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  1. IGB
  2. IGBF-3381

Investigate: ProtAnnot can no longer query InterProScan

    Details

    • Type: Task
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
      None

      Description

      I attempted to run a search of InterPro using ProtAnnot but the search did not execute properly. (See attached image for a view of ProtAnnot.)

      It looks like maybe the InterProScan Web service API has changed and ProtAnnot needs to be updated.

      Note:
      To understand how to run a search of InterPro using ProtAnnot, watch the video linked from the top page of https://apps.bioviz.org. The first part of the video explains how to install an IGB App using the App Store. You can skip the first part, since you probably should work with the development (current master branch) version of ProtAnnot available from the Downloads section of a ProtAnnot bitbucket repository. To just see how to run a search with ProtAnnot, you can skip ahead to 1:43 minutes into the video.

      The error, copied from IGB "log" tab:

      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

      For this task, determine if this error re-occurs in other searches.

      For your reference, one gene model searched. The gene model was "AT1G20920.7" from the "Araport" track of Arabidopsis genome version A_thaliana_Jun_2009.

      I discovered the error during final testing of IGBF-3202.

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              • Assignee:
                kgopu Kaushik Gopu
                Reporter:
                ann.loraine Ann Loraine
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                • Created:
                  Updated:
                  Resolved: