Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:
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Story Points:2
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Epic Link:
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Sprint:Fall 6, Fall 7
Description
Situation: If a user attempts to re-run a InterProScan job through ProtAnnot an error is thrown in the logs (see below).
Task: Investigate and fix the issue.
Steps to reproduce: Follow the IGB ProtAnnot SmokeTesting instructions. The error should appear after the step: Run the InterProScan again by selecting Run InterProScan under the InterProScan tab.
Exception in thread "AWT-EventQueue-0" java.lang.IndexOutOfBoundsException: Index 0 out of bounds for length 0 at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:100) at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:106) at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:302) at java.base/java.util.Objects.checkIndex(Objects.java:385) at java.base/java.util.ArrayList.get(ArrayList.java:427) at org.lorainelab.igb.protannot.model.InterProScanTableModel.getValueAt(InterProScanTableModel.java:90) at java.desktop/javax.swing.JTable.getValueAt(JTable.java:2769)
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Issue Links
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PR is merged.
Prior to testing, we need to increment the ProtAnnot version to 10.0.2.
This is required so that anyone who has ProtAnnot version 10.0.1 (or lower) installed will learn via the IGB interface or via the App Store interface that a new version of the software is available.
Update:
- The new bug-fixed version of ProtAnnot had the same version number as before (10.0.1), which caused the automatic bitbucket pipeline to run and over-write the old, non-fixed ProtAnnot jar file with version, so I re-ran the pipeline with commit f3f5934 as the target
- Meanwhile, I edited the pom.xml file using the bitbucket edit interface and changed the version to 10.0.2
- Saving the pom.xml edit triggered the pipeline and caused it to build a new jar with version 10.0.2
- Downloads section of the repository now has restored 10.0.1 jar file and the all-new 10.0.2 jar file
Ready for testing.
To test, using the ProtAnnot repository:
- Launch IGB
- Just to be on the safe side, de-activate all existing App repositories (using Preferences window, probably)
- Use the IGB interface (also the Preferences window, probably) to add this location as a new "app repository" : https://bitbucket.org/lorainelab/protannot/downloads/
- Check that ProtAnnot appears as an option to install. Check that it is shown as version 10.0.2
- Install it.
- Repeat "steps to reproduce" - see Description section above
- Confirm that the reported bug is no longer an issue.
Request for Paige Kulzer:
- Please take a look - is the bug fixed ?
This new version of ProtAnnot installs successfully and shows up correctly as version 10.0.2. I've confirmed that the reported bug is no longer an issue, ProtAnnot can be re-run multiple times without throwing an error in the Log.
For next steps, I will create a new ticket for releasing this new version of ProtAnnot to the IGB App Store. Marking this issue as complete!
I observed that the issue occurred when the first InterProScan run was performed using the "ProtAnnot -> Run InterProScan" option, and the second run was done via the "InterProScan tab -> Run InterProScan." However, I did not encounter any issues when both the first and second InterProScan runs were performed using the "InterProScan tab -> Run InterProScan" option.
Attaching the log files:
log.txt
Error_Log (2).txt
Instead of receiving the error "java.lang.IndexOutOfBoundsException: Index 0 out of bounds for length 0," mentioned in the ticket. I got the error "Server returned HTTP response code: 400 for URL: http://www.ebi.ac.uk/Tools/services/rest/iprscan5/run."