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 ] |
I have made the necessary changes to quickload module for the same.
I would suggest that someone who has prior knowledge about how the genome is loaded into IGB and how annots.xml works, should pick this up for the review. This way they'll be able to figure out quickly if I have missed anything which should have been handled.
The branch code can be found at :
https://bitbucket.org/pkulka10/igb_prutha/src/IGBF-1424/
| Assignee | Prutha Kulkarni [ prutha ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
You can use "https://quickload-testing.s3.amazonaws.com/noAnnotsQL/" hosted file for testing.
Steps for testing:
1) Run IGB and open preferences.
2) Go to Data sources tab and add a new Data Source by copying "https://quickload-testing.s3.amazonaws.com/noAnnotsQL/" url to the textbox.
3) "E_unicornus" named species will appear under the Species dropdown present in the right panel in IGB. Select it.
4) Select a Genome version which is available for the species.
5) It does not have an annots.xml file still the genome will be shown with a blank screen and a co-ordinate axis on it.
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Ann Loraine [ aloraine ] |
I added a question about Exception handling on the fork. Please take a look Prutha Kulkarni
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] | Prutha Kulkarni [ prutha ] |
Prof. [~aloraine], I have replied to the comment. Moving the ticket to In progress for further modifications.
Thanks.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Prof. [~aloraine], I have made the necessary changes and pushed those to the same branch. Also, I've improved the function validateURL a bit. Could you please have a look at those changes ?
Let me know if this is what you meant.
Changes can be found at:
https://bitbucket.org/pkulka10/igb_prutha/commits/d7aea8474f55848ea9a2cd3d0909e8d77b47dc0f
Thanks.
| 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 ] |
Please see comment on your branch
| Assignee | Ann Loraine [ aloraine ] | Prutha Kulkarni [ prutha ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Prof. [~aloraine], I have made the changes to the branch which can be found at.
https://bitbucket.org/pkulka10/igb_prutha/branch/IGBF-1424#diff
Space changes were not needed exactly.
| 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 ] |
Please submit PR. Thank you!
[~aloraine], a PR submitted for the same.
Changes are present at:
https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/752/igbf-1424-enable-igb-to-show-a-genome-from/diff
Could you please merge it into the master?
| 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 |
Validated the following scenarios:
1) Without annots.xml
2) Empty annots.xml
3) Malformed annots.xml
For the above three scenarios, it is working as expected loading blank screen.
| 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 ] |
Example quickload site with empty annots.xml file in A_thaliana_Jun_2009 genome directory: http://igbquickload.org/smokeTestingQuickload/