Details
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Type:
Bug
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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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Sprint:Summer 2018 Part 2
Description
Sample link from BAR:
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Sprint | Summer 2018 Part 2 [ 49 ] |
| Rank | Ranked higher |
| Description |
Sample link from BAR:
https://bioviz.org/bar.html?version=A_thaliana_Jun_2009 &annotation_set=Araport11 &server_url=http://lorainelab-quickload.scidas.org/bar &gene_id=AT1G07350 BAR code that forms these links: https://github.com/asully/eFP-Seq-Browser/blob/master/cgi-bin/core/custom.js |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Description |
Sample link from BAR:
https://bioviz.org/bar.html?version=A_thaliana_Jun_2009 &annotation_set=Araport11 &server_url=http://lorainelab-quickload.scidas.org/bar &gene_id=AT1G07350 BAR code that forms these links: https://github.com/asully/eFP-Seq-Browser/blob/master/cgi-bin/core/custom.js |
Sample link from BAR:
https://bioviz.org/bar.html?version=A_thaliana_Jun_2009 &annotation_set=Araport11 &server_url=bar &gene_id=AT1G07350 When forming the IGB localhost URL, use &server_url=http://lorainelab-quickload.scidas.org/bar BAR code that forms these links: https://github.com/asully/eFP-Seq-Browser/blob/master/cgi-bin/core/custom.js |
Residues are getting loaded after data from feature_url_0 are getting loaded. Appears to be a thread-related issue.
Workaround:
In the Javascript (bar.js) first make this call:
Wait a moment, then make this call:
This ensures that when IGB accesses the data set (feature_url_0), the reference sequence will already have been loaded.
http://bioviz.org/cgi-bin/geneIdLookup.py?gene_id=AT1G07350 returns JSON with gene coordinates
| Description |
Sample link from BAR:
https://bioviz.org/bar.html?version=A_thaliana_Jun_2009 &annotation_set=Araport11 &server_url=bar &gene_id=AT1G07350 When forming the IGB localhost URL, use &server_url=http://lorainelab-quickload.scidas.org/bar BAR code that forms these links: https://github.com/asully/eFP-Seq-Browser/blob/master/cgi-bin/core/custom.js |
Sample link from BAR:
https://bioviz.org/bar.html?version=A_thaliana_Jun_2009&annotation_set=Araport11&server_url=bar&gene_id=AT1G07350& |
BAR code that forms links: https://github.com/asully/eFP-Seq-Browser/blob/master/cgi-bin/core/custom.js
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Sneha Ramesh Watharkar [ jdaly ] | Ann Loraine [ aloraine ] |
| Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
You can find work on Branch: https://bitbucket.org/swathark/bioviz/branch/IGBF-1367#diff
| Status | Reviewing [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
PR submitted.
| Status | Pull Request Submitted [ 10101 ] | Needs Testing [ 10002 ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Status | Testing In Progress [ 10003 ] | In Progress [ 3 ] |
PR merged. Testing on https://ann.bioviz.org
| Comment | [ I don't understand "Handle old and new style BAR links" ? ] |
| Assignee | Ann Loraine [ aloraine ] | Sneha Ramesh Watharkar [ jdaly ] |
| Status | In Progress [ 3 ] | Open [ 1 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Prof [~aloraine] : Fixed footer of bar.html
Branch : https://bitbucket.org/swathark/bioviz/branch/IGBF-1367-barjsFooterFix#diff
| Assignee | Sneha Ramesh Watharkar [ jdaly ] | Ann Loraine [ aloraine ] |
| Status | Needs 1st Level Review [ 10005 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Ann Loraine [ aloraine ] | Sneha Ramesh Watharkar [ jdaly ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Merged to master.
| Resolution | Done [ 10000 ] | |
| Status | Pull Request Submitted [ 10101 ] | Closed [ 6 ] |
| Workflow | Loraine Lab Workflow [ 18063 ] | Fall 2019 Workflow Update [ 19928 ] |
| Workflow | Fall 2019 Workflow Update [ 19928 ] | Revised Fall 2019 Workflow Update [ 22048 ] |
Sample link to activate IGB on localhost:
http://localhost:7085/IGBControl?version=A_thaliana_Jun_2009&seq_id=Chr1&start=2257408&end=2260187&server_url=http://lorainelab-quickload.scidas.org/bar&loadresidues=True&feature_url_0=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam&query_url=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam
Note: query_url is the same as feature_url_0, feature_url_1, etc. For every feature_url_n, include an identical query_url. For example, if you have feature_url_0=foo&feature_url_1=bar, then include query_url=foo&query_url=bar
This is just how IGB 9.0.1 and below wants it. We will investigate why this is necessary later.