum DisplayType { - NETWORK = 'network', - SANKEY = 'sankey', -} - -@Component({ - selector: 'app-route-display', - templateUrl: './route-display.component.html', - styleUrls: ['./route-display.component.scss'], -}) -export class RouteDisplayComponent { - @Input() set displayType(displayType: DisplayType) { - this.currentDisplay = DisplayType[displayType]; - } - @Input() set graphData(graphData: GraphData) { - // Update vis js data - this.networkData = graphData; - - // Update sankey data - this.generateSankeyData(graphData.nodes, graphData.edges); - - // Update legend - this.setupLegend(graphData.nodes); - } - - currentDisplay: string; - - networkConfig: Options; - networkData: GraphData; - - sankeyConfig: any; - sankeyData: any; - - legend: Map; - - constructor() { - this.initVisJsSettings(); - this.initPlotlySankeySettings(); - this.legend = new Map(); - } - - initVisJsSettings() { - // Init vis js network settings - this.networkConfig = { - interaction: { - hover: true, - multiselect: true, - selectConnectedEdges: false, - }, - physics: { - enabled: true, - solver: 'barnesHut', - }, - edges: { - font: { - size: 12, - }, - length: 250, - widthConstraint: { - maximum: 90, - }, - }, - nodes: { - scaling: { - min: 25, - max: 50, - label: { - enabled: true, - min: 12, - max: 72, - maxVisible: 72, - drawThreshold: 5, - }, - }, - shape: 'box', - widthConstraint: { - maximum: 180, - }, - }, - }; - - this.networkData = { - nodes: [], - edges: [], - }; - } - - generateSankeyData(nodes: any[], edges: any[]) { - const source = []; - const target = []; - const value = []; - const label = []; - const color = []; - - const nodeIdentityMap = new Map(); - nodes.forEach((node, i) => { - nodeIdentityMap.set(node.id, i); - label.push(node.label); - color.push(node.color.border); - }); - - const seenEdges = new Map(); - edges.forEach((edge) => { - const sankeyEdge = [nodeIdentityMap.get(edge.from), nodeIdentityMap.get(edge.to)]; - if (seenEdges.has(sankeyEdge.toString())) { - value[seenEdges.get(sankeyEdge.toString())] += 1; - } else { - source.push(sankeyEdge[0]); - target.push(sankeyEdge[1]); - value.push(1); - seenEdges.set(sankeyEdge.toString(), value.length - 1); - } - }); - - this.sankeyData = { - type: 'sankey', - orientation: 'h', - node: { - arrangement: 'snap', - pad: 15, - thickness: 20, - line: { - color: 'black', - width: 0.5, - }, - label, - color, - }, - link: { - source, - target, - value, - }, - }; - } - - initPlotlySankeySettings() { - // Init plotly sankey settings - this.sankeyData = { - type: 'sankey', - orientation: 'h', - node: { - arrangement: 'snap', - pad: 15, - thickness: 20, - line: { - color: 'black', - width: 0.5, - }, - label: [], - color: [], - }, - - link: { - source: [], - target: [], - value: [], - }, - }; - - this.sankeyConfig = { - font: { - size: 10, - }, - }; - } - - /** - * Given a list of input nodes, generates a Map object representing a node legend. Keys are the label of the nodes, and values are a list - * of colors representing the border and background of the node. - * @param nodes list of node objects - */ - setupLegend(nodes: any) { - nodes.forEach((node) => { - if (!isNil(node.databaseLabel)) { - if (!this.legend.has(node.databaseLabel)) { - this.legend.set(node.databaseLabel, [node.color.border, node.color.background]); - } - } - }); - } -} diff --git a/client/src/app/shortest-path/containers/route-search.component.html b/client/src/app/shortest-path/containers/route-search.component.html deleted file mode 100644 index 542f90ab00..0000000000 --- a/client/src/app/shortest-path/containers/route-search.component.html +++ /dev/null @@ -1 +0,0 @@ -

route-search works!

diff --git a/client/src/app/shortest-path/containers/route-search.component.scss b/client/src/app/shortest-path/containers/route-search.component.scss deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/client/src/app/shortest-path/containers/route-search.component.spec.ts b/client/src/app/shortest-path/containers/route-search.component.spec.ts deleted file mode 100644 index f79732f27d..0000000000 --- a/client/src/app/shortest-path/containers/route-search.component.spec.ts +++ /dev/null @@ -1,29 +0,0 @@ -import { ComponentFixture, TestBed } from '@angular/core/testing'; - -import { configureTestSuite } from 'ng-bullet'; - -import { RootStoreModule } from 'app/root-store'; - -import { RouteSearchComponent } from './route-search.component'; - -describe('RouteSearchComponent', () => { - let component: RouteSearchComponent; - let fixture: ComponentFixture; - - configureTestSuite(() => { - TestBed.configureTestingModule({ - imports: [RootStoreModule], - declarations: [RouteSearchComponent], - }); - }); - - beforeEach(() => { - fixture = TestBed.createComponent(RouteSearchComponent); - component = fixture.componentInstance; - fixture.detectChanges(); - }); - - it('should create', () => { - expect(component).toBeTruthy(); - }); -}); diff --git a/client/src/app/shortest-path/containers/route-search.component.ts b/client/src/app/shortest-path/containers/route-search.component.ts deleted file mode 100644 index 5e6bacec0c..0000000000 --- a/client/src/app/shortest-path/containers/route-search.component.ts +++ /dev/null @@ -1,12 +0,0 @@ -import { Component, OnInit } from '@angular/core'; - -@Component({ - selector: 'app-route-search', - templateUrl: './route-search.component.html', - styleUrls: ['./route-search.component.scss'], -}) -export class RouteSearchComponent implements OnInit { - constructor() {} - - ngOnInit() {} -} diff --git a/client/src/app/shortest-path/containers/shortest-path.component.html b/client/src/app/shortest-path/containers/shortest-path.component.html deleted file mode 100644 index 3088da5831..0000000000 --- a/client/src/app/shortest-path/containers/shortest-path.component.html +++ /dev/null @@ -1,23 +0,0 @@ -
- -
- -
- - - -
- -
- -
diff --git a/client/src/app/shortest-path/containers/shortest-path.component.scss b/client/src/app/shortest-path/containers/shortest-path.component.scss deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/client/src/app/shortest-path/containers/shortest-path.component.spec.ts b/client/src/app/shortest-path/containers/shortest-path.component.spec.ts deleted file mode 100644 index f2d9e9ed51..0000000000 --- a/client/src/app/shortest-path/containers/shortest-path.component.spec.ts +++ /dev/null @@ -1,36 +0,0 @@ -import { ComponentFixture, TestBed } from '@angular/core/testing'; - -import { configureTestSuite } from 'ng-bullet'; -import { MockComponents } from 'ng-mocks'; - -import { RootStoreModule } from 'app/root-store'; -import { SharedModule } from 'app/shared/shared.module'; - -import { RouteBuilderComponent } from '../components/route-builder.component'; -import { RouteDisplayComponent } from '../components/route-display.component'; -import { ShortestPathComponent } from './shortest-path.component'; - -describe('ShortestPathComponent', () => { - let component: ShortestPathComponent; - let fixture: ComponentFixture; - - configureTestSuite(() => { - TestBed.configureTestingModule({ - imports: [RootStoreModule, SharedModule], - declarations: [ - ShortestPathComponent, - MockComponents(RouteBuilderComponent, RouteDisplayComponent), - ], - }); - }); - - beforeEach(() => { - fixture = TestBed.createComponent(ShortestPathComponent); - component = fixture.componentInstance; - fixture.detectChanges(); - }); - - it('should create', () => { - expect(component).toBeTruthy(); - }); -}); diff --git a/client/src/app/shortest-path/containers/shortest-path.component.ts b/client/src/app/shortest-path/containers/shortest-path.component.ts deleted file mode 100644 index 8e0a40ada3..0000000000 --- a/client/src/app/shortest-path/containers/shortest-path.component.ts +++ /dev/null @@ -1,50 +0,0 @@ -import { Component, OnDestroy } from '@angular/core'; - -import { combineLatest, Subscription } from 'rxjs'; - -import { GraphData } from 'app/interfaces/vis-js.interface'; -import { BackgroundTask } from 'app/shared/rxjs/background-task'; - -import { ShortestPathService } from '../services/shortest-path.service'; - -@Component({ - selector: 'app-shortest-path', - templateUrl: './shortest-path.component.html', - styleUrls: ['./shortest-path.component.scss'], -}) -export class ShortestPathComponent implements OnDestroy { - loadTask: BackgroundTask<[], any>; - shortestPathLoadedSub: Subscription; - - loadedQuery: number; - displayType: string; - graphData: GraphData; - - constructor(public shortestPathService: ShortestPathService) { - this.loadTask = new BackgroundTask(() => { - return combineLatest(this.shortestPathService.getShortestPathQueryResult(this.loadedQuery)); - }); - this.shortestPathLoadedSub = this.loadTask.results$.subscribe( - ({ result: [shortestPathResult], value: [] }) => { - this.graphData = { - nodes: shortestPathResult.nodes, - edges: shortestPathResult.edges, - }; - } - ); - } - - ngOnDestroy() { - this.shortestPathLoadedSub.unsubscribe(); - } - - changeDisplayType(type: string) { - this.displayType = type; - } - - loadNewQuery(query: number) { - this.graphData = null; - this.loadedQuery = query; - this.loadTask.update([]); - } -} diff --git a/client/src/app/shortest-path/services/shortest-path.service.ts b/client/src/app/shortest-path/services/shortest-path.service.ts deleted file mode 100644 index c4911d24fb..0000000000 --- a/client/src/app/shortest-path/services/shortest-path.service.ts +++ /dev/null @@ -1,26 +0,0 @@ -import { HttpClient } from '@angular/common/http'; -import { Injectable } from '@angular/core'; - -import { Observable } from 'rxjs'; -import { map } from 'rxjs/operators'; - -@Injectable({ - providedIn: 'root', -}) -export class ShortestPathService { - readonly kgAPI = '/api/knowledge-graph'; - - constructor(private http: HttpClient) {} - - getShortestPathQueryResult(queryId: number): Observable { - return this.http - .get<{ result: any }>(`${this.kgAPI}/shortest-path-query/${queryId}`, {}) - .pipe(map((resp: any) => resp.result)); - } - - getShortestPathQueryList(): Observable { - return this.http - .get<{ result: Map }>(`${this.kgAPI}/shortest-path-query-list`, {}) - .pipe(map((resp: any) => resp.result)); - } -} diff --git a/client/src/app/shortest-path/shortest-path.module.ts b/client/src/app/shortest-path/shortest-path.module.ts deleted file mode 100644 index d8cceb48f1..0000000000 --- a/client/src/app/shortest-path/shortest-path.module.ts +++ /dev/null @@ -1,22 +0,0 @@ -import { NgModule } from '@angular/core'; -import { CommonModule } from '@angular/common'; - -import { SharedModule } from 