Support for AnVIL duos_id (#6620) #6668

dsotirho-ucsc · 2024-10-30T18:04:01Z

Connected issues: #6620

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coveralls · 2024-10-30T18:25:46Z

coverage: 85.563% (+0.002%) from 85.561%
when pulling 3acd295 on issues/dsotirho-ucsc/6620-duos-id
into 7ea685b on develop.

codecov · 2024-10-30T18:27:25Z

Codecov Report

Attention: Patch coverage is 82.35294% with 3 lines in your changes missing coverage. Please review.

Project coverage is 85.54%. Comparing base (7ea685b) to head (3acd295).

Files with missing lines	Patch %	Lines
src/azul/terra.py	75.00%	2 Missing ⚠️
src/azul/plugins/repository/tdr_anvil/__init__.py	83.33%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #6668   +/-   ##
========================================
  Coverage    85.54%   85.54%           
========================================
  Files          153      153           
  Lines        20981    20990    +9     
========================================
+ Hits         17948    17956    +8     
- Misses        3033     3034    +1

☔ 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 · 2024-11-27T22:02:56Z

6686_IT_2024-11-27.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

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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

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achave11-ucsc previously approved these changes Nov 22, 2024

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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

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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 added 2 commits November 27, 2024 10:44

Refactor get_duos() to return the DUOS ID

94f2099

[r] Support for AnVIL duos_id (#6620)

3acd295

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 from 7b0b646 to 3acd295 Compare November 27, 2024 18:45

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Support for AnVIL duos_id (#6620) #6668

Support for AnVIL duos_id (#6620) #6668

dsotirho-ucsc commented Oct 30, 2024 •

edited by achave11-ucsc

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dsotirho-ucsc commented Nov 27, 2024

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

Support for AnVIL duos_id (#6620) #6668

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Support for AnVIL duos_id (#6620) #6668

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

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dsotirho-ucsc commented Oct 30, 2024 •

edited by achave11-ucsc

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