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  1. IGB
  2. IGBF-781

Update synonyms.txt for UCSC

        Details

        • Story Points:
          3
        • Epic Link:
        • Sprint:
          Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28

          Description

          Situation: When DAS support was restored in IGB additional genomes provided by UCSC were made available. However, many of these genomes appear oddly in the species or genome dropdown menus. This indicates these genomes may not be included in the synonyms.txt file.

          Task: Update the synonyms.txt file. Also make sure species listed in the main IGB QL site are represented in species.txt and synonyms.txt in the files that are packaged with IGB.

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              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-1165 Chromosome.txt files on remote Quickload sites are being ignored

              • Major - Major loss of function.
              • To-Do

              Task - A task that needs to be done. IGBB-90 update synonyms.txt

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3053 Investigate: M_musculus_Jun_2020 genome listed in Track Hubs table?

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1879 Ensure Galaxy default dbkey values are in synonyms.txt

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-2861 Investigate species synonyms lookup

              • Major - Major loss of function.
              • To-Do

              Task - A task that needs to be done. IGBF-2793 Restore DASv1 support

              • Major - Major loss of function.
              • Closed

                Activity

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                11 older comments
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                ann.loraine Ann Loraine added a comment -

                Modifying bioviz-playbooks "replace" role to edit genome dashboard util.js file during deployment to also use user-specified IGB repository and branch.

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                ann.loraine Ann Loraine added a comment - Modifying bioviz-playbooks "replace" role to edit genome dashboard util.js file during deployment to also use user-specified IGB repository and branch.
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                ann.loraine Ann Loraine added a comment -

                Deployed genome dashboard to bioviztest.bioviz.org using the proposed fork and branch. Confirmed that utils.js contains the following variables:

                const SPECIES = 'https://bitbucket.org/nfreese/nowlanfork-igb/IGBF-781/core/synonym-lookup/src/main/resources/species.txt';
const SYNONYMS = 'https://bitbucket.org/nfreese/nowlanfork-igb/raw/IGBF-781/core/synonym-lookup/src/main/resources/synonyms.txt';
const ALLQUICKLOADS = 'https://bitbucket.org/nfreese/nowlanfork-igb/raw/IGBF-781/core/igb-preferences/src/main/resources/igbDefaultPrefs.json';

                I see no difference between the genome dashboard deployed above and the version deployed on bioviz.org (main site). The only thing that looks a bit weird is that both sites don't have a picture for genome F_albicollis_Jun_2013 (collared flycatcher). This was added recently to IGB Quickload svn repository, and we (mainly me) forgot to add a photo to the genome dashboard repository. This has nothing to do with the current issue however.

                Based on the above review, I think it is fine to now merge the pull request.

                Show
                ann.loraine Ann Loraine added a comment - Deployed genome dashboard to bioviztest.bioviz.org using the proposed fork and branch. Confirmed that utils.js contains the following variables: const SPECIES = 'https: //bitbucket.org/nfreese/nowlanfork-igb/IGBF-781/core/synonym-lookup/src/main/resources/species.txt'; const SYNONYMS = 'https: //bitbucket.org/nfreese/nowlanfork-igb/raw/IGBF-781/core/synonym-lookup/src/main/resources/synonyms.txt'; const ALLQUICKLOADS = 'https: //bitbucket.org/nfreese/nowlanfork-igb/raw/IGBF-781/core/igb-preferences/src/main/resources/igbDefaultPrefs.json'; I see no difference between the genome dashboard deployed above and the version deployed on bioviz.org (main site). The only thing that looks a bit weird is that both sites don't have a picture for genome F_albicollis_Jun_2013 (collared flycatcher). This was added recently to IGB Quickload svn repository, and we (mainly me) forgot to add a photo to the genome dashboard repository. This has nothing to do with the current issue however. Based on the above review, I think it is fine to now merge the pull request.
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                ann.loraine Ann Loraine added a comment -

                Merged and built master branch installers. Ready for testing.

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                ann.loraine Ann Loraine added a comment - Merged and built master branch installers. Ready for testing.
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                nfreese Nowlan Freese added a comment -

                Tested on Mac master installer.

                Working correctly.

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                nfreese Nowlan Freese added a comment - Tested on Mac master installer. Working correctly.
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                omarne Omkar Marne (Inactive) added a comment -

                Tested on Windows and Linux. The species names aren't abbreviated. They are in their complete name.

                Closing the issue.

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                omarne Omkar Marne (Inactive) added a comment - Tested on Windows and Linux. The species names aren't abbreviated. They are in their complete name. Closing the issue.

                  People

                  • Assignee:
                    nfreese Nowlan Freese
                    Reporter:
                    ann.loraine Ann Loraine
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                    • Created:
                      Updated:
                      Resolved: