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SwissDataScienceCenter / renku-python

A Python library for the Renku collaborative data science platform.
https://renku-python.readthedocs.io/
Apache License 2.0
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Different dot-graphs with relative paths as outputdirectory #397

Open rcnijzink opened 5 years ago

rcnijzink commented 5 years ago

Describe the bug The knowledge graph generated with a dot-format differs depending on the way the outputdirectory is defined. Only when all paths are set down from the current work directory, the graph shows the directory as output. With relative paths going up, the graphs shows the individual files. This is mainly a problem in case there are many files produced.

To Reproduce https://renkulab.io/gitlab/remko.nijzink/vom_test commit c83ed73b2625fb6ad81789d7b0adb5359e43a656

This works fine: renku run bash src_sh/copy2dir.sh data/input/AdelaideRiver/dailyweather.prn work/AdelaideRiver/tmp_results2/ renku log --format dot resultfile | dot -Tpng > out1.png

This leads to a different graph showing the file as output instead of the directory: renku run bash ../../src_sh/copy2dir.sh ../../data/input/AdelaideRiver/dailyweather.prn tmp_results2/ renku log --format dot resultfile | dot -Tpng > out1.png

See also the graphs attached, the ascii formats do not seem to have this issue. outputdir_bug.txt outputdir_correct.txt

outputdir_bug

outputdir_correct

jirikuncar commented 5 years ago

@rcnijzink I can confirm that it's a problem. Unfortunately, I don't have a reliable solution that would generate a correct CWL description for running script with an output directory outside the repository root.