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:2
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Epic Link:
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Sprint:Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11
Description
Situation: The UCSC DAS data provider has access to a large number of genomes and datasets that are very useful for IGB users. However, the UCSC DAS endpoint can be slow and it is unclear how much longer UCSC will support it as they have created a new JSON API with the same functionality.
Task: Investigate the feasibility of altering the IGB UCSC DAS logic to add a new JSON API endpoint.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Rank | Ranked higher |
Some documentation:
DAS: https://genome.ucsc.edu/FAQ/FAQdownloads.html#download23
API: https://genome.ucsc.edu/goldenPath/help/api.html
What would the same query to DAS look like for the API?
| Sprint | Spring 5 2021 May 17 - May 28 [ 121 ] | Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11 [ 121, 122 ] |
| Rank | Ranked higher |
Suggestion: Investigate adding a new data provider that consumes data from the JSON API (without changing the current DAS data provider infrastructure).
| Summary | Investigate changing UCSC DAS data provider to JSON API | Investigate adding UCSCS JSON API as a new data provider |
| Summary | Investigate adding UCSCS JSON API as a new data provider | Investigate adding UCSC JSON API as a new data provider |
| Description |
Situation: The UCSC DAS data provider has access to a large number of genomes and datasets that are very useful for IGB users. However, the UCSC DAS endpoint can be slow and it is unclear how much longer UCSC will support it as they have created a new JSON API with the same functionality.
Task: Investigate the feasibility of altering the IGB UCSC DAS logic to instead use the JSON API endpoint. |
Situation: The UCSC DAS data provider has access to a large number of genomes and datasets that are very useful for IGB users. However, the UCSC DAS endpoint can be slow and it is unclear how much longer UCSC will support it as they have created a new JSON API with the same functionality.
Task: Investigate the feasibility of altering the IGB UCSC DAS logic to add a new JSON API endpoint. |
| Assignee | Omkar Marne [ omarne ] | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11 [ 121, 122 ] | Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25 [ 121, 122, 123 ] |
| Rank | Ranked higher |
| Sprint | Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25 [ 121, 122, 123 ] | Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11 [ 121, 122 ] |
| 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 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Nowlan Freese [ nfreese ] |
Nowlan Freese: suggests this could be a good project for a student engineer (1 to 2 months, 15 hours/week, including training?)
Current UCSC DAS genomes: https://genome.ucsc.edu/cgi-bin/das/dsn
Current UCSC API genomes: https://api.genome.ucsc.edu/list/ucscGenomes