Support for AnVIL duos_id (#6620) #6668

dsotirho-ucsc · 2024-10-30T18:04:01Z

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

Author (partiality)

Added p tag to titles of partial commits
This PR is labeled partial _{or completely resolves all connected issues}
This PR partially resolves each of the connected issues _{or does not have the partial label}

Author (chains)

This PR is blocked by previous PR in the chain _{or is not chained to another PR}
The blocking PR is labeled base _{or this PR is not chained to another PR}
This PR is labeled chained _{or is not chained to another PR}

Author (reindex, API changes)

Added r tag to commit title _{or the changes introduced by this PR will not require reindexing of any deployment}
This PR is labeled reindex:dev _{or the changes introduced by it will not require reindexing of dev}
This PR is labeled reindex:anvildev _{or the changes introduced by it will not require reindexing of anvildev}
This PR is labeled reindex:anvilprod _{or the changes introduced by it will not require reindexing of anvilprod}
This PR is labeled reindex:prod _{or the changes introduced by it will not require reindexing of prod}
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}
Documented upgrading of deployments in UPGRADING.rst _{or this PR does not require upgrading deployments}
Added u tag to commit title _{or this PR does not require upgrading deployments}
This PR is labeled upgrade _{or does not require upgrading deployments}
This PR is labeled deploy:shared _{or does not modify docker_images.json, and does not require deploying the shared component for any other reason}
This PR is labeled deploy:gitlab _{or does not require deploying the gitlab component}
This PR is labeled deploy:runner _{or does not require deploying the runner image}

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
Ran make requirements_update _{or this PR does not modify requirements*.txt, common.mk, Makefile and Dockerfile}
Added R tag to commit title _{or this PR does not modify requirements*.txt}
This PR is labeled reqs _{or does not modify requirements*.txt}
make integration_test passes in personal deployment _{or this PR does not modify functionality that could affect the IT outcome}

Peer reviewer (after approval)

PR is not a draft
Ticket is in Review requested column
PR is awaiting requested review from system administrator
PR is assigned to only the system administrator

System administrator (after approval)

Actually approved the PR
Labeled connected issues as demo or no demo
Commented on connected issues about demo expectations _{or all connected issues are labeled no demo}
Decided if PR can be labeled no sandbox
A comment to this PR details the completed security design review
PR title is appropriate as title of merge commit
N reviews label is accurate
Moved connected issues to Approved column
PR is assigned to only the operator

Operator (before pushing merge the commit)

System administrator

Background migrations for dev.gitlab are complete _{or this PR is not labeled deploy:gitlab}
Background migrations for anvildev.gitlab are complete _{or this PR is not labeled deploy:gitlab}
PR is assigned to only the operator

Operator (before pushing merge the commit)

Operator (chain shortening)

Changed the target branch of the blocked PR to develop _{or this PR is not labeled base}
Removed the chained label from the blocked PR _{or this PR is not labeled base}
Removed the blocking relationship from the blocked PR _{or this PR is not labeled base}
Removed the base label from this PR _{or this PR is not labeled base}

Operator (after pushing the merge commit)

Operator (reindex)

Operator

Propagated the deploy:shared, deploy:gitlab, deploy:runner, API, reindex:partial, reindex:anvilprod and reindex:prod labels to the next promotion PRs _{or this PR carries none of these labels}
Propagated any specific instructions related to the deploy:shared, deploy:gitlab, deploy:runner, API, reindex:partial, reindex:anvilprod and reindex:prod labels, from the description of this PR to that of the next promotion PRs _{or this PR carries none of these labels}
PR is assigned to no one

Shorthand for review comments

L line is too long
W line wrapping is wrong
Q bad quotes
F other formatting problem

coveralls · 2024-10-30T18:25:46Z

coverage: 85.714% (+0.03%) from 85.686%
when pulling 6492eef on issues/dsotirho-ucsc/6620-duos-id
into 0bb6aab on develop.

codecov · 2024-10-30T18:27:25Z

Codecov Report

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

Project coverage is 85.69%. Comparing base (0bb6aab) to head (6492eef).

Files with missing lines	Patch %	Lines
src/azul/terra.py	71.42%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #6668      +/-   ##
===========================================
+ Coverage    85.66%   85.69%   +0.02%     
===========================================
  Files          149      149              
  Lines        20996    21002       +6     
===========================================
+ Hits         17987    17998      +11     
+ Misses        3009     3004       -5

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

dsotirho-ucsc · 2024-11-21T23:11:28Z

6668_IT_2024-11-21.txt

achave11-ucsc · 2024-11-22T14:53:19Z

src/azul/plugins/repository/tdr_anvil/__init__.py

@@ -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']


dsotirho-ucsc · 2024-11-22T19:29:28Z

6668_IT-2024-11-22.txt

achave11-ucsc

LGTM ✅

hannes-ucsc · 2024-11-26T18:00:27Z

src/azul/plugins/repository/tdr_anvil/__init__.py

@@ -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)


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.

hannes-ucsc · 2024-11-26T18:00:41Z

src/azul/plugins/repository/tdr_anvil/__init__.py

+            duos_id = None
+            description = None


Suggested change

duos_id = None

description = None

duos_id, description = None, None

dsotirho-ucsc · 2024-12-02T20:30:50Z

6668_IT_2024-12-02.txt

dsotirho-ucsc · 2024-12-18T18:08:39Z

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 · 2025-01-09T01:11:49Z

6668_IT_2024-01-08.txt

dsotirho-ucsc · 2025-01-09T01:14:07Z

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
}

hannes-ucsc · 2025-01-13T18:59:46Z

src/azul/plugins/metadata/anvil/service/response.py

@@ -210,6 +210,7 @@ def _non_pivotal_fields_by_entity_type(self) -> dict[str, set[str]]:
            },
            'datasets': {
                'dataset_id',
+                'duos_id',


Makes sense.

hannes-ucsc

~~Please add DUOS ID to compact manifest as well. I upped the estimate for that.~~

hannes-ucsc · 2025-01-13T19:26:25Z

test/service/test_manifest.py

@@ -1845,6 +1845,12 @@ def test_compact_manifest(self):
                '',
                ''
            ),
+            (
+                'datasets.duos_id',


This test is indexing the DUOS bundle so I would expect the DUOS ID to be included in the resulting manifest. Please find out why it's not.

The DUOS ID value is not being included in the manifest since the DUOS bundle is only added to the datasets and bundles indices, and not the files index which the manifest pulls values from.

dsotirho-ucsc · 2025-01-17T18:51:43Z

6668_IT_2025-01-17.txt

hannes-ucsc · 2025-01-17T23:48:26Z

src/azul/plugins/metadata/anvil/__init__.py

+            # duos_id is omitted from manifests since the field isn't included
+            # in the `files` index.


This isn't very informative. The reason is that there is only one DUOS bundle per dataset and that that bundle only contributes to outer entities of the datasets type, and not to entities of the other types, such as files, which the manifest is generated from.

This comment should also appear in the test assertion, the one that prompted my review comment, as we discussed.

dsotirho-ucsc · 2025-01-18T02:35:14Z

6668_IT-2025-01-17.txt

github-actions bot added the orange [process] Done by the Azul team label Oct 30, 2024

dsotirho-ucsc added reindex:anvildev [process] PR requires reindexing anvildev reindex:anvilprod [process] PR requires reindexing anvilprod labels Oct 30, 2024

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6620-duos-id branch from 677649b to 85b0fd6 Compare November 8, 2024 18:27

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

dsotirho-ucsc requested a review from achave11-ucsc November 21, 2024 23:49

dsotirho-ucsc assigned achave11-ucsc Nov 21, 2024

achave11-ucsc requested changes Nov 22, 2024

View reviewed changes

achave11-ucsc removed their assignment Nov 22, 2024

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6620-duos-id branch from f9f87ff to 7b0b646 Compare November 22, 2024 18:41

dsotirho-ucsc requested a review from achave11-ucsc November 22, 2024 19:29

dsotirho-ucsc assigned achave11-ucsc Nov 22, 2024

achave11-ucsc previously approved these changes Nov 22, 2024

View reviewed changes

achave11-ucsc marked this pull request as ready for review November 22, 2024 19:30

achave11-ucsc requested a review from hannes-ucsc as a code owner November 22, 2024 19:30

achave11-ucsc assigned hannes-ucsc and unassigned achave11-ucsc Nov 22, 2024

hannes-ucsc requested changes Nov 26, 2024

View reviewed changes

hannes-ucsc added the 0 reviews [process] Lead didn't request any changes label Nov 26, 2024

hannes-ucsc removed their assignment Nov 26, 2024

dsotirho-ucsc dismissed achave11-ucsc’s stale review via 3acd295 November 27, 2024 18:45

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

dsotirho-ucsc requested a review from hannes-ucsc December 2, 2024 22:59

hannes-ucsc removed their assignment Dec 13, 2024

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 force-pushed the issues/dsotirho-ucsc/6620-duos-id branch 3 times, most recently from a1c6657 to 3215614 Compare January 8, 2025 23:24

dsotirho-ucsc requested a review from hannes-ucsc January 9, 2025 19:25

dsotirho-ucsc assigned hannes-ucsc Jan 9, 2025

hannes-ucsc approved these changes Jan 13, 2025

View reviewed changes

hannes-ucsc requested changes Jan 13, 2025

View reviewed changes

hannes-ucsc removed their assignment Jan 13, 2025

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6620-duos-id branch 2 times, most recently from 543ad12 to ebc86e4 Compare January 17, 2025 18:14

