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ISA-tools / ISAvalidator-ISAconverter-BIImanager

The ISAvalidator, ISA converter and BII data manager tools
http://www.isa-tools.org
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Protocol Type not reported but with ontology REF and accession #47

Closed proccaserra closed 10 years ago

proccaserra commented 10 years ago

Spotted with a test export from Golm Database July 2013: if Protocol Name value exists if Protocol Type value absent if Protocol Type Term Source REF value exists if Protocol Type Term Source Accession value exists

then upon validation, a ArrayIndexOutOfBoundsException is thrown:

Getting ontology object for CMO: oo = null Exception in thread "Thread-17" java.lang.ArrayIndexOutOfBoundsException: 1 at org.isatools.isacreator.io.IOUtils.processOntologyField(IOUtils.java:144) at org.isatools.isacreator.io.exportisa.exportadaptors.ISASectionExportAdaptor.processSectionOntologyFields(ISASectionExportAdaptor.java:89) at org.isatools.isacreator.io.exportisa.exportadaptors.ISASectionExportAdaptor.exportISASectionAsString(ISASectionExportAdaptor.java:117) at org.isatools.isacreator.io.exportisa.exportadaptors.ISASectionExportAdaptor.exportISASectionAsString(ISASectionExportAdaptor.java:102) at org.isatools.isacreator.io.exportisa.ISAFileOutput.printStudy(ISAFileOutput.java:115) at org.isatools.isacreator.gui.io.exportisa.OutputISAFilesFromGUI.saveISAFiles(OutputISAFilesFromGUI.java:99) at org.isatools.isacreator.gui.ISAcreator.saveISATab(ISAcreator.java:1174) at org.isatools.isacreator.validateconvert.ui.ValidateUI$1.run(ValidateUI.java:154) at java.lang.Thread.run(Thread.java:680) Sun Jul 07 16:51:35 BST 2013

proccaserra commented 10 years ago

Not the root cause of error, seems down to unability to resolve the ontology resource declared in the Ontology Section