Details
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Type:
Improvement
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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: 10.1.0
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Labels:None
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Story Points:1
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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, Spring 10
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
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- Closed
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Activity
PR is merged into "main" branch as per usual. Installers are built and deployed to bioviz.org "early access" section.
Ready for testing.
Raised the pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1014. Please review and let me know if there are any issues.
Will raise the pull request once this one is merged as both have a same commit: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1013
Tested Sravani's branch on Mac:
BioViz Connect - worked
Public trackhubs - worked
Galaxy - worked
I was able to load data without seeing the seqid error when genome was only available from UCSC REST.
Ready for pull request
Fixed the issue with the loading when the genome is not present in IGB Quickload, had to change the genome version name that was sent to GeneralLoadView initVersion method, before a wrong version name was sent because of which if the data is no there in IGB Quickload it wasn't able to load the chromosomes using that version name for the remaining providers. Also, had to add the autoload functionality for UCSC to load the data which is done as part of this ticket: https://jira.bioviz.org/browse/IGBF-3633. Updated code is present at the branch: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-2862. Testing is completed, working as expected.
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]
Tested using main branch installer on Mac.
With only the UCSC REST data provider activated, I was able to load genomes from public trackhubs and Galaxy without seeing the seqid error.
Closing ticket.