'app/shared/shared.module'; - -import { ShortestPathComponent } from './containers/shortest-path.component'; -import { RouteSearchComponent } from './containers/route-search.component'; -import { RouteBuilderComponent } from './components/route-builder.component'; -import { RouteDisplayComponent } from './components/route-display.component'; - -const components = [ - ShortestPathComponent, - RouteSearchComponent, - RouteBuilderComponent, - RouteDisplayComponent, -]; - -@NgModule({ - declarations: [...components], - imports: [CommonModule, SharedModule], -}) -export class ShortestPathModule {} diff --git a/client/src/app/visualization/components/sidenav-type-view/sidenav-type-view.component.ts b/client/src/app/visualization/components/sidenav-type-view/sidenav-type-view.component.ts index 52106675c1..487a698b70 100644 --- a/client/src/app/visualization/components/sidenav-type-view/sidenav-type-view.component.ts +++ b/client/src/app/visualization/components/sidenav-type-view/sidenav-type-view.component.ts @@ -1,5 +1,7 @@ import { Component, Input } from '@angular/core'; +import { IdType } from 'vis-network'; + import { VisNode } from 'app/interfaces'; import { AssociatedType, @@ -98,7 +100,7 @@ export class SidenavTypeViewComponent { ); } - getSnippets(node1Id: number, node2Id: number, limit: number, page: number) { + getSnippets(node1Id: IdType, node2Id: IdType, limit: number, page: number) { this.visualizationService.getSnippetsForNodePair(node1Id, node2Id, page, limit).subscribe( (result) => { this.queryData = result.queryData; diff --git a/client/src/app/visualization/components/visualization-canvas/visualization-canvas.component.spec.ts b/client/src/app/visualization/components/visualization-canvas/visualization-canvas.component.spec.ts index 0797abfb1d..dec150c61f 100644 --- a/client/src/app/visualization/components/visualization-canvas/visualization-canvas.component.spec.ts +++ b/client/src/app/visualization/components/visualization-canvas/visualization-canvas.component.spec.ts @@ -575,7 +575,7 @@ describe('VisualizationCanvasComponent', () => { await expect(instance.clusters.size).toEqual(2); }); - it('isNotAClusterEdge should detect whether an edge is a cluster edge or not', () => { + it('isNotAClusteredEdge should detect whether an edge is a cluster edge or not', () => { spyOn(visualizationService, 'getReferenceTableData').and.returnValue( of(mockGetReferenceTableDataResultOutgoing) ); @@ -590,7 +590,7 @@ describe('VisualizationCanvasComponent', () => { relationship: 'Mock Edge', direction: Direction.FROM, } as ClusterData); - expect(instance.isNotAClusterEdge(clusterEdge)).toBeFalse(); + expect(instance.isNotAClusteredEdge(clusterEdge)).toBeFalse(); }); it('collapseNeighbors should remove all edges connected to the given node', () => { @@ -628,13 +628,13 @@ describe('VisualizationCanvasComponent', () => { expect(instance.edges.get(103)).toBeTruthy(); }); - it('expandOrCollapseNode should collapse the node if it is expanded', () => { + it('toggleNodeExpandState should collapse the node if it is expanded', () => { const updatedNodeState = { ...instance.nodes.get(1), expanded: true }; instance.nodes.update(updatedNodeState); expect(instance.nodes.get(1).expanded).toBeTrue(); - instance.expandOrCollapseNode(1); + instance.toggleNodeExpandState(1); expect(instance.nodes.get(1)).toBeTruthy(); expect(instance.nodes.get(2)).toBeNull(); @@ -644,7 +644,7 @@ describe('VisualizationCanvasComponent', () => { expect(instance.edges.get(102)).toBeNull(); }); - it('expandOrCollapseNode should destroy any connected clusters of the given node', () => { + it('toggleNodeExpandState should destroy any connected clusters of the given node', () => { spyOn(visualizationService, 'getReferenceTableData').and.returnValue( of(mockGetReferenceTableDataResultOutgoing) ); @@ -654,7 +654,7 @@ describe('VisualizationCanvasComponent', () => { instance.nodes.update(updatedNodeState); instance.groupNeighborsWithRelationship(mockGroupRequestOutgoing); - instance.expandOrCollapseNode(1); + instance.toggleNodeExpandState(1); expect(instance.clusters.size).toEqual(0); @@ -666,16 +666,6 @@ describe('VisualizationCanvasComponent', () => { expect(instance.edges.get(102)).toBeNull(); }); - it('expandOrCollapseNode should request a node expansion from the parent if the node is collapsed', () => { - const expandNodeSpy = spyOn(instance.expandNode, 'emit'); - - // Technically, node 1 is "expanded" in the sense that it has connections, but for the purpose - // of this test we only care if the "expanded" property is set to false on the node - instance.expandOrCollapseNode(1); - - expect(expandNodeSpy).toHaveBeenCalled(); - }); - it('getEdgesBetweenNodes should get all the edges between the two given nodes', () => { const edges = instance.getEdgesBetweenNodes(1, 2); @@ -906,12 +896,12 @@ describe('VisualizationCanvasComponent', () => { }); it('should expand/collapse a node if it is double clicked', () => { - const expandOrCollapseNodeSpy = spyOn(instance, 'expandOrCollapseNode'); + const toggleNodeExpandStateSpy = spyOn(instance, 'toggleNodeExpandState'); spyOn(instance.networkGraph, 'getNodeAt').and.returnValue(1); instance.onDoubleClickCallback(mockCallbackParams); - expect(expandOrCollapseNodeSpy).toHaveBeenCalledWith(1); + expect(toggleNodeExpandStateSpy).toHaveBeenCalledWith(1); }); it('should show tooltip and update selected cluster nodes if an unselected cluster is right-clicked', () => { diff --git a/client/src/app/visualization/components/visualization-canvas/visualization-canvas.component.ts b/client/src/app/visualization/components/visualization-canvas/visualization-canvas.component.ts index 4a4c6c3863..644f02e824 100644 --- a/client/src/app/visualization/components/visualization-canvas/visualization-canvas.component.ts +++ b/client/src/app/visualization/components/visualization-canvas/visualization-canvas.component.ts @@ -1,9 +1,10 @@ import { Component, Input, EventEmitter, OnInit, Output, AfterViewInit } from '@angular/core'; import { isNil } from 'lodash-es'; +import { NgbModalRef } from '@ng-bootstrap/ng-bootstrap'; import { Options } from '@popperjs/core'; -import { Subject, Subscription } from 'rxjs'; -import { skip, first } from 'rxjs/operators'; +import { BehaviorSubject, Subject, Subscription } from 'rxjs'; +import { first } from 'rxjs/operators'; import { DataSet } from 'vis-data'; import { Network, IdType } from 'vis-network'; @@ -16,15 +17,16 @@ import { } from 'app/interfaces/neo4j.interface'; import { AssociatedType, + BulkReferenceTableDataRequest, ClusterData, DuplicateNodeEdgePair, Direction, DuplicateEdgeConnectionData, EdgeConnectionData, - ExpandNodeResult, - ExpandNodeRequest, + GetBulkReferenceTableDataResult, GetClusterSnippetsResult, GetEdgeSnippetsResult, + GetReferenceTableDataResult, GroupRequest, NewClusterSnippetsPageRequest, NewEdgeSnippetsPageRequest, @@ -40,9 +42,12 @@ import { SidenavSnippetData, SidenavTypeEntity, } from 'app/interfaces/visualization.interface'; +import { Progress } from 'app/interfaces/common-dialog.interface'; import { MessageType } from 'app/interfaces/message-dialog.interface'; +import { ProgressDialogComponent } from 'app/shared/components/dialog/progress-dialog.component'; import { SNIPPET_PAGE_LIMIT } from 'app/shared/constants'; import { MessageArguments, MessageDialog } from 'app/shared/services/message-dialog.service'; +import { ProgressDialog } from 'app/shared/services/progress-dialog.service'; import { uuidv4 } from 'app/shared/utils'; import { ContextMenuControlService } from 'app/visualization/services/context-menu-control.service'; import { VisualizationService } from 'app/visualization/services/visualization.service'; @@ -56,8 +61,6 @@ import { VisualizationService } from 'app/visualization/services/visualization.s export class VisualizationCanvasComponent implements OnInit, AfterViewInit { - @Output() expandNode = new EventEmitter(); - @Output() openLoadingClustersDialog = new EventEmitter(); @Output() finishedClustering = new EventEmitter(); @Output() getSnippetsForEdge = new EventEmitter(); @Output() getSnippetsForCluster = new EventEmitter(); @@ -65,89 +68,6 @@ export class VisualizationCanvasComponent @Input() nodes: DataSet; @Input() edges: DataSet; - @Input() set expandNodeResult(result: ExpandNodeResult) { - try { - if (!isNil(result)) { - const edgeLabelsOfExpandedNode = this.getConnectedEdgeLabels(result.expandedNode); - let newClusterCount = 0; - edgeLabelsOfExpandedNode.forEach( - (directionList) => (newClusterCount += directionList.length) - ); - - if (edgeLabelsOfExpandedNode.size === 0) { - this.messageDialog.display({ - title: 'Auto-Cluster Error!', - message: - 'Something strange occurred: attempted to cluster a node with zero relationships!', - type: MessageType.Error, - } as MessageArguments); - return; - } - - // When the last relationship is finished clustering, emit - this.clusteringSubscription = this.clusterCreatedSource - .asObservable() - .pipe(skip(this.openClusteringRequests + newClusterCount - 1), first()) - .subscribe(() => { - this.finishedClustering.emit(true); - }); - - edgeLabelsOfExpandedNode.forEach((directionList, relationship) => { - directionList.forEach((direction) => { - const neighborNodesWithRel = this.getNeighborsWithRelationship( - relationship, - result.expandedNode, - direction - ); - const duplicateNodeEdgePairs = this.createDuplicateNodesAndEdges( - neighborNodesWithRel, - relationship, - result.expandedNode, - direction - ); - - // This is very similar to the implementation of `updateGraphWithDuplicates`, except that here we only delete - // the existing nodes/edges, and don't add the duplicates. We will add the duplicates later, in `createCluster` - const nodesToRemove = []; - const edgesToRemove = []; - - duplicateNodeEdgePairs.forEach((pair) => { - const duplicateNode = pair.node; - const duplicateEdge = pair.edge; - const edges = this.networkGraph.getConnectedEdges(duplicateNode.duplicateOf); - - if (edges.length === 1) { - // If the original node is being clustered on its last unclustered edge, - // remove it entirely from the canvas. - nodesToRemove.push(duplicateNode.duplicateOf); - edgesToRemove.push(duplicateEdge.duplicateOf); - } else if ( - this.networkGraph.getConnectedNodes(duplicateNode.duplicateOf).length === 1 - ) { - // Otherwise, don't remove the original node, and only remove the original edge if the - // candidate node is not connected to any other node. - edgesToRemove.push(duplicateEdge.duplicateOf); - } - }); - - this.edges.remove(edgesToRemove); - this.nodes.remove(nodesToRemove); - - this.createCluster(result.expandedNode, relationship, duplicateNodeEdgePairs); - }); - }); - } - } catch (error) { - this.messageDialog.display({ - title: 'Clustering Error', - message: error, - type: MessageType.Error, - } as MessageArguments); - this.clusteringSubscription.unsubscribe(); - this.openClusteringRequests = 0; - this.finishedClustering.emit(true); - } - } @Input() set getEdgeSnippetsResult(result: GetEdgeSnippetsResult) { if (!isNil(result)) { try { @@ -242,7 +162,7 @@ export class VisualizationCanvasComponent selectedNodeEdgeLabelData: Map; selectedEdges: IdType[]; referenceTableData: DuplicateNodeEdgePair[]; - clusters: Map; + clusters: Map; openClusteringRequests: number; selectedClusterNodeData: VisNode[]; @@ -253,10 +173,15 @@ export class VisualizationCanvasComponent settingsFormValues: SettingsFormValues; + loadingClustersDialogRef: Omit & { + componentInstance: ProgressDialogComponent; + }; + constructor( private contextMenuControlService: ContextMenuControlService, - private messageDialog: MessageDialog, - private visService: VisualizationService + private visService: VisualizationService, + private readonly messageDialog: MessageDialog, + private readonly progressDialog: ProgressDialog ) { this.networkContainerId = uuidv4(); @@ -277,7 +202,7 @@ export class VisualizationCanvasComponent placement: 'right-start', }; - this.clusters = new Map(); + this.clusters = new Map(); this.openClusteringRequests = 0; this.clusterCreatedSource = new Subject(); this.selectedClusterNodeData = []; @@ -342,11 +267,9 @@ export class VisualizationCanvasComponent } updateSelectedEdges() { - this.selectedEdges = this.networkGraph.getSelectedEdges().filter( - // Cluster edges are strings, normal edges are numbers. We do NOT want to include cluster edges - // in our list of selected edges at the moment. - (edgeId) => typeof edgeId === 'number' - ); + this.selectedEdges = this.networkGraph + .getSelectedEdges() + .filter((edgeId) => this.isNotAClusteredEdge(edgeId)); } updateSelectedNodesAndEdges() { @@ -378,7 +301,7 @@ export class VisualizationCanvasComponent // If a previously connected node has no remaining edges (i.e. it is not connected // to any other neighbor), remove it. - const nodesToRemove = connectedNodes.map((connectedNodeId: number) => { + const nodesToRemove = connectedNodes.map((connectedNodeId: IdType) => { if (this.networkGraph.findNode(connectedNodeId).length !== 0) { const connectedEdges = this.networkGraph.getConnectedEdges(connectedNodeId); if (connectedEdges.length === 0) { @@ -389,27 +312,79 @@ export class VisualizationCanvasComponent this.nodes.remove(nodesToRemove); } - expandOrCollapseNode(nodeId: number) { + toggleNodeExpandState(nodeId: IdType) { const nodeRef = this.nodes.get(nodeId); if (nodeRef.expanded) { - // Updates node expand state - const updatedNodeState = { ...nodeRef, expanded: !nodeRef.expanded }; - this.nodes.update(updatedNodeState); - // 'Collapse' all neighbor nodes that do not themselves have neighbors - this.collapseNeighbors(nodeRef); + this.collapseNode(nodeRef); } else { // Need to request new data from the parent when nodes are expanded const filterLabels = Array.from(this.legend.keys()).filter( (key) => this.settingsFormValues[key].value ); - this.expandNode.emit({ - nodeId, - filterLabels, - }); + this.expandNode(nodeId, filterLabels); } } + collapseNode(nodeRef: VisNode) { + // Updates node expand state + const updatedNodeState = { ...nodeRef, expanded: !nodeRef.expanded }; + this.nodes.update(updatedNodeState); + // 'Collapse' all neighbor nodes that do not themselves have neighbors + this.collapseNeighbors(nodeRef); + } + + expandNode(nodeId: IdType, filterLabels: string[]) { + if (filterLabels.length === 0) { + this.openNoResultsFromExpandDialog(); + return; + } + + this.openLoadingClustersDialog(); + + this.visService.expandNode(nodeId, filterLabels).subscribe( + (bulkResult: GetBulkReferenceTableDataResult) => { + // If the expanded node has no connecting relationships, notify the user + if (bulkResult.referenceTables.length === 0) { + this.loadingClustersDialogRef.close(); + this.openNoResultsFromExpandDialog(); + return; + } + + // Set the origin node's expand state to true + let nodeRef = this.nodes.get(nodeId) as VisNode; + nodeRef = { ...nodeRef, expanded: true }; + this.nodes.update(nodeRef); + + bulkResult.referenceTables + // Sorting the tables by length makes creating clusters faster by doing the smallest tables first + .sort((a, b) => a.referenceTableRows.length - b.referenceTableRows.length) + .forEach((table: GetReferenceTableDataResult) => { + const { referenceTableRows, direction, description } = table; + const duplicateNodeEdgePairs = table.duplicateNodeEdgePairs.map((pair) => { + return { + node: this.visService.convertNodeToVisJSFormat(pair.node, this.legend), + edge: this.visService.convertEdgeToVisJSFormat(pair.edge), + } as DuplicateNodeEdgePair; + }); + this.processGetReferenceTableResults( + nodeId, + duplicateNodeEdgePairs, + referenceTableRows, + description, + direction + ); + }); + // Done loading clusters so close the dialog automatically + this.loadingClustersDialogRef.close(); + }, + (error) => { + this.loadingClustersDialogRef.close(); + this.openErrorDialog('Node Expansion Error', error); + } + ); + } + fitToScreen(event: EventEmitter) { this.networkGraph.fit(); } @@ -425,14 +400,18 @@ export class VisualizationCanvasComponent /** * Check that the input is a normal edge and that it isn't currently clustered. - * Normal edges are numbers, cluster edges are strings. `getClusteredEdges` is - * used here to deterimine if the input edge is currently clustered; The - * output of getClusteredEdges is the input edge + any cluster edges it is contained - * in if any. * @param edge the id of the edge to check */ - isNotAClusterEdge(edge: IdType) { - return typeof edge !== 'string' && this.networkGraph.getClusteredEdges(edge).length === 1; + isNotAClusteredEdge(edge: IdType) { + const baseEdges = this.networkGraph.getBaseEdges(edge); + // If 'edge' is a base edge, the value of `getBaseEdges` should be a list with a single value: the edge id itself. If it were a + // cluster, it could still be a list with a single value, but that value would NOT be the cluster edge id, it would be whatever + // base edge was clustered. + const notAClusterEdge = baseEdges.length === 1 && baseEdges.includes(edge); + // Furthermore, we can quickly check that 'edge' is not in a cluster by checking the length of `getClusteredEdges`: if it is more + // than 1, the edge is in at least one cluster. + const notInAClusterEdge = this.networkGraph.getClusteredEdges(edge).length === 1; + return notAClusterEdge && notInAClusterEdge; } /** @@ -450,7 +429,7 @@ export class VisualizationCanvasComponent .filter((edgeId) => { const edge = this.edges.get(edgeId); // First check if this is the correct relationship - if (this.isNotAClusterEdge(edgeId) && edge.label === relationship) { + if (this.isNotAClusteredEdge(edgeId) && edge.label === relationship) { // Then, check that it is in the correct direction if (direction === Direction.FROM && edge.from === node) { return true; @@ -479,7 +458,7 @@ export class VisualizationCanvasComponent this.networkGraph .getConnectedEdges(selectedNode) - .filter((edge) => this.isNotAClusterEdge(edge)) + .filter((edge) => this.isNotAClusteredEdge(edge)) .forEach((edgeId) => { const edge = this.edges.get(edgeId); const { label, from, to } = edge; @@ -524,70 +503,84 @@ export class VisualizationCanvasComponent } createClusterSvg(referenceTableRows: ReferenceTableRow[]) { - const maxSnippetCount = referenceTableRows[0].snippetCount; - const maxRowsToShow = this.settingsFormValues.maxClusterShownRows.value; - const numRowsToShow = - referenceTableRows.length > maxRowsToShow ? maxRowsToShow : referenceTableRows.length; - - const maxNodesCellText = `Showing ${numRowsToShow} of ${referenceTableRows.length} clustered nodes`; - const rowsHTMLString = referenceTableRows - .slice(0, maxRowsToShow) - .map((row, index) => { - const percentOfMax = - row.snippetCount === 0 ? row.snippetCount : (row.snippetCount / maxSnippetCount) * 100; - let rowHTMLString = ` - - ${row.nodeDisplayName} - (${row.snippetCount}) - -
- - `; - if (index === numRowsToShow - 1) { - rowHTMLString += ` - - ${maxNodesCellText} - - `; - } - return rowHTMLString; - }) - .join('\n'); - const ctx = document.getElementsByTagName('canvas')[0].getContext('2d'); - const longestName = referenceTableRows - .slice(0, maxRowsToShow) - .sort( - (a, b) => - ctx.measureText(b.nodeDisplayName).width - ctx.measureText(a.nodeDisplayName).width - )[0].nodeDisplayName; - - // Get width of SVG + let svgHeight; + let svgWidth; + let rowsHTMLString; + const FLUFF_HEIGHT = 15 + 5 + 4; // height of rows + padding height + border height const FLUFF_WIDTH = 21 + 6; // padding + border const WIDTH_MULTIPLIER = 1.5; // multiplier to massage the width to about what we want - const svgWidth = Math.max( - // width of biggest name + max width of counts + max width of bars + constant width - Math.floor( - ctx.measureText(longestName).width * WIDTH_MULTIPLIER + - ctx.measureText(`(${maxSnippetCount})`).width * WIDTH_MULTIPLIER + - 100 + - FLUFF_WIDTH - ), - // OR width of the max-nodes-cell + constant width - Math.floor(ctx.measureText(maxNodesCellText).width * WIDTH_MULTIPLIER + FLUFF_WIDTH) - ); + const ctx = document.getElementsByTagName('canvas')[0].getContext('2d'); - // Get height of SVG - const FLUFF_HEIGHT = 15 + 5 + 4; // height of rows + padding height + border height - // Add a single extra row to accomodate the max-nodes-cell - const numRows = referenceTableRows.slice(0, maxRowsToShow).length + 1; - // constant height * # of rows - const svgHeight = FLUFF_HEIGHT * numRows; - - const svg = ` -
+ + `; + if (index === numRowsToShow - 1) { + rowHTMLString += ` + + ${maxNodesCellText} + + `; + } + return rowHTMLString; + }) + .join('\n'); + const longestName = referenceTableRows + .slice(0, maxRowsToShow) + .sort( + (a, b) => + ctx.measureText(b.nodeDisplayName).width - ctx.measureText(a.nodeDisplayName).width + )[0].nodeDisplayName; + + // Get width of SVG + svgWidth = Math.max( + // width of biggest name + max width of counts + max width of bars + constant width + Math.floor( + ctx.measureText(longestName).width * WIDTH_MULTIPLIER + + ctx.measureText(`(${maxSnippetCount})`).width * WIDTH_MULTIPLIER + + 100 + + FLUFF_WIDTH + ), + // OR width of the max-nodes-cell + constant width + Math.floor(ctx.measureText(maxNodesCellText).width * WIDTH_MULTIPLIER + FLUFF_WIDTH) + ); + + // Get height of SVG + // Add a single extra row to accomodate the max-nodes-cell + const numRows = referenceTableRows.slice(0, maxRowsToShow).length + 1; + // constant height * # of rows + svgHeight = FLUFF_HEIGHT * numRows; + } else { + const cellText = 'Showing 0 of 0 clustered nodes'; + svgWidth = ctx.measureText(cellText).width * WIDTH_MULTIPLIER + FLUFF_WIDTH; + svgHeight = FLUFF_HEIGHT; + rowsHTMLString = ` + + ${cellText} + + `; + } + const svg = ` + - -
- ${rowsHTMLString}
+ +
+ ${rowsHTMLString}
 `; @@ -683,7 +676,7 @@ export class VisualizationCanvasComponent createDuplicateEdgeFromOriginal( originalEdge: VisEdge, - clusterOrigin: number, + clusterOrigin: IdType, duplicateNode: DuplicateVisNode ) { const newDuplicateEdgeId = 'duplicateEdge:' + uuidv4(); @@ -782,7 +775,7 @@ export class VisualizationCanvasComponent edges = edges.filter((id) => { const edge = this.edges.get(id); // Make sure the edges we duplicate have the grouped relationship and that they are connected to the cluster origin - if (this.isNotAClusterEdge(id) && edge.label === relationship) { + if (this.isNotAClusteredEdge(id) && edge.label === relationship) { // Then, check that it is in the correct direction if (direction === Direction.FROM && edge.from === clusterOrigin) { return true; @@ -802,7 +795,7 @@ export class VisualizationCanvasComponent const newDuplicateEdge = this.createDuplicateEdgeFromOriginal( this.edges.get(edges[0]), - clusterOrigin as number, + clusterOrigin as IdType, newDuplicateNode ); @@ -862,7 +855,7 @@ export class VisualizationCanvasComponent // Clean up the cluster this.networkGraph.openCluster(clusterNodeId); - this.clusters.delete(clusterNodeId as string); + this.clusters.delete(clusterNodeId as IdType); this.cleanUpDuplicates(nodesInCluster); } @@ -877,20 +870,87 @@ export class VisualizationCanvasComponent // Destroy the cluster this.networkGraph.openCluster(clusterNodeId); - this.clusters.delete(clusterNodeId as string); + this.clusters.delete(clusterNodeId as IdType); this.nodes.remove(nodesInCluster); this.edges.remove(edgesInCluster); } - createCluster( + resetClustersOnRelationshipAndDirection( originNode: IdType, relationship: string, - duplicateNodeEdgePairs: DuplicateNodeEdgePair[] + direction: string ) { - this.openClusteringRequests += 1; + // Remove any existing clusters connected to the origin node on this relationship/direction first. Any + // nodes within should have been included in the duplicateNodeEdgePairs array sent to the appserver. + this.networkGraph.getConnectedNodes(originNode).forEach((nodeId) => { + if (this.networkGraph.isCluster(nodeId)) { + const cluster = this.clusters.get(nodeId); + if (cluster.relationship === relationship && cluster.direction === direction) { + this.destroyCluster(nodeId); + } + } + }); + } + + addClusterToGraph( + svgUrl: string, + duplicateNodeEdgePairs: DuplicateNodeEdgePair[], + referenceTableRows: ReferenceTableRow[], + relationship: string, + direction: Direction + ) { + this.networkGraph.cluster({ + joinCondition: (n) => duplicateNodeEdgePairs.map((pair) => pair.node.id).includes(n.id), + clusterNodeProperties: { + image: svgUrl, + label: null, + shape: 'image', + shapeProperties: { + useImageSize: true, + }, + size: this.config.nodes.size, + // This setting is valid as described under 'clusterNodeProperties' + // here: https://visjs.github.io/vis-network/docs/network/index.html#optionsObject + // @ts-ignore + allowSingleNodeCluster: true, + }, + clusterEdgeProperties: { + label: relationship, + }, + processProperties: (clusterOptions) => { + const newClusterId = `cluster:${uuidv4()}`; + this.clusters.set(newClusterId, { referenceTableRows, relationship, direction }); + return { ...clusterOptions, id: newClusterId }; + }, + }); + } - const referenceTableDataRequest = { + processGetReferenceTableResults( + originNode: IdType, + duplicateNodeEdgePairs: DuplicateNodeEdgePair[], + referenceTableRows: ReferenceTableRow[], + relationship: string, + direction: Direction + ) { + const url = this.createClusterSvg(referenceTableRows); + + this.resetClustersOnRelationshipAndDirection(originNode, relationship, direction); + this.updateGraphWithDuplicates(duplicateNodeEdgePairs); + // TODO: Would be nice to have some indication that the cluster has been selected. + // A bit tricky, since clusters are SVGs, but maybe this can be done. + this.addClusterToGraph( + url, + duplicateNodeEdgePairs, + referenceTableRows, + relationship, + direction + ); + this.updateSelectedNodeEdgeLabelData(originNode); + } + + getReferenceTableDataRequestObject(duplicateNodeEdgePairs: DuplicateNodeEdgePair[]) { + return { nodeEdgePairs: duplicateNodeEdgePairs.map((pair) => { return { node: { @@ -906,57 +966,58 @@ export class VisualizationCanvasComponent } as ReferenceTablePair; }), } as ReferenceTableDataRequest; + } - this.visService.getReferenceTableData(referenceTableDataRequest).subscribe((result) => { - const { referenceTableRows, direction } = result; - const url = this.createClusterSvg(referenceTableRows); - - // Remove any existing clusters connected to the origin node on this relationship/direction first. Any - // nodes within should have been included in the duplicateNodeEdgePairs array sent to the appserver. - this.networkGraph.getConnectedNodes(originNode).forEach((nodeId) => { - if (this.networkGraph.isCluster(nodeId)) { - const cluster = this.clusters.get(nodeId); - if (cluster.relationship === relationship && cluster.direction === direction) { - this.destroyCluster(nodeId); - } - } - }); + createCluster( + originNode: IdType, + relationship: string, + duplicateNodeEdgePairs: DuplicateNodeEdgePair[] + ) { + this.openClusteringRequests += 1; - this.updateGraphWithDuplicates(duplicateNodeEdgePairs); - - // TODO: Would be nice to have some indication that the cluster has been selected. - // A bit tricky, since clusters are SVGs, but maybe this can be done. - this.networkGraph.cluster({ - joinCondition: (n) => duplicateNodeEdgePairs.map((pair) => pair.node.id).includes(n.id), - clusterNodeProperties: { - image: url, - label: null, - shape: 'image', - shapeProperties: { - useImageSize: true, - }, - size: this.config.nodes.size, - // This setting is valid as described under 'clusterNodeProperties' - // here: https://visjs.github.io/vis-network/docs/network/index.html#optionsObject - // @ts-ignore - allowSingleNodeCluster: true, - }, - clusterEdgeProperties: { - label: relationship, - }, - processProperties: (clusterOptions) => { - const newClusterId = `cluster:${uuidv4()}`; - this.clusters.set(newClusterId, { referenceTableRows, relationship, direction }); - return { ...clusterOptions, id: newClusterId }; - }, - }); + const referenceTableDataRequest = + this.getReferenceTableDataRequestObject(duplicateNodeEdgePairs); - this.updateSelectedNodeEdgeLabelData(originNode); + this.visService.getReferenceTableData(referenceTableDataRequest).subscribe((result) => { + const { referenceTableRows, direction } = result; + this.processGetReferenceTableResults( + originNode, + duplicateNodeEdgePairs, + referenceTableRows, + relationship, + direction + ); this.openClusteringRequests -= 1; this.clusterCreatedSource.next(true); }); } + getBulkReferenceTableDataRequestObj(associations: Map) { + return { + associations: Array.from(associations.keys()).map((key) => { + const [description, direction] = key.split('$'); + return { + description, + direction: direction as Direction, + nodeEdgePairs: associations.get(key).map((pair) => { + return { + node: { + id: pair.node.id, + displayName: pair.node.displayName, + label: pair.node.primaryLabel, + }, + edge: { + originalFrom: pair.edge.originalFrom, + originalTo: pair.edge.originalTo, + label: pair.edge.label, + }, + } as ReferenceTablePair; + }), + } as ReferenceTableDataRequest; + }), + } as BulkReferenceTableDataRequest; + } + getDuplicateNodeEdgePairsFromCluster(clusterNodeId: IdType) { const clusteredNodeIds = this.networkGraph.getNodesInCluster(clusterNodeId); const duplicateNodeEdgePairs = []; @@ -976,7 +1037,7 @@ export class VisualizationCanvasComponent /** * Creates a cluster node of all the neighbors connected to the currently selected * node connected by the input relationship. - * @param rel a string representing the relationship the neighbors will be clustered on + * @param groupRequest an object representing the relationship the neighbors will be clustered on */ groupNeighborsWithRelationship(groupRequest: GroupRequest) { const { relationship, node, direction } = groupRequest; @@ -1017,14 +1078,13 @@ export class VisualizationCanvasComponent title: 'Clustering Error!', message: `An error occurred while trying to cluster node with ID ${node} on relationship ` + - `${relationship} in direction "${direction}". `, + `${relationship} in direction '${direction}'. `, type: MessageType.Error, } as MessageArguments); return; } - // Rquest that the parent open the "Loading clusters" dialog - this.openLoadingClustersDialog.emit(true); + this.openLoadingClustersDialog(); // When finished clustering, emit this.clusteringSubscription = this.clusterCreatedSource @@ -1308,7 +1368,7 @@ export class VisualizationCanvasComponent // Check if event is double clicking a node if (hoveredNode) { - this.expandOrCollapseNode(hoveredNode as number); + this.toggleNodeExpandState(hoveredNode as string); } } @@ -1317,7 +1377,7 @@ export class VisualizationCanvasComponent const hoveredEdge = this.networkGraph.getEdgeAt(params.pointer.DOM); if (this.networkGraph.isCluster(hoveredNode)) { - const nodeIdToSnippetCountMap = new Map(); + const nodeIdToSnippetCountMap = new Map(); this.clusters .get(hoveredNode) .referenceTableRows.forEach((nodeRow) => @@ -1377,4 +1437,36 @@ export class VisualizationCanvasComponent } // End Callback Functions + + // Start Dialog Display Functions + + openNoResultsFromExpandDialog() { + this.messageDialog.display({ + title: 'No Relationships', + message: 'Expanded node had no connected relationships.', + type: MessageType.Info, + } as MessageArguments); + } + + openLoadingClustersDialog() { + this.loadingClustersDialogRef = this.progressDialog.display({ + title: `Node Expansion`, + progressObservables: [ + new BehaviorSubject( + new Progress({ + status: 'Loading clusters...', + }) + ), + ], + onCancel: () => {}, + }); + } + + openErrorDialog(title: string, error: string) { + this.messageDialog.display({ + title, + message: error, + type: MessageType.Error, + } as MessageArguments); + } } diff --git a/client/src/app/visualization/containers/visualization/visualization.component.html