Details
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Type: Improvement
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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:
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Story Points:2
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Epic Link:
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Sprint:Winter 2018 Sprint 1, Winter 2018 Sprint 2, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov
Description
Sometimes we have a genome sequence available but no annotation files.
In such a case, it makes sense to provide the sequence (2bit) file, the genome.txt file, but not the annots.xml file, since the annots.xml file would contain no files.
However, IGB gives an error if there is no annots.xml file to load.
Change this so that if a Quickload genome directory lacks an annots.xml file, IGB can still show the genome sequence and load files from the users desktop.
To do this task, you will need to dig into the DataProviders system. You will need to understand what happens when a Quickload site's genome directory is accessed.
To get familiar with it,
- review the Quickload documentation on wiki.transvar.org
- search and review previous Quickload-related issues in Jira
Attachments
Activity
Ann Loraine
created issue -
Ann Loraine
made changes -
Field | Original Value | New Value |
---|---|---|
Sprint | Fall 2018 Sprint 3 [ 53 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Summary | Enable IGB to show a genome from Quickload even if annots.xml is empty | Enable IGB to show a genome from Quickload even if annots.xml is not available |
Ann Loraine
made changes -
Description |
Sometimes we have a genome sequence available but no annotations.
However, currently, if there are no annotations available, IGB refuses to load a genome from a Quickload site. Let's change this. If a genome version directory has no annots.xml file or if the annots.xml file contains no data, IGB should still load and display the assembly. |
Sometimes we have a genome sequence available but no annotation files. In such a case, it makes sense to provide the sequence (2bit) file, the genome.txt file, but not the annots.xml file, since the annots.xml file would contain no files. However, IGB gives an error if there is no annots.xml file to load. Change this so that if a Quickload genome directory lacks an annots.xml file, IGB can still show the genome sequence and load files from the users desktop. |
Ann Loraine
made changes -
Description |
Sometimes we have a genome sequence available but no annotation files. In such a case, it makes sense to provide the sequence (2bit) file, the genome.txt file, but not the annots.xml file, since the annots.xml file would contain no files. However, IGB gives an error if there is no annots.xml file to load. Change this so that if a Quickload genome directory lacks an annots.xml file, IGB can still show the genome sequence and load files from the users desktop. |
Sometimes we have a genome sequence available but no annotation files.
In such a case, it makes sense to provide the sequence (2bit) file, the genome.txt file, but not the annots.xml file, since the annots.xml file would contain no files. However, IGB gives an error if there is no annots.xml file to load. Change this so that if a Quickload genome directory lacks an annots.xml file, IGB can still show the genome sequence and load files from the users desktop. To do this task, you will need to dig into the DataProviders system. You will need to understand what happens when a Quickload site's genome directory is accessed. |
Ann Loraine
made changes -
Description |
Sometimes we have a genome sequence available but no annotation files.
In such a case, it makes sense to provide the sequence (2bit) file, the genome.txt file, but not the annots.xml file, since the annots.xml file would contain no files. However, IGB gives an error if there is no annots.xml file to load. Change this so that if a Quickload genome directory lacks an annots.xml file, IGB can still show the genome sequence and load files from the users desktop. To do this task, you will need to dig into the DataProviders system. You will need to understand what happens when a Quickload site's genome directory is accessed. |
Sometimes we have a genome sequence available but no annotation files.
