Fix: Indexing integration test is complicated and inefficient (#6676) #6677

nadove-ucsc · 2024-11-01T09:54:52Z

Connected issues: #6676

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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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Shorthand for review comments

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

…script (#6669)

#6669)

coveralls · 2024-11-01T10:16:42Z

coverage: 85.522% (+0.2%) from 85.368%
when pulling 6ac46de on issues/nadove-ucsc/6676-indexing-it-complicated-inefficient
into 24aaa42 on develop.

codecov · 2024-11-01T10:44:09Z

Codecov Report

Attention: Patch coverage is 31.68317% with 69 lines in your changes missing coverage. Please review.

Project coverage is 85.50%. Comparing base (24aaa42) to head (6ac46de).

Files with missing lines	Patch %	Lines
test/integration_test.py	0.00%	66 Missing ⚠️
src/azul/plugins/__init__.py	33.33%	2 Missing ⚠️
src/azul/indexer/__init__.py	96.15%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #6677      +/-   ##
===========================================
+ Coverage    85.35%   85.50%   +0.15%     
===========================================
  Files          155      155              
  Lines        20779    20758      -21     
===========================================
+ Hits         17735    17749      +14     
+ Misses        3044     3009      -35

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

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

nadove-ucsc added 4 commits October 30, 2024 17:16

Rename, relocate, and document method

96301ec

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

ea3e362

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

3735676

…script (#6669)

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

bfc2010

#6669)

github-actions bot added the orange [process] Done by the Azul team label Nov 1, 2024

nadove-ucsc force-pushed the issues/nadove-ucsc/6676-indexing-it-complicated-inefficient branch from 975ec25 to 050fe4c Compare November 1, 2024 10:04

nadove-ucsc force-pushed the issues/nadove-ucsc/6676-indexing-it-complicated-inefficient branch from 050fe4c to c3ea16a Compare November 1, 2024 10:22

nadove-ucsc force-pushed the issues/nadove-ucsc/6676-indexing-it-complicated-inefficient branch 2 times, most recently from d3077f9 to 74fccf3 Compare November 1, 2024 23:19

nadove-ucsc and others added 8 commits November 1, 2024 22:52

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

d5d6b41

Fix formatting

c79bee1

Fix missing parameter in inactive code

8ae55de

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

Clarify and enforce bundle FQID equality semantics (#6671)

91d9cf7

fixup! Clarify and enforce bundle FQID equality semantics (#6671)

48b5fa4

Use SourcedBundleFQID in catalog_complete subtest

69f1a70

Eliminate old-style type annotations in integration tests

6d75a5d

Refactor SourceRef prefix assignment

d000642

nadove-ucsc force-pushed the issues/nadove-ucsc/6676-indexing-it-complicated-inefficient branch from 74fccf3 to ca24970 Compare November 3, 2024 21:52

Fix: Indexing integration test is complicated and inefficient (#6676)

6ac46de

nadove-ucsc force-pushed the issues/nadove-ucsc/6676-indexing-it-complicated-inefficient branch from ca24970 to 6ac46de Compare November 3, 2024 22:33

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Fix: Indexing integration test is complicated and inefficient (#6676) #6677

Fix: Indexing integration test is complicated and inefficient (#6676) #6677

nadove-ucsc commented Nov 1, 2024 •

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coveralls commented Nov 1, 2024 •

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Fix: Indexing integration test is complicated and inefficient (#6676) #6677

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Fix: Indexing integration test is complicated and inefficient (#6676) #6677

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nadove-ucsc commented Nov 1, 2024 • edited 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 Nov 1, 2024 • edited Loading

codecov bot commented Nov 1, 2024 • edited Loading

Codecov Report

nadove-ucsc commented Nov 1, 2024 •

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coveralls commented Nov 1, 2024 •

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codecov bot commented Nov 1, 2024 •

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