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  1. IGB
  2. IGBF-4412

Fix issue with DAS test

        Details

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

          Description

          Build was failing with tests on DasDataProviderTest.

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              Task - A task that needs to be done. IGBF-4411 Add more SAMtags to SAMtags filter function

              • 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-1531 [ 17617 ]
                nfreese Nowlan Freese made changes -
                Link This issue blocks IGBF-4411 [ IGBF-4411 ]
                nfreese Nowlan Freese made changes -
                Description Build was failing with tests on DasDataProviderTest.
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                nfreese Nowlan Freese added a comment -

                Issue was that UCSC updated URLs that we were pulling data from when testing DAS files.

                Branch: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-4412
                Commit: https://bitbucket.org/nfreese/nowlanfork-igb/commits/93719277274927d837b124f2b4809724d9e77dae
                PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1105

                Show
                nfreese Nowlan Freese added a comment - Issue was that UCSC updated URLs that we were pulling data from when testing DAS files. Branch: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-4412 Commit: https://bitbucket.org/nfreese/nowlanfork-igb/commits/93719277274927d837b124f2b4809724d9e77dae PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1105
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                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 ]
                nfreese Nowlan Freese made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
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                ann.loraine Ann Loraine added a comment -

                PR is merged and new installers are deployed to "early access" section of bioviz.org.
                Ready for testing.

                Show
                ann.loraine Ann Loraine added a comment - PR is merged and new installers are deployed to "early access" section of bioviz.org. Ready for testing.
                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 Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
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                nfreese Nowlan Freese added a comment -

                When building IGB the test file is completed successfully.

                Note that there is a test file das-dsn-test-data.xml that has the old version of the URL that includes the port 80. That file is currently correct, as the file on UCSC still reports the links with the port 80.

                For example:
                Link: https://genome.cse.ucsc.edu/cgi-bin/das/dsn
                Output:

                <DSN>
<SOURCE id="hs1" version="1.00">Jan. 2022 (T2T CHM13v2.0/hs1) at UCSC</SOURCE>
<DESCRIPTION>Human Jan. 2022 (T2T CHM13v2.0/hs1) Genome at UCSC</DESCRIPTION>
<MAPMASTER>http://genome.ucsc.edu:80/cgi-bin/das/hs1</MAPMASTER>
</DSN>

                Closing ticket.

                Show
                nfreese Nowlan Freese added a comment - When building IGB the test file is completed successfully. Note that there is a test file das-dsn-test-data.xml that has the old version of the URL that includes the port 80. That file is currently correct, as the file on UCSC still reports the links with the port 80. For example: Link: https://genome.cse.ucsc.edu/cgi-bin/das/dsn Output: <DSN> <SOURCE id="hs1" version="1.00">Jan. 2022 (T2T CHM13v2.0/hs1) at UCSC</SOURCE> <DESCRIPTION>Human Jan. 2022 (T2T CHM13v2.0/hs1) Genome at UCSC</DESCRIPTION> <MAPMASTER>http://genome.ucsc.edu:80/cgi-bin/das/hs1</MAPMASTER> </DSN> Closing ticket.
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]

                  People

                  • Assignee:
                    nfreese Nowlan Freese
                    Reporter:
                    nfreese Nowlan Freese
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                    Dates

                    • Created:
                      Updated:
                      Resolved: