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Set allow_duplicate_entries="False" for built-in Tool Data Tables. #2644

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merged 2 commits into from Jul 22, 2016

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@blankenberg
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commented Jul 21, 2016

Prevents duplicate entries from appearing in data table when they exist in the files. Prevents cases where a duplicate entry occurs and is then passed as a comma separated list onto the command line (which breaks most tools).

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commented Jul 21, 2016

@blankenberg should this not the default setting?

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commented Jul 21, 2016

Its a backwards compatibility issue. There are cases where it could possibly be desirable for a tool data table to allow duplicate entries.

@blankenberg blankenberg removed the major label Jul 21, 2016

@jmchilton jmchilton merged commit 0808015 into galaxyproject:dev Jul 22, 2016

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commented Aug 10, 2016

I agree with @blankenberg it is a backwards compatibility issue, but also with @bgruening in that the default should be false.

e.g. Allowing duplicates has broken BLAST unit tests: https://lists.galaxyproject.org/pipermail/galaxy-dev/2016-August/024771.html

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commented Aug 10, 2016

Sorry, unless I am still overlooking something, adding allow_duplicate_entries="False" has not fixed the comma separated duplicates in the BLAST+ tests:
peterjc/galaxy_blast@55a747e e.g. https://travis-ci.org/peterjc/galaxy_blast/builds/151204086

Was there a separate issue for where the comma-separated entries come from?

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commented Aug 11, 2016

As of this peterjc/galaxy_blast@ebfc584 commit my TravisCI tests pass. The change was removing my manipulation of the *.loc files where combining this with planemo test seems to have resulted in duplicate entries. This was despite peterjc/galaxy_blast@55a747e setting allow_duplicate_entries="False" so there could be a Galaxy problem lurking here?

Your thoughts @blankenberg @jmchilton? Should I file a new issue on this? Thanks.

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