Fix: Invalid columns in compact manifest for AnVIL (#6110) #6566
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #6566 +/- ##
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- Coverage 85.36% 85.34% -0.03%
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Files 155 155
Lines 20770 20782 +12
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+ Hits 17731 17736 +5
- Misses 3039 3046 +7 ☔ View full report in Codecov by Sentry. |
nadove-ucsc
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Sep 13, 2024
hannes-ucsc
requested changes
Sep 13, 2024
| @@ -277,6 +277,19 @@ def facets(self) -> Sequence[str]: | |||
| def manifest_config(self) -> ManifestConfig: | |||
| result = defaultdict(dict) | |||
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|
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| # This is used to modify the field names from how they are specified in | |||
| # the field mapping. Keys are field paths in an ES hit, and values are | |||
| # the desired manifest column name, or None to omit from the manifest. | |||
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Suggested change
| # the desired manifest column name, or None to omit from the manifest. | |
| # the desired manifest column name, or None to omit the column from the manifest. |
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| custom_field_names = { | ||
| ('bundles', 'uuid'): 'files.bundle_uuid', | ||
| ('bundles', 'version'): 'files.bundle_version', | ||
| ('contents', 'activities', 'activity_table'): None, | ||
| ('contents', 'files', 'uuid'): None, | ||
| ('contents', 'files', 'version'): None, | ||
| ('sources', 'id'): 'sources.source_id', | ||
| ('sources', 'spec'): 'sources.source_spec', | ||
| } |
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The intent of this translation is to make the column names match the response property paths, so this is a brittle coupling to wherever the latter are defined. Think of a way to alleviate or avoid that brittle coupling and propose that in PL.
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| # Add a file URL column. It isn't an indexed field so isn't in the field | ||
| # mapping, rather it is dynamically added in during manifest generation. |
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| # Add a file URL column. It isn't an indexed field so isn't in the field | |
| # mapping, rather it is dynamically added in during manifest generation. | |
| # The file URL is synthesized from the `uuid` and `version` fields. Above, we already configured these two fields to be omitted from the manifest since they are not informative to the user. |
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hannes-ucsc
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| # Note that there is a brittle coupling that must be maintained between | ||
| # the keys here and the keys in `custom_field_names`. |
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| # Note that there is a brittle coupling that must be maintained between | |
| # the keys here and the keys in `custom_field_names`. | |
| # Note that there is a brittle coupling that must be maintained between | |
| # the keys here and those used in the custom field name lookup in `self.manifest_config`. |
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| # Note that there is a brittle coupling that must be maintained between | ||
| # the keys here and the keys in `self._field_mapping`. |
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We discussed another brittle coupling that should be clarified via a comment.
hannes-ucsc
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achave11-ucsc
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Connected issues: #6110
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Author
developissues/<GitHub handle of author>/<issue#>-<slug>1 when the issue title describes a problem, the corresponding PR
title is
Fix:followed by the issue titleAuthor (partiality)
ptag to titles of partial commitspartialor completely resolves all connected issuespartiallabelAuthor (chains)
baseor this PR is not chained to another PRchainedor is not chained to another PRAuthor (reindex, API changes)
rtag to commit title or the changes introduced by this PR will not require reindexing of any deploymentreindex:devor the changes introduced by it will not require reindexing ofdevreindex:anvildevor the changes introduced by it will not require reindexing ofanvildevreindex:anvilprodor the changes introduced by it will not require reindexing ofanvilprodreindex:prodor the changes introduced by it will not require reindexing ofprodreindex:partialand its description documents the specific reindexing procedure fordev,anvildev,anvilprodandprodor requires a full reindex or carries none of the labelsreindex:dev,reindex:anvildev,reindex:anvilprodandreindex:prodAPIor this PR does not modify a REST APIa(A) tag to commit title for backwards (in)compatible changes or this PR does not modify a REST APIapp.pyor this PR does not modify a REST APIAuthor (upgrading deployments)
