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  1. IGB
  2. IGBF-2813

Add URL option to Custom Genome

        Details

        • Story Points:
          3
        • Epic Link:
        • Sprint:
          Winter 6 Mar 8 - Mar 19, Spring 1 2021 Mar 22 - Apr 2, Spring 2 2021 Apr 5 - Apr 16

          Description

          Situation: In IGB, when a user selects File > Open Genome from File... a window opens that allows the user to provide a Reference Sequence for the new genome. However, only local files are allowed, not URLs.

          Task: Add ability to use URLs when opening custom genomes.

            Attachments

              Issue Links

              relates to

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-2783 Improve Open Genome from File UI

              • Major - Major loss of function.
              • Closed

              Documentation - When documentation is missing or wrong IGBF-2838 Update Custom Genomes IGB User's Guide Page

              • Minor - Minor loss of function, or other problem where easy workaround is present.
              • Closed

                Activity

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                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-1765 [ 17855 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2783 [ IGBF-2783 ]
                ann.loraine Ann Loraine made changes -
                Assignee Karthik Raveendran [ karthik ]
                ann.loraine Ann Loraine made changes -
                Fix Version/s 9.1.8 Major Release [ 10605 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Winter 6 Mar 8 - Mar 19 [ 116 ] Winter 6 Mar 8 - Mar 19, Spring 1 Mar 22 - Apr 2 [ 116, 117 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Issue Type Task [ 3 ] New Feature [ 2 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
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                ann.loraine Ann Loraine added a comment -

                Kindly provide comments describing work thus far.

                Show
                ann.loraine Ann Loraine added a comment - Kindly provide comments describing work thus far.
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                karthik Karthik Raveendran added a comment -

                In the new changes, the 'Reference Sequence' text field in 'Open Genome from File UI' can be used to enter a URL as well as a local system file path to load a custom genome. The new logic checks the prefix of the link to determine if its URL or local file path.
                The changes need testing against different file paths that includes special characters or spaces.

                Show
                karthik Karthik Raveendran added a comment - In the new changes, the 'Reference Sequence' text field in 'Open Genome from File UI' can be used to enter a URL as well as a local system file path to load a custom genome. The new logic checks the prefix of the link to determine if its URL or local file path. The changes need testing against different file paths that includes special characters or spaces.
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
                ann.loraine Ann Loraine made changes -
                Sprint Winter 6 Mar 8 - Mar 19, Spring 1 2021 Mar 22 - Apr 2 [ 116, 117 ] Winter 6 Mar 8 - Mar 19, Spring 1 2021 Mar 22 - Apr 2, Spring 2 2021 Apr 5 - Apr 16 [ 116, 117, 118 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
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                nfreese Nowlan Freese added a comment -

                Karthik's branch installers: https://bitbucket.org/KarthikRavee91/karthikfork-igb/downloads/

                Test loading the following files both online (by adding the URL) or locally (by downloading the file and choosing it locally):
                https://data.cyverse.org/dav-anon/iplant/home/nowlanf/nowlanTESTDontChange/relativeFixed/E_unicornis_Jul_2043/down%20stream/E_unicornis_Jul_2043.2bit

                http://igbquickload.org/quickload/A_thaliana_Jun_2009/A_thaliana_Jun_2009.2bit

                Show
                nfreese Nowlan Freese added a comment - Karthik's branch installers: https://bitbucket.org/KarthikRavee91/karthikfork-igb/downloads/ Test loading the following files both online (by adding the URL) or locally (by downloading the file and choosing it locally): https://data.cyverse.org/dav-anon/iplant/home/nowlanf/nowlanTESTDontChange/relativeFixed/E_unicornis_Jul_2043/down%20stream/E_unicornis_Jul_2043.2bit http://igbquickload.org/quickload/A_thaliana_Jun_2009/A_thaliana_Jun_2009.2bit
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
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                nfreese Nowlan Freese added a comment - - edited

                Karthik Raveendran

                Can this import be removed: import static com.affymetrix.genometry.symloader.ProtocolConstants.FILE_PROTOCOL_SCHEME;

                Tested the above 2bit files on Mac and they worked correctly, could load the sequence.

                I also tested the fasta file: https://data.cyverse.org/dav-anon/iplant/home/nowlanf/S_SARS-CoV-2_Wuhan-Hu-1_Jan_2020.fa
                It was able to load the correct chromosome and sequence.

                Show
                nfreese Nowlan Freese added a comment - - edited Karthik Raveendran Can this import be removed: import static com.affymetrix.genometry.symloader.ProtocolConstants.FILE_PROTOCOL_SCHEME; Tested the above 2bit files on Mac and they worked correctly, could load the sequence. I also tested the fasta file: https://data.cyverse.org/dav-anon/iplant/home/nowlanf/S_SARS-CoV-2_Wuhan-Hu-1_Jan_2020.fa It was able to load the correct chromosome and sequence.
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Karthik Raveendran [ karthik ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                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 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
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                nfreese Nowlan Freese added a comment -

                Looks good, recommend pull request.

                Show
                nfreese Nowlan Freese added a comment - Looks good, recommend pull request.
                nfreese Nowlan Freese made changes -
                Assignee Karthik Raveendran [ karthik ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese 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 -
                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 -
                Assignee Karthik Raveendran [ karthik ]
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                ann.loraine Ann Loraine added a comment -

                Pull request is merged. Master branch installers are been built and ready for testing.

                Show
                ann.loraine Ann Loraine added a comment - Pull request is merged. Master branch installers are been built and ready for testing.
                rweidenh Logan Weidenhammer (Inactive) made changes -
                Assignee Rachel Weidenhammer [ rweidenh ]
                rweidenh Logan Weidenhammer (Inactive) made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
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                rweidenh Logan Weidenhammer (Inactive) added a comment -

                Tested on Windows 10
                All of the files in the previous comments do load correctly via URL.
                I also tested the unicorn link locally and it works that way as well.

                Looks good. Moving to Done.

                Show
                rweidenh Logan Weidenhammer (Inactive) added a comment - Tested on Windows 10 All of the files in the previous comments do load correctly via URL. I also tested the unicorn link locally and it works that way as well. Looks good. Moving to Done.
                rweidenh Logan Weidenhammer (Inactive) made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                rweidenh Logan Weidenhammer (Inactive) made changes -
                Assignee Rachel Weidenhammer [ rweidenh ] Karthik Raveendran [ karthik ]
                rweidenh Logan Weidenhammer (Inactive) made changes -
                Link This issue relates to IGBF-2838 [ IGBF-2838 ]

                  People

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

                    • Created:
                      Updated:
                      Resolved: