Look for report TSV file required to build spectral libraries from DIA-NN results #514
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…o files are required to build the library - a .speclib file and a report TSV file. The .blib lists only the .speclib file. We have to guess the name of the TSV report. - Skyline error when TSV is missing: unable to determine DIA-NN report filename for 'report-lib.parquet.skyline.speclib': the TSV report is required to read speclib files and must be in the same directory as the speclib and share some leading characters (e.g. somedata-tsv.speclib and somedata-report.tsv) - We look for TSV files in the same directory as the .speclib file; find a file with the longest matching prefix that also contains some expected column headers. - Display additional error message on the validation page if the report TSV could not be found.
labkey-jeckels
approved these changes
Feb 26, 2025
panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicValidationTest.java
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panoramapublic/src/org/labkey/panoramapublic/speclib/LibSourceFile.java
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Rationale
Building a spectral library in Skyline from DIA-NN results requires a .speclib file and a report TSV file. The name of the speclib file is in the SpectrumSourceFiles table of the SQLite blib file. However, the name of the report TSV is not included.
Skyline displays this error if the TSV file is missing while building the library:
ERROR: unable to determine DIA-NN report filename for 'report-lib.parquet.skyline.speclib': the TSV report is required to read speclib files and must be in the same directory as the speclib and share some leading characters (e.g. somedata-tsv.speclib and somedata-report.tsv)The report TSV should be uploaded to pass Panorama Public data validation.
Changes