Details
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Type:
New Feature
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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:1
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Epic Link:
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Sprint:Fall 7 2021 Nov 8 - Nov 24, Fall 8 2021 Nov 29 - Dec 10, Fall 9 2021 Dec 13 - Dec 24
Description
A method for determining whether or not a UCSC genome name can be mapped to an IGB genome version is needed in order to decide which genome versions in the trackhub table UI can be made to have the option of utilizing IGB's 'open genome' endpoint located at http://localhost:7085/IGBControl?version=GENOME. Since this functionality may be needed in future services, an endpoint can be added to the trackhub facade API that returns the primary IGB genome version name corresponding to the provided UCSC genome version. This can be accomplished by searching the master synonyms.txt in an attempt to find an entry that matches the UCSC genome name. The first entry of the corresponding row would then be returned as the primary IGB genome version name.
It may be useful to extend IGB's endpoint to also include an 'species' query parameter, which could allow users to open converted trackhubs whose genome versions do not map to those associated with an IGB-supported organism.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2831 [ 19524 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description | A method for determining whether or not a UCSC genome name can be mapped to an IGB genome version is needed in order to decide which genome versions in the trackhub table UI can be made to have the option of utilizing IGB's 'open genome' endpoint located at http://localhost:7085/IGBControl?version=${genome}. Since this functionality may be needed in future services, an endpoint can be added to the trackhub facade API that returns the primary IGB genome version name corresponding to the provided UCSC genome version. This can be accomplished by searching the master [synonyms.txt|https://bitbucket.org/lorainelab/integrated-genome-browser/raw/3ea35fe2b8fd3c9dc59c1f3390744b41461f90ae/core/synonym-lookup/src/main/resources/synonyms.txt] in an attempt to find an entry that matches the UCSC genome name. The first entry of the corresponding row would then be returned as the primary IGB genome version name. |
| Description | A method for determining whether or not a UCSC genome name can be mapped to an IGB genome version is needed in order to decide which genome versions in the trackhub table UI can be made to have the option of utilizing IGB's 'open genome' endpoint located at http://localhost:7085/IGBControl?version=${genome}. Since this functionality may be needed in future services, an endpoint can be added to the trackhub facade API that returns the primary IGB genome version name corresponding to the provided UCSC genome version. This can be accomplished by searching the master [synonyms.txt|https://bitbucket.org/lorainelab/integrated-genome-browser/raw/3ea35fe2b8fd3c9dc59c1f3390744b41461f90ae/core/synonym-lookup/src/main/resources/synonyms.txt] in an attempt to find an entry that matches the UCSC genome name. The first entry of the corresponding row would then be returned as the primary IGB genome version name. | A method for determining whether or not a UCSC genome name can be mapped to an IGB genome version is needed in order to decide which genome versions in the trackhub table UI can be made to have the option of utilizing IGB's 'open genome' endpoint located at http://localhost:7085/IGBControl?version=GENOME. Since this functionality may be needed in future services, an endpoint can be added to the trackhub facade API that returns the primary IGB genome version name corresponding to the provided UCSC genome version. This can be accomplished by searching the master [synonyms.txt|https://bitbucket.org/lorainelab/integrated-genome-browser/raw/3ea35fe2b8fd3c9dc59c1f3390744b41461f90ae/core/synonym-lookup/src/main/resources/synonyms.txt] in an attempt to find an entry that matches the UCSC genome name. The first entry of the corresponding row would then be returned as the primary IGB genome version name. |
| Description | A method for determining whether or not a UCSC genome name can be mapped to an IGB genome version is needed in order to decide which genome versions in the trackhub table UI can be made to have the option of utilizing IGB's 'open genome' endpoint located at http://localhost:7085/IGBControl?version=GENOME. Since this functionality may be needed in future services, an endpoint can be added to the trackhub facade API that returns the primary IGB genome version name corresponding to the provided UCSC genome version. This can be accomplished by searching the master [synonyms.txt|https://bitbucket.org/lorainelab/integrated-genome-browser/raw/3ea35fe2b8fd3c9dc59c1f3390744b41461f90ae/core/synonym-lookup/src/main/resources/synonyms.txt] in an attempt to find an entry that matches the UCSC genome name. The first entry of the corresponding row would then be returned as the primary IGB genome version name. |
A method for determining whether or not a UCSC genome name can be mapped to an IGB genome version is needed in order to decide which genome versions in the trackhub table UI can be made to have the option of utilizing IGB's 'open genome' endpoint located at http://localhost:7085/IGBControl?version=GENOME. Since this functionality may be needed in future services, an endpoint can be added to the trackhub facade API that returns the primary IGB genome version name corresponding to the provided UCSC genome version. This can be accomplished by searching the master [synonyms.txt|https://bitbucket.org/lorainelab/integrated-genome-browser/raw/3ea35fe2b8fd3c9dc59c1f3390744b41461f90ae/core/synonym-lookup/src/main/resources/synonyms.txt] in an attempt to find an entry that matches the UCSC genome name. The first entry of the corresponding row would then be returned as the primary IGB genome version name.
