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Bug in planemo test workflow with subworkflows #1345

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lldelisle opened this issue Jan 13, 2023 · 1 comment
Open

Bug in planemo test workflow with subworkflows #1345

lldelisle opened this issue Jan 13, 2023 · 1 comment

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@lldelisle
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Hi,
I found a bug in planemo test when testing workflow with subworkflow. It seems that planemo does not wait for the subworkflow to finish before testing the outputs...
Here is a minimal test to reproduce the error:
test.tar.gz
The command line used was:

$ planemo test --galaxy_url https://usegalaxy.org/ --galaxy_user_key xxxx stupid-workflow2.ga 
waiting for invocation 1f1b4765b9fcc485
galaxy.tool_util.verify INFO: ## files diff on '/home/ldelisle/Documents/mygit/iwc/test/test-data/input file.txt' and '/tmp/tmpo0rffprzinput file.txt': lines_diff = 0, found diff = 7
galaxy.tool_util.verify INFO: ## files diff on '/home/ldelisle/Documents/mygit/iwc/test/test-data/input file.txt' and '/tmp/tmpdb2rh8_ainput file.txt': lines_diff = 0, found diff = 7
None
There were problems with 1 test(s) - out of 1 test(s) executed. See /home/ldelisle/Documents/mygit/iwc/test/tool_test_output.html for detailed breakdown.
stupid-workflow2.ga_0: failed

If you check the html, you can see:
image
The subworkflow did not started at the time the output was analysed.

@mvdbeek
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mvdbeek commented Jan 13, 2023

Arg, I should have known this when I changed the polling in https://github.com/galaxyproject/planemo/pull/1297/files#diff-782ba15d4458fed978058ad9cb3874e0d49a029eee86757df40cabd0951fe957R737 ... if you're up for a new adventure in planemo you could look at _wait_for_invocation_jobs ... this should also look at all subworkflow invocations.

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