In such a case, it makes sense to provide the sequence (2bit) file, the genome.txt file, but not the annots.xml file, since the annots.xml file would contain no files. However, IGB gives an error if there is no annots.xml file to load. Change this so that if a Quickload genome directory lacks an annots.xml file, IGB can still show the genome sequence and load files from the users desktop. To do this task, you will need to dig into the DataProviders system. You will need to understand what happens when a Quickload site's genome directory is accessed. To get familiar with it, * review the Quickload documentation on wiki.transvar.org * search and review previous Quickload-related issues in Jira |
Ann Loraine
made changes -
Fix Version/s | 9.1.0 Major Release [ 10601 ] | |
Sprint | Winter 2018 Sprint 1 [ 56 ] | |
Labels | Intermediate |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 1 [ 56 ] | Winter 2018 Sprint 1, Winter 2018 Sprint 2 [ 56, 57 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 1, Winter 2018 Sprint 2 [ 56, 57 ] | Winter 2018 Sprint 1, Winter 2018 Sprint 2, Winter 2018 Sprint 3 [ 56, 57, 58 ] |
Srishti Tiwari (Inactive)
made changes -
Assignee | Srishti Tiwari [ stiwari8 ] |
Ann Loraine
made changes -
Assignee | Srishti Tiwari [ stiwari8 ] | Ann Loraine [ aloraine ] |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] |
Ann Loraine
made changes -
Fix Version/s | 9.1.0 Major Release [ 10601 ] | |
Sprint | Winter 2018 Sprint 1, Winter 2018 Sprint 2, Winter 2018 Sprint 3 [ 56, 57, 58 ] | Winter 2018 Sprint 1, Winter 2018 Sprint 2 [ 56, 57 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Workflow | Loraine Lab Workflow [ 18130 ] | Fall 2019 Workflow Update [ 18910 ] |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 1, Winter 2018 Sprint 2 [ 56, 57 ] | Winter 2018 Sprint 1, Winter 2018 Sprint 2, Fall 2019 Sprint 4 [ 56, 57, 75 ] |
Ann Loraine
made changes -
Rank | Ranked lower |
Ann Loraine
made changes -
Story Points | 1 | 2 |
Ann Loraine
made changes -
Summary | Enable IGB to show a genome from Quickload even if annots.xml is not available | Investigate: Can we enable IGB to show a genome from Quickload even if annots.xml is not available? |
Ann Loraine
made changes -
Epic Link | IGBF-1765 [ 17855 ] |
Prutha Kulkarni (Inactive)
made changes -
Assignee | Prutha Kulkarni [ prutha ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 1, Winter 2018 Sprint 2, Fall 4 : 30 Sep to 11 Oct [ 56, 57, 75 ] | Winter 2018 Sprint 1, Winter 2018 Sprint 2, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct [ 56, 57, 75, 76 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Workflow | Fall 2019 Workflow Update [ 18910 ] | Revised Fall 2019 Workflow Update [ 21037 ] |
Status | Open [ 1 ] | To-Do [ 10305 ] |
Prutha Kulkarni (Inactive)
made changes -
Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Prutha Kulkarni (Inactive)
made changes -
Assignee | Prutha Kulkarni [ prutha ] |
Prutha Kulkarni (Inactive)
made changes -
Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
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 ] | To-Do [ 10305 ] |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] | Prutha Kulkarni [ prutha ] |
Prutha Kulkarni (Inactive)
made changes -
Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Prutha Kulkarni (Inactive)
made changes -
Assignee | Prutha Kulkarni [ prutha ] |
Prutha Kulkarni (Inactive)
made changes -
Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 1, Winter 2018 Sprint 2, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct [ 56, 57, 75, 76 ] | Winter 2018 Sprint 1, Winter 2018 Sprint 2, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov [ 56, 57, 75, 76, 77 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Ann Loraine
made changes -
Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] | Prutha Kulkarni [ prutha ] |
Prutha Kulkarni (Inactive)
made changes -
Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Prutha Kulkarni (Inactive)
made changes -
Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Prutha Kulkarni (Inactive)
made changes -
Assignee | Prutha Kulkarni [ prutha ] |
Ann Loraine
made changes -
Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Ann Loraine
made changes -
Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Ann Loraine
made changes -
Assignee | Prutha Kulkarni [ prutha ] |
Prutha Kulkarni (Inactive)
made changes -
Assignee | Prutha Kulkarni [ prutha ] |
Prutha Kulkarni (Inactive)
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 ] |
Pawan Bole (Inactive)
made changes -
Assignee | Pawan Bole [ pbole ] |
Ann Loraine
made changes -
Sprint | Winter 2018 Sprint 1, Winter 2018 Sprint 2, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov [ 56, 57, 75, 76, 77 ] | Winter 2018 Sprint 1, Winter 2018 Sprint 2, Fall 4 : 30 Sep to 11 Oct, Fall 5 : 14 Oct to 25 Oct, Fall 6 : 28 Oct to 8 Nov, Fall 7 : 11 Nov to 22 Nov [ 56, 57, 75, 76, 77, 78 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Pawan Bole (Inactive)
made changes -
Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Pawan Bole (Inactive)
made changes -
Resolution | Done [ 10000 ] | |
Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Pawan Bole (Inactive)
made changes -
Assignee | Pawan Bole [ pbole ] | Prutha Kulkarni [ prutha ] |