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: 9.0.2 Minor Release
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Labels:
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Story Points:0.25
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Sprint:Fall 2018 Sprint 3, Fall 2018 Sprint 4, Fall 2018 Sprint 5
Description
IGB Quickload sites are Web sites that host data for IGB. The IGB preferences system includes some default Quickload sites that are automatically available in IGB.
Add 2 new such sites to IGB:
name: DNA-Seq
address: http://lorainelab-quickload.scidas.org/dnaseq/
name: ChIP-Seq
address: http://lorainelab-quickload.scidas.org/chipseq/
To test DNA-Seq:
- Visit Solanum lycopersicum (tomato) Feb 2014 genome in IGB
- Confirm that you now see a folder named "DNA-Seq" in Available Data section of the Data Access tabbed panel
To test ChIP-Seq:
- Visit Arabidopisis thaliana Jun 2009 genome in IGB
- Confirm that you now see a folder named "ChIP-Seq" in Available Data section of the Data Access tabbed panel
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Assignee | Ann Loraine [ aloraine ] |
| Rank | Ranked higher |
| Summary | Add DNA-Seq Quickload source | Add DNA-Seq and ChIP-Seq Quickload sources |
| Description |
IGB Quickload sites are Web sites that host data for IGB. The IGB preferences system includes some default Quickload sites that are automatically available in IGB.
Add a new such site to IGB: name: DNA-Seq address: http://lorainelab-quickload.scidas.org/dnaseq/ To test: * Visit Solanum lycopersicum (tomato) Feb 2014 genome in IGB * Confirm that you now see a folder named "DNA-Seq" in the Available Data section of the Data Access tabbed panel |
IGB Quickload sites are Web sites that host data for IGB. The IGB preferences system includes some default Quickload sites that are automatically available in IGB.
Add 2 new such sites to IGB: name: DNA-Seq address: http://lorainelab-quickload.scidas.org/dnaseq/ name: ChIP-Seq address: http://lorainelab-quickload.scidas.org/chipseq/ To test DNA-Seq: * Visit Solanum lycopersicum (tomato) Feb 2014 genome in IGB * Confirm that you now see a folder named "DNA-Seq" in Available Data section of the Data Access tabbed panel To test ChIP-Seq: * Visit Arabidopisis thaliana Jun 2009 genome in IGB * Confirm that you now see a folder named "ChIP-Seq" in Available Data section of the Data Access tabbed panel |
| Sprint | Fall 2018 Sprint 3 [ 53 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Assignee | Srishti Tiwari [ stiwari8 ] |
| Status | Open [ 1 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Srishti Tiwari [ stiwari8 ] |
| Assignee | Pranav Sanjay Tambvekar [ ptambvek ] |
| Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
Seems As expected during the Code and Functional Review
| Status | Reviewing [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Pranav Sanjay Tambvekar [ ptambvek ] | Srishti Tiwari [ stiwari8 ] |
Pull request submitted.
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Open [ 1 ] |
- See comment on pull request regarding id.
- Review: "Case Study: Fixing duplicate Quickload Sites in Data Sources Tab
IGBF-1206" (on IGB Canvas class)
Note: I should have labeled this issue "Intermediate" or "Advanced" rather than "Beginner" because it touches on the data provider subsystem which is not well documented and also fragile.
The change required to the JSON file is simple, but a lot can go wrong if it is not done correctly. And "correctly" is not well-documented.
| Status | Open [ 1 ] | Open [ 1 ] |
To test:
- Reset preferences to defaults
- Run branch
- Visit Arabidopsis genome
- Check that data Sources listed in Data Access Panel look right:
On the top: "RNA-Seq"
Next: "DNA-Seq"
Next: "BioAnalytic Resource"
Next: "Quickload"
FIxed ids as per review comment and tested locally.
Currently, they are getting listed in this order for Arabidopsis thaliana Jun 2009:
Chip
RNA-Seq
Bio-Analytic Resource
IGB Quickload
for Solanum Lycopersicum (Feb 2014) tomato:
DNA-Seq
IGB Quickload
Please confirm if this is correct.
Quick question:
Is it "Chip" or "ChIP-Seq" ?
It is being displayed as Chip on the UI. However, in IgbDefaultPrefs.json, the name is entered as "ChIP-Seq".
| Status | Open [ 1 ] | Reviewing [ 10301 ] |
| Assignee | Srishti Tiwari [ stiwari8 ] | Ann Loraine [ aloraine ] |
| Status | Reviewing [ 10301 ] | Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Assignee | Mason Meyer [ mason ] |
| Rank | Ranked higher |
| Sprint | Fall 2018 Sprint 3 [ 53 ] | Fall 2018 Sprint 3, Fall 2018 Sprint 4 [ 53, 54 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Sprint | Fall 2018 Sprint 3, Fall 2018 Sprint 4 [ 53, 54 ] | Fall 2018 Sprint 3, Fall 2018 Sprint 4, Fall 2018 Sprint 5 [ 53, 54, 55 ] |
| Rank | Ranked lower |
| Assignee | Mason Meyer [ mason ] | Ann Loraine [ aloraine ] |
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 18108 ] | Fall 2019 Workflow Update [ 19943 ] |
| Workflow | Fall 2019 Workflow Update [ 19943 ] | Revised Fall 2019 Workflow Update [ 22063 ] |
Hello,
Added the quickload resources in JSON file.
Please review the changes on:
https://bitbucket.org/srishtitiwari/integrated-genome-browser/src/IGBF-1403/
Thanks,
Srishti