Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:1
-
Epic Link:
-
Sprint:Fall 9
Description
Situation: The External View tab does not appear to be working for UCSC. Based on the following URL, it looks like UCSC is blocking programmatic access to the site:
https://genome.ucsc.edu/cgi-bin/hgTracks?pix=800&db=hg19&position=chr1:6203693-6206373
There is a FAQ on the UCSC website that says programmatic access can be restored with an API key:
https://genome.ucsc.edu/FAQ/FAQdownloads.html#CAPTCHA
Task: Email the UCSC team to determine if we can get an API key for IGB or if they can whitelist us. In the meantime, disable the external view tab.
Attachments
Issue Links
- relates to
-
IGBF-4355 Investigate com.affymetrix.igb.external.LoaderTest failing
-
- Closed
-
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
In the External View tab there is a settings button. Clicking on it and following the directions there to add a UCSC user id does work to enable the External View to work. My recommendation would be that we leave the External View tab enabled and add some additional documentation to the IGB users guide saying that it is now a requirement to add a UCSC user id.
Updated documentation:
User's guide: https://wiki.bioviz.org/confluence/display/igbman/External+View
Release testing: https://wiki.bioviz.org/confluence/display/ITD/External+View
To test, follow the instructions provided in the documentation above. Make sure that it works and the instructions are clear.
Once testing is complete and successful, this ticket can be closed.
| Assignee | Nowlan Freese [ nfreese ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
At Step 4 in the User's Guide documentation, I had to click a hyperlink that read, "Show as updateable table." in order to see an hguid field to copy. You'll need to add this step to the Release testing documentation, as well.
After step 6, I had to click "update" again in order to get rid of the error in the External View tab.
All else looks good! It's easy to follow and no obvious grammatical/spelling issues.
| Assignee | Paige Kulzer [ pkulzer ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Paige Kulzer [ pkulzer ] | Nowlan Freese [ nfreese ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Good catch!
Documentation should be updated for user's guide and release documentation.
| Assignee | Nowlan Freese [ nfreese ] | Paige Kulzer [ pkulzer ] |
| 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 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Looks good! Closing ticket.
| 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 | Paige Kulzer [ pkulzer ] | Nowlan Freese [ nfreese ] |
| Link | This issue relates to IGBF-4383 [ IGBF-4383 ] |
I have emailed the UCSC team.