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ISA-tools / isa-configurations

ISAconfiguration files which have been created by the ISAconfigurator. These can be used by ISAcreator, ISAvalidator, ISAconverter and the BII Data Management Tool
http://isa-tools.org
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Default configurations do not validate #5

Open isthisthat opened 11 years ago

isthisthat commented 11 years ago

Errors remaining:

error - a_study_protein-protein interaction detection_protein microarray.txt Invalid ISA-TAB: unexpected field Derived Data File found in section transcriptomics_pipeline

warning - a_study_cell sorting_flow cytometry.txt the column "Image File" (#12) is in a wrong position, or some other column is missing before this. Please check the ISATAB specification. error - a_study_cell sorting_flow cytometry.txt Errors in fields order/structure with the file "a_study_cell sorting_flow cytometry.txt", see the log messages for details

warning - a_study_cell counting_flow cytometry.txt WARNING: The field "Data Transformation Name" should be preceded by the field "Normalization Name" warning - a_study_cell counting_flow cytometry.txt the column "Image File" (#12) is in a wrong position, or some other column is missing before this. Please check the ISATAB specification. error - a_study_cell counting_flow cytometry.txt Errors in fields order/structure with the file "a_study_cell counting_flow cytometry.txt", see the log messages for details

warning - a_study_protein-DNA binding site identification_DNA microarray.txt the column "Array Data Matrix File" (#27) is in a wrong position, or some other column is missing before this. Please check the ISATAB specification. error - a_study_protein-DNA binding site identification_DNA microarray.txt Errors in fields order/structure with the file "a_study_protein-DNA binding site identification_DNA microarray.txt", see the log messages for details

eamonnmag commented 11 years ago

Yes, this is now correct. Your file a_study_protein-protein interaction detection_protein microarray.txt needs to be edited and the column Derived Data File should be renamed to Derived Array Data File.

isthisthat commented 11 years ago

Please have a look at https://github.com/ISA-tools/Configuration-Files/blob/master/isaconfig-default_v2013-02-13/ppi_detection_micro.xml That file still has it as "Derived Data File".

Please fix the rest of the "warnings" as well. They result to errors preventing the user from passing validation.

Thanks.

eamonnmag commented 11 years ago

Sorry, I was looking at a different XML file. Updated now. The warnings will not stop validation, they are simply shown alongside errors, if errors appeared. If there are only warnings, validation will be successful, unless validation is 'strict'. I'll have to ask @proccaserra to fix the ordering issues.

thanks!

isthisthat commented 11 years ago

Hi Eamonn, Regarding "The warnings will not stop validation, they are simply shown alongside errors, if errors appeared." You are right. However, in cases where these is a column ordering issue, I've noticed that the warning results into an error. That's why I've particularly included those warnings above (even though there were many more "silent" warnings). You can check for yourself.

eamonnmag commented 11 years ago

Sure, and we'll sort those existing problems with validation asap. Thanks for your patience. Are your other problems solved now?

isthisthat commented 11 years ago

OK for now! Cheers.