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compomics / reporter

Protein quantification based on reporter ions
http://compomics.github.io/projects/reporter.html
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problems exporting PSM reports #15

Closed jcanderan closed 3 years ago

jcanderan commented 3 years ago

Hello,

I can successfully export Peptide/Protein reports (both in windows and linux), but cannot export any form of a PSM report regardless of the psdb used.

Here's a sample error log from trying in Windows GUI:

java.lang.NullPointerException: Cannot read the array length because "keys" is null
    at eu.isas.reporter.export.report.sections.ReporterPsmSection.writeSection(ReporterPsmSection.java:188)
    at eu.isas.reporter.export.report.ReporterExportFactory.writeExport(ReporterExportFactory.java:482)
    at eu.isas.reporter.gui.export.ReportDialog$11.run(ReportDialog.java:447)

Here's a sample error log from trying in linux command-line with a different psdb:

java.lang.NullPointerException
        at eu.isas.reporter.export.report.sections.ReporterPsmSection.writeSection(ReporterPsmSection.java:188)
        at eu.isas.reporter.export.report.ReporterExportFactory.writeExport(ReporterExportFactory.java:482)
        at eu.isas.reporter.cli.CLIExportMethods.exportReport(CLIExportMethods.java:91)
        at eu.isas.reporter.cli.ReporterCLI.call(ReporterCLI.java:581)
        at eu.isas.reporter.cli.ReporterCLI.main(ReporterCLI.java:845)

Thanks!

hbarsnes commented 3 years ago

Thanks for letting us know! This has now been fixed and a new version will be released soon.

hbarsnes commented 3 years ago

I've just released a new version of Reporter that should solve this issue. If you still have issues with the PSM reports, please let me know and I'll reopen the issue.

jcanderan commented 3 years ago

Thanks for working on this!

It gets further than it did but now a new error when exporting report type 4 pops up:

java.lang.IllegalArgumentException: No best match found for spectrum -3083128518393361966.
        at eu.isas.reporter.export.report.sections.ReporterPsmSection.writeSection(ReporterPsmSection.java:275)
        at eu.isas.reporter.export.report.ReporterExportFactory.writeExport(ReporterExportFactory.java:482)
        at eu.isas.reporter.cli.CLIExportMethods.exportReport(CLIExportMethods.java:91)
        at eu.isas.reporter.cli.ReporterCLI.call(ReporterCLI.java:581)
        at eu.isas.reporter.cli.ReporterCLI.main(ReporterCLI.java:845)

Here's the error for a different file:

java.lang.IllegalArgumentException: No best match found for spectrum -5146861328799035303.
        at eu.isas.reporter.export.report.sections.ReporterPsmSection.writeSection(ReporterPsmSection.java:275)
        at eu.isas.reporter.export.report.ReporterExportFactory.writeExport(ReporterExportFactory.java:482)
        at eu.isas.reporter.cli.CLIExportMethods.exportReport(CLIExportMethods.java:91)
        at eu.isas.reporter.cli.ReporterCLI.call(ReporterCLI.java:581)
        at eu.isas.reporter.cli.ReporterCLI.main(ReporterCLI.java:845)
hbarsnes commented 3 years ago

I've just released a new version of Reporter attempting to fix the issue. Please give it a go and let me know if it solves the problem?

jcanderan commented 3 years ago

Fixed the issue for the files I've tested.

Thanks!