[IGBF-1367] Modify bar.js to handle new query params - JIRA UNCC

Details

Type: Bug
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
None

Sprint:
Summer 2018 Part 2

Description

Sample link from BAR:

Anns' test server:
https://ann.bioviz.org/bar.html?version=A_thaliana_Jun_2009&annotation_set=Araport11&server_url=bar&gene_id=AT1G07350&feature_url_0=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam

Live link from BAR:
http://bioviz.org/bar.html?version=A_thaliana_Jun_2009&annotation_set=Araport11&server_url=bar&gene_id=AT1G07350&feature_url_0=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam

Attachments

Issue Links

relates to

IGBF-1364 Turn off "zoom in and click load data" message if using position bookmark

Closed

IGBF-1353 Optimize IGB Javascript bridge code

Closed

Activity

Ascending order - Click to sort in descending order

Hide

Permalink

Ann Loraine added a comment - 19/Jul/18 3:54 PM - edited

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.

Show

Ann Loraine added a comment - 19/Jul/18 3:54 PM - edited 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.

4 older comments

Hide

Permalink

Sneha Ramesh Watharkar (Inactive) added a comment - 20/Jul/18 12:15 PM

PR submitted.

Show

Sneha Ramesh Watharkar (Inactive) added a comment - 20/Jul/18 12:15 PM PR submitted.

Hide

Permalink

Ann Loraine added a comment - 20/Jul/18 1:49 PM

PR merged. Testing on https://ann.bioviz.org

Show

Ann Loraine added a comment - 20/Jul/18 1:49 PM PR merged. Testing on https://ann.bioviz.org

Hide

Permalink

Ann Loraine added a comment - 20/Jul/18 1:49 PM - edited

Fix bar.html to show footer correctly.

Show

Ann Loraine added a comment - 20/Jul/18 1:49 PM - edited Fix bar.html to show footer correctly.

Hide

Permalink

Sneha Ramesh Watharkar (Inactive) added a comment - 24/Jul/18 5:31 PM

Prof [~aloraine] : Fixed footer of bar.html
Branch : https://bitbucket.org/swathark/bioviz/branch/IGBF-1367-barjsFooterFix#diff

Show

Sneha Ramesh Watharkar (Inactive) added a comment - 24/Jul/18 5:31 PM Prof [~aloraine] : Fixed footer of bar.html Branch : https://bitbucket.org/swathark/bioviz/branch/IGBF-1367-barjsFooterFix#diff

Hide

Permalink

Ann Loraine added a comment - 26/Jul/18 1:53 PM

Merged to master.

Show

Ann Loraine added a comment - 26/Jul/18 1:53 PM Merged to master.

People

Assignee:

Sneha Ramesh Watharkar (Inactive)

Reporter:

Sneha Ramesh Watharkar (Inactive)

Votes:

0 Vote for this issue

Watchers:

2 Start watching this issue

Dates

Created:

19/Jul/18 11:42 AM

Updated:

31/Jul/18 10:19 AM

Resolved:

26/Jul/18 1:54 PM