Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Minor
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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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Story Points:0.5
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Epic Link:
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Sprint:Summer 2 2023 May 29, Summer 4 2023 June 26, Summer 5 2023 July 10
Description
In the ProtAnnot app, a link connecting to an InterPro web page takes the user to a '404 page not found' page which will redirect to the correct page. Replace the existing link with the working link: http://www.ebi.ac.uk/interpro/about/interpro/
To find the dead link in ProtAnnot:
1. Open IGB.
2. Plug-ins > Launch App Manager
3. Install ProtAnnot
4. Open a genome
5. Click and drag to select some data to compare
6. In upper left, Tools > Start ProtAnnot
7. In ProtAnnot, click Run InterProScan...
8. In the new Job Configuration window, in bottom left notice the link "visit the Interpro Web page at EBI."
9. Clicking this link takes the user to "http://www.ebi.ac.uk/interpro/about.html/". Which is not valid, but redirects to the site's current About page.
Change the link so it takes the user directly to the InterPro About page: "http://www.ebi.ac.uk/interpro/about/interpro/"
Attachments
Issue Links
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- Closed
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Activity
I have updated the version of the project. https://bitbucket.org/kaushik-gopu/kgopu_proant/downloads/
The new version of the jar has been build in the downloads folder of the repo.
Tested ProtAnnot version from Kaushik's downloads folder. When installed on IGB release 9.1.10 version shows as 9.1.4.
Ready for pull request.
Squashed the commits to keep repository history readable and understandable.
Ready for pull request: https://bitbucket.org/kaushik-gopu/kgopu_proant/pull-requests/4
PR is now merged. Ready for testing.
To test, add this location as a new bundle repository (app store):
Test this using IGB version 9.1.10 or lower. Version higher than 9.1.10 will not work because it will use/have a different google guava library version than what is being used by the App.
I installed ProtAnnot using the "downloads" folder as the bundle repository and confirmed that the link now works.
However, I discovered what appears to be a new problem.
When I attempted to run an InterPro Search, the search failed with the following error. Lines lines preceding the error are included for context.
01:20:10.863 INFO com.affymetrix.igb.IGB - Completed loading sequence for Chr1 : 7,284,963 - 7,290,069 from IGB Quickload http://lorainelab-quickload.scidas.org/quickload/
01:21:04.688 INFO o.l.i.p.i.InterProscanServiceRest - iprscan5-R20230710-072102-0693-74435734-p1m
01:21:05.129 ERROR o.l.i.p.i.InterProscanServiceRest - No enum constant org.lorainelab.igb.protannot.interproscan.api.InterProscanService.Status.QUEUED
java.lang.IllegalArgumentException: No enum constant org.lorainelab.igb.protannot.interproscan.api.InterProscanService.Status.QUEUED
at java.lang.Enum.valueOf(Enum.java:238) ~[na:1.8.0_332]
at org.lorainelab.igb.protannot.interproscan.api.InterProscanService$Status.valueOf(InterProscanService.java:29) ~[-1688969961404:na]
at org.lorainelab.igb.protannot.interproscan.InterProscanServiceRest.status(InterProscanServiceRest.java:106) ~[-1688969961404:na]
at org.lorainelab.igb.protannot.ProtAnnotService$5.run(ProtAnnotService.java:692) [-1688969961404:na]
at java.util.TimerThread.mainLoop(Timer.java:555) [na:1.8.0_332]
at java.util.TimerThread.run(Timer.java:505) [na:1.8.0_332]
01:21:05.130 INFO o.l.igb.protannot.ProtAnnotService - iprscan5-R20230710-072102-0693-74435734-p1m Error
Opening a new ticket (IGBF-3381) to investigate / reproduce the error, and then fix the error.
Link has been updated and tested in local.
Link to branch IGBF-3202