Default configurations do not validate

[isthisthat]

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]

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]

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]

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]

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]

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

[isthisthat]

OK for now!
Cheers.