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Enable Support of 2 'Sample Name' chaining to allow representation/tracking of Aliquots #191

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proccaserra opened this issue Feb 7, 2017 · 1 comment
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@proccaserra
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proccaserra commented Feb 7, 2017

Required by Imperial (and most likely all phenome centres): requested by Jake Pearce/Nourredin Sadawi

Protocol type should be set to 'aliquoting' to allow standard parsing.

ISAcreator-1.7+ currently support multiple Sample Name occuring on the Assay Table
<field header="Sample Name" data-type="String" is-file-field="false"
is-multiple-value="true" is-required="true" is-hidden="false" is-forced-ontology="false">


[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]

In case, ISA users were to prefer coding aliquoting event at the 'studySample' level, it would require
modifying ISA configuration to set the 'is_multiple_value' to 'true' in the studySample.xml file:




and amend the ISA java parser/validator, which seems confused if multiple 'Sample Name' header appear in that Table.

TODO: Check if and how ISA-API and ISA python validator/converter handle these representations

TODO: produce ISA-TAB files for testing

@agbeltran agbeltran added this to the Release 0.8 milestone Mar 20, 2017
djcomlab added a commit that referenced this issue Mar 28, 2017
djcomlab added a commit to ISA-tools/ISAdatasets that referenced this issue Mar 28, 2017
@djcomlab djcomlab self-assigned this Mar 28, 2017
djcomlab added a commit that referenced this issue Mar 28, 2017
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Fixed in develop, closing

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