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Support for AnVIL duos_id (#6620) #6668

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@dsotirho-ucsc dsotirho-ucsc commented Oct 30, 2024

Connected issues: #6620

Checklist

Author

  • PR is a draft
  • Target branch is develop
  • Name of PR branch matches issues/<GitHub handle of author>/<issue#>-<slug>
  • On ZenHub, PR is connected to all issues it (partially) resolves
  • PR description links to connected issues
  • PR title matches1 that of a connected issue or comment in PR explains why they're different
  • PR title references all connected issues
  • For each connected issue, there is at least one commit whose title references that issue

1 when the issue title describes a problem, the corresponding PR
title is Fix: followed by the issue title

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  • Added p tag to titles of partial commits
  • This PR is labeled partial or completely resolves all connected issues
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  • This PR is blocked by previous PR in the chain or is not chained to another PR
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Author (reindex, API changes)

  • Added r tag to commit title or the changes introduced by this PR will not require reindexing of any deployment
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  • This PR is labeled reindex:partial and its description documents the specific reindexing procedure for dev, anvildev, anvilprod and prod or requires a full reindex or carries none of the labels reindex:dev, reindex:anvildev, reindex:anvilprod and reindex:prod
  • This PR and its connected issues are labeled API or this PR does not modify a REST API
  • Added a (A) tag to commit title for backwards (in)compatible changes or this PR does not modify a REST API
  • Updated REST API version number in app.py or this PR does not modify a REST API

Author (upgrading deployments)

  • Ran make docker_images.json and committed the resulting changes or this PR does not modify azul_docker_images, or any other variables referenced in the definition of that variable
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Author (hotfixes)

  • Added F tag to main commit title or this PR does not include permanent fix for a temporary hotfix
  • Reverted the temporary hotfixes for any connected issues or the none of the stable branches (anvilprod and prod) have temporary hotfixes for any of the issues connected to this PR

Author (before every review)

  • Rebased PR branch on develop, squashed old fixups
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  • Actually approved the PR
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  • Ran _select anvildev.shared && CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unused or this PR is not labeled deploy:shared
  • Ran _select anvildev.gitlab && CI_COMMIT_REF_NAME=develop make -C terraform/gitlab apply or this PR is not labeled deploy:gitlab
  • Checked the items in the next section or this PR is labeled deploy:gitlab
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  • Background migrations for dev.gitlab are complete or this PR is not labeled deploy:gitlab
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Operator (before pushing merge the commit)

  • Ran _select dev.gitlab && make -C terraform/gitlab/runner or this PR is not labeled deploy:runner
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  • Deleted unreferenced indices in sandbox or this PR does not remove catalogs or otherwise causes unreferenced indices in dev
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  • Started reindex in sandbox or this PR is not labeled reindex:dev
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  • Changed the target branch of the blocked PR to develop or this PR is not labeled base
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Operator (after pushing the merge commit)

  • Pushed merge commit to GitLab dev
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  • Ran _select dev.shared && make -C terraform/shared apply or this PR is not labeled deploy:shared
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  • Deindexed all unreferenced catalogs in dev or this PR is neither labeled reindex:partial nor reindex:dev
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Shorthand for review comments

  • L line is too long
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  • Q bad quotes
  • F other formatting problem

@github-actions github-actions bot added the orange [process] Done by the Azul team label Oct 30, 2024
@dsotirho-ucsc dsotirho-ucsc added reindex:anvildev [process] PR requires reindexing anvildev reindex:anvilprod [process] PR requires reindexing anvilprod labels Oct 30, 2024
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coveralls commented Oct 30, 2024

Coverage Status

coverage: 85.678% (+0.03%) from 85.65%
when pulling 00c13a2 on issues/dsotirho-ucsc/6620-duos-id
into 27c948d on develop.

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codecov bot commented Oct 30, 2024

Codecov Report

Attention: Patch coverage is 86.66667% with 2 lines in your changes missing coverage. Please review.

Project coverage is 85.66%. Comparing base (27c948d) to head (00c13a2).

Files with missing lines Patch % Lines
src/azul/terra.py 71.42% 2 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #6668      +/-   ##
===========================================
+ Coverage    85.63%   85.66%   +0.02%     
===========================================
  Files          149      149              
  Lines        20950    20956       +6     
===========================================
+ Hits         17940    17951      +11     
+ Misses        3010     3005       -5     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6620-duos-id branch from 677649b to 85b0fd6 Compare November 8, 2024 18:27
@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6620-duos-id branch 2 times, most recently from 89e199b to 9032559 Compare November 21, 2024 21:17
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6668_IT_2024-11-21.txt

@@ -457,14 +457,16 @@ def _supplementary_bundle(self, bundle_fqid: TDRAnvilBundleFQID) -> TDRAnvilBund
def _duos_bundle(self, bundle_fqid: TDRAnvilBundleFQID) -> TDRAnvilBundle:
assert not bundle_fqid.is_batched, bundle_fqid
duos_info = self.tdr.get_duos(bundle_fqid.source)
duos_id = None if duos_info is None else one(duos_info['consentGroups'])['datasetIdentifier']
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L

@achave11-ucsc achave11-ucsc removed their assignment Nov 22, 2024
@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6620-duos-id branch from f9f87ff to 7b0b646 Compare November 22, 2024 18:41
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6668_IT-2024-11-22.txt

achave11-ucsc
achave11-ucsc previously approved these changes Nov 22, 2024
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LGTM ✅

@achave11-ucsc achave11-ucsc marked this pull request as ready for review November 22, 2024 19:30
@@ -457,14 +457,20 @@ def _supplementary_bundle(self, bundle_fqid: TDRAnvilBundleFQID) -> TDRAnvilBund
def _duos_bundle(self, bundle_fqid: TDRAnvilBundleFQID) -> TDRAnvilBundle:
assert not bundle_fqid.is_batched, bundle_fqid
duos_info = self.tdr.get_duos(bundle_fqid.source)
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As far as I can tell, get_duos() already uses the ID and could return it. If that is not the case, I would like to understand why. If it is, that method should return a tuple of the ID and the info, after asserting that the ID used to look up the info, and the ID embedded in it are equal.

Comment on lines 461 to 484
duos_id = None
description = None
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Suggested change
duos_id = None
description = None
duos_id, description = None, None

@hannes-ucsc hannes-ucsc added the 0 reviews [process] Lead didn't request any changes label Nov 26, 2024
@hannes-ucsc hannes-ucsc removed their assignment Nov 26, 2024
@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6620-duos-id branch 2 times, most recently from 3acd295 to 06cb30a Compare December 2, 2024 19:15
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6668_IT_2024-12-02.txt

@hannes-ucsc hannes-ucsc removed their assignment Dec 3, 2024
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#6668 (comment)

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@hannes-ucsc hannes-ucsc removed their assignment Dec 6, 2024
@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6620-duos-id branch from a7594de to a1520bd Compare December 10, 2024 18:32
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6620_IT_2024-12-10.txt

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Please squash all commits into a single one.

Comment on lines 668 to 669
require(duos_id == consent_group['datasetIdentifier'],
duos_id, consent_group['datasetIdentifier'])
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Suggested change
require(duos_id == consent_group['datasetIdentifier'],
duos_id, consent_group['datasetIdentifier'])
require(duos_id == consent_group['datasetIdentifier'],
"Mismatched identifiers", duos_id, consent_group)

@hannes-ucsc hannes-ucsc removed their assignment Dec 13, 2024
@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6620-duos-id branch from a1520bd to d3d5723 Compare December 13, 2024 01:00
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6668_IT_2024-12-12.txt

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I'm surprised that there aren't aren't any changes to test_response_anvil.py and why there isn't an entry for the new field in azul.plugins.metadata.anvil.Plugin._field_mapping. I noticed that there isn't a mapping entry for the description either, or any coverage of that field in test_response_anvil.py so I think there is some existing test debt.

Most importantly, does this work? Can you actually see the added field in the service response of your deployment?

Please discuss this with @nadove-ucsc. The three of us should then discuss whether we should remediate the debt in this PR or in a follow-up issue.

@@ -210,6 +210,7 @@ def _non_pivotal_fields_by_entity_type(self) -> dict[str, set[str]]:
},
'datasets': {
'dataset_id',
'duos_id',
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Do you know why description isn't listed here?

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This list is in _non_pivotal_fields_by_entity_type. In non-datasets endpoints, the datasets inner entity only contains a small subset of datasets fields.

$ http 'https://service.explore.anvilproject.org/index/activities?size=2' | jq '.hits[].datasets'
[
  {
    "dataset_id": [
      "8a756d17-c54c-3b33-312b-c767552a8516"
    ],
    "title": [
      "ANVIL_1000G_high_coverage_2019"
    ]
  }
]
[
  {
    "dataset_id": [
      "8a756d17-c54c-3b33-312b-c767552a8516"
    ],
    "title": [
      "ANVIL_1000G_high_coverage_2019"
    ]
  }
]

@@ -498,6 +498,7 @@ def _duos_types(cls) -> FieldTypes:
return {
'document_id': null_str,
'description': null_str,
'duos_id': null_str,
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We should also change azul.plugins.metadata.anvil.indexer.transform.SingletonTransformer._is_duos to use duos_id instead of description.

@hannes-ucsc hannes-ucsc removed their assignment Dec 13, 2024
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dsotirho-ucsc commented Dec 18, 2024

I'm surprised that there aren't aren't any changes to test_response_anvil.py

The tests in that file index a primary bundle, not a DUOS bundle.

and why there isn't an entry for the new field in azul.plugins.metadata.anvil.Plugin._field_mapping.

It is there. 7aeec0b

I noticed that there isn't a mapping entry for the description either

Having an entry in _field_mapping causes the field to be included in the compact manifest. I suspect this is why description was omitted from _field_mapping.

or any coverage of that field in test_response_anvil.py so I think there is some existing test debt.

The field is tested in test_anvil.py with test_dataset_description()

Most importantly, does this work? Can you actually see the added field in the service response of your deployment?

Yes

$ http 'https://service.daniel2.anvil.gi.ucsc.edu/index/datasets' | jq '.hits[].datasets[] | {"document_id": .document_id, "title": .title, "duos_id": .duos_id, "description": .description[:50]}'
{
  "document_id": "677dd55c-3fa3-4b07-8c98-985d94d7577e",
  "title": "ANVIL_1000G_2019_Dev",
  "duos_id": null,
  "description": null
}
{
  "document_id": "748f9698-8d05-40e8-85de-75c86e959873",
  "title": "ANVIL_CCDG_Sample_1",
  "duos_id": "DUOS-000668",
  "description": "GTEx test study description content"
}
{
  "document_id": "95edef18-cac2-46c9-b1d1-10f885836490",
  "title": "ANVIL_CMG_Sample_1",
  "duos_id": "DUOS-000667",
  "description": "This is an example of a description for GREGoR, fo"
}

However the duos_id field (like description) is omitted from the response when there is no DUOS bundle

$ http 'https://service.daniel2.anvil.gi.ucsc.edu/index/datasets' | jq '.hits[0].datasets[]'
{
  "document_id": "677dd55c-3fa3-4b07-8c98-985d94d7577e",
  "source_datarepo_row_ids": [
    "workspace_attributes:95684a9c-e0a1-4c05-9f1f-de628a38420c"
  ],
  "dataset_id": "385290c3-dff5-fb6d-2501-fa0ba3ad1c35",
  "consent_group": [
    null
  ],
  "data_use_permission": [
    null
  ],
  "owner": [
    null
  ],
  "principal_investigator": [
    null
  ],
  "registered_identifier": [
    null
  ],
  "title": "ANVIL_1000G_2019_Dev",
  "data_modality": [
    null
  ],
  "accessible": true
}

@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6620-duos-id branch 2 times, most recently from 0b6e556 to ab479b3 Compare December 21, 2024 00:04
@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6620-duos-id branch 2 times, most recently from bf4cde5 to a1c6657 Compare January 8, 2025 02:35
@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6620-duos-id branch from a1c6657 to 3215614 Compare January 8, 2025 23:24
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6668_IT_2024-01-08.txt

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Most importantly, does this work? Can you actually see the added field in the service response of your deployment?

Yes …

http 'https://service.daniel2.anvil.gi.ucsc.edu/index/datasets' | jq '.hits[1].datasets[]'
{
  "document_id": "748f9698-8d05-40e8-85de-75c86e959873",
  "source_datarepo_row_ids": [
    "workspace_attributes:37828c3d-95d5-405a-ac36-214ad9785604"
  ],
  "dataset_id": "b16cc52e-84a0-bb91-70e6-30512935b474",
  "consent_group": [
    null
  ],
  "data_use_permission": [
    null
  ],
  "owner": [
    null
  ],
  "principal_investigator": [
    null
  ],
  "registered_identifier": [
    null
  ],
  "title": "ANVIL_CCDG_Sample_1",
  "data_modality": [
    null
  ],
  "description": "GTEx test study description content",
  "duos_id": "DUOS-000668",
  "accessible": false
}

… however due to #6609 both the description and duos_id fields are omitted from dataset 385290c3 (ANVIL_1000G_2019_Dev) on my personal deployment.

$ http 'https://service.daniel2.anvil.gi.ucsc.edu/index/datasets' | jq '.hits[0].datasets[]'
{
  "document_id": "677dd55c-3fa3-4b07-8c98-985d94d7577e",
  "source_datarepo_row_ids": [
    "workspace_attributes:95684a9c-e0a1-4c05-9f1f-de628a38420c"
  ],
  "dataset_id": "385290c3-dff5-fb6d-2501-fa0ba3ad1c35",
  "consent_group": [
    null
  ],
  "data_use_permission": [
    null
  ],
  "owner": [
    null
  ],
  "principal_investigator": [
    null
  ],
  "registered_identifier": [
    null
  ],
  "title": "ANVIL_1000G_2019_Dev",
  "data_modality": [
    null
  ],
  "accessible": true
}

I tried a reindex with a updated version of Noa's patch applied …

Index: src/azul/plugins/repository/tdr_anvil/__init__.py
IDEA additional info:
Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP
<+>UTF-8
===================================================================
diff --git a/src/azul/plugins/repository/tdr_anvil/__init__.py b/src/azul/plugins/repository/tdr_anvil/__init__.py
--- a/src/azul/plugins/repository/tdr_anvil/__init__.py (revision 00c13a2241e3c0453e51e70535b971a1df502ea3)
+++ b/src/azul/plugins/repository/tdr_anvil/__init__.py (date 1736384121828)
@@ -279,7 +279,10 @@
                 FROM {backtick(self._full_table_name(spec, BundleType.duos.value))}
             '''))
             dataset_row_id = row['datarepo_row_id']
-            if dataset_row_id.startswith(prefix):
+            common_prefix = spec.prefix.common
+            assert prefix.startswith(common_prefix), (prefix, spec)
+            partition_prefix = prefix.removeprefix(common_prefix)
+            if dataset_row_id[len(common_prefix):].startswith(partition_prefix):
                 bundle_uuid = change_version(dataset_row_id,
                                              self.datarepo_row_uuid_version,
                                              self.bundle_uuid_version)

… and the duos_id and description fields were returned for this dataset.

$ http 'https://service.daniel2.anvil.gi.ucsc.edu/index/datasets' | jq '.hits[0].datasets[]'
{
  "document_id": "677dd55c-3fa3-4b07-8c98-985d94d7577e",
  "source_datarepo_row_ids": [
    "workspace_attributes:95684a9c-e0a1-4c05-9f1f-de628a38420c"
  ],
  "dataset_id": "385290c3-dff5-fb6d-2501-fa0ba3ad1c35",
  "consent_group": [
    null
  ],
  "data_use_permission": [
    null
  ],
  "owner": [
    null
  ],
  "principal_investigator": [
    null
  ],
  "registered_identifier": [
    null
  ],
  "title": "ANVIL_1000G_2019_Dev",
  "data_modality": [
    null
  ],
  "description": null,
  "duos_id": null,
  "accessible": true
}

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