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Add EDAM topic(s) and operation(s) elements to XSD file. #3221

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merged 1 commit into from Nov 28, 2016

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@hmenager
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commented Nov 25, 2016

This is a proposal to add EDAM-related elements declaration to the Galaxy XSD file. The current Galaxy tools which include EDAM topic(s) or operation(s) will fail validation with the XSD.

For instance, with https://github.com/galaxyproject/galaxy/blob/dev/tools/filters/bed_to_bigbed.xml:

$ xmllint --noout --schema ~/galaxy/lib/galaxy/tools/xsd/galaxy.xsd bed_to_bigbed.xml 
bed_to_bigbed.xml:3: element edam_operations: Schemas validity error : Element 'edam_operations': This element is not expected. Expected is one of ( macros, requirements, parallelism, version_command, action, environment_variables, command, request_parameter_translation, configfiles, outputs ).
bed_to_bigbed.xml fails to validate

Or with https://github.com/galaxyproject/galaxy/blob/dev/tools/stats/gsummary.xml:

$ xmllint --noout --schema ~/galaxy/lib/galaxy/tools/xsd/galaxy.xsd gsummary.xml 
gsummary.xml:3: element edam_topics: Schemas validity error : Element 'edam_topics': This element is not expected. Expected is one of ( macros, requirements, parallelism, version_command, action, environment_variables, command, request_parameter_translation, configfiles, outputs ).
gsummary.xml fails to validate

This PR declares the EDAM related elements to avoid these errors.

@bgruening

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commented Nov 25, 2016

Very nice @hmenager! Thanks a lot!

@galaxybot galaxybot added the triage label Nov 25, 2016

@galaxybot galaxybot added this to the 17.01 milestone Nov 25, 2016

@jmchilton

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commented Nov 28, 2016

@galaxybot test this

@jmchilton jmchilton merged commit c8ea393 into galaxyproject:dev Nov 28, 2016

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@jmchilton

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commented Nov 28, 2016

Awesome - thanks @hmenager!

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