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  1. IGB
  2. IGBF-2058

Limit View in IGB to correct file types (Terrain)

        Details

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

          Description

          Task: Limit the View in IGB button within BioViz-CyVerse to only the files that are viewable in IGB. This list/database will need to be updatable, as new filetypes are added to IGB on a regular basis.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-2083 Color View in IGB Based on Public/Owner

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-1621 Limit View in IGB to accepted file types

              • Major - Major loss of function.
              • Closed

                Activity

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                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-1482 [ 17568 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-1621 [ IGBF-1621 ]
                chaitanya Chaitanya Kintali (Inactive) made changes -
                Status Open [ 1 ] To-Do [ 10305 ]
                chaitanya Chaitanya Kintali (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 4 : 30 Sep to 11 Oct [ 75 ] Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct [ 75, 76 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                chaitanya Chaitanya Kintali (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                chaitanya Chaitanya Kintali (Inactive) made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                chaitanya Chaitanya Kintali (Inactive) made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                chaitanya Chaitanya Kintali (Inactive) made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 20815 ] Revised Fall 2019 Workflow Update [ 21164 ]
                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 ]
                chaitanya Chaitanya Kintali (Inactive) made changes -
                Assignee Chaitanya Kintali [ chaitanya ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Assignee Srishti Tiwari [ stiwari8 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                Hide
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                stiwari8 Srishti Tiwari (Inactive) added a comment -

                View in IGB button is not getting displayed for bed files.

                Show
                stiwari8 Srishti Tiwari (Inactive) added a comment - View in IGB button is not getting displayed for bed files.
                Hide
                Permalink
                nfreese Nowlan Freese added a comment -

                Are we handling gzipped files (.gz)? Many bed files are gzipped.

                Show
                nfreese Nowlan Freese added a comment - Are we handling gzipped files (.gz)? Many bed files are gzipped.
                Hide
                Permalink
                stiwari8 Srishti Tiwari (Inactive) added a comment -

                I think in the Cyverse Environment we need to have all file types. Once that is done, this ticket will be thoroughly tested for all file types

                Show
                stiwari8 Srishti Tiwari (Inactive) added a comment - I think in the Cyverse Environment we need to have all file types. Once that is done, this ticket will be thoroughly tested for all file types
                Hide
                Permalink
                nfreese Nowlan Freese added a comment - - edited

                I will add in the smoketest files and will update this comment when it is complete.

                Edit: Files are in nowlanf > SmokeTesting > H_sapiens_Dec_2013

                All of the files except for the indexes (.bai and .tbi) should be viewable in IGB.

                It looks like some of the .gz files and bedGraph are not showing correctly.

                Show
                nfreese Nowlan Freese added a comment - - edited I will add in the smoketest files and will update this comment when it is complete. Edit: Files are in nowlanf > SmokeTesting > H_sapiens_Dec_2013 All of the files except for the indexes (.bai and .tbi) should be viewable in IGB. It looks like some of the .gz files and bedGraph are not showing correctly.
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status Post-merge Testing In Progress [ 10003 ] Merged Needs Testing [ 10002 ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Assignee Srishti Tiwari [ stiwari8 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2083 [ IGBF-2083 ]
                Hide
                Permalink
                chaitanya Chaitanya Kintali (Inactive) added a comment -

                Code changes done and merged.
                Srishti Tiwari Can you please test the ticket if we can see the button based on the viewable file Formats.
                NOTE: Regarding whether to grey it out or not depending upon user permissions we have created another ticket. https://jira.transvar.org/browse/IGBF-2083 which is pushed onto next sprint.

                Show
                chaitanya Chaitanya Kintali (Inactive) added a comment - Code changes done and merged. Srishti Tiwari Can you please test the ticket if we can see the button based on the viewable file Formats. NOTE: Regarding whether to grey it out or not depending upon user permissions we have created another ticket. https://jira.transvar.org/browse/IGBF-2083 which is pushed onto next sprint.
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                Hide
                Permalink
                nfreese Nowlan Freese added a comment - - edited

                Chaitanya fixed the issue with .gz and bedgraph files. The smoke testing data has the correct files showing with View in IGB.

                Closing issue.

                Show
                nfreese Nowlan Freese added a comment - - edited Chaitanya fixed the issue with .gz and bedgraph files. The smoke testing data has the correct files showing with View in IGB. Closing issue.
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Chaitanya Kintali [ chaitanya ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    chaitanya Chaitanya Kintali (Inactive)
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: