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:0.5
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Sprint:B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2
Description
IGB has a REST API that allows users to control the application. We are using this to enable users to load data from external servers by clicking links that then get forwarded to a JavaScript "bridge" program running on BioViz.org.
For example, here is a link from the BAR Web site. Note that it refers to a Web page on BioViz that contains JavaScript code that then tries to open a link on localhost, where IGB is running. IGB contains a build-in Web server that listens on a port for requests.
Note that the "sym_name" parameter is supposed to specify track label.
However, it does not appear to be working correctly.
For example,
Should result in a new track appearing in IGB with FOOBARBAZ as the track label.
This should be fixed so that IGB respects the given parameters.
Attachments
Issue Links
- relates to
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IGBF-1353 Optimize IGB Javascript bridge code
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Sprint | B - Summer 2018 [ 48 ] |
| Rank | Ranked higher |
| Summary | investigate whether | investigate why REST API parameter not respected |
| Rank | Ranked higher |
| Story Points | 0.5 |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Summary | investigate why REST API parameter not respected | REST API parameter sym_name not respected |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Open [ 1 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Attachment | test.html [ 14101 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Rank | Ranked higher |
| Sprint | B - Summer 2018 [ 48 ] | B - Summer 2018, Summer 2018 Part 2 [ 48, 49 ] |
| Rank | Ranked higher |
| Fix Version/s | 9.0.2 [ 10600 ] |
| Assignee | Kiran Korey [ kkorey ] |
| Status | Needs 1st Level Review [ 10005 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Ivory Blakley [ ieclabau ] |
| Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
| Assignee | Ivory Blakley [ ieclabau ] | Kiran Korey [ kkorey ] |
| Status | Reviewing [ 10301 ] | Open [ 1 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Kiran Korey [ kkorey ] |
| Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
| Assignee | Sneha Ramesh Watharkar [ jdaly ] |
| Assignee | Sneha Ramesh Watharkar [ jdaly ] | Kiran Korey [ kkorey ] |
| Status | Reviewing [ 10301 ] | Open [ 1 ] |
| Assignee | Kiran Korey [ kkorey ] | Sneha Ramesh Watharkar [ jdaly ] |
| Status | Open [ 1 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
| Status | Reviewing [ 10301 ] | Needs 1st Level Review [ 10005 ] |
| Rank | Ranked higher |
| Sprint | B - Summer 2018, Summer 2018 Part 2 [ 48, 49 ] | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3 [ 48, 49, 50 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
| Status | Reviewing [ 10301 ] | Open [ 1 ] |
| Assignee | Sneha Ramesh Watharkar [ jdaly ] | Kiran Korey [ kkorey ] |
| Assignee | Kiran Korey [ kkorey ] | Sneha Ramesh Watharkar [ jdaly ] |
| Status | Open [ 1 ] | Reviewing [ 10301 ] |
| Status | Reviewing [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Reviewing [ 10301 ] |
| Status | Reviewing [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Sneha Ramesh Watharkar [ jdaly ] | Kiran Korey [ kkorey ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Needs Testing [ 10002 ] |
| Assignee | Kiran Korey [ kkorey ] |
| Rank | Ranked higher |
| Sprint | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3 [ 48, 49, 50 ] | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1 [ 48, 49, 50, 51 ] |
| Rank | Ranked lower |
| Rank | Ranked higher |
| Sprint | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1 [ 48, 49, 50, 51 ] | B - Summer 2018, Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Fall 2018 Sprint 2 [ 48, 49, 50, 51, 52 ] |
| Attachment | Error1287Jira.PNG [ 14150 ] |
| Assignee | Kiran Korey [ kkorey ] |
| Assignee | Kiran Korey [ kkorey ] | Ivory Blakley [ ieclabau ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Status | Testing In Progress [ 10003 ] | Open [ 1 ] |
| Assignee | Ivory Blakley [ ieclabau ] | Kiran Korey [ kkorey ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs Testing [ 10002 ] |
| Assignee | Kiran Korey [ kkorey ] |
| Comment |
[ http://bioviz.org/bar.html?version=Arabidopsis_thaliana_TAIR10&feature_url_0=http://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam&sym_name_0=FOOBARBAZ&sym_method_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&server_url=bar
The above bookmark should load a track with the name "FOOBARBAZ". Using an installer from master, it does not do that. Something is broken. ] |
| Comment |
[ When testing this issue on master,
I noticed that the track name is not same as sym_name! It is displaying a long string and not the string value passed as sym_name. Steps followed. Running IGB on latest master. Clicking links in the issue description. IGB app opens the data set with some long string as track name. Attaching the screen shot for reference. Assigning it to [~kkorey] to check it once on master to verify this behaviour. ] |
| Comment |
[ I think one of the other commits or the merge process has caused this issue, need to investigate more.
] |
| Comment | [ BioViz: https://bitbucket.org/lorainelab/bioviz ] |
| Comment |
[ See:
BookmarkUnibrowControlServlet. It uses loadFromFile to trigger loading of a data set hosted on Galaxy or BAR into IGB. * To start, it moves IGB view to requested seq_id, start, and end if provided in the REST URL. * Next, it checks whether server_url parameter matches a loaded data provider. * If not, it invokes loadFromURL. Note: If server_url is absent, new track is not loaded. ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Assignee | Ivory Blakley [ ieclabau ] |
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Ivory Blakley [ ieclabau ] | Kiran Korey [ kkorey ] |
| Fix Version/s | 9.0.2 Minor Release [ 10600 ] | |
| Labels | Advanced |
| Fix Version/s | 9.0.2 Minor Release [ 10600 ] |
| Workflow | Loraine Lab Workflow [ 17978 ] | Fall 2019 Workflow Update [ 19878 ] |
| Workflow | Fall 2019 Workflow Update [ 19878 ] | Revised Fall 2019 Workflow Update [ 21997 ] |