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: 9.1.8 Major Release
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Labels:None
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Story Points:3
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Epic Link:
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Sprint:Winter 6 Mar 8 - Mar 19, Spring 1 2021 Mar 22 - Apr 2, Spring 2 2021 Apr 5 - Apr 16
Description
Situation: In IGB, when a user selects File > Open Genome from File... a window opens that allows the user to provide a Reference Sequence for the new genome. However, only local files are allowed, not URLs.
Task: Add ability to use URLs when opening custom genomes.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Fix Version/s | 9.1.8 Major Release [ 10605 ] |
| Rank | Ranked higher |
| Sprint | Winter 6 Mar 8 - Mar 19 [ 116 ] | Winter 6 Mar 8 - Mar 19, Spring 1 Mar 22 - Apr 2 [ 116, 117 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Rank | Ranked higher |
| Issue Type | Task [ 3 ] | New Feature [ 2 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
In the new changes, the 'Reference Sequence' text field in 'Open Genome from File UI' can be used to enter a URL as well as a local system file path to load a custom genome. The new logic checks the prefix of the link to determine if its URL or local file path.
The changes need testing against different file paths that includes special characters or spaces.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Sprint | Winter 6 Mar 8 - Mar 19, Spring 1 2021 Mar 22 - Apr 2 [ 116, 117 ] | Winter 6 Mar 8 - Mar 19, Spring 1 2021 Mar 22 - Apr 2, Spring 2 2021 Apr 5 - Apr 16 [ 116, 117, 118 ] |
| Rank | Ranked higher |
Karthik's branch installers: https://bitbucket.org/KarthikRavee91/karthikfork-igb/downloads/
Test loading the following files both online (by adding the URL) or locally (by downloading the file and choosing it locally):
https://data.cyverse.org/dav-anon/iplant/home/nowlanf/nowlanTESTDontChange/relativeFixed/E_unicornis_Jul_2043/down%20stream/E_unicornis_Jul_2043.2bit
http://igbquickload.org/quickload/A_thaliana_Jun_2009/A_thaliana_Jun_2009.2bit
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Nowlan Freese [ nfreese ] |
Can this import be removed: import static com.affymetrix.genometry.symloader.ProtocolConstants.FILE_PROTOCOL_SCHEME;
Tested the above 2bit files on Mac and they worked correctly, could load the sequence.
I also tested the fasta file: https://data.cyverse.org/dav-anon/iplant/home/nowlanf/S_SARS-CoV-2_Wuhan-Hu-1_Jan_2020.fa
It was able to load the correct chromosome and sequence.
| Assignee | Nowlan Freese [ nfreese ] | Karthik Raveendran [ karthik ] |
| 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 ] |
| Assignee | Karthik Raveendran [ karthik ] |
Looks good, recommend pull request.
| Assignee | Karthik Raveendran [ karthik ] |
| 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 | Karthik Raveendran [ karthik ] |
Pull request is merged. Master branch installers are been built and ready for testing.
| Assignee | Rachel Weidenhammer [ rweidenh ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Tested on Windows 10
All of the files in the previous comments do load correctly via URL.
I also tested the unicorn link locally and it works that way as well.
Looks good. Moving to Done.
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Rachel Weidenhammer [ rweidenh ] | Karthik Raveendran [ karthik ] |
Kindly provide comments describing work thus far.