Details

    • Type: Bug
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
      None
    • Story Points:
      0.25
    • Sprint:
      Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23

      Description

      Attempting to submit an app using a URL creates an error.
      Tried https://bitbucket.org/lorainelab/super-simple-igb-app/downloads/super-simple-igb-app-0.0.1.jar with devappstore5.bioviz.org.

      To test, enter a jar file from the Downloads section of one of the IGB Apps available from https://bitbucket.org/lorainelab/workspace/projects/IAQ.

        Attachments

          Activity

          ann.loraine Ann Loraine created issue -
          ann.loraine Ann Loraine made changes -
          Field Original Value New Value
          Epic Link IGBF-2563 [ 18746 ]
          ann.loraine Ann Loraine made changes -
          Description Attempting to submit an app creates an error. Attempting to submit an app creates an error.
          Tried it on devappstore5.bioviz.org
          ann.loraine Ann Loraine made changes -
          Assignee Sameer Shanbhag [ sameer ]
          ann.loraine Ann Loraine made changes -
          Description Attempting to submit an app creates an error.
          Tried it on devappstore5.bioviz.org
          Attempting to submit an app creates an error.
          Tried it on devappstore5.bioviz.org

          To test, you can enter a jar file from the Downloads section of one of the IGB Apps available from https://bitbucket.org/lorainelab/workspace/projects/IAQ.
          ann.loraine Ann Loraine made changes -
          Description Attempting to submit an app creates an error.
          Tried it on devappstore5.bioviz.org

          To test, you can enter a jar file from the Downloads section of one of the IGB Apps available from https://bitbucket.org/lorainelab/workspace/projects/IAQ.
          Attempting to submit an app creates an error. Tried https://bitbucket.org/lorainelab/super-simple-igb-app/downloads/super-simple-igb-app-0.0.1.jar with devappstore5.bioviz.org.

          To test, you can enter a jar file from the Downloads section of one of the IGB Apps available from https://bitbucket.org/lorainelab/workspace/projects/IAQ.
          ann.loraine Ann Loraine made changes -
          Description Attempting to submit an app creates an error. Tried https://bitbucket.org/lorainelab/super-simple-igb-app/downloads/super-simple-igb-app-0.0.1.jar with devappstore5.bioviz.org.

          To test, you can enter a jar file from the Downloads section of one of the IGB Apps available from https://bitbucket.org/lorainelab/workspace/projects/IAQ.
          Attempting to submit an app using a URL creates an error.
          Tried https://bitbucket.org/lorainelab/super-simple-igb-app/downloads/super-simple-igb-app-0.0.1.jar with devappstore5.bioviz.org.

          To test, enter a jar file from the Downloads section of one of the IGB Apps available from https://bitbucket.org/lorainelab/workspace/projects/IAQ.
          ann.loraine Ann Loraine made changes -
          Comment [ * App type - How an App changes the IGB interface

          Application - Application Apps add new windows to the IGB Interface
          Plugin - Plugin Apps add new menus to the IGB interface
          Panel - Panel Apps introduced a new tabbed panel to the IGB interface

          * Biology - Apps categorized by biological research area

          Epigenome - Apps for visualizing or searching DNA or histone modification diversity
          Alternative splicing - Apps that show splicing pattern diversity
          Microbial genomics - Apps for analysis and visualization of microbial genomic data
          Plant genomics - Apps for analysis and visualization of genomes from photosynthetic organisms
          Protein - Apps for searching or visualizing of protein structure or function
          Transcriptome - Apps that display RNA expression data

          * Data - Apps categorized by data formats and data types

          Bisulfite - Apps that display DNA from bisulfite sequencing to detect DNA methylation
          ChIP-Seq - Apps that display DNA sequenced from chromatin precipitation experiments
          DNA-Seq - Apps that display genomic DNA sequencing results
          RNA-Seq - Apps that display RNA sequence alignments and genome graphs










          ]
          ann.loraine Ann Loraine made changes -
          Sprint Fall 5 Nov 9 - Nov 20 [ 108 ] Fall 5 Nov 9 - Nov 20, Fall 6 Nov 23 - Dec 4 [ 108, 109 ]
          ann.loraine Ann Loraine made changes -
          Rank Ranked higher
          Hide
          sameer Sameer Shanbhag (Inactive) added a comment -

          Reason:

          • PermissionError: [Errno 13] Permission denied: '/home/ubuntu/appstore/submit_appmerge-annotation-operator-9.1.0.jar'

          Currently fixing the issue.

