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PRIDE-Toolsuite / pride-converter-2

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ConverterException exception during writing of result file. #15

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Load 8 mascot.dat files in batch mode

What is the expected output? What do you see instead?

I get the following exception when performing the final step:

Error while generating PRIDE XML file: Report object contains peptide not 
returned by DAO: 6960_1 
uk.ac.ebi.pride.tools.converter.utils.ConverterException: Report object 
contains peptide not returned by DAO: 6960_1 at 
uk.ac.ebi.pride.tools.converter.conversion.io.PrideXmlWriter.finalizeIdentificat
ion(PrideXmlWriter.java:394) at 
uk.ac.ebi.pride.tools.converter.conversion.io.PrideXmlWriter.writeXml(PrideXmlWr
iter.java:241) at 
uk.ac.ebi.pride.tools.converter.gui.forms.FileExportForm.finish(FileExportForm.j
ava:182) at 
uk.ac.ebi.pride.tools.converter.gui.NavigationPanel$4.doInBackground(NavigationP
anel.java:334) at javax.swing.SwingWorker$1.call(SwingWorker.java:296) at 
java.util.concurrent.FutureTask.run(FutureTask.java:262) at 
javax.swing.SwingWorker.run(SwingWorker.java:335) at 
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) 
at 
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) 
at java.lang.Thread.run(Thread.java:744) MODULE: WRAPPER-EXPORT

What version of the product are you using? On what operating system?
2.1.0 on Linux 64bit

Original issue reported on code.google.com by p...@japps.nl on 8 Jul 2014 at 1:13

GoogleCodeExporter commented 9 years ago 
Btw this is a fatal exception; the converter crashes after this.

Original comment by p...@japps.nl on 8 Jul 2014 at 1:14

GoogleCodeExporter commented 9 years ago 
Sorry my version is:

2.0.20 (build 20131031-1454)

Original comment by p...@japps.nl on 8 Jul 2014 at 1:17

GoogleCodeExporter commented 9 years ago 
I have the following result when looking for references to the peptide with 
identifier "9660_1" in the contents of the 8 "dat-report.xml" files:

command: grep "<UniqueIdentifier>6960_1</UniqueIdentifier>" *report.xml 
--before-context 7

