ISA converter - use of default configuration - update needed to cope with new assay definitions
proccaserra opened this issue · 0 comments
proccaserra commented
Symptoms:
Conversion from ISA-JSON to ISA-TAB drops unrecognized assays if measurement type and technology types not found in
/resources/config/json/default
by the converter
- strict requirement on
measurement type.term
andtechnology type.term
value: exact match needed. - strict requirement on
protocol_type.term
value: exact match needed. - strict requirement on the sequence of processes and input/output (no support for optional steps, e.g. optional Labeling events during sample processing
TODO:
- add set of assay configurations to cover Metabolights definitions:
https://github.com/EBI-Metabolights/MtblsWS-Py/blob/master/resources/MetaboLightsAssayMaster.tsv - catch unrecognised assay definitions (measurement type + technology type) and raise an ERROR to users and point to curation actions to take.
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