          Show
          sameer Sameer Shanbhag (Inactive) added a comment - Reason: PermissionError: [Errno 13] Permission denied: '/home/ubuntu/appstore/submit_appmerge-annotation-operator-9.1.0.jar' Currently fixing the issue.
          Hide
          sameer Sameer Shanbhag (Inactive) added a comment -

          Hi Professor [~aloraine],

          Currently the above error can be caused because there was inconsistency on how we were opening the temp file for writing and before closing the file we open it for writing which causes the permission issue, on windows it gives a specific error saying file is being used by another process, I have updated it so that this wont happen

          Show
          sameer Sameer Shanbhag (Inactive) added a comment - Hi Professor [~aloraine] , Currently the above error can be caused because there was inconsistency on how we were opening the temp file for writing and before closing the file we open it for writing which causes the permission issue, on windows it gives a specific error saying file is being used by another process, I have updated it so that this wont happen https://bitbucket.org/lorainelab/appstore/pull-requests/229/igbf-2659-fix-the-permission-issue-due-to
          sameer Sameer Shanbhag (Inactive) made changes -
          Status To-Do [ 10305 ] Pull Request Submitted [ 10101 ]
          Hide
          ann.loraine Ann Loraine added a comment -

          I have merged in the PR and deployed the new code to https://devappstore5.bioviz.org
          I am still seeing an "Internal Server Error" upon attempting to submit jar via a URL.
          attn: Sameer Shanbhag

          Show
          ann.loraine Ann Loraine added a comment - I have merged in the PR and deployed the new code to https://devappstore5.bioviz.org I am still seeing an "Internal Server Error" upon attempting to submit jar via a URL. attn: Sameer Shanbhag
          Hide
          sameer Sameer Shanbhag (Inactive) added a comment -

          Hi Professor [~aloraine],

          This confirms that the windows and linux have two different problem, In windows the problem is caused due to the above reason where as in ubuntu the problem is caused due to lack of permissions for the user trying to create a temp file

          • we might need to change this in the Playbooks (give write permission to apache process on submit_app directory)

          Error:

          • PermissionError: [Errno 13] Permission denied: '/home/ubuntu/appstore/submit_app/merge-annotation-operator-9.1.0.jar'
          Show
          sameer Sameer Shanbhag (Inactive) added a comment - Hi Professor [~aloraine] , This confirms that the windows and linux have two different problem, In windows the problem is caused due to the above reason where as in ubuntu the problem is caused due to lack of permissions for the user trying to create a temp file we might need to change this in the Playbooks (give write permission to apache process on submit_app directory) Error: PermissionError: [Errno 13] Permission denied: '/home/ubuntu/appstore/submit_app/merge-annotation-operator-9.1.0.jar'
          Hide
          ann.loraine Ann Loraine added a comment -

          Thanks for the clarification!
          I am working on figuring out what needs to be done to fix the playbooks.

          Show
          ann.loraine Ann Loraine added a comment - Thanks for the clarification! I am working on figuring out what needs to be done to fix the playbooks.
          ann.loraine Ann Loraine made changes -
          Sprint Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11 [ 108, 109 ] Fall 5 Nov 9 - Nov 20, Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23 [ 108, 109, 110 ]
          ann.loraine Ann Loraine made changes -
          Rank Ranked higher
          ann.loraine Ann Loraine made changes -
          Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
          ann.loraine Ann Loraine made changes -
          Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
          sameer Sameer Shanbhag (Inactive) made changes -
          Assignee Sameer Shanbhag [ sameer ]
          ssegu Sai Supreeth Segu (Inactive) made changes -
          Assignee Sai Supreeth Segu [ ssegu ]
          ssegu Sai Supreeth Segu (Inactive) made changes -
          Assignee Sai Supreeth Segu [ ssegu ]
          ssegu Sai Supreeth Segu (Inactive) made changes -
          Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
          ssegu Sai Supreeth Segu (Inactive) made changes -
          Assignee Sai Supreeth Segu [ ssegu ]
          Hide
          ssegu Sai Supreeth Segu (Inactive) added a comment -

          Everything works fine. Moving to closed

          Show
          ssegu Sai Supreeth Segu (Inactive) added a comment - Everything works fine. Moving to closed
          ssegu Sai Supreeth Segu (Inactive) made changes -
          Resolution Done [ 10000 ]
          Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
          ssegu Sai Supreeth Segu (Inactive) made changes -
          Assignee Sai Supreeth Segu [ ssegu ] Sameer Shanbhag [ sameer ]

            People

            • Assignee:
              sameer Sameer Shanbhag (Inactive)
              Reporter:
              ann.loraine Ann Loraine
            • Votes:
              0 Vote for this issue
              Watchers:
              3 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved: