Uploaded image for project: 'IGB'
  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.

            Attachments

              Issue Links

              relates to

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

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-1765 [ 17855 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2399 [ IGBF-2399 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Description Please also raise a ticket for an image name change, otherwise, images won't be visible for some.

                		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:

                * Fork this repo https://bitbucket.org/lorainelab/genome-dashboard
                * Images to change are in genome-dashboard/public/images

                *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 [~cdias1] or [~pbadzuh] for help.
                ann.loraine Ann Loraine made changes -
                Labels Beginner Intern
                ann.loraine Ann Loraine made changes -
                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:

                * Fork this repo https://bitbucket.org/lorainelab/genome-dashboard
                * Images to change are in genome-dashboard/public/images

                *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 [~cdias1] or [~pbadzuh] for help.                 		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:

                * Fork this repo https://bitbucket.org/lorainelab/genome-dashboard
                * Images to change are in genome-dashboard/public/images
                * Not all will need to be changed.

                *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 [~cdias1] or [~pbadzuh] for help.
                pbadzuh Philip Badzuh (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                pbadzuh Philip Badzuh (Inactive) made changes -
                Assignee Philip Badzuh [ pbadzuh ]
                pbadzuh Philip Badzuh (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Hide
                Permalink
                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
                pbadzuh Philip Badzuh (Inactive) made changes -
                Assignee Philip Badzuh [ pbadzuh ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Please use attached image for Cannabis sativa instead.

                Show
                ann.loraine Ann Loraine added a comment - Please use attached image for Cannabis sativa instead.
                ann.loraine Ann Loraine made changes -
                Attachment C_sativa_CBDRx.png [ 14747 ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                This image is from wikipedia.

                Show
                ann.loraine Ann Loraine added a comment - This image is from wikipedia.
                ann.loraine Ann Loraine made changes -
                Assignee Philip Badzuh [ pbadzuh ]
                Hide
                Permalink
                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.
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                Hide
                Permalink
                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.
                pbadzuh Philip Badzuh (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                pbadzuh Philip Badzuh (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                pbadzuh Philip Badzuh (Inactive) made changes -
                Assignee Philip Badzuh [ pbadzuh ]
                Hide
                Permalink
                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.
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Assignee Philip Badzuh [ pbadzuh ]
                Hide
                Permalink
                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
                pbadzuh Philip Badzuh (Inactive) made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                pbadzuh Philip Badzuh (Inactive) made changes -
                Assignee Philip Badzuh [ pbadzuh ]
                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 ]
                Hide
                Permalink
                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.
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Assignee Philip Badzuh [ pbadzuh ]

                  People

                  • Assignee:
                    pbadzuh Philip Badzuh (Inactive)
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: