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PRIDE-Archive / jmzTab

Java implementation of the PSI-PI mzTab specification
http://pride-utilities.github.io/jmzTab
Apache License 2.0
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IndexOutOfBoundsException when validating mzid file #13

Closed mbelmadani closed 5 years ago

mbelmadani commented 5 years ago

Hi all,

I was trying to validate files output from Percolator from the crux-toolkit (using the option --mzid-output T). I'm using Java 1.8.0-openjdk on ubuntu 18. 

$ /usr/lib/jvm/java-1.8.0-openjdk-amd64/bin/java -Xms4096m -jar mzIdentMLValidator-1.4.34-SNAPSHOT.jar
W|15:51:58.308|MzIdentMLElement                        |MzIdentML Configuration file: jar:file:/home/z/workshop/mzIdentMLValidator_GUI_v1.4.34-SNAPSHOT/Validator/mzIdentMLValidator-1.4.34-SNAPSHOT.jar!/MzIdentMLElement.cfg.xml
D|15:51:58.422|XmlXpathIndexer                         |Indexing and keeping track of line numbers.
D|15:52:08.977|AXmlElementExtractor                    |Detected charset ISO-8859-1 for input: file:/home/z/local/mbelmadani_22_04_2019_percolator_trypsinp/percolator-out_indiv/trypsinp/comet-out/RawData/myfile_b04_01.mzML.gz/comet.target.txt/percolator.target.mzid
D|15:52:08.980|AXmlElementExtractor                    |Detected charset ISO-8859-1 for input: file:/home/z/local/mbelmadani_22_04_2019_percolator_trypsinp/percolator-out_indiv/trypsinp/comet-out/RawData/myfile_b04_01.mzML.gz/comet.target.txt/percolator.target.mzid
Exception in thread "Thread-2" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
    at java.util.ArrayList.rangeCheck(ArrayList.java:657)
    at java.util.ArrayList.get(ArrayList.java:433)
    at uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory$MzIdentMLIndexerImpl.extractMzIdentMLStartTag(MzIdentMLIndexerFactory.java:298)
    at uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory$MzIdentMLIndexerImpl.<init>(MzIdentMLIndexerFactory.java:106)
    at uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory$MzIdentMLIndexerImpl.<init>(MzIdentMLIndexerFactory.java:59)
    at uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory.buildIndex(MzIdentMLIndexerFactory.java:56)
    at uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory.buildIndex(MzIdentMLIndexerFactory.java:44)
    at uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller.<init>(MzIdentMLUnmarshaller.java:60)
    at psidev.psi.pi.validator.MzIdentMLValidator.startValidation(MzIdentMLValidator.java:466)
    at psidev.psi.pi.validator.MzIdentMLValidatorGUI$4.construct(MzIdentMLValidatorGUI.java:706)
    at psidev.psi.pi.validator.swingworker.SwingWorker.lambda$new$1(SwingWorker.java:138)
    at java.lang.Thread.run(Thread.java:748)

Is this a bug or is there something I can configure to work around this? In this snippet I doubled the memory but I had the same issue with the original settings.

nilshoffmann commented 5 years ago

Hi, could you please move your issue to the following repository: https://github.com/PRIDE-Utilities/jmzIdentML

This repository is for the mzTab 1.0 reference implementation jmzTab. From your stack trace, I only see jmzIdentML being used.

With kind regards, Nils

Am 23.04.2019 um 00:57 schrieb Manuel Belmadani notifications@github.com:

Hi all,

I was trying to validate files output from Percolator from the crux-toolkit (using the option --mzid-output T). I'm using Java 1.8.0-openjdk on ubuntu 18.

$ /usr/lib/jvm/java-1.8.0-openjdk-amd64/bin/java -Xms4096m -jar mzIdentMLValidator-1.4.34-SNAPSHOT.jar W|15:51:58.308|MzIdentMLElement |MzIdentML Configuration file: jar:file:/home/z/workshop/mzIdentMLValidator_GUI_v1.4.34-SNAPSHOT/Validator/mzIdentMLValidator-1.4.34-SNAPSHOT.jar!/MzIdentMLElement.cfg.xml D|15:51:58.422|XmlXpathIndexer |Indexing and keeping track of line numbers. D|15:52:08.977|AXmlElementExtractor |Detected charset ISO-8859-1 for input: file:/home/z/local/mbelmadani_22_04_2019_percolator_trypsinp/percolator-out_indiv/trypsinp/comet-out/RawData/myfile_b04_01.mzML.gz/comet.target.txt/percolator.target.mzid D|15:52:08.980|AXmlElementExtractor |Detected charset ISO-8859-1 for input: file:/home/z/local/mbelmadani_22_04_2019_percolator_trypsinp/percolator-out_indiv/trypsinp/comet-out/RawData/myfile_b04_01.mzML.gz/comet.target.txt/percolator.target.mzid Exception in thread "Thread-2" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 at java.util.ArrayList.rangeCheck(ArrayList.java:657) at java.util.ArrayList.get(ArrayList.java:433) at uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory$MzIdentMLIndexerImpl.extractMzIdentMLStartTag(MzIdentMLIndexerFactory.java:298) at uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory$MzIdentMLIndexerImpl.(MzIdentMLIndexerFactory.java:106) at uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory$MzIdentMLIndexerImpl.(MzIdentMLIndexerFactory.java:59) at uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory.buildIndex(MzIdentMLIndexerFactory.java:56) at uk.ac.ebi.jmzidml.xml.xxindex.MzIdentMLIndexerFactory.buildIndex(MzIdentMLIndexerFactory.java:44) at uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller.(MzIdentMLUnmarshaller.java:60) at psidev.psi.pi.validator.MzIdentMLValidator.startValidation(MzIdentMLValidator.java:466) at psidev.psi.pi.validator.MzIdentMLValidatorGUI$4.construct(MzIdentMLValidatorGUI.java:706) at psidev.psi.pi.validator.swingworker.SwingWorker.lambda$new$1(SwingWorker.java:138) at java.lang.Thread.run(Thread.java:748)

Is this a bug or is there something I can configure to work around this? In this snippet I doubled the memory but I had the same issue with the original settings.

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mbelmadani commented 5 years ago

My bad, thanks for the pointer!