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:1
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Epic Link:
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Sprint:Fall 7 : 11 Nov to 22 Nov, Fall 8 : 25 Nov to 6 Dec, Fall 9 : 9 Dec to 20 Dec
Description
Situation: Loading a BAI by itself requires the chromosomes and their lengths. This information is being provided by IGB as long as a genome has been loaded. Versions of IGB previous to 9.1 required users to load a genome before loading data. As of 9.1 we now allow users to load data when no genome is selected. However, this will not work for BAI file, as the genome information is required.
Task: Implement the popup seen in IGB pre 9.1 warning the user that they must select a genome before loading a BAI file. Make sure that the warning only pops up for BAI files.
Attachments
Issue Links
- relates to
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IGBF-1920 Visualizing the index
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
|
| Assignee | Srishti Tiwari [ stiwari8 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Fall 7 : 11 Nov to 22 Nov [ 78 ] | Fall 7 : 11 Nov to 22 Nov, Fall 8 : 25 Nov to 6 Dec [ 78, 79 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Srishti Tiwari [ stiwari8 ] | Sai Charan Reddy Vallapureddy [ svallapu ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
I made a small request regarding imports. Otherwise it looks fine to me. However Sai Charan Reddy Vallapureddy should review, as requested by Srishti Tiwari.
Hi Professor, sorry about that. This is happening automatically in the latest IntelliJ. Reverting the same.
| 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 ] |
| Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] | Nowlan Freese [ nfreese ] |
The code is working correctly for File > Open File and dragging and dropping a bai file. However, I don't think the changes were implemented for loading via URL (openURLAction).
Moving to To Do.
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Nowlan Freese
branch: https://bitbucket.org/svallapu/charan_igb/branch/IGBF-2104-veryNew
Open URL requirement is not fixed.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Nowlan Freese [ nfreese ] |
Code is working correctly for File > Open File, dragging and dropping, and loading via URL.
Ready for pull request.
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Nowlan Freese [ nfreese ] | Sai Charan Reddy Vallapureddy [ svallapu ] |
[~aloraine]Nowlan Freese
Pull request submitted
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | To-Do [ 10305 ] |
| Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
Sai Charan Reddy Vallapureddy please check my one comment on the - see your branch/commit in bitbucket. I had a quick request for clarification regarding and apache commons import.
Comment is copied below:
"Can you please double-check that the bundle containing package org.apache.commons.io.FilenameUtils is properly imported? I’m wondering if might not be because I did not see an “apache” bundle explicitly included in the dependencies in the POM.xml file. However, in the maven bundle plugin configuration, the import packages directive is “*;resolution:=optional”
I’m not completely sure about this, but I think what’s happening is that we are telling the bnd tool that all packages are imported and even if they are not available in the run-time, the bundle should still resolve. Which means there could potentially be a run-time error?
Could yo double-check the bundle’s MANIFEST.MF file to make sure the needed apache commons packages is listed? Also, make sure it is properly listed in the bundle’s POM as a provided dependency?"
cc: Nowlan Freese
| Status | To-Do [ 10305 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
| Link | This issue relates to IGBF-2189 [ IGBF-2189 ] |
IGBF-2189 ticket is created for this issue.
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Sprint | Fall 7 : 11 Nov to 22 Nov, Fall 8 : 25 Nov to 6 Dec [ 78, 79 ] | Fall 7 : 11 Nov to 22 Nov, Fall 8 : 25 Nov to 6 Dec, Fall 9 : 9 Dec to 20 Dec [ 78, 79, 80 ] |
| Rank | Ranked higher |
Load genome requirement working correctly for URL, file, and drag and drop.
Closing issue.
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Nowlan Freese [ nfreese ] | Sai Charan Reddy Vallapureddy [ svallapu ] |
Ready for first level review:
https://bitbucket.org/srishtitiwari/integrated-genome-browser/commits/86fa90adcb025efb27632479656458900e7423dc