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elixir-europe / plant-brapi-to-isa

BSD 3-Clause "New" or "Revised" License
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Protocol declaration problem #49

Closed bedroesb closed 5 years ago

bedroesb commented 5 years ago

Protocols are implemented + correctly dumped in the ISA-tab files, yet the validator is giving these errors:

"message": "Missing Protocol declaration",
"supplemental": "Protocol(s) of type ['Phenotyping'] defined in the ISA-configuration expected as a between 'Sample Name' and 'Assay Name' but has not been found, in the file 'a_VIB_study___55_plant.txt'",
"code": 1007
"message": "Missing Protocol declaration",
"supplemental": "Protocol(s) of type ['Growth'] defined in the ISA-configuration expected as a between 'Source Name' and 'Sample Name' but has not been found, in the file 's_VIB_study___55.txt'",
"code": 1007
bedroesb commented 5 years ago

"It is meaningless to have a value in the Study Assay Measurement Type Term Source REF and Study Assay Technology Type Term Source REF, if the respective Study Assay Measurement Type Term Accession Number and Study Assay Technology Type Term Accession Number are empty."

bedroesb commented 5 years ago

"Create a file with the ontology URIs for the ontologies / ontology prefixes that are used most commonly, and have the script place them in this section where applicable."

bedroesb commented 5 years ago

leaving out the protocol parameters in the assay file when phenotyping is the protocol