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  1. IGB
  2. IGBF-3550

Add CRAM to list of supported files for BioViz Connect

    Details

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

      Description

      Situation: BioViz Connect uses a hardcoded list of IGB accepted file format extensions in order to correctly populate the View in IGB button. As we have now added support for cram, we need to update the list of file formats in BioViz Connect.

      Task: Update BioViz Connect so that CRAM is an accepted file format. Note that as previous versions of IGB do not support the cram format, we will need to add some additional logic to BioViz Connect to check the version number of IGB and limit the View in IGB button for cram to newer versions.

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            nfreese Nowlan Freese created issue -
            nfreese Nowlan Freese made changes -
            Field Original Value New Value
            Epic Link IGBF-2376 [ 18533 ]
            nfreese Nowlan Freese made changes -
            Link This issue is blocked by IGBF-3478 [ IGBF-3478 ]
            nfreese Nowlan Freese made changes -
            Description Situation: BioViz Connect uses a hardcoded list of IGB accepted file format extensions in order to correctly populate the View in IGB button. As we have now added support for cram, we need to update the list of file formats in BioViz Connect.

            Task: Update BioViz Connect so that cram is an accepted file format.
            Situation: BioViz Connect uses a hardcoded list of IGB accepted file format extensions in order to correctly populate the View in IGB button. As we have now added support for cram, we need to update the list of file formats in BioViz Connect.

            Task: Update BioViz Connect so that cram is an accepted file format. Note that as previous versions of IGB do not support the cram format, we will need to add some additional logic to BioViz Connect to check the version number of IGB and limit the View in IGB button for cram to newer versions.
            ann.loraine Ann Loraine made changes -
            Assignee Karthik Raveendran [ karthik ]
            ann.loraine Ann Loraine made changes -
            Summary Add Cram to list of supported files for BioViz Connect Add CRAM to list of supported files for BioViz Connect
            ann.loraine Ann Loraine made changes -
            Description Situation: BioViz Connect uses a hardcoded list of IGB accepted file format extensions in order to correctly populate the View in IGB button. As we have now added support for cram, we need to update the list of file formats in BioViz Connect.

            Task: Update BioViz Connect so that cram is an accepted file format. Note that as previous versions of IGB do not support the cram format, we will need to add some additional logic to BioViz Connect to check the version number of IGB and limit the View in IGB button for cram to newer versions.
            Situation: BioViz Connect uses a hardcoded list of IGB accepted file format extensions in order to correctly populate the View in IGB button. As we have now added support for cram, we need to update the list of file formats in BioViz Connect.

            Task: Update BioViz Connect so that CRAM is an accepted file format. Note that as previous versions of IGB do not support the cram format, we will need to add some additional logic to BioViz Connect to check the version number of IGB and limit the View in IGB button for cram to newer versions.
            ann.loraine Ann Loraine made changes -
            Description Situation: BioViz Connect uses a hardcoded list of IGB accepted file format extensions in order to correctly populate the View in IGB button. As we have now added support for cram, we need to update the list of file formats in BioViz Connect.

            Task: Update BioViz Connect so that CRAM is an accepted file format. Note that as previous versions of IGB do not support the cram format, we will need to add some additional logic to BioViz Connect to check the version number of IGB and limit the View in IGB button for cram to newer versions.
            Situation: BioViz Connect uses a hardcoded list of IGB accepted file format extensions in order to correctly populate the View in IGB button. As we have now added support for cram, we need to update the list of file formats in BioViz Connect.

            Task: Update BioViz Connect so that CRAM is an accepted file format. Note that as previous versions of IGB do not support the cram format, we will need to add some additional logic to BioViz Connect to check the version number of IGB and limit the View in IGB button for cram to newer versions.

            Hide
            pkulzer Paige Kulzer added a comment -

            Here is some additional information on the CRAM file format if anyone would like to better familiarize themselves: https://academic.oup.com/bioinformatics/article/38/6/1497/6499262

            Show
            pkulzer Paige Kulzer added a comment - Here is some additional information on the CRAM file format if anyone would like to better familiarize themselves: https://academic.oup.com/bioinformatics/article/38/6/1497/6499262
            karthik Karthik Raveendran made changes -
            Assignee Karthik Raveendran [ karthik ]
            karthik Karthik Raveendran made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            karthik Karthik Raveendran made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            Hide
            karthik Karthik Raveendran added a comment -

            Added cram to IGB supported file format. See commit

            Show
            karthik Karthik Raveendran added a comment - Added cram to IGB supported file format. See commit
            nfreese Nowlan Freese made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            Hide
            nfreese Nowlan Freese added a comment -

            Karthik Raveendran - how do we want to tackle version checking for cram?

            Option 1: Do nothing, any user who is using an older version of IGB will see the View in IGB button for a CRAM file, but when clicked it will throw an error in IGB.
            Option 2: Update logic in BioViz Connect to check the IGB version (major/minor/patch) and anything less than 10.0.0 will not show the View in IGB button for CRAM files.
            Option 3: Update logic in BioViz Connect to check the IGB version (major/minor/patch) and anything less than 10.0.0 will show a modal informing the user "To view a CRAM file in IGB, please update your IGB to the most recent version".

            I think we are checking IGB version in cyverse.js and there is a popup_modals.html warning for older versions of IGB.

            Show
            nfreese Nowlan Freese added a comment - Karthik Raveendran - how do we want to tackle version checking for cram? Option 1: Do nothing, any user who is using an older version of IGB will see the View in IGB button for a CRAM file, but when clicked it will throw an error in IGB. Option 2: Update logic in BioViz Connect to check the IGB version (major/minor/patch) and anything less than 10.0.0 will not show the View in IGB button for CRAM files. Option 3: Update logic in BioViz Connect to check the IGB version (major/minor/patch) and anything less than 10.0.0 will show a modal informing the user "To view a CRAM file in IGB, please update your IGB to the most recent version". I think we are checking IGB version in cyverse.js and there is a popup_modals.html warning for older versions of IGB.
            nfreese Nowlan Freese made changes -
            Assignee Karthik Raveendran [ karthik ]
            nfreese Nowlan Freese made changes -
            Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
            nfreese Nowlan Freese made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            Hide
            karthik Karthik Raveendran added a comment -

            Implemented Option 3 from the prev comment by Dr. Nowlan Freese. See commit

            Show
            karthik Karthik Raveendran added a comment - Implemented Option 3 from the prev comment by Dr. Nowlan Freese . See commit
            karthik Karthik Raveendran made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            karthik Karthik Raveendran made changes -
            Assignee Karthik Raveendran [ karthik ]
            Show
            karthik Karthik Raveendran added a comment - PR Submitted. https://bitbucket.org/nfreese/bioviz-connect/pull-requests/291
            karthik Karthik Raveendran made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            karthik Karthik Raveendran made changes -
            Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
            karthik Karthik Raveendran made changes -
            Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
            ann.loraine Ann Loraine made changes -
            Sprint Spring 3 [ 187 ] Spring 3, Spring 4 [ 187, 188 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            nfreese Nowlan Freese made changes -
            Sprint Spring 3, Spring 4 [ 187, 188 ] Spring 3, Spring 5 [ 187, 189 ]
            Hide
            ann.loraine Ann Loraine added a comment -

            To deploy testing and new versions using code in bioviz connect playbooks repository.

            AL request: Karthik Raveendran to take over deploying new versions of bioviz connect code, using playbooks.

            Show
            ann.loraine Ann Loraine added a comment - To deploy testing and new versions using code in bioviz connect playbooks repository. AL request: Karthik Raveendran to take over deploying new versions of bioviz connect code, using playbooks.
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ]
            nfreese Nowlan Freese made changes -
            Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
            nfreese Nowlan Freese made changes -
            Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
            Hide
            nfreese Nowlan Freese added a comment - - edited

            Merged and deployed to connect.bioviz.org/

            Deployed following instructions from bioviz-connect-playbooks repo with:

            ansible-playbook -i inventory.ini setup.yml

            Once the playbook was completed I had to hit the SyncAppDataToBioViz endpoint to see the change:

            https://connect.bioviz.org/SyncAppDataToBioViz/?accesstoken=<validKeyCloakAccessToken>
            

            I first tested the changes on bvctest7 (Nowlan has access to start/stop the instance).

            Note that you will need to proper crt files and key. You will also need to have a properly filled out inventory.ini and group_vars > setup_vars.yml files. I also specify my repo in the roles > clone > defaults > main.yml file:

            repo: https://bitbucket.org/nfreese/bioviz-connect.git
            Show
            nfreese Nowlan Freese added a comment - - edited Merged and deployed to connect.bioviz.org/ Deployed following instructions from bioviz-connect-playbooks repo with: ansible-playbook -i inventory.ini setup.yml Once the playbook was completed I had to hit the SyncAppDataToBioViz endpoint to see the change: https: //connect.bioviz.org/SyncAppDataToBioViz/?accesstoken=<validKeyCloakAccessToken> I first tested the changes on bvctest7 (Nowlan has access to start/stop the instance). Note that you will need to proper crt files and key. You will also need to have a properly filled out inventory.ini and group_vars > setup_vars.yml files. I also specify my repo in the roles > clone > defaults > main.yml file: repo: https: //bitbucket.org/nfreese/bioviz-connect.git
            nfreese Nowlan Freese made changes -
            Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
            Hide
            nfreese Nowlan Freese added a comment -

            I uploaded a folder with matching cram/bam/sam files. I was able to modify the metadata to specify the Arabidopsis genome for the CRAM file. Once the CRAM file and its index were made public I was able to click View in IGB and view the files in IGB. If I tried to load a CRAM file into a version of IGB less than 10.0.0 I saw a warning from BioViz Connect that I should upgrade my version of IGB.

            Closing ticket.

            Show
            nfreese Nowlan Freese added a comment - I uploaded a folder with matching cram/bam/sam files. I was able to modify the metadata to specify the Arabidopsis genome for the CRAM file. Once the CRAM file and its index were made public I was able to click View in IGB and view the files in IGB. If I tried to load a CRAM file into a version of IGB less than 10.0.0 I saw a warning from BioViz Connect that I should upgrade my version of IGB. Closing ticket.
            nfreese Nowlan Freese made changes -
            Assignee Nowlan Freese [ nfreese ] Karthik Raveendran [ karthik ]
            nfreese Nowlan Freese made changes -
            Resolution Done [ 10000 ]
            Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

              People

              • Assignee:
                karthik Karthik Raveendran
                Reporter:
                nfreese Nowlan Freese
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                Dates

                • Created:
                  Updated:
                  Resolved: