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Bugfix during error handling with linked files during upload #4858

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merged 1 commit into from Nov 1, 2017

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ieguinoa commented Oct 25, 2017

Just add the same conditions to the if as it is in the finish method.
The problem is, if the upload runs ok but then the job wrapper finish method fails, the runner calls fail() method afterwards: [https://github.com/galaxyproject/galaxy/blob/f4d45549cf9e59a6b3fe00b44744ef69683a149a/lib/galaxy/jobs/runners/init.py#L633]
If cases of upload by linking are not taken into account then the fail method overwrites the files that you are trying to link!

Not sure what are the odds of finish method failing, in my case it was because the data in peek was containing unicode character and that couldn't be inserted in the database with latin-1 coding format.This can happen, for example, when trying to link a pdf as fastqsanger.bz2.
Then your input pdf is overwritten !!!!!

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jmchilton commented Oct 26, 2017

@galaxybot test this

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bgruening commented Oct 28, 2017

LGTM. @natefoo we probably want to have this in 17.09.

@bgruening bgruening added kind/bug and removed triage labels Oct 28, 2017

@jmchilton jmchilton changed the title otherwise it will overwrite linking source file Bugfix during error handling with linked files during upload Nov 1, 2017

@jmchilton jmchilton merged commit 055d777 into galaxyproject:dev Nov 1, 2017

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jmchilton commented Nov 1, 2017

@bgruening I'll open a backport.

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jmchilton commented Nov 1, 2017

@ieguinoa Thanks a bunch for your contribution - this seems like a really solid fix and makes a lot of sense.

@jmchilton jmchilton referenced this pull request Nov 1, 2017

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[17.09] Backport #4858 #4911

martenson added a commit that referenced this pull request Nov 2, 2017

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