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
| Field | Original Value | New Value |
|---|---|---|
| Sprint | Fall 2018 Sprint 3 [ 53 ] |
| Rank | Ranked higher |
| 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 |
| 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. |
| 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. |
| 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 |
| Fix Version/s | 9.1.0 Major Release [ 10601 ] | |
| Sprint | Winter 2018 Sprint 1 [ 56 ] | |
| Labels | Intermediate |
| Rank | Ranked higher |
| Sprint | Winter 2018 Sprint 1 [ 56 ] | Winter 2018 Sprint 1, Winter 2018 Sprint 2 [ 56, 57 ] |
| Rank | Ranked higher |
| 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 ] |
| Assignee | Srishti Tiwari [ stiwari8 ] |
| Assignee | Srishti Tiwari [ stiwari8 ] | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] |
| 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 ] |
| Rank | Ranked higher |
| Workflow | Loraine Lab Workflow [ 18130 ] | Fall 2019 Workflow Update [ 18910 ] |
| 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 ] |
| Rank | Ranked lower |
| Story Points | 1 | 2 |
| 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? |
| Epic Link | IGBF-1765 [ 17855 ] |
| Assignee | Prutha Kulkarni [ prutha ] |
| Rank | Ranked higher |
| 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 ] |
| Rank | Ranked higher |
| Workflow | Fall 2019 Workflow Update [ 18910 ] | Revised Fall 2019 Workflow Update [ 21037 ] |
| Status | Open [ 1 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Prutha Kulkarni [ prutha ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] | Prutha Kulkarni [ prutha ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Prutha Kulkarni [ prutha ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Ann Loraine [ aloraine ] |
| 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 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] | Prutha Kulkarni [ prutha ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Prutha Kulkarni [ prutha ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Prutha Kulkarni [ prutha ] |
| Assignee | Prutha Kulkarni [ prutha ] |
| 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 | Pawan Bole [ pbole ] |
| 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 ] |
| Rank | Ranked higher |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Pawan Bole [ pbole ] | Prutha Kulkarni [ prutha ] |