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  1. IGB
  2. IGBF-2405

Change image names to match genome version prefix

        Details

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

          Description

          Genome dashboard (https://bioviz.org/genome-dashboard) displays images for each species available to load into IGB from IGB Quickload sites.

          Recently, we changed how Genome Dashboard locates the images. Now, the Genome Dashboard expects that the image names match the genome version prefix.

          For example, Genome Dashboard expects to find an image named G_species_text_text.png or G_species_text_text.jpg if the genome version prefix is G_species_text_text.

          For this task, use "git mv" to change the names of the Genome Dashboard images that do not match the proper pattern.

          Logistics:

          Note: You will need to run the Genome Dashboard on your local computer to test your changes. Instructions are in the repository itself. If you need assistance, ask Chester Dias or Philip Badzuh for help.

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              Task - A task that needs to be done. IGBF-2399 Avoid colliding image names for species

              • Major - Major loss of function.
              • Closed

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                pbadzuh Philip Badzuh (Inactive) added a comment -

                Please see my branch here:
                https://bitbucket.org/pbadzuh/genome-dashboard_pbdev/branch/IGBF-2405#diff

                • Change genome image names to a prefix, consisting of everything in the genome name except the date.
                • For genomes that refer to the same image, use symbolic links rather than duplicating images.
                • Add an image for the Cannabis sativa genome
                Show
                pbadzuh Philip Badzuh (Inactive) added a comment - Please see my branch here: https://bitbucket.org/pbadzuh/genome-dashboard_pbdev/branch/IGBF-2405#diff Change genome image names to a prefix, consisting of everything in the genome name except the date. For genomes that refer to the same image, use symbolic links rather than duplicating images. Add an image for the Cannabis sativa genome
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                ann.loraine Ann Loraine added a comment -

                Please use attached image for Cannabis sativa instead.

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                ann.loraine Ann Loraine added a comment - Please use attached image for Cannabis sativa instead.
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                ann.loraine Ann Loraine added a comment -

                This image is from wikipedia.

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                ann.loraine Ann Loraine added a comment - This image is from wikipedia.
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                ann.loraine Ann Loraine added a comment - - edited

                A question:

                We should not need to use symbolic links because all genome versions for a species will appear under one single picture, named using the genome version prefix. So I'm wondering about this commit message:

                For genomes that refer to the same image, use symbolic links rather than duplicating images.

                Show
                ann.loraine Ann Loraine added a comment - - edited A question: We should not need to use symbolic links because all genome versions for a species will appear under one single picture, named using the genome version prefix. So I'm wondering about this commit message: For genomes that refer to the same image, use symbolic links rather than duplicating images.
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                pbadzuh Philip Badzuh (Inactive) added a comment - - edited

                It seems that currently each genome prefix has its own dedicated card/tile, so different strains, for example, produce unique prefixes and distinct cards. They may, however, belong to the same genus and species, so they would use the same image asset. Pease let me know if this is the expected behavior.

                Show
                pbadzuh Philip Badzuh (Inactive) added a comment - - edited It seems that currently each genome prefix has its own dedicated card/tile, so different strains, for example, produce unique prefixes and distinct cards. They may, however, belong to the same genus and species, so they would use the same image asset. Pease let me know if this is the expected behavior.
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                ann.loraine Ann Loraine added a comment -

                OK thanks! Makes sense. Nice use of git's ability to track links! Do please submit PR at your earliest convenience.

                Show
                ann.loraine Ann Loraine added a comment - OK thanks! Makes sense. Nice use of git's ability to track links! Do please submit PR at your earliest convenience.
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                pbadzuh Philip Badzuh (Inactive) added a comment -

                Thanks!

                Please see the PR here:
                https://bitbucket.org/lorainelab/genome-dashboard/pull-requests/11/igbf-2405-change-image-names-to-match/diff

                Show
                pbadzuh Philip Badzuh (Inactive) added a comment - Thanks! Please see the PR here: https://bitbucket.org/lorainelab/genome-dashboard/pull-requests/11/igbf-2405-change-image-names-to-match/diff
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                ann.loraine Ann Loraine added a comment -

                Merged and deployed to https://test.bioviz.org/genome-dashboard.
                All the expected images are present.
                Moving to Closed.

                Show
                ann.loraine Ann Loraine added a comment - Merged and deployed to https://test.bioviz.org/genome-dashboard . All the expected images are present. Moving to Closed.

                  People

                  • Assignee:
                    pbadzuh Philip Badzuh (Inactive)
                    Reporter:
                    ann.loraine Ann Loraine
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                    • Created:
                      Updated:
                      Resolved: