Fix: Various problems in can_bundle script (#6669) by nadove-ucsc · Pull Request #6670 · DataBiosphere/azul

nadove-ucsc · 2024-10-31T00:22:12Z

Connected issues: #6669

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Shorthand for review comments

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

codecov · 2024-10-31T00:41:56Z

Codecov Report

Attention: Patch coverage is 26.66667% with 11 lines in your changes missing coverage. Please review.

Project coverage is 85.42%. Comparing base (787c416) to head (d53b159).
Report is 8 commits behind head on develop.

Files with missing lines	Patch %	Lines
test/integration_test.py	0.00%	10 Missing ⚠️
src/azul/plugins/__init__.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #6670      +/-   ##
===========================================
+ Coverage    85.40%   85.42%   +0.01%     
===========================================
  Files          155      155              
  Lines        20783    20777       -6     
===========================================
- Hits         17749    17748       -1     
+ Misses        3034     3029       -5

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

coveralls · 2024-10-31T00:43:16Z

coverage: 85.439% (+0.02%) from 85.419%
when pulling d53b159 on issues/nadove-ucsc/6669-various-problems-can-bundle-script
into 787c416 on develop.

dsotirho-ucsc · 2024-10-31T16:27:51Z

scripts/can_bundle.py

+    table_name = args.table_name
+    if table_name is not None:
+        fields['table_name'] = table_name


Suggested change

table_name = args.table_name

if table_name is not None:

fields['table_name'] = table_name

if args.table_name is not None:

fields['table_name'] = args.table_name

dsotirho-ucsc · 2024-10-31T16:31:02Z

scripts/can_bundle.py

    raise ValueError(f'No repository using source {source!r}')


+def parse_fqid_fields(args: argparse.Namespace) -> JSON:


Since parse_fqid_fields() is called before fetch_bundle(), it would make more sense to have it moved up so it is defined before fetch_bundle().

dsotirho-ucsc

Approved.

hannes-ucsc · 2024-11-02T05:43:56Z

…script (#6669)

#6669)

This fix is untested since it touches code that is disabled (conditional upon DSS direct access).

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dsotirho-ucsc marked this pull request as ready for review November 1, 2024 16:49

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hannes-ucsc dismissed stale reviews from dsotirho-ucsc and themself via 8ae55de November 2, 2024 07:51

hannes-ucsc force-pushed the issues/nadove-ucsc/6669-various-problems-can-bundle-script branch from c6799f3 to 8ae55de Compare November 2, 2024 07:51

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hannes-ucsc assigned achave11-ucsc and unassigned hannes-ucsc Nov 2, 2024

achave11-ucsc added the sandbox [process] Resolution is being verified in sandbox deployment label Nov 5, 2024

achave11-ucsc dismissed hannes-ucsc’s stale review via 1a6d5e3 November 5, 2024 07:21

achave11-ucsc force-pushed the issues/nadove-ucsc/6669-various-problems-can-bundle-script branch 2 times, most recently from 1a6d5e3 to 8ae55de Compare November 5, 2024 19:41

achave11-ucsc removed their assignment Nov 5, 2024

nadove-ucsc added 2 commits November 5, 2024 11:48

Rename, relocate, and document method

cad323c

Fix: Inaccurate module-level docstring in can_bundle script (#6669)

644377f

nadove-ucsc and others added 5 commits November 5, 2024 11:48

Fix: Faulty/brittle default value for source parameter in can_bundle …

8da52fb

…script (#6669)

Fix: Incorrect help message for version parameter in can_bundle script (

2b0d7d8

#6669)

can_bundle script requires explicit table name for AnVIL sources (#6669)

f0be49d

Fix formatting

85b36ea

Fix missing parameter in inactive code

d53b159

This fix is untested since it touches code that is disabled (conditional upon DSS direct access).

nadove-ucsc force-pushed the issues/nadove-ucsc/6669-various-problems-can-bundle-script branch from 8ae55de to d53b159 Compare November 5, 2024 19:48

nadove-ucsc assigned achave11-ucsc Nov 5, 2024

achave11-ucsc requested a review from hannes-ucsc November 5, 2024 20:51

achave11-ucsc assigned hannes-ucsc and unassigned achave11-ucsc Nov 5, 2024

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hannes-ucsc removed the sandbox [process] Resolution is being verified in sandbox deployment label Nov 5, 2024

achave11-ucsc added the sandbox [process] Resolution is being verified in sandbox deployment label Nov 6, 2024

achave11-ucsc merged commit bee4a60 into develop Nov 6, 2024

achave11-ucsc deleted the issues/nadove-ucsc/6669-various-problems-can-bundle-script branch November 6, 2024 16:14

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hannes-ucsc linked an issue Sep 12, 2025 that may be closed by this pull request

Various problems in can_bundle script #6669

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Fix: Various problems in can_bundle script (#6669)#6670

Fix: Various problems in can_bundle script (#6669)#6670
achave11-ucsc merged 7 commits intodevelopfrom
issues/nadove-ucsc/6669-various-problems-can-bundle-script

nadove-ucsc commented Oct 31, 2024 •

edited by achave11-ucsc

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		raise ValueError(f'No repository using source {source!r}')


		def parse_fqid_fields(args: argparse.Namespace) -> JSON:

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nadove-ucsc commented Oct 31, 2024 •

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