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SRA export does not support genome seq/nucleotide seq measurement/technology combination #67

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djcomlab opened this issue Jul 25, 2016 · 0 comments
Open

SRA export does not support genome seq/nucleotide seq measurement/technology combination #67

djcomlab opened this issue Jul 25, 2016 · 0 comments
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@djcomlab
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If using genome sequencing and nucleotide sequencing measurement/technology type in the input ISA tab for the SRA converter, the converter does not write out an appropriate set of XML tags for the library descriptor.

On inspection of https://github.com/ISA-tools/ISAvalidator-ISAconverter-BIImanager/blob/master/import_layer/src/main/java/org/isatools/isatab/export/sra/SraExportPipelineComponent.java it looks like there are some unimplemented types (especially now with the SRA 1.5 update) that needs to be added.
djcomlab added a commit that referenced this issue Jul 27, 2016
@djcomlab
Fixes to address problems reported by COPO, linked to issues #67 #63,…
f4d6ff0 
… as well as a few others.

* Add missing STUDY_SET element to study.xml output
* Modifications to SraExportPipelineComponent for new and updated assay types supported by SRA 1.5

Note, some of these changes may affect ISAcreator and ISAconfigurator builds. Until tested with those, keep these changes in this hotfix/copo-sra-export branch.
djcomlab added a commit that referenced this issue Jul 29, 2016
@djcomlab
Fixes to access generated XmlBeans because of schema update #67
a4a9063
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