dsotirho-ucsc requested a review from hannes-ucsc January 17, 2025 18:52

dsotirho-ucsc assigned hannes-ucsc Jan 17, 2025

hannes-ucsc requested changes Jan 17, 2025

View reviewed changes

hannes-ucsc added 2 reviews [process] Lead requested changes twice and removed 1 review [process] Lead requested changes once labels Jan 17, 2025

hannes-ucsc removed their assignment Jan 17, 2025

dsotirho-ucsc added 3 commits January 17, 2025 17:08

Add DUOS bundle to response test

a4156f8

[r] Support for AnVIL duos_id (#6620)

3bb81f0

fixup! [r] Support for AnVIL duos_id (#6620)

6492eef

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6620-duos-id branch from ebc86e4 to 6492eef Compare January 18, 2025 01:15

dsotirho-ucsc requested a review from hannes-ucsc January 18, 2025 02:35

dsotirho-ucsc assigned hannes-ucsc Jan 18, 2025

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Support for AnVIL duos_id (#6620) #6668

Support for AnVIL duos_id (#6620) #6668

dsotirho-ucsc commented Oct 30, 2024 •

edited by achave11-ucsc

Loading

coveralls commented Oct 30, 2024 •

edited

Loading

codecov bot commented Oct 30, 2024 •

edited

Loading

dsotirho-ucsc commented Nov 21, 2024

achave11-ucsc Nov 22, 2024

dsotirho-ucsc commented Nov 22, 2024

achave11-ucsc left a comment

hannes-ucsc Nov 26, 2024

hannes-ucsc Nov 26, 2024

dsotirho-ucsc commented Dec 2, 2024

dsotirho-ucsc commented Dec 18, 2024 •

edited

Loading

dsotirho-ucsc commented Jan 9, 2025

dsotirho-ucsc commented Jan 9, 2025

hannes-ucsc Jan 13, 2025

hannes-ucsc left a comment •

edited

Loading

hannes-ucsc Jan 13, 2025

dsotirho-ucsc Jan 17, 2025

dsotirho-ucsc commented Jan 17, 2025

hannes-ucsc Jan 17, 2025

dsotirho-ucsc commented Jan 18, 2025

	duos_id = None
	description = None
	duos_id, description = None, None

		# duos_id is omitted from manifests since the field isn't included
		# in the `files` index.

Support for AnVIL duos_id (#6620) #6668

Are you sure you want to change the base?

Support for AnVIL duos_id (#6620) #6668

Conversation

dsotirho-ucsc commented Oct 30, 2024 • edited by achave11-ucsc Loading

Checklist

Author

Author (partiality)

Author (chains)

Author (reindex, API changes)

Author (upgrading deployments)

Author (hotfixes)

Author (before every review)

Peer reviewer (after approval)

System administrator (after approval)

Operator (before pushing merge the commit)

System administrator

Operator (before pushing merge the commit)

Operator (chain shortening)

Operator (after pushing the merge commit)

Operator (reindex)

Operator

Shorthand for review comments

coveralls commented Oct 30, 2024 • edited Loading

codecov bot commented Oct 30, 2024 • edited Loading

Codecov Report

dsotirho-ucsc commented Nov 21, 2024

achave11-ucsc Nov 22, 2024

Choose a reason for hiding this comment

dsotirho-ucsc commented Nov 22, 2024

achave11-ucsc left a comment

Choose a reason for hiding this comment

hannes-ucsc Nov 26, 2024

Choose a reason for hiding this comment

hannes-ucsc Nov 26, 2024

Choose a reason for hiding this comment

dsotirho-ucsc commented Dec 2, 2024

dsotirho-ucsc commented Dec 18, 2024 • edited Loading

dsotirho-ucsc commented Jan 9, 2025

dsotirho-ucsc commented Jan 9, 2025

hannes-ucsc Jan 13, 2025

Choose a reason for hiding this comment

hannes-ucsc left a comment • edited Loading

Choose a reason for hiding this comment

hannes-ucsc Jan 13, 2025

Choose a reason for hiding this comment

dsotirho-ucsc Jan 17, 2025

Choose a reason for hiding this comment

dsotirho-ucsc commented Jan 17, 2025

hannes-ucsc Jan 17, 2025

Choose a reason for hiding this comment

dsotirho-ucsc commented Jan 18, 2025

dsotirho-ucsc commented Oct 30, 2024 •

edited by achave11-ucsc

Loading

coveralls commented Oct 30, 2024 •

edited

Loading

codecov bot commented Oct 30, 2024 •

edited

Loading

dsotirho-ucsc commented Dec 18, 2024 •

edited

Loading

hannes-ucsc left a comment •

edited

Loading