Details
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Type:
Improvement
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Status: To-Do (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:3
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Epic Link:
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Sprint:Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9, Summer 3 2021 Jul 12 - Jul 23
Description
Situation: Many genomes in IGB are provided by UCSC DAS, a service that is similar to Quickload. Galaxy is a website that provides analysis tools for genomes. The data produced by Galaxy can then be viewed in IGB by clicking a link in Galaxy. The link works through the BookmarkUnibrowControlServlet.java class to parse out the genome and other information.
However, there is an edge case where if the genome is provided by UCSC DAS in IGB (as opposed to IGB Quickload) and the user has not first selected the correct genome, clicking the link in Galaxy will cause an error (see comment). This is because seqid is null. The seqid should be set to a chromosome/scaffold/contig of the genome. My guess is that because the genome is provided by UCSC DAS, which behaves differently than Quickload, the current methods to retrieve the seqid for the genome are returning null.
Task: Implement a fix.
Attachments
Issue Links
- relates to
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- Closed
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Activity
To replicate:
In IGB, navigate to File > Preferences... and then select the Data Sources tab
Disable all data sources except for UCSC DAS
Close and reopen IGB (do not reset preferences to default)
In a web browser, paste the following link:
No seqid: The bookmark did not specify a valid seqid: specified 'null'
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14:22:20.856 ERROR c.a.i.b.BookmarkUnibrowControlServlet - Error while loading bookmark.
java.lang.NullPointerException: null
at com.affymetrix.igb.bookmarks.BookmarkUnibrowControlServlet$1.runInBackground(BookmarkUnibrowControlServlet.java:224) ~[classes/:na]
at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) [genometry-9.1.8.jar:na]
at javax.swing.SwingWorker$1.call(SwingWorker.java:295) [na:1.8.0_191]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_191]
at javax.swing.SwingWorker.run(SwingWorker.java:334) [na:1.8.0_191]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_191]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_191]
at java.lang.Thread.run(Thread.java:748) [na:1.8.0_191]