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:Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15
Description
Add a button to the manual trackhub-converter page to hit the "Add Data Source" endpoint in IGB. Parameters required for the request:
1) quickloadurl (eg. https://translate.bioviz.org/api/?hubUrl=https://raw.githubusercontent.com/mhalushka/miROme/main/UCSC/hub.txt&filePath=/) and 2) quickloadname: short label in the hubUrl file (use the hubUrl in the above link to see a short label example)
Use the following endpoint: http://127.0.0.1:7085/igbDataSource for the request call.
Attachments
Issue Links
Activity
Karthik Raveendran
created issue -
Karthik Raveendran
made changes -
Field | Original Value | New Value |
---|---|---|
Epic Link | IGBF-2831 [ 19524 ] |
Karthik Raveendran
made changes -
Karthik Raveendran
made changes -
Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Karthik Raveendran
made changes -
Description |
Add a button to the track hub table to hit the Add Data Source endpoint in IGB. Parameters required for the request: quickloadurl and quickloadname.
Use the following for the request: http://127.0.0.1:7085/igbDataSource |
Add a button to the trackhub-converter page to hit the Add Data Source endpoint in IGB. Parameters required for the request: quickloadurl and quickloadname.
Use the following for the request: http://127.0.0.1:7085/igbDataSource |
Karthik Raveendran
made changes -
Summary | Add data source button to Track Hub table | Add data source button to Track Hub webpages |
Karthik Raveendran
made changes -
Description |
Add a button to the trackhub-converter page to hit the Add Data Source endpoint in IGB. Parameters required for the request: quickloadurl and quickloadname.
Use the following for the request: http://127.0.0.1:7085/igbDataSource |
Add a button to the trackhub-converter page to hit the "Add Data Source" endpoint in IGB. Parameters required for the request:
1) quickloadurl (eg. https://translate.bioviz.org/api/?hubUrl=https://raw.githubusercontent.com/mhalushka/miROme/main/UCSC/hub.txt&filePath=/) and 2) quickloadname: short label in the hubUrl file (use the hubUrl in the above link to see a short label example) Use the following endpoint: http://127.0.0.1:7085/igbDataSource for the request call. |
Karthik Raveendran
made changes -
Description |
Add a button to the trackhub-converter page to hit the "Add Data Source" endpoint in IGB. Parameters required for the request:
1) quickloadurl (eg. https://translate.bioviz.org/api/?hubUrl=https://raw.githubusercontent.com/mhalushka/miROme/main/UCSC/hub.txt&filePath=/) and 2) quickloadname: short label in the hubUrl file (use the hubUrl in the above link to see a short label example) Use the following endpoint: http://127.0.0.1:7085/igbDataSource for the request call. |
Add a button to the manual trackhub-converter page to hit the "Add Data Source" endpoint in IGB. Parameters required for the request:
1) quickloadurl (eg. https://translate.bioviz.org/api/?hubUrl=https://raw.githubusercontent.com/mhalushka/miROme/main/UCSC/hub.txt&filePath=/) and 2) quickloadname: short label in the hubUrl file (use the hubUrl in the above link to see a short label example) Use the following endpoint: http://127.0.0.1:7085/igbDataSource for the request call. |
Karthik Raveendran
made changes -
Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Karthik Raveendran
made changes -
Assignee | Karthik Raveendran [ karthik ] |
Ann Loraine
made changes -
Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] |
Ann Loraine
made changes -
Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Ann Loraine
made changes -
Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Ann Loraine
made changes -
Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
Ann Loraine
made changes -
Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] |
Ann Loraine
made changes -
Sprint | Summer 5 2022 July 18 [ 151 ] | Summer 5 2022 July 18, Summer 6 2022 Aug 1 [ 151, 152 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Nowlan Freese
made changes -
Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Nowlan Freese
made changes -
Assignee | Nowlan Freese [ nfreese ] |
Nowlan Freese
made changes -
Status | Post-merge Testing In Progress [ 10003 ] | Merged Needs Testing [ 10002 ] |
Nowlan Freese
made changes -
Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Nowlan Freese
made changes -
Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
Nowlan Freese
made changes -
Assignee | Nowlan Freese [ nfreese ] | Karthik Raveendran [ karthik ] |
Karthik Raveendran
made changes -
Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Karthik Raveendran
made changes -
Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Karthik Raveendran
made changes -
Assignee | Karthik Raveendran [ karthik ] |
Nowlan Freese
made changes -
Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Nowlan Freese
made changes -
Assignee | Nowlan Freese [ nfreese ] |
Nowlan Freese
made changes -
Assignee | Nowlan Freese [ nfreese ] | Karthik Raveendran [ karthik ] |
Nowlan Freese
made changes -
Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Karthik Raveendran
made changes -
Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Ann Loraine
made changes -
Sprint | Summer 5 2022 July 18, Summer 6 2022 Aug 1 [ 151, 152 ] | Summer 5 2022 July 18, Summer 6 2022 Aug 1, Fall 1 2022 Aug 15 [ 151, 152, 153 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Assignee | Karthik Raveendran [ karthik ] | Ann Loraine [ aloraine ] |
Ann Loraine
made changes -
Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
Ann Loraine
made changes -
Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] |
Nowlan Freese
made changes -
Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Nowlan Freese
made changes -
Assignee | Karthik Raveendran [ karthik ] |
Nowlan Freese
made changes -
Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
Karthik Raveendran
made changes -
Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Karthik Raveendran
made changes -
Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Karthik Raveendran
made changes -
Assignee | Karthik Raveendran [ karthik ] |
Nowlan Freese
made changes -
Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Nowlan Freese
made changes -
Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Nowlan Freese
made changes -
Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Ann Loraine
made changes -
Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
Ann Loraine
made changes -
Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Nowlan Freese
made changes -
Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Nowlan Freese
made changes -
Assignee | Nowlan Freese [ nfreese ] |
Nowlan Freese
made changes -
Nowlan Freese
made changes -
Assignee | Nowlan Freese [ nfreese ] | Karthik Raveendran [ karthik ] |
Nowlan Freese
made changes -
Resolution | Done [ 10000 ] | |
Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
For the manual trackhub converter page, the 'Add Data Source to IGB' button and the method has been implemented. The button appears only after the UCSC trackhub is converted and the quickload data source URL is copied from the result for the 'quickloadurl' parameter. For the 'quickloadname' parameter, the UCSC trackhub url is called and the 'shortLabel' is used. Thus, the 'add data source' endpoint URL is built.
However, when the igbDataSource endpoint is hit, I run into an error in IGB:
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException: genomeVersionNamePrefix is a required field.
When sample parameters are used(like "bioviz.org" and "karthik" for quickloadurl and quickloadname respectively) right after the 'built' URL above is called, both data sources are added to IGB.
See Nowlan Freese comments in
IGBF-3131where a list of testing issues are mentioned, Issue 2 "Invalid quickload (incorrect URL that returns HTML) "For public trackhub page, I assume that the same error will appear. A design for 'Add Data Source' button needs to finalized as well.