Details
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Type:
Task
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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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Labels:None
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Story Points:3
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Epic Link:
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Sprint:Spring 7
Description
Task: Release the UCSC GenArk IGB App to the app store.
- Create a name for the app
- Create a logo for the app
- Create an AppDescription.md with instructions on how to use the app
Attachments
Issue Links
- relates to
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IGBF-4211 Improve the Species and Genome Version names shown from GenArk
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- To-Do
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-4086 [ 23382 ] |
| Sprint | Spring 7 [ 216 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Nowlan Freese [ nfreese ] |
AppDescription:
- Can we put the GenArk tab to the right of the Advanced Search tab?
- I'm leaning towards getting rid of the bullet point "View genome-specific metadata..."
- I would change the bullet point "To learn more about a genome..." to something that informs the user that data for the selected genome can be found under the Data Access tab in the Available Data window.
Readme:
- Do we need to specify Zulu or can we just say JDK21? Also, does it need to be the JDK21 + JavaFX version?
- Under the How to use this IGB App: I would add a bullet point that informs the user that data for the selected genome can be found under the Data Access tab in the Available Data window.
I vote for the name GenArk Genomes
| Assignee | Nowlan Freese [ nfreese ] | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Modified the markdown files accordingly and fixed a small sorting issue as well. Updated code is present in the branch: https://bitbucket.org/jaya-sravani/ucsc-genark-data-provider/branch/IGBF-4189. Please review and let me know if there's any other issue. Checked whether this app needs JDK21 + JavaFX version; no dependencies require JavaFX, so changed the bullet point requirement to just JDK21.
Pushed the bitbucket-pipelines.yaml file as well. Once the issue with the release artifacts pipeline for the main branch of IGB is resolved, will rerun this pipeline to generate the repository files in the Download folder.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
Able to set up the Bitbucket pipelines now. It's working as expected, and the files are available in the downloads folder.
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Comment |
[ As per discussion in today's scrum and yesterday via email, [~jsirigin] decided to stop using repository variable
{code} ${BB_AUTH_STRING} {code} in the bitbucket pipeline script and change to using {code} ${BITBUCKET_USERNAME}:${BITBUCKET_APP_PASSWORD} {code} instead because this is more consistent with the Atlassian bitbucket cloud documentation and also is more intuitive for users, because our individual accounts have "app password" options in our bitbucket user account settings. She also investigated whether BITBUCKET_USERNAME environment variable is provided in the pipeline environment. It is not. So, we need to set both variables as repository environment variables for the pipeline to run. We both had an issue with remembering how to create BB_AUTH_STRING. It's supposed to be a concatenation of a user name and an app password, with a colon character. This is hard to remember and easy to forget. [~jsirigin] reimplemented the pipeline code and I have updated the lorainelab fork. The pipeline ran as expected and new artifacts were built and transferred the the Download section as expeced. ] |
| Attachment | GenArk-Genome_logo.png [ 18682 ] |
Released the app to bioviz.org, installed and tested it, everything's working as expected. Moving this ticket to merged needs testing.
Ann Loraine I have added the logo file to the resources folder in my workspace repo, so the lorainelab fork needs to be updated with that.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] | Nowlan Freese [ nfreese ] |
| Assignee | Nowlan Freese [ nfreese ] | Paige Kulzer [ pkulzer ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Tested the new UCSC GenArk App on my Mac using IGB 10.2.0. The app installs and uninstalls properly. The GenArk Genomes tab appears in the bottom tray once the app is installed. The search, load, and information aspects of the table are all working as expected. No errors in the Log.
I suggest investigating the possibility of changing what is displayed in the Species and Genome Version drop-down menus once GenArk genomes are loaded into IGB. Currently, the Assembly Version is being displayed in the Species drop-down while the Accession Number is being displayed in the Genome Version drop-down. Instead, I think displaying the Scientific Name in the Species menu and the Assembly Version in the Genome Version menu would be more consistent. Nowlan Freese will make an investigate ticket for this and relate it to this ticket.
Marking this as Done!
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Paige Kulzer [ pkulzer ] | Jaya Sravani Sirigineedi [ jsirigin ] |
Added the AppDescription.md and README.md files. Here is the branch with the updated code: https://bitbucket.org/jaya-sravani/ucsc-genark-data-provider/branch/IGBF-4189. Please review and let me know if there are any issues.
Few suggestions for the app name:
Let me know which options you'd prefer, and if you have any more suggestions, feel free to add them.
Note: Once the app name is finalised, will change the name in the markdown files and application.