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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Sprint:Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar
Description
Situation: Need to revert changes to how the bookmark url encoding works in order to get bookmarks to work with special characters.
Task: Revert changes to bookmark url encoding.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
|
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | Bed_HomoSapiensChr1 SPACE.bed [ 14652 ] | |
| Attachment | BedGraph_HomoSapien_noName SPACE.bedGraph [ 14653 ] |
| Assignee | Nowlan Freese [ nfreese ] | Karthik Raveendran [ karthik ] |
| Summary | Handle spaces in filenames | Revert changes to URL encoding in bookmarks |
| Description |
Situation: If there is a space in a filename it is causing the metadata colors to not be loaded correctly - though the file does load.
Task: Handle spaces in filenames correctly. |
Situation: Need to revert changes to how the bookmark url encoding works in order to get bookmarks to work with special characters.
Task: Revert changes to bookmark url encoding. |
| Assignee | Karthik Raveendran [ karthik ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Epic Link |
|
| Sprint | Spring 3 : 17 Feb to 28 Feb [ 87 ] | Spring 3 : 17 Feb to 28 Feb, Spring 4 : 2 Mar to 13 Mar [ 87, 89 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Prutha Kulkarni [ prutha ] |
I have tested the issue using the instructions mentioned above.
1) Downloaded the files and the branch installer.
2) Opened those files and created a bookmark.
3) Removed those files and selected a different genome.
4) Double clicked bookmark to check if the custom genome is not being loaded if a user is already in a genome when opening data that is not associated with a genome.
Everything is working fine. Nowlan Freese, please go ahead and submit a PR for the same.
| Assignee | Prutha Kulkarni [ prutha ] | Nowlan Freese [ nfreese ] |
| Status | First Level Review in Progress [ 10301 ] | 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 ] |
| Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
Nowlan Freese - Bookmarks are getting loaded but once I close IGB and try to reload, null pointer exception is thrown.
| Assignee | Noor Zahara [ noor91zahara ] | Nowlan Freese [ nfreese ] |
| Status | Post-merge Testing In Progress [ 10003 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
The issue Noor found is an existing issue with how bookmarks works with custom genomes. What is happening is that when a user loads data without selecting a genome, IGB creates a custom genome. The data is then loaded within this custom genome. When the user creates a bookmark, the version is set as custom genome. When the user closes IGB the custom genome is removed. When the user reopens IGB and tries to load the bookmark, IGB cannot find a genome version of custom genome, and thus generates a null pointer. This behavior has been around for a while. CyVerse and Galaxy use a separate bookmark logic to load custom genomes to avoid this problem. This seems like an edge case as I'm not sure how often users would be creating bookmarks in custom genomes.
Since the other functionality appears to be working, I'm closing this issue.
| 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 ] |
Changes made in
IGBF-32were interfering with bookmarks created from files with spaces being loaded correctly. As the associated changes in the Galaxy codebase associated withIGBF-32were not pushed, I reverted the changes in the directlyLoadFile and loadUnknownData methods. The loadUnknownData method was also modified to match the loadCyVerseDataMethod (now removed) fromIGBF-1632. The loadUnknownData method now does not load a custom genome if a user is already in a genome when opening data that is not associated with a genome.To test:
To test IGB bookmarks, load the attached files into IGB and create a bookmark. Remove the files from IGB and then double-click on the bookmark to see if it loads correctly.
My IGB branch with changes: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-2273-SpaceInName