b/client/src/app/visualization/containers/visualization/visualization.component.html index ede18667f2..da8eeaaf39 100644 --- a/client/src/app/visualization/containers/visualization/visualization.component.html +++ b/client/src/app/visualization/containers/visualization/visualization.component.html @@ -12,15 +12,11 @@ *ngIf="networkGraphData && !hideDisplay" [nodes]="nodes" [edges]="edges" - [expandNodeResult]="expandNodeResult" [getEdgeSnippetsResult]="getEdgeSnippetsResult" [getClusterSnippetsResult]="getClusterSnippetsResult" [getSnippetsError]="getSnippetsError" [legend]="legend" [config]="networkGraphConfig" - (expandNode)="expandNode($event)" - (openLoadingClustersDialog)="openLoadingClustersDialog()" - (finishedClustering)="finishedClustering($event)" (getNodeData)="nodeSelectedCallback()" (getSnippetsForEdge)="getSnippetsForEdge($event)" (getSnippetsForCluster)="getSnippetsForCluster($event)" diff --git a/client/src/app/visualization/containers/visualization/visualization.component.spec.ts b/client/src/app/visualization/containers/visualization/visualization.component.spec.ts index 869699e93f..ed522b6a9c 100644 --- a/client/src/app/visualization/containers/visualization/visualization.component.spec.ts +++ b/client/src/app/visualization/containers/visualization/visualization.component.spec.ts @@ -9,7 +9,6 @@ import { of } from 'rxjs'; import { DataSet } from 'vis-data'; import { - ExpandNodeRequest, GraphNode, GraphRelationship, Neo4jResults, @@ -137,71 +136,54 @@ describe('VisualizationComponent', () => { expect(fixture).toBeTruthy(); }); - it('convertNodeToVisJSFormat should convert a graph node to vis js format', () => { - const convertedMockNode = instance.convertNodeToVisJSFormat(mockGraphNode); - expect(convertedMockNode).toEqual({ - ...mockGraphNode, - expanded: false, - primaryLabel: mockGraphNode.label, - font: { - color: instance.legend.get(mockGraphNode.label)[0], - }, - color: { - background: '#FFFFFF', - border: instance.legend.get(mockGraphNode.label)[1], - hover: { - background: '#FFFFFF', - border: instance.legend.get(mockGraphNode.label)[1], - }, - highlight: { - background: '#FFFFFF', - border: instance.legend.get(mockGraphNode.label)[1], - }, - }, - label: - mockGraphNode.displayName.length > 64 - ? mockGraphNode.displayName.slice(0, 64) + '...' - : mockGraphNode.displayName, - }); - }); - - it('convertEdgeToVisJSFormat should convert an edge node to vis js format', () => { - const convertedMockEdge = instance.convertEdgeToVisJSFormat(mockGraphRelationship); - expect(convertedMockEdge).toEqual({ - ...mockGraphRelationship, - label: mockGraphRelationship.data.description, - arrows: 'to', - color: { - color: '#0c8caa', - }, - }); - }); - - it('convertToVisJSFormat should convert neo4j query results to vis js format', () => { - const convertedMockNode = instance.convertNodeToVisJSFormat(mockGraphNode); - const convertedMockEdge = instance.convertEdgeToVisJSFormat(mockGraphRelationship); - const convertedNeo4jResults = instance.convertToVisJSFormat(mockNeo4jResults); - - expect(convertedNeo4jResults).toEqual({ - nodes: [convertedMockNode], - edges: [convertedMockEdge], - }); - }); - - it('should call expandNode service when child requests a node to be expanded', () => { - const expandNodeSpy = spyOn(instance, 'expandNode'); - const visualizationCanvasComponentMock = fixture.debugElement.query( - By.directive(VisualizationCanvasComponent) - ).componentInstance as VisualizationCanvasComponent; - const mockExpandNodeRequest = { - nodeId: 1, - filterLabels: ['Chemicals', 'Diseases', 'Genes'], - } as ExpandNodeRequest; - - visualizationCanvasComponentMock.expandNode.emit(mockExpandNodeRequest); - - expect(expandNodeSpy).toHaveBeenCalledWith(mockExpandNodeRequest); - }); + // TODO: These should be moved to the visualization service + // it('convertNodeToVisJSFormat should convert a graph node to vis js format', () => { + // const convertedMockNode = instance.convertNodeToVisJSFormat(mockGraphNode); + // expect(convertedMockNode).toEqual({ + // ...mockGraphNode, + // expanded: false, + // primaryLabel: mockGraphNode.label, + // font: { + // color: instance.legend.get(mockGraphNode.label)[0], + // }, + // color: { + // background: '#FFFFFF', + // border: instance.legend.get(mockGraphNode.label)[1], + // hover: { + // background: '#FFFFFF', + // border: instance.legend.get(mockGraphNode.label)[1], + // }, + // highlight: { + // background: '#FFFFFF', + // border: instance.legend.get(mockGraphNode.label)[1], + // } + // }, + // label: mockGraphNode.displayName.length > 64 ? mockGraphNode.displayName.slice(0, 64) + '...' : mockGraphNode.displayName, + // }); + // }); + + // it('convertEdgeToVisJSFormat should convert an edge node to vis js format', () => { + // const convertedMockEdge = instance.convertEdgeToVisJSFormat(mockGraphRelationship); + // expect(convertedMockEdge).toEqual({ + // ...mockGraphRelationship, + // label: mockGraphRelationship.data.description, + // arrows: 'to', + // color: { + // color: '#0c8caa', + // } + // }); + // }); + + // it('convertGraphToVisJSFormat should convert neo4j query results to vis js format', () => { + // const convertedMockNode = instance.convertNodeToVisJSFormat(mockGraphNode); + // const convertedMockEdge = instance.convertEdgeToVisJSFormat(mockGraphRelationship); + // const convertedNeo4jResults = instance.convertGraphToVisJSFormat(mockNeo4jResults); + + // expect(convertedNeo4jResults).toEqual({ + // nodes: [convertedMockNode], + // edges: [convertedMockEdge], + // }); + // }); it('should emit getSnippetsForEdge subject when child requests snippets for edge', () => { const getSnippetsFromEdgeSpy = spyOn(instance.getEdgeSnippetsSubject, 'next'); diff --git a/client/src/app/visualization/containers/visualization/visualization.component.ts b/client/src/app/visualization/containers/visualization/visualization.component.ts index 2a9356de39..a71bf80ac7 100644 --- a/client/src/app/visualization/containers/visualization/visualization.component.ts +++ b/client/src/app/visualization/containers/visualization/visualization.component.ts @@ -3,13 +3,11 @@ import { Component, OnDestroy, OnInit } from '@angular/core'; import { ActivatedRoute } from '@angular/router'; import { isArray, isNil } from 'lodash-es'; -import { BehaviorSubject, EMPTY as empty, merge, of, Subject, Subscription } from 'rxjs'; -import { filter, map, switchMap, take, tap } from 'rxjs/operators'; +import { EMPTY as empty, merge, of, Subject, Subscription, forkJoin } from 'rxjs'; +import { filter, switchMap, take, tap } from 'rxjs/operators'; import { DataSet } from 'vis-data'; import { - ExpandNodeRequest, - ExpandNodeResult, GetClusterSnippetsResult, GetEdgeSnippetsResult, GraphNode, @@ -28,14 +26,9 @@ import { getGraphQueryParams, GraphQueryParameters, } from 'app/search/utils/search'; -import { ProgressDialog } from 'app/shared/services/progress-dialog.service'; -import { MessageArguments, MessageDialog } from 'app/shared/services/message-dialog.service'; -import { MessageType } from 'app/interfaces/message-dialog.interface'; -import { Progress } from 'app/interfaces/common-dialog.interface'; import { GraphSearchParameters } from 'app/search/graph-search'; import { TrackingService } from 'app/shared/services/tracking.service'; import { TRACKING_ACTIONS, TRACKING_CATEGORIES } from 'app/shared/schemas/tracking'; -import { getURLFromSnapshot } from 'app/shared/utils/router'; import { VisualizationService } from '../../services/visualization.service'; @@ -54,7 +47,6 @@ export class VisualizationComponent implements OnInit, OnDestroy { nodes: DataSet; edges: DataSet; - expandNodeResult: ExpandNodeResult; getEdgeSnippetsResult: GetEdgeSnippetsResult; getClusterSnippetsResult: GetClusterSnippetsResult; getSnippetsError: HttpErrorResponse; @@ -69,8 +61,6 @@ export class VisualizationComponent implements OnInit, OnDestroy { // data, biocyc, etc... legend: Map; - loadingClustersDialogRef; - // TODO: Will we need to add more of these? LITERATURE_LABELS = ['literaturedisease', 'literaturechemical', 'literaturegene']; @@ -79,8 +69,6 @@ export class VisualizationComponent implements OnInit, OnDestroy { private visService: VisualizationService, private legendService: LegendService, private workspaceManager: WorkspaceManager, - private readonly progressDialog: ProgressDialog, - private readonly messageDialog: MessageDialog, private readonly tracking: TrackingService ) { this.legend = new Map(); @@ -137,7 +125,27 @@ export class VisualizationComponent implements OnInit, OnDestroy { } ngOnInit() { - this.legendService.getAnnotationLegend().subscribe((legend) => { + const getDocumentObsverable = this.route.queryParams.pipe( + tap((params) => { + if (params.q != null) { + this.params = createGraphSearchParamsFromQuery(params as GraphQueryParameters); + } + }), + filter((params) => params.data), + switchMap((params) => { + if (!params.data) { + return empty; + } + return this.visService.getDocument(params.data); + }), + take(1) + ); + + // Join the two observables so we don't create any race conditions. I.e., they both have to complete before we set any data. + forkJoin({ + legend: this.legendService.getAnnotationLegend(), + neo4jResults: getDocumentObsverable, + }).subscribe(({ legend, neo4jResults }) => { Object.keys(legend).forEach((label) => { if (this.LITERATURE_LABELS.includes(label)) { // Keys of the result dict are all lowercase, need to change the first character @@ -150,31 +158,13 @@ export class VisualizationComponent implements OnInit, OnDestroy { this.legend.set(formattedLabel, [legend[label].color, '#0c8caa']); } }); - }); - this.route.queryParams - .pipe( - tap((params) => { - if (params.q != null) { - this.params = createGraphSearchParamsFromQuery(params as GraphQueryParameters); - } - }), - filter((params) => params.data), - switchMap((params) => { - if (!params.data) { - return empty; - } - return this.visService.getBatch(params.data).pipe(map((result: Neo4jResults) => result)); - }), - take(1) - ) - .subscribe((result) => { - if (result) { - this.networkGraphData = this.setupInitialProperties(result); - this.nodes = new DataSet(this.networkGraphData.nodes); - this.edges = new DataSet(this.networkGraphData.edges); - } - }); + if (neo4jResults) { + this.networkGraphData = this.setupInitialProperties(neo4jResults); + this.nodes = new DataSet(this.networkGraphData.nodes); + this.edges = new DataSet(this.networkGraphData.edges); + } + }); this.getClusterSnippetsResult = null; this.getEdgeSnippetsResult = null; @@ -218,35 +208,24 @@ export class VisualizationComponent implements OnInit, OnDestroy { this.getSnippetsSubscription.unsubscribe(); } - openNoResultsFromExpandDialog() { - this.messageDialog.display({ - title: 'No Relationships', - message: 'Expanded node had no connected relationships.', - type: MessageType.Info, - } as MessageArguments); - } - - openLoadingClustersDialog() { - this.loadingClustersDialogRef = this.progressDialog.display({ - title: `Node Expansion`, - progressObservables: [ - new BehaviorSubject( - new Progress({ - status: 'Loading clusters...', - }) - ), - ], - onCancel: () => {}, + /** + * Redirects to the visualizer search page with the new query term as a URL parameter. + * @param query string to search for + */ + search(query: string) { + this.tracking.register({ + category: TRACKING_CATEGORIES.visualiser, + action: TRACKING_ACTIONS.search, + label: query, + url: this.tracking.toString(), }); - } - finishedClustering(event: boolean) { - this.loadingClustersDialogRef.close(); + this.workspaceManager.navigateByUrl({ url: `/search?q=${query}` }); } /** * Used for adding properties custom properties on initial setup. - * Is different from convertToVisJSFormat which is a reusable utility + * Is different from convertGraphToVisJSFormat which is a reusable utility * function to rearrange custom properties. * @param result - neo4j results from AP call */ @@ -256,115 +235,9 @@ export class VisualizationComponent implements OnInit, OnDestroy { const setExpandProperty = result.nodes.map((n) => { return { ...n, expanded: false }; }); - return this.convertToVisJSFormat({ nodes: setExpandProperty, edges: result.edges }); - } - - /** - * This function is used to modify the API response to a format - * vis.js will understand. vis.js uses a limited set - * of properties for rendering the network graph. - * @param result - a list of nodes and edges for conversion - */ - convertToVisJSFormat({ nodes, edges }: Neo4jResults) { - return { - nodes: nodes - .map((n: GraphNode) => this.convertNodeToVisJSFormat(n)) - .filter((val) => val !== null), - edges: edges.map((e: GraphRelationship) => this.convertEdgeToVisJSFormat(e)), - }; - } - - convertNodeToVisJSFormat(n: GraphNode): VisNode { - if (isNil(n.displayName) || isNil(n.label)) { - console.error(`Node does not have expected label and displayName properties ${n}`); - return null; - } - const color = this.legend.get(n.label) ? this.legend.get(n.label)[0] : '#000000'; - const border = this.legend.get(n.label) ? this.legend.get(n.label)[1] : '#000000'; - return { - ...n, - expanded: false, - primaryLabel: n.label, - font: { - color, - }, - color: { - background: '#FFFFFF', - border, - hover: { - background: '#FFFFFF', - border, - }, - highlight: { - background: '#FFFFFF', - border, - }, - }, - label: n.displayName.length > 64 ? n.displayName.slice(0, 64) + '...' : n.displayName, - }; - } - - convertEdgeToVisJSFormat(e: GraphRelationship): VisEdge { - return { - ...e, - color: { - color: '#0c8caa', - }, - label: e.data.description, - arrows: 'to', - }; - } - - expandNode(expandNodeRequest: ExpandNodeRequest) { - const { nodeId, filterLabels } = expandNodeRequest; - - this.openLoadingClustersDialog(); - - this.tracking.register({ - category: TRACKING_CATEGORIES.visualiser, - action: TRACKING_ACTIONS.expandNode, - label: 'nodeId', - value: nodeId, - // Stringified ActivatedRoute is object definition, not the actual URL - // url: this.route.toString() - url: getURLFromSnapshot(this.route.snapshot).toString(), - }); - - if (filterLabels.length === 0) { - this.openNoResultsFromExpandDialog(); - return; - } - - this.visService.expandNode(nodeId, filterLabels).subscribe( - (r: Neo4jResults) => { - const nodeRef = this.nodes.get(nodeId) as VisNode; - const visJSDataFormat = this.convertToVisJSFormat(r); - let { nodes } = visJSDataFormat; - const { edges } = visJSDataFormat; - - // If the expanded node has no connecting relationships, notify the user - if (edges.length === 0) { - this.openNoResultsFromExpandDialog(); - this.loadingClustersDialogRef.close(); - return; - } - - // Sets the node expand state to true - nodes = nodes.map((n) => { - if (n.id === nodeId) { - return { ...n, expanded: !nodeRef.expanded }; - } - return n; - }); - - this.nodes.update(nodes); - this.edges.update(edges); - - this.expandNodeResult = { nodes, edges, expandedNode: nodeId } as ExpandNodeResult; - }, - (error) => { - this.loadingClustersDialogRef.close(); - } + return this.visService.convertGraphToVisJSFormat( + { nodes: setExpandProperty, edges: result.edges }, + this.legend ); } @@ -383,7 +256,7 @@ export class VisualizationComponent implements OnInit, OnDestroy { updateCanvasWithSingleNode(data: GraphNode) { this.nodes.clear(); this.edges.clear(); - const node = this.convertNodeToVisJSFormat(data); + const node = this.visService.convertNodeToVisJSFormat(data, this.legend); if (node !== null) { this.nodes.add(node); } diff --git a/client/src/app/visualization/services/visualization.service.ts b/client/src/app/visualization/services/visualization.service.ts index c32c13d8f2..fe90b6e624 100644 --- a/client/src/app/visualization/services/visualization.service.ts +++ b/client/src/app/visualization/services/visualization.service.ts @@ -1,8 +1,10 @@ import { Injectable } from '@angular/core'; import { HttpClient } from '@angular/common/http'; +import { isNil } from 'lodash-es'; import { of } from 'rxjs'; import { map, catchError } from 'rxjs/operators'; +import { IdType } from 'vis-network'; import { GetClusterSnippetsResult, @@ -15,6 +17,11 @@ import { AssociatedTypeSnippetCountRequest, GetAssociatedTypeResult, GetNodePairSnippetsResult, + GraphNode, + GraphRelationship, + VisNode, + VisEdge, + GetBulkReferenceTableDataResult, } from 'app/interfaces'; @Injectable() @@ -23,10 +30,64 @@ export class VisualizationService { constructor(private http: HttpClient) {} - getBatch(query: string) { - return this.http - .get<{ result: Neo4jResults }>(`${this.baseUrl}/batch`, { params: { data: query } }) - .pipe(map((resp) => resp.result)); + /** + * This function is used to modify the API response to a format + * vis.js will understand. vis.js uses a limited set + * of properties for rendering the network graph. + * @param result - a list of nodes and edges for conversion + */ + convertGraphToVisJSFormat({ nodes, edges }: Neo4jResults, legend: Map) { + return { + nodes: nodes + .map((n: GraphNode) => this.convertNodeToVisJSFormat(n, legend)) + .filter((val) => val !== null), + edges: edges.map((e: GraphRelationship) => this.convertEdgeToVisJSFormat(e)), + }; + } + + convertNodeToVisJSFormat(n: GraphNode, legend: Map): VisNode { + if (isNil(n.displayName) || isNil(n.label)) { + console.error(`Node does not have expected label and displayName properties ${n}`); + return null; + } + const color = legend.get(n.label) ? legend.get(n.label)[0] : '#000000'; + const border = legend.get(n.label) ? legend.get(n.label)[1] : '#000000'; + return { + ...n, + expanded: false, + primaryLabel: n.label, + font: { + color, + }, + color: { + background: '#FFFFFF', + border, + hover: { + background: '#FFFFFF', + border, + }, + highlight: { + background: '#FFFFFF', + border, + }, + }, + label: n.displayName.length > 64 ? n.displayName.slice(0, 64) + '...' : n.displayName, + }; + } + + convertEdgeToVisJSFormat(e: GraphRelationship): VisEdge { + return { + ...e, + color: { + color: '#0c8caa', + }, + label: e.data.description, + arrows: 'to', + }; + } + + getDocument(id: IdType) { + return this.http.get(`${this.baseUrl}/document/${id}`); } /** @@ -34,31 +95,18 @@ export class VisualizationService { * of the depth of 1. * @param nodeId the node id from the database */ - expandNode(nodeId: number, filterLabels: string[]) { + expandNode(nodeId: IdType, filterLabels: string[]) { return this.http - .post<{ result: Neo4jResults }>(`${this.baseUrl}/expand`, { nodeId, filterLabels }) + .post<{ result: GetBulkReferenceTableDataResult }>(`${this.baseUrl}/expand`, { + nodeId, + filterLabels, + }) .pipe(map((resp) => resp.result)); } getReferenceTableData(request: ReferenceTableDataRequest) { return this.http - .post<{ result: GetReferenceTableDataResult }>(`${this.baseUrl}/get-reference-table-data`, { - nodeEdgePairs: [...request.nodeEdgePairs].sort( - ( - { node: { displayName: a1 }, edge: { originalFrom: a2, originalTo: a3 } }, - { node: { displayName: b1 }, edge: { originalFrom: b2, originalTo: b3 } } - ) => { - const a = `${a1}${a2}${a3}`; - const b = `${b1}${b2}${b3}`; - if (a > b) { - return -1; - } else if (a < b) { - return 1; - } - return 0; - } - ), - }) + .post<{ result: GetReferenceTableDataResult }>(`${this.baseUrl}/get-reference-table`, request) .pipe(map((resp) => resp.result)); } @@ -94,13 +142,13 @@ export class VisualizationService { `${this.baseUrl}/get-associated-type-snippet-count`, { source_node: request.source_node, - associated_nodes: [...request.associated_nodes].sort((a, b) => a - b), + associated_nodes: [...request.associated_nodes], } ) .pipe(map((resp) => resp.result.associatedData)); } - getSnippetsForNodePair(node1Id: number, node2Id: number, page: number, limit: number) { + getSnippetsForNodePair(node1Id: IdType, node2Id: IdType, page: number, limit: number) { return this.http .post<{ result: GetNodePairSnippetsResult }>(`${this.baseUrl}/get-snippets-for-node-pair`, { page, diff --git a/deployment b/deployment index 859bae595a..0f1943080f 160000 --- a/deployment +++ b/deployment @@ -1 +1 @@ -Subproject commit 859bae595a46d50dd6c22e785d7cc9dcb10d64a6 +Subproject commit 0f1943080f4dd462a64535248e2f63ede809faa2 diff --git a/docker-compose.override.yml b/docker-compose.override.yml index 203b9de7d1..ca4ec289d8 100644 --- a/docker-compose.override.yml +++ b/docker-compose.override.yml @@ -21,11 +21,6 @@ x-appserver: &appserver # ElasticSearch - ELASTICSEARCH_HOSTS=http://elasticsearch:9200 - ELASTIC_FILE_INDEX_ID=file_dev - # Neo4j - - NEO4J_SCHEME=bolt - - NEO4J_HOST=graphdatabase - - NEO4J_AUTH=neo4j/password - - NEO4J_PORT=7687 # Arango - ARANGO_HOST=http://arangodb:8529 - ARANGO_USERNAME=root @@ -50,7 +45,6 @@ x-appserver: &appserver # - lmdb:/home/n4j/neo4japp/services/annotations/lmdb depends_on: - elasticsearch - - graphdatabase - pgdatabase - redis - pdfparser @@ -101,11 +95,11 @@ services: - FLASK_APP_CONFIG=Development - FLASK_DEBUG=1 - FLASK_ENV=development - # Neo4j - - NEO4J_SCHEME=bolt - - NEO4J_HOST=graphdatabase - - NEO4J_AUTH=neo4j/password - - NEO4J_PORT=7687 + # Arango + - ARANGO_HOST=http://arangodb:8529 + - ARANGO_USERNAME=root + - ARANGO_PASSWORD=password + - ARANGO_DB_NAME=lifelike # Redis - REDIS_HOST=redis - REDIS_PORT=6379 @@ -120,19 +114,19 @@ services: networks: - backend depends_on: - - graphdatabase + - arangodb - redis cache-invalidator: container_name: cache-invalidator build: ./cache-invalidator environment: - - LOG_LEVEL=debug - # Neo4j - - NEO4J_SCHEME=bolt - - NEO4J_HOST=graphdatabase - - NEO4J_AUTH=neo4j/password - - NEO4J_PORT=7687 + - LOG_LEVEL=DEBUG + # Arango + - ARANGO_HOST=http://arangodb:8529 + - ARANGO_USERNAME=root + - ARANGO_PASSWORD=password + - ARANGO_DB_NAME=lifelike # Redis - REDIS_HOST=redis - REDIS_PORT=6379 @@ -144,7 +138,7 @@ services: - backend depends_on: - redis - - graphdatabase + - arangodb pdfparser: container_name: pdfparser @@ -167,18 +161,6 @@ services: networks: - backend - graphdatabase: - container_name: graphdatabase - image: neo4j:4.4-community - environment: - - NEO4J_AUTH=neo4j/password - - NEO4JLABS_PLUGINS=["apoc", "n10s"] - ports: - - "7474:7474" - - "7687:7687" - networks: - - backend - arangodb: build: # Note that this Dockerfile simply adds a user directory and installs the helper scripts into it, and then executes the default arango diff --git a/docs/wiki/appserver/logging-guide.md b/docs/wiki/appserver/logging-guide.md index 83f0d10221..dd4b1d59ab 100644 --- a/docs/wiki/appserver/logging-guide.md +++ b/docs/wiki/appserver/logging-guide.md @@ -48,7 +48,7 @@ When you don't have the username information, another class `EventLog` can be us ```python from neo4japp.constants import LogEventType -@bp.route('/viz-search-temp', methods=['POST']) +@bp.route('/visualizer-temp', methods=['POST']) @jsonify_with_class(SimpleSearchRequest) def visualizer_search_temp(req: SimpleSearchRequest): ... diff --git a/statistical-enrichment/Pipfile b/statistical-enrichment/Pipfile index f900adbc1b..4646c16270 100644 --- a/statistical-enrichment/Pipfile +++ b/statistical-enrichment/Pipfile @@ -13,7 +13,6 @@ flask-httpauth = "==3.3.0" flask-marshmallow = "==0.11.0" Flask = "==1.1.2" gunicorn = "==20.0.4" -neo4j = "==4.2.1" pandas = "==1.3.3" pyjwt = "==2.0.0" redis = "==3.5.2" @@ -27,6 +26,7 @@ ipython = "==7.28.0" jupyter = "==1.0.0" sympy = "==1.9" nose = "==1.3.7" +python-arango = "==7.5.2" jinja2 = "<3.1.0" itsdangerous = "<=2.0.1" werkzeug = "==0.16.0" diff --git a/statistical-enrichment/Pipfile.lock b/statistical-enrichment/Pipfile.lock index beb70c2646..ec732d59cd 100644 --- a/statistical-enrichment/Pipfile.lock +++ b/statistical-enrichment/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "a979a7297628c4ab913e539d9dcf9fe6da739459ef23a5f16caee695f94a1778" + "sha256": "88eb0ec16c4eeaf04710818138cd2f825d3ce3e46e988215ba2574473f4b59c9" }, "pipfile-spec": 6, "requires": { @@ -21,7 +21,7 @@ "sha256:cfdb2b588b9fc25ede96d8db56ed50848b0b649dca3dd1df0b11f683bb9e0b5f", "sha256:f7ed51751b2c2add651e5747c891b47e26d2a21be5d32d9311dfe9692f3e5d7a" ], - "markers": "python_full_version >= '3.8.0'", + "markers": "python_version >= '3.8'", "version": "==4.0.0" }, "appnope": { @@ -72,7 +72,7 @@ "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80", "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85" ], - "markers": "python_full_version >= '3.8.0'", + "markers": "python_version >= '3.8'", "version": "==1.3.0" }, "async-lru": { @@ -80,7 +80,7 @@ "sha256:b8a59a5df60805ff63220b2a0c5b5393da5521b113cd5465a44eb037d81a5627", "sha256:ff02944ce3c288c5be660c42dbcca0742b32c3b279d6dceda655190240b99224" ], - "markers": "python_full_version >= '3.8.0'", + "markers": "python_version >= '3.8'", "version": "==2.0.4" }, "attrs": { @@ -93,11 +93,11 @@ }, "babel": { "hashes": [ - "sha256:04c3e2d28d2b7681644508f836be388ae49e0cfe91465095340395b60d00f210", - "sha256:fbfcae1575ff78e26c7449136f1abbefc3c13ce542eeb13d43d50d8b047216ec" + "sha256:33e0952d7dd6374af8dbf6768cc4ddf3ccfefc244f9986d4074704f2fbd18900", + "sha256:7077a4984b02b6727ac10f1f7294484f737443d7e2e66c5e4380e41a3ae0b4ed" ], "markers": "python_version >= '3.7'", - "version": "==2.13.0" + "version": "==2.13.1" }, "backcall": { "hashes": [ @@ -119,15 +119,15 @@ "sha256:0a31f1837963c41d46bbf1331b8778e1308ea0791db03cc4e7357b97cf42a8fe", "sha256:3225f354cfc436b9789c66c4ee030194bee0568fbf9cbdad3bc8b5c26c5f12b6" ], - "markers": "python_full_version >= '3.8.0'", + "markers": "python_version >= '3.8'", "version": "==6.1.0" }, "blinker": { "hashes": [ - "sha256:152090d27c1c5c722ee7e48504b02d76502811ce02e1523553b4cf8c8b3d3a8d", - "sha256:296320d6c28b006eb5e32d4712202dbcdcbf5dc482da298c2f44881c43884aaa" + "sha256:c3f865d4d54db7abc53758a01601cf343fe55b84c1de4e3fa910e420b438d5b9", + "sha256:e6820ff6fa4e4d1d8e2747c2283749c3f547e4fee112b98555cdcdae32996182" ], - "version": "==1.6.3" + "version": "==1.7.0" }, "certifi": { "hashes": [ @@ -192,104 +192,104 @@ 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"sha256:9b232b9430c8f57288c1024b34a8f0251ddcc47268927367a0dd3eeaca40deb5", + "sha256:baf991e61542da48fe8aef8b779a9ea0aa38d8a54166ee250d5af5ecf4486619" ], - "markers": "python_full_version >= '3.8.0'", - "version": "==5.11.2" + "markers": "python_version >= '3.8'", + "version": "==5.13.0" }, "types-python-dateutil": { "hashes": [ @@ -1697,18 +1698,18 @@ }, "urllib3": { "hashes": [ - "sha256:7a7c7003b000adf9e7ca2a377c9688bbc54ed41b985789ed576570342a375cd2", - "sha256:b19e1a85d206b56d7df1d5e683df4a7725252a964e3993648dd0fb5a1c157564" + "sha256:c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84", + "sha256:fdb6d215c776278489906c2f8916e6e7d4f5a9b602ccbcfdf7f016fc8da0596e" ], "markers": "python_version >= '3.7'", - "version": "==2.0.6" + "version": "==2.0.7" }, "wcwidth": { "hashes": [ - "sha256:77f719e01648ed600dfa5402c347481c0992263b81a027344f3e1ba25493a704", - "sha256:8705c569999ffbb4f6a87c6d1b80f324bd6db952f5eb0b95bc07517f4c1813d4" + "sha256:9a929bd8380f6cd9571a968a9c8f4353ca58d7cd812a4822bba831f8d685b223", + "sha256:a675d1a4a2d24ef67096a04b85b02deeecd8e226f57b5e3a72dbb9ed99d27da8" ], - "version": "==0.2.8" + "version": "==0.2.9" }, "webargs": { "hashes": [ @@ -1737,7 +1738,7 @@ "sha256:084072e0a7f5f347ef2ac3d8698a5e0b4ffbfcab607628cadabc650fc9a83a24", "sha256:b3324019b3c28572086c4a319f91d1dcd44e6e11cd340232978c684a7650d0df" ], - "markers": "python_full_version >= '3.8.0'", + "markers": "python_version >= '3.8'", "version": "==1.6.4" }, "werkzeug": { @@ -1841,7 +1842,7 @@ "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31", "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0" ], - "markers": "python_full_version >= '3.8.0'", + "markers": "python_version >= '3.8'", "version": "==3.17.0" } }, @@ -1974,10 +1975,10 @@ }, "wcwidth": { "hashes": [ - "sha256:77f719e01648ed600dfa5402c347481c0992263b81a027344f3e1ba25493a704", - "sha256:8705c569999ffbb4f6a87c6d1b80f324bd6db952f5eb0b95bc07517f4c1813d4" + "sha256:9a929bd8380f6cd9571a968a9c8f4353ca58d7cd812a4822bba831f8d685b223", + "sha256:a675d1a4a2d24ef67096a04b85b02deeecd8e226f57b5e3a72dbb9ed99d27da8" ], - "version": "==0.2.8" + "version": "==0.2.9" } } } diff --git a/statistical-enrichment/statistical_enrichment/config.py b/statistical-enrichment/statistical_enrichment/config.py index 29ed492990..8daa4b4c19 100644 --- a/statistical-enrichment/statistical_enrichment/config.py +++ b/statistical-enrichment/statistical_enrichment/config.py @@ -4,13 +4,12 @@ class Base: """Default values""" - JWKS_URL = environ.get('JWKS_URL', None) - JWT_SECRET = environ.get('JWT_SECRET', 'secrets') - JWT_ALGORITHM = environ.get('JWT_ALGORITHM', 'HS256') - JWT_AUDIENCE = environ.get('JWT_AUDIENCE', None) - - NEO4J_HOST = environ.get('NEO4J_HOST') - NEO4J_SCHEME = environ.get('NEO4J_SCHEME') - NEO4J_AUTH = environ.get('NEO4J_AUTH') - NEO4J_PORT = environ.get('NEO4J_PORT') - NEO4J_DATABASE = environ.get('NEO4J_DATABASE') + JWKS_URL = environ.get('JWKS_URL', None) or None + JWT_SECRET = environ.get('JWT_SECRET', 'secrets') or 'secrets' + JWT_ALGORITHM = environ.get('JWT_ALGORITHM', 'HS256') or 'HS256' + JWT_AUDIENCE = environ.get('JWT_AUDIENCE', None) or None + + ARANGO_HOST = environ.get('ARANGO_HOST', 'http://localhost:8529') + ARANGO_USERNAME = environ.get('ARANGO_USERNAME', 'root') + ARANGO_PASSWORD = environ.get('ARANGO_PASSWORD', 'password') + ARANGO_DB_NAME = environ.get('ARANGO_DB_NAME', 'lifelike') diff --git a/statistical-enrichment/statistical_enrichment/database.py b/statistical-enrichment/statistical_enrichment/database.py new file mode 100644 index 0000000000..c7f3dd44d0 --- /dev/null +++ b/statistical-enrichment/statistical_enrichment/database.py @@ -0,0 +1,24 @@ +from arango import ArangoClient +from arango.http import DefaultHTTPClient +import os +from flask import g + + +def create_arango_client(hosts=None) -> ArangoClient: + # Need a custom HTTP client for Arango because the default timeout is only 60s + class CustomHTTPClient(DefaultHTTPClient): + REQUEST_TIMEOUT = 1000 + + hosts = hosts or os.getenv('ARANGO_HOST') + return ArangoClient( + hosts=hosts, + # Without this setting any requests to Arango will fail because we don't have a valid cert + verify_override=False, + http_client=CustomHTTPClient(), + ) + + +def get_or_create_arango_client() -> ArangoClient: + if not hasattr(g, "arango_conn"): + g.arango_client = create_arango_client() + return g.arango_client diff --git a/statistical-enrichment/statistical_enrichment/services/__init__.py b/statistical-enrichment/statistical_enrichment/services/__init__.py index f50db97d48..d37499789b 100644 --- a/statistical-enrichment/statistical_enrichment/services/__init__.py +++ b/statistical-enrichment/statistical_enrichment/services/__init__.py @@ -1,3 +1,2 @@ from .rcache import * from .enrichment import * -from .graphdb import * diff --git a/statistical-enrichment/statistical_enrichment/services/arangodb.py b/statistical-enrichment/statistical_enrichment/services/arangodb.py new file mode 100644 index 0000000000..bd69c16560 --- /dev/null +++ b/statistical-enrichment/statistical_enrichment/services/arangodb.py @@ -0,0 +1,22 @@ +from arango import ArangoClient +from arango.database import StandardDatabase +from flask import current_app +from typing import Any, List, Optional + + +def get_db( + arango_client: ArangoClient, + name: Optional[str] = None, + username: Optional[str] = None, + password: Optional[str] = None, +): + return arango_client.db( + name=name or current_app.config.get('ARANGO_DB_NAME'), + username=username or current_app.config.get('ARANGO_USERNAME'), + password=password or current_app.config.get('ARANGO_PASSWORD'), + ) + + +def execute_arango_query(db: StandardDatabase, query: str, **bind_vars) -> List[Any]: + cursor = db.aql.execute(query, ttl=600, max_runtime=600, bind_vars=bind_vars) + return [row for row in cursor] diff --git a/statistical-enrichment/statistical_enrichment/services/enrichment/__init__.py b/statistical-enrichment/statistical_enrichment/services/enrichment/__init__.py index 3f925ecd10..e69de29bb2 100644 --- a/statistical-enrichment/statistical_enrichment/services/enrichment/__init__.py +++ b/statistical-enrichment/statistical_enrichment/services/enrichment/__init__.py @@ -1,10 +0,0 @@ -from flask import g -from ..graphdb import get_neo4j_db -from .enrichment_visualisation import EnrichmentVisualisationService - - -def get_enrichment_visualisation_service(): - if 'enrichment_visualisation_service' not in g: - graph = get_neo4j_db() - g.enrichment_visualisation_service = EnrichmentVisualisationService(graph=graph) - return g.enrichment_visualisation_service diff --git a/statistical-enrichment/statistical_enrichment/services/enrichment/enrichment_visualisation.py b/statistical-enrichment/statistical_enrichment/services/enrichment/enrichment_visualisation.py index 420281a433..dc95ef4864 100644 --- a/statistical-enrichment/statistical_enrichment/services/enrichment/enrichment_visualisation.py +++ b/statistical-enrichment/statistical_enrichment/services/enrichment/enrichment_visualisation.py @@ -1,118 +1,166 @@ -import json +from arango import ArangoClient from flask import current_app from functools import partial +import json +import pandas as pd from typing import List -import pandas as pd +from ..arangodb import execute_arango_query, get_db from .enrich_methods import fisher from ..rcache import redis_cached, redis_server -class EnrichmentVisualisationService: - def __init__(self, graph): - self.graph = graph +def enrich_go(arango_client: ArangoClient, gene_names: List[str], analysis, organism): + if analysis == 'fisher': + GO_terms = redis_server.get(f"GO_for_{organism.id}") + if GO_terms is not None: + df = pd.read_json(GO_terms) + go_count = len(df) + mask = ~df.geneNames.map(set(gene_names).isdisjoint) + go = df[mask] + else: + go = redis_cached( + f"get_go_terms_{organism}_{','.join(gene_names)}_x", + partial(get_go_terms, arango_client, organism.id, gene_names), + load=json.loads, + dump=json.dumps, + ) + go_count = redis_cached( + f"go_term_count_{organism.id}", + partial(get_go_term_count, arango_client, organism.id), + load=json.loads, + dump=json.dumps, + ) + return fisher(gene_names, go, go_count) + raise NotImplementedError - def enrich_go(self, gene_names: List[str], analysis, organism): - if analysis == 'fisher': - GO_terms = redis_server.get(f"GO_for_{organism.id}") - if GO_terms is not None: - df = pd.read_json(GO_terms) - go_count = len(df) - mask = ~df.geneNames.map(set(gene_names).isdisjoint) - go = df[mask] - else: - go = self.get_go_terms(organism, gene_names) - go_count = self.get_go_term_count(organism) - return fisher(gene_names, go, go_count) - raise NotImplementedError - def query_go_term(self, organism_id, gene_names): - r = self.graph.read_transaction( - lambda tx: list( - tx.run( - """ - UNWIND $gene_names AS geneName - MATCH (g:Gene)-[:HAS_TAXONOMY]-(t:Taxonomy {eid:$taxId}) - WHERE g.name=geneName - CALL { - // Make simple run by relations we has from GO db - WITH g - MATCH (g)-[:GO_LINK]-(go:db_GO) - WITH DISTINCT go - // GO db 'GO_LINK's has tax_id property so we can filter in this way - MATCH (go)-[:GO_LINK {tax_id:$taxId}]-(go_gene:Gene) - RETURN go, go_gene - UNION - // Fetch GO relations defined in BioCyc - WITH g - MATCH (g)-[:IS]-(:db_BioCyc)-[:ENCODES]-(:Protein)-[:GO_LINK]-(go:db_GO) - WITH DISTINCT go - // BioCyc db 'GO_LINK's does not have tax_id property so we need to filter in this way - MATCH (go)-[:GO_LINK]-(:Protein)-[:ENCODES]-(:db_BioCyc)-[:IS]-(go_gene:Gene {tax_id:$taxId}) - RETURN go, go_gene - } - WITH - DISTINCT go, - collect(DISTINCT go_gene) AS go_genes - RETURN - go.eid AS goId, - go.name AS goTerm, - // Return all but 'db_GO' labels - [lbl IN labels(go) WHERE lbl <> 'db_GO'] AS goLabel, - [g IN go_genes |g.name] AS geneNames - """, - taxId=organism_id, - gene_names=gene_names, - ).data() - ) +def get_go_terms(arango_client: ArangoClient, tax_id, gene_names: List[str]): + result = execute_arango_query( + db=get_db(arango_client), + query=go_term_query(), + gene_names=gene_names, + tax_id=tax_id, + ) + if not result: + current_app.logger.warning( + f'Could not find related GO terms for organism id: {tax_id}' ) - if not r: - current_app.logger.warning( - f'Could not find related GO terms for organism id: {organism_id}' - ) - return r + return result + - def get_go_terms(self, organism, gene_names): - cache_id = f"get_go_terms_{organism}_{','.join(gene_names)}" - return redis_cached( - cache_id, - partial(self.query_go_term, organism.id, gene_names), - load=json.loads, - dump=json.dumps, +def get_go_term_count(arango_client: ArangoClient, tax_id): + result = execute_arango_query( + db=get_db(arango_client), query=go_term_count_query(), tax_id=tax_id + ) + if not result: + current_app.logger.warning( + f'Could not find related GO terms for organism id: {tax_id}' ) + return None + return result[0] - def query_go_term_count(self, organism_id): - r = self.graph.read_transaction( - lambda tx: list( - tx.run( - """ - MATCH (g:Gene)-[:HAS_TAXONOMY]-(t:Taxonomy {eid:$taxId}) - CALL { - WITH g - MATCH (g)-[:GO_LINK]-(go:db_GO) - RETURN go - UNION - WITH g - MATCH (g)-[:IS]-(:db_BioCyc)-[:ENCODES]-(:Protein)-[:GO_LINK]-(go:db_GO) - RETURN go + +def go_term_query(): + return """ + LET original_master_genes = ( + FOR organism IN taxonomy + FILTER organism.eid == @tax_id + FOR master_gene IN INBOUND organism has_taxonomy + FILTER "Gene" IN master_gene.labels + FILTER master_gene.name IN @gene_names + RETURN master_gene + ) + LET organism_genes = ( + FOR organism IN taxonomy + FILTER organism.eid == @tax_id + FOR gene IN INBOUND organism has_taxonomy + RETURN gene + ) + FOR original_gene IN original_master_genes + LET results = UNION( + ( + FOR go_term IN OUTBOUND original_gene go_link + LET linked_gene_names = ( + FOR gene IN organism_genes + FOR link IN go_link + FILTER link._from == gene._id + FILTER link._to == go_term._id + RETURN gene.name + ) + RETURN DISTINCT { + "goId": go_term.eid, + "goTerm": go_term.name, + "goLabel": go_term.labels, + "geneNames": linked_gene_names } - return count(distinct go) as go_count - """, - taxId=organism_id, + ), + ( + LET biocyc_go_terms = ( + FOR biocyc_gene IN INBOUND original_gene is + FOR protein IN OUTBOUND biocyc_gene encodes + FOR go_term IN OUTBOUND protein go_link + RETURN DISTINCT go_term + ) + LET gene_names_and_linked_protein_ids = ( + FOR gene IN organism_genes + FOR biocyc_gene IN INBOUND gene is + FOR protein IN OUTBOUND biocyc_gene encodes + RETURN {"geneName": gene.name, "protein_id": protein._id} ) + FOR go_term IN biocyc_go_terms + LET linked_gene_names = ( + FOR pair IN gene_names_and_linked_protein_ids + FOR link IN go_link + FILTER link._from == pair.protein_id + FILTER link._to == go_term._id + RETURN pair.geneName + ) + RETURN DISTINCT { + "goId": go_term.eid, + "goTerm": go_term.name, + "goLabel": go_term.labels, + "geneNames": linked_gene_names + } ) ) - if not r: - current_app.logger.warning( - f'Could not find related GO terms for organism id: {organism_id}' - ) - return r[0]['go_count'] + FOR result IN results + COLLECT id = result.goId, term = result.goTerm, label = result.goLabel INTO genes = result.geneNames + RETURN DISTINCT { + "goId": id, + "goTerm": term, + "goLabel": label, + "geneNames": UNIQUE(FLATTEN(genes)) + } + """ - def get_go_term_count(self, organism): - cache_id = f"go_term_count_{organism}" - return redis_cached( - cache_id, - partial(self.query_go_term_count, organism.id), - load=json.loads, - dump=json.dumps, - ) + +def go_term_count_query(): + return """ + LET linked_gene_names = ( + FOR organism IN taxonomy + FILTER organism.eid == @tax_id + FOR linked_gene IN INBOUND organism has_taxonomy + FILTER "Gene" IN linked_gene.labels + RETURN linked_gene + ) + + LET go_terms = ( + FOR gene IN linked_gene_names + LET results = UNION( + ( + FOR go_term IN OUTBOUND gene go_link + RETURN DISTINCT go_term + ), + ( + FOR biocyc_gene IN INBOUND gene is + FOR protein IN OUTBOUND biocyc_gene encodes + FOR go_term IN OUTBOUND protein go_link + RETURN DISTINCT go_term + ) + ) + FOR result IN results + RETURN DISTINCT result + ) + RETURN COUNT(go_terms) + """ diff --git a/statistical-enrichment/statistical_enrichment/services/graphdb.py b/statistical-enrichment/statistical_enrichment/services/graphdb.py deleted file mode 100644 index 10283d304a..0000000000 --- a/statistical-enrichment/statistical_enrichment/services/graphdb.py +++ /dev/null @@ -1,17 +0,0 @@ -import os - -from flask import g -from neo4j import GraphDatabase, basic_auth - -host = os.getenv('NEO4J_HOST', '0.0.0.0') -scheme = os.getenv('NEO4J_SCHEME', 'bolt') -port = os.getenv('NEO4J_PORT', '7687') -url = f'{scheme}://{host}:{port}' -username, password = os.getenv('NEO4J_AUTH', 'neo4j/password').split('/') -driver = GraphDatabase.driver(url, auth=basic_auth(username, password)) - - -def get_neo4j_db(): - if not hasattr(g, 'neo4j_db'): - g.neo4j_db = driver.session() - return g.neo4j_db diff --git a/statistical-enrichment/statistical_enrichment/views.py b/statistical-enrichment/statistical_enrichment/views.py index 290a3d7eb1..f49584917a 100644 --- a/statistical-enrichment/statistical_enrichment/views.py +++ b/statistical-enrichment/statistical_enrichment/views.py @@ -4,9 +4,10 @@ from .app import app from .auth import login_exempt -from .services.rcache import redis_cached +from .database import get_or_create_arango_client from .schemas import EnrichmentSchema -from .services import get_enrichment_visualisation_service +from .services.enrichment.enrichment_visualisation import enrich_go +from .services.rcache import redis_cached @app.route('/', methods=['GET', 'POST']) @@ -24,14 +25,14 @@ def healthz(): @app.route('/enrich-with-go-terms', methods=['POST']) @login_exempt @use_args(EnrichmentSchema) -def enrich_go(args): +def enrich_with_go_terms(args): gene_names = args['geneNames'] organism = args['organism'] analysis = args['analysis'] cache_id = '_'.join(['enrich_go', ','.join(gene_names), analysis, str(organism)]) - enrichment_visualisation = get_enrichment_visualisation_service() + arango_client = get_or_create_arango_client() return redis_cached( cache_id, - partial(enrichment_visualisation.enrich_go, gene_names, analysis, organism), + partial(enrich_go, arango_client, gene_names, analysis, organism), dump=dumps, ), dict(mimetype='application/json')