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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

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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

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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
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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.

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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.
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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.

                  People

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

                    • Created:
                      Updated:
                      Resolved: