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
Checking to make sure local file bookmarks are still good:
(I'm including these links for future inspection. Since they are for local files, they will only work on my machine.)
--> that link seems to be working fine!
--> The sym_name argument is respected! (sym_name_1=MyLocalFile+with+C.+sabeus+genes) Good!
Lastly, local file, with no sym_name arg:
http://localhost:7085/IGBControl?version=C_sabeus_Mar_2014&seqid=chr8&start=97021529&end=97021597&loadresidues=false&create=2018%2F09%2F17+13%3A20%3A04&modified=2018%2F09%2F17+13%3A20%3A04&feature_url_0=http%3A%2F%2F18.222.191.240%2FQuickload_IGBF-1401_C.sabaeus%2FC_sabeus_Mar_2014%2FC_sabeus_Mar_2014.mRNAs_withDesc.bed.gz&sym_method_0=http%3A%2F%2F18.222.191.240%2FQuickload_IGBF-1401_C.sabaeus%2FC_sabeus_Mar_2014%2FC_sabeus_Mar_2014.mRNAs_withDesc.bed.gz&sym_ypos_0=0&sym_yheight_0=50&sym_col_0=0x000000&sym_bg_0=0xFFFFFF&sym_name_0=C.+sabeus+genes&feature_url_1=file%3A%2FUsers%2Fivory%2FDesktop%2FlocalQuickloadTestSet%2FQuickload_C.sabaeus%2FC_sabeus_Mar_2014.mRNAs_withDesc.bed.gz&sym_method_1=file%3A%2FUsers%2Fivory%2FDesktop%2FlocalQuickloadTestSet%2FQuickload_C.sabaeus%2FC_sabeus_Mar_2014.mRNAs_withDesc.bed.gz&sym_ypos_1=0&sym_yheight_1=50&sym_col_1=0x0247FE&sym_bg_1=0xFFFFFF&query_url=http%3A%2F%2F18.222.191.240%2FQuickload_IGBF-1401_C.sabaeus%2FC_sabeus_Mar_2014%2FC_sabeus_Mar_2014.mRNAs_withDesc.bed.gz&query_url=file%3A%2FUsers%2Fivory%2FDesktop%2FlocalQuickloadTestSet%2FQuickload_C.sabaeus%2FC_sabeus_Mar_2014.mRNAs_withDesc.bed.gz&server_url=http%3A%2F%2F18.222.191.240%2FQuickload_IGBF-1401_C.sabaeus%2F&server_url=
--> the url works! with no sym_name arugment, the track is added with the file path as the name.
Its a little odd to use the entire file path. When I just add a file directly, the track is named based on the file name, not the full path.
A quick regression test with 9.0.1... 9.0.1 also uses the entire file path.
I think everything I know to check looks good here. : )
Doing a functional review:
Between each test, remove the track and return to the home screen by hitting the "species" link.
I should be able to click this link and see the A thaliana genome, and a track called "FOOBARBAZ":
http://localhost:7085/IGBControl?server_url=kiki&version=Arabidopsis_thaliana_TAIR10&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&sym_name_0=FOOBARBAZ
--> Good!
I should be able to follow this link (modified from above) and the track will be named based on its file name (accepted_hits.bam):
http://localhost:7085/IGBControl?server_url=kiki&version=Arabidopsis_thaliana_TAIR10&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
--> Good!
I should be able to follow this link (modified from above) and the track will be named "newName":
http://localhost:7085/IGBControl?server_url=kiki&sym_name_0=newName&version=Arabidopsis_thaliana_TAIR10&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
--> Good!
In terms of the initial issue description, this looks great!
Dr. Loraine –
I don't know how to interpret that last comment... is that added instructions for testing? or a tip for figuring out a problem? ... ?
I got the last master branch, did a clean and build, ran IGB.
When I follow each of those last three links I get:
- http://localhost:7085/IGBControl -->
"This page isn’t working
localhost didn’t send any data.
ERR_EMPTY_RESPONSE" - http://localhost:7085/IgbGalaxyDataView -->
"Invalid Request!" - http://127.0.0.1:7085/igbStatusCheck -->
var igbIsRunning = true
BookmarkHTTPRequestHandler
invokes
BookmarkUnibrowControllerServlet
See: goToBookmark - used by endpoints:
Also, we have;
The REST API is closely related to IGB's bookmark syntax.
Review what the User's guide says about location and location+data bookmarks.
Note that you can right-click a bookmark in IGB and choose option "copy bookmark as URL".
You can also see the bookmark parameters by click "Details" in the Bookmarks tab.
I am moving this to done and reassigning it to Kiran so records show that he tackled the issue.