Details
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Type:
Improvement
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Story Points:0.5
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Epic Link:
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Sprint:Spring 9 : 25 May to 8 Jun
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
- 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 Chester Dias or Philip Badzuh for help.
Attachments
Issue Links
- relates to
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IGBF-2399 Avoid colliding image names for species
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Rank | Ranked higher |
| 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. |
| Labels | Beginner Intern |
| 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. |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
Please use attached image for Cannabis sativa instead.
| Attachment | C_sativa_CBDRx.png [ 14747 ] |
This image is from wikipedia.
| Assignee | Philip Badzuh [ pbadzuh ] |
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.
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
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.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
OK thanks! Makes sense. Nice use of git's ability to track links! Do please submit PR at your earliest convenience.
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
Thanks!
Please see the PR here:
https://bitbucket.org/lorainelab/genome-dashboard/pull-requests/11/igbf-2405-change-image-names-to-match/diff
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Merged and deployed to https://test.bioviz.org/genome-dashboard.
All the expected images are present.
Moving to Closed.
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
Please see my branch here:
https://bitbucket.org/pbadzuh/genome-dashboard_pbdev/branch/IGBF-2405#diff