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      Description

      Situation: A user has asked for the UCSC DAS functionality to be returned to IGB.

      Task: Revert the changes to remove DASv1 support from IGB.

        Issue Links

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          Hide
          nfreese Nowlan Freese added a comment -

          Branch: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-2793

          To test:
          Open the mouse genome (M_musculus_Dec_2011)
          Navigate to chr1:52,182,882-52,235,630
          Select the External View tab
          In the dropdown menu, select UCSC (should be UCSC by default)
          Click update (Gene annotations should appear in the External View tab)
          Next, select View > View Region in UCSC Browser (a web browser should open to genome.ucsc.edu)
          Next, select the Data Access tab
          Under Available Data, there should be a folder for UCSC (DAS)
          Click the arrow to see all of the options under UCSC (DAS)
          Select ncbiRefSeqCurated (note that the DAS menu and data may move slowly as they utilize an external resource)
          Once the track has appeared in IGB, click Load Data (gene models should appear)

          Show
          nfreese Nowlan Freese added a comment - Branch: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-2793 To test: Open the mouse genome (M_musculus_Dec_2011) Navigate to chr1:52,182,882-52,235,630 Select the External View tab In the dropdown menu, select UCSC (should be UCSC by default) Click update (Gene annotations should appear in the External View tab) Next, select View > View Region in UCSC Browser (a web browser should open to genome.ucsc.edu ) Next, select the Data Access tab Under Available Data, there should be a folder for UCSC (DAS) Click the arrow to see all of the options under UCSC (DAS) Select ncbiRefSeqCurated (note that the DAS menu and data may move slowly as they utilize an external resource) Once the track has appeared in IGB, click Load Data (gene models should appear)
          Hide
          nfreese Nowlan Freese added a comment -

          Restoring DASv1 support in IGB fixes the issues with the External View tab (IGBF-2776) and the View Region in UCSC Browser (IGBF-2777), as they both used DAS to determine what genomes were available in UCSC (initUCSCSources() method in UCSCViewAction.java).

          The issue with the DAS files not loading in IGB was due to the XML being returned containing a link to a dead dtd file (http://www.biodas.org/dtd/dasgff.dtd). At some point in the last couple of years the biodas.org website appears to have gone offline. IGB versions prior to 8.4.0 did not validate the XML using dtd and thus had no issues. IGB versions 8.4.0 to 9.1.6 attempt to validate the XML using dtd and because the biodas.org link is no longer active failed to validate causing the DAS data to fail to load in IGB.

          Show
          nfreese Nowlan Freese added a comment - Restoring DASv1 support in IGB fixes the issues with the External View tab ( IGBF-2776 ) and the View Region in UCSC Browser ( IGBF-2777 ), as they both used DAS to determine what genomes were available in UCSC (initUCSCSources() method in UCSCViewAction.java). The issue with the DAS files not loading in IGB was due to the XML being returned containing a link to a dead dtd file ( http://www.biodas.org/dtd/dasgff.dtd ). At some point in the last couple of years the biodas.org website appears to have gone offline. IGB versions prior to 8.4.0 did not validate the XML using dtd and thus had no issues. IGB versions 8.4.0 to 9.1.6 attempt to validate the XML using dtd and because the biodas.org link is no longer active failed to validate causing the DAS data to fail to load in IGB.
          Hide
          nfreese Nowlan Freese added a comment - - edited

          Many files were removed/edited when DASv1 support was removed from IGB. I reverted three commits to restore the functionality, but this required resolving several merge conflicts. In addition, I tried to maintain the removal of DASv2 support as it does not appear to be necessary. However, many of the merge conflicts were due to commenting out both DASv1 and DASv2 at the same time.

          Show
          nfreese Nowlan Freese added a comment - - edited Many files were removed/edited when DASv1 support was removed from IGB. I reverted three commits to restore the functionality, but this required resolving several merge conflicts. In addition, I tried to maintain the removal of DASv2 support as it does not appear to be necessary. However, many of the merge conflicts were due to commenting out both DASv1 and DASv2 at the same time.
          Hide
          nfreese Nowlan Freese added a comment - - edited

          Many of the functions provided by DAS can be accomplished with the newer UCSC Rest API. At some point it would be good to replace the DAS functionality with the REST API, though this may require extensive work.

          Show
          nfreese Nowlan Freese added a comment - - edited Many of the functions provided by DAS can be accomplished with the newer UCSC Rest API . At some point it would be good to replace the DAS functionality with the REST API, though this may require extensive work.
          Hide
          rweidenh Rachel Weidenhammer added a comment - - edited

          (reviewed on Windows 10 OS)
          Functional Review:

          Following the steps from the first comment works as instructed.
          I encountered no errors.

          Code Review:

          I don't feel like I am able to understand the changes well enough to review them.
          It looks like the DAS Parser was told not to support DTD, and some other files were added but then removed.

          But thank you for all of the information in the previous comments on this issue. They are very informative and helpful.

          Show
          rweidenh Rachel Weidenhammer added a comment - - edited (reviewed on Windows 10 OS) Functional Review: Following the steps from the first comment works as instructed. I encountered no errors. Code Review: I don't feel like I am able to understand the changes well enough to review them. It looks like the DAS Parser was told not to support DTD, and some other files were added but then removed. But thank you for all of the information in the previous comments on this issue. They are very informative and helpful.
          Show
          nfreese Nowlan Freese added a comment - Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/865/igbf-2793
          Hide
          pbadzuh Philip Badzuh added a comment -

          Testing on macOS following the instructions in the first comment, everything seems to be working as expected. Closing issue.

          Show
          pbadzuh Philip Badzuh added a comment - Testing on macOS following the instructions in the first comment, everything seems to be working as expected. Closing issue.
          Hide
          aloraine Ann Loraine added a comment -

          From the Wayback Machine.

          Show
          aloraine Ann Loraine added a comment - From the Wayback Machine.

            People

            • Assignee:
              nfreese Nowlan Freese
              Reporter:
              nfreese Nowlan Freese
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              4 Start watching this issue

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                Updated:
                Resolved:

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