It may be useful to extend IGB's endpoint to also include an 'species' query parameter, which could allow users to open converted trackhubs whose genome versions do not map to those associated with an IGB-supported organism. |
| Sprint | Fall 7 2021 Nov 8 - Nov 24 [ 133 ] | Fall 7 2021 Nov 8 - Nov 24, Fall 8 2021 Nov 29 - Dec 10 [ 133, 134 ] |
| Rank | Ranked higher |
That is fine.
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Summary | Add trackhub facade API endpoint to check for UCSC-IGB genome version match | Add trackhub facade API endpoint to translate UCSC genome names to IGB synonym equivalents |
Please see my changes here.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Code looks good. It is nice to see formatted comment string for the new method "get_igb_genome_versions". I actually am not familiar with the proper way to format this type of comment in python, so this was helpful for me. Please submit PR when ready.
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Ann Loraine [ aloraine ] | Philip Badzuh [ pbadzuh ] |
That's good to hear, thanks. Please see the PR here.
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
The PR targets developer's repository, not team repository.
Philip Badzuh - please re-submit the PR with the team repository as the target.
| Assignee | Philip Badzuh [ pbadzuh ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| 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 ] |
Sorry about that. Please see the correct PR here.
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
Merged.
Deployed to the main track hub (production) site. Ready for testing.
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Notes for testing:
This code adds the new endpoint igbGenomeVersion.
For description of how to invoke this endpoint, visit the repository address in your browser and scroll down the page.
| Assignee | Omkar Marne [ omarne ] |
| Sprint | Fall 7 2021 Nov 8 - Nov 24, Fall 8 2021 Nov 29 - Dec 10 [ 133, 134 ] | Fall 7 2021 Nov 8 - Nov 24, Fall 8 2021 Nov 29 - Dec 10, Fall 9 2021 Dec 13 - Dec 24 [ 133, 134, 135 ] |
| Rank | Ranked higher |
| Attachment | screenshot-1.png [ 17020 ] |
I clone the hub-facade repository.
After performing the steps in the bitbucket repository I got the above output. Please let me know if that's an expected output. Please see attached screenshot.
Philip Badzuh Please take a look.
A reminder for Omkar Marne:
I'm not sure if you are intending to do more work on this, or if you are blocked and waiting for input from the developer.
No-one will notice your comment above until you either:
- either move this ticket back to "To-Do" (because the dev needs to answer your question before you can proceed)
or
- you "@" the dev with your question.
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
| Assignee | Omkar Marne [ omarne ] | Philip Badzuh [ pbadzuh ] |
Hey Omkar Marne, you'll need to test the endpoint using the POST http method. You can do so by using Postman, which offers a GUI, or curl in the command line. Thanks. Adding the http method accepted by each of the endpoints could be something that we could add to the readme later.
| Assignee | Philip Badzuh [ pbadzuh ] | Omkar Marne [ omarne ] |
Hey Omkar Marne, sorry for any confusion. There was some information missing from the readme, which I have updated. You can see my latest code here and the latest testing instructions here. Please let me know if you have any questions.
| Attachment | Postman.png [ 17021 ] |
After copying the changes that Philip Badzuh made in his repository I am getting the expected output. Please check the attached snapshot 'Postman'. I have used the postman app web version instead of the local agent to display the POST method.
Philip Badzuh Please submit the pull requests to merge your changes.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| 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 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Omkar Marne [ omarne ] | Philip Badzuh [ pbadzuh ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
Please review the changes linked to in my previous comment.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Assignee | Omkar Marne [ omarne ] |
| Assignee | Omkar Marne [ omarne ] | Ann Loraine [ aloraine ] |
Changes are good! Please submit PR.
| 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 | Ann Loraine [ aloraine ] | Philip Badzuh [ pbadzuh ] |
Great! Please see PR here.
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
Merged and deployed to back end site for testing: https://translate.bioviz.org. Ready for testing.
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Omkar Marne [ omarne ] |
| Attachment | screenshot-2.png [ 17023 ] |
| Attachment | screenshot-1.png [ 17020 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Omkar Marne [ omarne ] | Philip Badzuh [ pbadzuh ] |
After performing the testing instructions from the read me the file I am getting the expected output.
While executing the URL I had to install Postman app desktop agent to display the POST method result on the localhost.
Please see screenshot 2.
Closing the ticket.
I started by implementing the endpoint to take a single UCSC genome and return the IGB equivalent, however, this would require many requests that would increase latency for the front-end.
As a second version, I updated the endpoint to take multiple UCSC genome versions for conversion.
In testing, there was a CORS issue, so I configured our django server to allow requests from all origins in the browser. We can update this to limit it to bioviz.org, if you see this as an issue, [~aloraine].