result:
F005143.dat-report.xml-  <Peptide>
F005143.dat-report.xml-    <Sequence>GSQQYR</Sequence>
F005143.dat-report.xml-    <CuratedSequence></CuratedSequence>
F005143.dat-report.xml-    <Start>277</Start>
F005143.dat-report.xml-    <End>282</End>
F005143.dat-report.xml-    <SpectrumReference>6960</SpectrumReference>
F005143.dat-report.xml-    <isSpecific>false</isSpecific>
F005143.dat-report.xml:    <UniqueIdentifier>6960_1</UniqueIdentifier>
--
F005143.dat-report.xml-  <Peptide>
F005143.dat-report.xml-    <Sequence>GSQQYR</Sequence>
F005143.dat-report.xml-    <CuratedSequence></CuratedSequence>
F005143.dat-report.xml-    <Start>277</Start>
F005143.dat-report.xml-    <End>282</End>
F005143.dat-report.xml-    <SpectrumReference>6960</SpectrumReference>
F005143.dat-report.xml-    <isSpecific>false</isSpecific>
F005143.dat-report.xml:    <UniqueIdentifier>6960_1</UniqueIdentifier>
--
F005143.dat-report.xml-  <Peptide>
F005143.dat-report.xml-    <Sequence>GSQQYR</Sequence>
F005143.dat-report.xml-    <CuratedSequence></CuratedSequence>
F005143.dat-report.xml-    <Start>277</Start>
F005143.dat-report.xml-    <End>282</End>
F005143.dat-report.xml-    <SpectrumReference>6960</SpectrumReference>
F005143.dat-report.xml-    <isSpecific>false</isSpecific>
F005143.dat-report.xml:    <UniqueIdentifier>6960_1</UniqueIdentifier>
--
F005143.dat-report.xml-  <Peptide>
F005143.dat-report.xml-    <Sequence>GSQQYR</Sequence>
F005143.dat-report.xml-    <CuratedSequence></CuratedSequence>
F005143.dat-report.xml-    <Start>277</Start>
F005143.dat-report.xml-    <End>282</End>
F005143.dat-report.xml-    <SpectrumReference>6960</SpectrumReference>
F005143.dat-report.xml-    <isSpecific>false</isSpecific>
F005143.dat-report.xml:    <UniqueIdentifier>6960_1</UniqueIdentifier>
--
F005143.dat-report.xml-  <Peptide>
F005143.dat-report.xml-    <Sequence>GSQQYR</Sequence>
F005143.dat-report.xml-    <CuratedSequence></CuratedSequence>
F005143.dat-report.xml-    <Start>277</Start>
F005143.dat-report.xml-    <End>282</End>
F005143.dat-report.xml-    <SpectrumReference>6960</SpectrumReference>
F005143.dat-report.xml-    <isSpecific>false</isSpecific>
F005143.dat-report.xml:    <UniqueIdentifier>6960_1</UniqueIdentifier>
--
F005143.dat-report.xml-  <Peptide>
F005143.dat-report.xml-    <Sequence>GSQQYR</Sequence>
F005143.dat-report.xml-    <CuratedSequence></CuratedSequence>
F005143.dat-report.xml-    <Start>277</Start>
F005143.dat-report.xml-    <End>282</End>
F005143.dat-report.xml-    <SpectrumReference>6960</SpectrumReference>
F005143.dat-report.xml-    <isSpecific>false</isSpecific>
F005143.dat-report.xml:    <UniqueIdentifier>6960_1</UniqueIdentifier>
--
F005143.dat-report.xml-  <Peptide>
F005143.dat-report.xml-    <Sequence>GSQQYR</Sequence>
F005143.dat-report.xml-    <CuratedSequence></CuratedSequence>
F005143.dat-report.xml-    <Start>277</Start>
F005143.dat-report.xml-    <End>282</End>
F005143.dat-report.xml-    <SpectrumReference>6960</SpectrumReference>
F005143.dat-report.xml-    <isSpecific>false</isSpecific>
F005143.dat-report.xml:    <UniqueIdentifier>6960_1</UniqueIdentifier>
--
F005143.dat-report.xml-  <Peptide>
F005143.dat-report.xml-    <Sequence>GSQQYR</Sequence>
F005143.dat-report.xml-    <CuratedSequence></CuratedSequence>
F005143.dat-report.xml-    <Start>208</Start>
F005143.dat-report.xml-    <End>213</End>
F005143.dat-report.xml-    <SpectrumReference>6960</SpectrumReference>
F005143.dat-report.xml-    <isSpecific>false</isSpecific>
F005143.dat-report.xml:    <UniqueIdentifier>6960_1</UniqueIdentifier>
--
F005157.dat-report.xml-  <Peptide>
F005157.dat-report.xml-    <Sequence>SEGEVAR</Sequence>
F005157.dat-report.xml-    <CuratedSequence></CuratedSequence>
F005157.dat-report.xml-    <Start>270</Start>
F005157.dat-report.xml-    <End>276</End>
F005157.dat-report.xml-    <SpectrumReference>6960</SpectrumReference>
F005157.dat-report.xml-    <isSpecific>true</isSpecific>
F005157.dat-report.xml:    <UniqueIdentifier>6960_1</UniqueIdentifier>

Hope this is of any help....

Original comment by p...@japps.nl on 8 Jul 2014 at 1:42

GoogleCodeExporter commented 9 years ago 
In the code above it seems strange that the unique identifier is found 8 times 
in the F005143.dat-reportxml file and once in the F005157.dat-report.xml.

Original comment by p...@japps.nl on 8 Jul 2014 at 1:45

GoogleCodeExporter commented 9 years ago 
This error does no longer occurs when I create all the dat-report.xml files in 
one go rather than in multiple separate single .dat file runs.

Original comment by p...@japps.nl on 9 Jul 2014 at 9:29

GoogleCodeExporter commented 9 years ago 
It seems that I get this problem when I use dat-report files that were created 
in different runs of the converter than the one that I was currently running. 
Is this now how dat-report.xml files should be used?

Original comment by p...@japps.nl on 10 Jul 2014 at 8:42