Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-2243

Deploy Genoviz SDK Javadocs on Bioviz

    Details

    • Type: Task
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
      None
    • Story Points:
      0.25
    • Sprint:
      Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May

      Description

      To help developers understand how to use the Genoviz SDK, we should deploy the javadocs on an easy to reach location.

      For this task, add new menu item to BioViz.org under "For Developers" - call it "GenViz SDK Javadocs"

        Attachments

          Issue Links

            Activity

            ann.loraine Ann Loraine created issue -
            ann.loraine Ann Loraine made changes -
            Field Original Value New Value
            Epic Link IGBF-1531 [ 17617 ]
            ann.loraine Ann Loraine made changes -
            Link This issue relates to IGBF-2228 [ IGBF-2228 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
            ann.loraine Ann Loraine made changes -
            Sprint Spring 3 : 3 Feb to 14 Feb [ 86 ] Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 21 Feb [ 86, 87 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            nfreese Nowlan Freese made changes -
            Sprint Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb [ 86, 87 ] Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 86, 87, 89 ]
            nfreese Nowlan Freese made changes -
            Rank Ranked higher
            nfreese Nowlan Freese made changes -
            Sprint Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 86, 87, 89 ] Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 86, 87, 89, 90 ]
            nfreese Nowlan Freese made changes -
            Rank Ranked higher
            noor91zahara Noor Zahara (Inactive) made changes -
            Assignee Noor Zahara [ noor91zahara ]
            noor91zahara Noor Zahara (Inactive) made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            Hide
            noor91zahara Noor Zahara (Inactive) added a comment -

            [~aloraine]

            Should I link the menu to 'http://bitbucket.org/lorainelab/genoviz-sdk/downloads/genoviz-1.1.8-javadoc.jar' ?

            Show
            noor91zahara Noor Zahara (Inactive) added a comment - [~aloraine] Should I link the menu to 'http://bitbucket.org/lorainelab/genoviz-sdk/downloads/genoviz-1.1.8-javadoc.jar' ?
            nfreese Nowlan Freese made changes -
            Sprint Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar [ 86, 87, 89, 90 ] Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10 [ 86, 87, 89, 90, 91 ]
            nfreese Nowlan Freese made changes -
            Rank Ranked higher
            noor91zahara Noor Zahara (Inactive) made changes -
            Attachment javadoc.sh [ 14688 ]
            Hide
            noor91zahara Noor Zahara (Inactive) added a comment -

            [~aloraine] - I have attached the script file. Kindly let me know if it is fine.

            Show
            noor91zahara Noor Zahara (Inactive) added a comment - [~aloraine] - I have attached the script file. Kindly let me know if it is fine.
            Hide
            noor91zahara Noor Zahara (Inactive) added a comment -

            Code Diff - https://bitbucket.org/noorzahara/bioviz-local/branch/IGBF-2243#diff

            Testing Steps -

            Run javadoc.sh from within the application
            Check if Genoviz SDK Javadocs option is added under "Developers" tab on bioviz application
            Click on 'Genoviz SDK Javadocs', a page containing javadoc details should open.

            Show
            noor91zahara Noor Zahara (Inactive) added a comment - Code Diff - https://bitbucket.org/noorzahara/bioviz-local/branch/IGBF-2243#diff Testing Steps - Run javadoc.sh from within the application Check if Genoviz SDK Javadocs option is added under "Developers" tab on bioviz application Click on 'Genoviz SDK Javadocs', a page containing javadoc details should open.
            noor91zahara Noor Zahara (Inactive) made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            noor91zahara Noor Zahara (Inactive) made changes -
            Assignee Noor Zahara [ noor91zahara ]
            ann.loraine Ann Loraine made changes -
            Sprint Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10 [ 86, 87, 89, 90, 91 ] Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr [ 86, 87, 89, 90, 91, 92 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            ann.loraine Ann Loraine made changes -
            Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
            ann.loraine Ann Loraine made changes -
            Assignee Noor Zahara [ noor91zahara ]
            Hide
            ann.loraine Ann Loraine added a comment -

            Please see comments on the committed files for above branch.
            cc: Noor Zahara

            Show
            ann.loraine Ann Loraine added a comment - Please see comments on the committed files for above branch. cc: Noor Zahara
            Hide
            noor91zahara Noor Zahara (Inactive) added a comment -
            Show
            noor91zahara Noor Zahara (Inactive) added a comment - I have made changes as per the comments https://bitbucket.org/noorzahara/bioviz-local/branch/IGBF-2243#diff
            noor91zahara Noor Zahara (Inactive) made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            noor91zahara Noor Zahara (Inactive) made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            noor91zahara Noor Zahara (Inactive) made changes -
            Assignee Noor Zahara [ noor91zahara ]
            Hide
            ann.loraine Ann Loraine added a comment -

            Thanks - this looks fine. I have not tried to run it, but it looks like it should work.