make docker_images.jsonand committed the resulting changes or this PR does not modifyazul_docker_images, or any other variables referenced in the definition of that variableutag to commit title or this PR does not require upgrading deploymentsupgradeor does not require upgrading deploymentsdeploy:sharedor does not modifydocker_images.json, and does not require deploying thesharedcomponent for any other reasondeploy:gitlabor does not require deploying thegitlabcomponentdeploy:runneror does not require deploying therunnerimageAuthor (hotfixes)
Ftag to main commit title or this PR does not include permanent fix for a temporary hotfixanvilprodandprod) have temporary hotfixes for any of the issues connected to this PRAuthor (before every review)
develop, squashed old fixupsmake requirements_updateor this PR does not modifyrequirements*.txt,common.mk,MakefileandDockerfileRtag to commit title or this PR does not modifyrequirements*.txtreqsor does not modifyrequirements*.txtmake integration_testpasses in personal deployment or this PR does not modify functionality that could affect the IT outcomePeer reviewer (after approval)
System administrator (after approval)
demoorno demono demono sandboxN reviewslabel is accurateOperator (before pushing merge the commit)
reindex:…labels andrcommit title tagno demodevelop_select dev.shared && CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unusedor this PR is not labeleddeploy:shared_select dev.gitlab && CI_COMMIT_REF_NAME=develop make -C terraform/gitlab applyor this PR is not labeleddeploy:gitlab_select anvildev.shared && CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unusedor this PR is not labeleddeploy:shared_select anvildev.gitlab && CI_COMMIT_REF_NAME=develop make -C terraform/gitlab applyor this PR is not labeleddeploy:gitlabdeploy:gitlabdeploy:gitlabSystem administrator
dev.gitlabare complete or this PR is not labeleddeploy:gitlabanvildev.gitlabare complete or this PR is not labeleddeploy:gitlabOperator (before pushing merge the commit)
_select dev.gitlab && make -C terraform/gitlab/runneror this PR is not labeleddeploy:runner_select anvildev.gitlab && make -C terraform/gitlab/runneror this PR is not labeleddeploy:runnersandboxlabel or PR is labeledno sandboxdevor PR is labeledno sandboxanvildevor PR is labeledno sandboxsandboxdeployment or PR is labeledno sandboxanvilboxdeployment or PR is labeledno sandboxsandboxdeployment or PR is labeledno sandboxanvilboxdeployment or PR is labeledno sandboxsandboxor this PR does not remove catalogs or otherwise causes unreferenced indices indevanvilboxor this PR does not remove catalogs or otherwise causes unreferenced indices inanvildevsandboxor this PR is not labeledreindex:devanvilboxor this PR is not labeledreindex:anvildevsandboxor this PR is not labeledreindex:devanvilboxor this PR is not labeledreindex:anvildevpif the PR is also labeledpartialOperator (chain shortening)
developor this PR is not labeledbasechainedlabel from the blocked PR or this PR is not labeledbasebasebaselabel from this PR or this PR is not labeledbaseOperator (after pushing the merge commit)
devanvildevdevdevanvildevanvildev_select dev.shared && make -C terraform/shared applyor this PR is not labeleddeploy:shared_select anvildev.shared && make -C terraform/shared applyor this PR is not labeleddeploy:shareddevanvildevOperator (reindex)
devor this PR is neither labeledreindex:partialnorreindex:devanvildevor this PR is neither labeledreindex:partialnorreindex:anvildevdevor this PR is neither labeledreindex:partialnorreindex:devanvildevor this PR is neither labeledreindex:partialnorreindex:anvildevdevor this PR is neither labeledreindex:partialnorreindex:devanvildevor this PR is neither labeledreindex:partialnorreindex:anvildevdevor this PR does not require reindexingdevanvildevor this PR does not require reindexinganvildevdevor this PR does not require reindexingdevanvildevor this PR does not require reindexinganvildevdevor this PR does not require reindexingdevanvildevor this PR does not require reindexinganvildevOperator
deploy:shared,deploy:gitlab,deploy:runner,API,reindex:partial,reindex:anvilprodandreindex:prodlabels to the next promotion PRs or this PR carries none of these labelsdeploy:shared,deploy:gitlab,deploy:runner,API,reindex:partial,reindex:anvilprodandreindex:prodlabels, from the description of this PR to that of the next promotion PRs or this PR carries none of these labelsShorthand for review comments
Lline is too longWline wrapping is wrongQbad quotesFother formatting problem