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‎.github/workflows/docs.yaml

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with:
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fetch-depth: 0
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- name: Set up Python
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: 3.10.8
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- name: Install and configure Poetry

‎.github/workflows/pytest.yaml

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with:
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fetch-depth: 1
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- name: Set up Python
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: 3.10.8
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- name: Install and configure Poetry
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run: poetry install --no-interaction --no-root
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- name: Install library
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run: poetry install --no-interaction
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- name: Check dependencies
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run: poetry run deptry .
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- name: Run tests
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run: poetry run pytest
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- name: Upload coverage to Codecov

‎.pre-commit-config.yaml

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- id: check-json
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- id: check-toml
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- id: check-yaml
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- id: pretty-format-json
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args:
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- --autofix
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- --no-ensure-ascii
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- --no-sort-keys
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- id: check-ast
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- id: debug-statements
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- id: check-docstring-first
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rev: 0.3.8
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hooks:
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- id: pydoclint
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- repo: https://github.com/pre-commit/mirrors-prettier
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rev: "v3.0.3"
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hooks:
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- id: prettier
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args: ["--staged"]

‎.vscode/extensions.json

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"ms-python.isort",
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"ms-python.mypy-type-checker",
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"ms-python.python",
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"ms-python.black-formatter"
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"ms-python.black-formatter",
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"esbenp.prettier-vscode"
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],
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"unwantedRecommendations": [
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"ms-python.flake8"
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]
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"unwantedRecommendations": ["ms-python.flake8"]
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}

‎.vscode/launch.json

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"program": "${file}",
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"console": "integratedTerminal",
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"justMyCode": true,
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"args": [
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"--config-dir=./configs"
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]
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"args": ["--config-dir=./configs"]
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},
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{
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"name": "Python: Current File [local]",
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"program": "${file}",
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"console": "integratedTerminal",
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"justMyCode": true,
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"args": [
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"--config-dir=./configs",
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"environment=local"
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]
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"args": ["--config-dir=./configs", "environment=local"]
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}
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]
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}

‎.vscode/settings.json

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"source.organizeImports": true
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}
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},
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"python.terminal.launchArgs": [
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"-m",
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"IPython",
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"--no-autoindent"
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],
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"python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"],
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"[jsonc]": {
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"editor.tabSize": 2,
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"editor.insertSpaces": true,
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}
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},
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"json.format.keepLines": true,
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"isort.args": [
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"--profile",
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"black"
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],
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"isort.args": ["--profile", "black"],
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"autoDocstring.docstringFormat": "google",
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"python.testing.pytestArgs": [
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".",
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"--doctest-modules",
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"--cov=src/"
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],
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"python.testing.pytestArgs": [".", "--doctest-modules", "--cov=src/"],
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"python.testing.unittestEnabled": false,
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"python.testing.pytestEnabled": true,
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"mypy-type-checker.severity": {

‎LICENSE.md

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‎README.md

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[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/opentargets/genetics_etl_python/main.svg)](https://results.pre-commit.ci/badge/github/opentargets/genetics_etl_python)
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# Genetics Portal Data Pipeline (experimental)
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- [Documentation](https://opentargets.github.io/genetics_etl_python/)

‎codecov.yml

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comment:
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layout: "reach, diff, flags, files"
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behavior: default
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require_changes: false # if true: only post the comment if coverage changes
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require_changes: false # if true: only post the comment if coverage changes
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coverage:
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status:

‎commitlint.config.js

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module.exports = {extends: ['@commitlint/config-conventional']};
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module.exports = { extends: ["@commitlint/config-conventional"] };

‎config/datasets/gcp.yaml

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javierre: gs://genetics-portal-input/v2g_input/javierre_2016_preprocessed.parquet
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jung: gs://genetics-portal-raw/pchic_jung2019/jung2019_pchic_tableS3.csv
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thurman: gs://genetics-portal-input/v2g_input/thurman2012/genomewideCorrs_above0.7_promoterPlusMinus500kb_withGeneNames_32celltypeCategories.bed8.gz
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catalog_associations: ${datasets.inputs}/v2d/gwas_catalog_v1.0.2-associations_e110_r2023-09-11.tsv
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catalog_studies: ${datasets.inputs}/v2d/gwas-catalog-v1.0.3-studies-r2023-09-11.tsv
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catalog_ancestries: ${datasets.inputs}/v2d/gwas-catalog-v1.0.3-ancestries-r2023-09-11.tsv
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catalog_sumstats_lut: ${datasets.inputs}/v2d/harmonised_list-r2023-09-11.txt
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catalog_associations: ${datasets.inputs}/v2d/gwas_catalog_v1.0.2-associations_e110_r2023-11-24.tsv
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catalog_studies:
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# To get a complete representation of all GWAS Catalog studies, we need to ingest the list of unpublished studies from a different file.
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- ${datasets.inputs}/v2d/gwas-catalog-v1.0.3-studies-r2023-11-24.tsv
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- ${datasets.inputs}/v2d/gwas-catalog-v1.0.3-unpublished-studies-r2023-11-24.tsv
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catalog_ancestries:
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- ${datasets.inputs}/v2d/gwas-catalog-v1.0.3-ancestries-r2023-11-24.tsv
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- ${datasets.inputs}/v2d/gwas-catalog-v1.0.3-unpublished-ancestries-r2023-11-24.tsv
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catalog_sumstats_lut: ${datasets.inputs}/v2d/harmonised_list-r2023-11-24a.txt
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ukbiobank_manifest: gs://genetics-portal-input/ukb_phenotypes/neale2_saige_study_manifest.190430.tsv
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l2g_gold_standard_curation: ${datasets.inputs}/l2g/gold_standard/curation.json
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gene_interactions: ${datasets.inputs}/l2g/interaction # 23.09 data

‎config/step/gwas_catalog.yaml renamed to ‎config/step/gwas_catalog_ingestion.yaml

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_target_: otg.gwas_catalog.GWASCatalogStep
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catalog_studies_file: ${datasets.catalog_studies}
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catalog_ancestry_file: ${datasets.catalog_ancestries}
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catalog_study_files: ${datasets.catalog_studies}
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catalog_ancestry_files: ${datasets.catalog_ancestries}
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catalog_associations_file: ${datasets.catalog_associations}
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catalog_sumstats_lut: ${datasets.catalog_sumstats_lut}
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variant_annotation_path: ${datasets.variant_annotation}
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ld_index_path: ${datasets.ld_index}
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catalog_studies_out: ${datasets.catalog_study_index}
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catalog_associations_out: ${datasets.catalog_study_locus}

‎config/step/gwas_catalog_sumstat_preprocess.yaml

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_target_: otg.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep
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raw_sumstats_path: ???
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out_sumstats_path: ???

‎docs/assets/javascripts/extra.js

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$('.contributors img[data-src]').each(function () {
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src = $(this).attr("data-src");
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$(this).attr('src', src);
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$(".contributors img[data-src]").each(function () {
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src = $(this).attr("data-src");
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$(this).attr("src", src);
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});

‎docs/assets/overrides/partials/source-file.html

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<hr />
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<ul class="metadata page-metadata" data-bi-name="page info" lang="en-us" dir="ltr">
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{% if page.meta.git_creation_date_localized %}
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<li>
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<span class="icon twemoji">
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{% include ".icons/material/clock-plus-outline.svg" %}
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</span>
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<span class="label">
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{{ page.meta.git_creation_date_localized }}
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</span>
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</li>
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{% endif %}
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<small>
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<ul
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class="metadata page-metadata"
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data-bi-name="page info"
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lang="en-us"
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dir="ltr"
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>
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<!-- mkdocs-git-revision-date-plugin -->
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{% if page.meta.git_creation_date_localized %}
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<li>
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<span class="icon twemoji">
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{% include ".icons/material/clock-plus-outline.svg" %}
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</span>
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<span class="label"> {{ page.meta.git_creation_date_localized }} </span>
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</li>
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{% endif %} {% if page.meta.git_revision_date_localized %}
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<li>
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<span class="icon twemoji">
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{% include ".icons/material/clock-edit-outline.svg" %}
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</span>
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<span class="label"> {{ page.meta.git_revision_date_localized }} </span>
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{% endif %}
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{% if page.meta.git_revision_date_localized %}
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{% include ".icons/material/clock-edit-outline.svg" %}
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<span class="label">
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Contributors
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</span>
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</li>
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<li class="contributors-holder">
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<ul class="contributors" data-bi-name="contributors">
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{%- for user in committers -%}
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<li><a href="{{ user.url }}" title="{{ user.name }}" data-bi-name="contributorprofile"
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target="_blank"><img src="{{ user.avatar }}" alt="{{ user.name }}"></a></li>
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{%- endfor -%}
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</li>
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<li>
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<span class="icon twemoji">
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<span class="label"> Contributors </span>
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</li>
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<li class="contributors-holder">
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<ul class="contributors" data-bi-name="contributors">
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{%- for user in committers -%}
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<li>
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<a
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href="{{ user.url }}"
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title="{{ user.name }}"
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data-bi-name="contributorprofile"
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target="_blank"
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><img src="{{ user.avatar }}" alt="{{ user.name }}"
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/></a>
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</li>
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{%- endfor -%}
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</li>
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</ul>
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</small>
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‎docs/assets/stylesheets/extra.css

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.metadata {
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list-style: none;
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padding: 0;
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margin: 0;
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margin-bottom: 15px;
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list-style: none;
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padding: 0;
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margin: 0;
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display: inline-block;
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display: flex !important;
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align-items: center;
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display: flex !important;
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flex-direction: row;
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margin-bottom: 0 !important;
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list-style: none;
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display: flex;
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flex-direction: row;
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justify-content: center;
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align-items: center;
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display: inline-flex;
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margin: 0 !important;
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padding: 0 !important;
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border-radius: 50%;
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filter: grayscale(100%);
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-webkit-filter: grayscale(100%);
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opacity: 0.8;
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vertical-align: middle;
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width: 1.6rem;
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transition: all 0.2s ease-in-out;
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border-radius: 50%;
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filter: grayscale(100%);
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-webkit-filter: grayscale(100%);
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opacity: 0.8;
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-webkit-filter: grayscale(0%);
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