            For the next steps, please squash the commits (rebase -i) into one commit and submit a PR.

            Show
            ann.loraine Ann Loraine added a comment - Thanks - this looks fine. I have not tried to run it, but it looks like it should work. For the next steps, please squash the commits (rebase -i) into one commit and submit a PR.
            ann.loraine Ann Loraine made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            ann.loraine Ann Loraine made changes -
            Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
            Hide
            ann.loraine Ann Loraine added a comment -

            Please squash commits and submit a PR.

            Show
            ann.loraine Ann Loraine added a comment - Please squash commits and submit a PR.
            ann.loraine Ann Loraine made changes -
            Assignee Noor Zahara [ noor91zahara ]
            Show
            noor91zahara Noor Zahara (Inactive) added a comment - I squashed the changes and created a PR https://bitbucket.org/lorainelab/bioviz/pull-requests/38/igbf-2243-deploy-genoviz-sdk-javadocs-on/diff
            noor91zahara Noor Zahara (Inactive) made changes -
            Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
            noor91zahara Noor Zahara (Inactive) made changes -
            Assignee Noor Zahara [ noor91zahara ]
            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 ]
            Hide
            ann.loraine Ann Loraine added a comment -

            To test:

            • Deploy bioviz site on an EC2
            • Run the script
            • Check that the javadocs can be navigated
            Show
            ann.loraine Ann Loraine added a comment - To test: Deploy bioviz site on an EC2 Run the script Check that the javadocs can be navigated
            Hide
            ann.loraine Ann Loraine added a comment -

            I followed the above steps and observed an error when running the script.

            I tested the "tar" command and noticed this error:

            AnnBioviz root $ tar xvzf genoviz-1.1.9-javadoc.jar
            gzip: stdin has more than one entry--rest ignored
            tar: Child returned status 2
            tar: Error is not recoverable: exiting now

            Returning to To-Do for Noor Zahara to take a look.

            Show
            ann.loraine Ann Loraine added a comment - I followed the above steps and observed an error when running the script. I tested the "tar" command and noticed this error: AnnBioviz root $ tar xvzf genoviz-1.1.9-javadoc.jar gzip: stdin has more than one entry--rest ignored tar: Child returned status 2 tar: Error is not recoverable: exiting now Returning to To-Do for Noor Zahara to take a look.
            ann.loraine Ann Loraine made changes -
            Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
            ann.loraine Ann Loraine made changes -
            Status Post-merge Testing In Progress [ 10003 ] To-Do [ 10305 ]
            ann.loraine Ann Loraine made changes -
            Assignee Noor Zahara [ noor91zahara ]
            Hide
            noor91zahara Noor Zahara (Inactive) added a comment - - edited

            [~aloraine] - Could you try the same command without the z i.e tar xvf genoviz-1.1.9-javadoc.jar ?

            I have made the changes to the script.

            Show
            noor91zahara Noor Zahara (Inactive) added a comment - - edited [~aloraine] - Could you try the same command without the z i.e tar xvf genoviz-1.1.9-javadoc.jar ? I have made the changes to the script.
            ann.loraine Ann Loraine made changes -
            Sprint Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr [ 86, 87, 89, 90, 91, 92 ] Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar, Spring 5 : 16 Mar to 27 Mar, Spring 6 : 30 Mar to Apr 10, Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May [ 86, 87, 89, 90, 91, 92, 93 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            Hide
            ann.loraine Ann Loraine added a comment -

            Migrated the command to ansible playbook which will be used to deploy and provision bioviz Web sites.
            Also, as part of the provisioning process, added creation of a sub-directory under "releases" named for the version of genoviz.
            A symbolic link "current" links to the current release.
            Also, changed the link in BioViz hmtl to "current" instead of "releases/index.html".
            Moving this to Done.

            Show
            ann.loraine Ann Loraine added a comment - Migrated the command to ansible playbook which will be used to deploy and provision bioviz Web sites. Also, as part of the provisioning process, added creation of a sub-directory under "releases" named for the version of genoviz. A symbolic link "current" links to the current release. Also, changed the link in BioViz hmtl to "current" instead of "releases/index.html". Moving this to Done.
            ann.loraine Ann Loraine made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            ann.loraine Ann Loraine made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            ann.loraine Ann Loraine made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            ann.loraine Ann Loraine made changes -
            Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
            ann.loraine Ann Loraine made changes -
            Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
            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 ]
            ann.loraine Ann Loraine made changes -
            Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
            ann.loraine Ann Loraine made changes -
            Resolution Done [ 10000 ]
            Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

              People

              • Assignee:
                noor91zahara Noor Zahara (Inactive)
                Reporter:
                ann.loraine Ann Loraine
              • Votes:
                0 Vote for this issue
                Watchers:
                2 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: