Details
-
Type:
Improvement
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: 9.0.2 Minor Release
-
Labels:
-
Story Points:0.5
-
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
-
IGBF-1353 Optimize IGB Javascript bridge code
-
- Closed
-
Activity
BookmarkHTTPRequestHandler
invokes
BookmarkUnibrowControllerServlet
See: goToBookmark - used by endpoints:
Also, we have;
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
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!
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. : )
I am moving this to done and reassigning it to Kiran so records show that he tackled the issue.
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.