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TES tests: improve Nextflow log parsing#561

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paulineribeyre merged 3 commits into
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tes-unskip
Jun 2, 2026
Merged

TES tests: improve Nextflow log parsing#561
paulineribeyre merged 3 commits into
masterfrom
tes-unskip

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@paulineribeyre
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Link to JIRA ticket if there is one:

New Features

Breaking Changes

Bug Fixes

Improvements

Dependency updates

Deployment changes

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github-actions Bot commented Jun 1, 2026

The style in this PR agrees with black. ✔️

This formatting comment was generated automatically by a script in uc-cdis/wool.

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github-actions Bot commented Jun 1, 2026

Integration Tests on Kind

Test summary after running integration tests

filepath passed failed skipped SUBTOTAL
tests/test_gen3_workflow.py 2 2 1 5
TOTAL 2 2 1 5

Test summary after rerunning failed integration tests

filepath failed SUBTOTAL
tests/test_gen3_workflow.py 2 2
TOTAL 2 2

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github-actions Bot commented Jun 1, 2026

Integration Tests

filepath passed SUBTOTAL
tests/test_gen3_workflow.py 5 5
TOTAL 5 5

Please find the detailed integration test report here

Please find the Github Action logs here

@paulineribeyre paulineribeyre changed the title Enable more TES tests TES tests: improve Nextflow log parsing Jun 2, 2026
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github-actions Bot commented Jun 2, 2026

Integration Tests on Kind

filepath skipped SUBTOTAL
tests/test_gen3_workflow.py 3 3
TOTAL 3 3

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github-actions Bot commented Jun 2, 2026

Integration Tests

filepath passed SUBTOTAL
tests/test_gen3_workflow.py 3 3
TOTAL 3 3

Please find the detailed integration test report here

Please find the Github Action logs here

nss10
nss10 previously approved these changes Jun 2, 2026
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Function looks good, left a comment about variable names. They seem slightly confusing.

if task["process_name"] not in res:
res[task["process_name"]] = task
continue
prev_timestamp = parser.parse(task["timestamp"])
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Wait, does prev_timestamp mean previous timestamp? It seems like we are storing the current/new timestamp in here and storing the timestamp of an already processed line in the new_timestamp.

Can we rename prev_timestamp --> current_timestamp and new_timestamp --> stored_timestamp

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yes i just noticed this! pushing a fix

@paulineribeyre paulineribeyre merged commit 6875b45 into master Jun 2, 2026
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@paulineribeyre paulineribeyre deleted the tes-unskip branch June 2, 2026 17:21
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2 participants