Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Critical
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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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Story Points:5
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Sprint:Fall 7 : 11 Nov to 22 Nov, Fall 8 : 25 Nov to 6 Dec, Fall 9 : 9 Dec to 20 Dec, Spring 1 : 25 Dec to 17 Jan, Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb, Spring 3 : 17 Feb to 28 Feb
Description
Situation: Until the new endpoints have been finished in IGB, we will try to use the existing IGB bookmarks endpoint for receiving metadata from IGB-CyVerse.
Task: Investigate and implement code changes so that the metadata from IGB-CyVerse (genome version, foreground, background) is sent and processed by IGB Bookmarks. The end result should be that when a user clicks on View in IGB in IGB-CyVerse, the genome version, foreground and background are sent to IGB. IGB loads the specified genome version, loads the data track, and colors the foreground and background.
Note: Look at IGBF-1635 for important files.
Attachments
Issue Links
Activity
Updated branch with changes to address server_url issue when a genome is specified: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-2133-CyVerseMetadataBridge
Ready for testing.
Tested the ticket:
Steps involved in Testing:
1) Open IGB and do not load any data. Change the foreground, background, Genome version at Biovizconnect and click on "view in igb" and IGB should load the data with foreground, background, and genome version loaded correctly in the data tracks and bookmarks.
2) Open IGB and load human species data. Change the foreground, background, Genome version at Biovizconnect and click on "view in igb" and IGB should load the data with foreground, background and genome version loaded correctly in the data tracks and bookmarks.
3) Open IGB and load human species data. Change the foreground, background and put Genome version blank or "version" and click on "view in igb" and IGB should load the data with foreground, background with the new values and genome version with the previously loaded values.
4) Also tested with the url's mentioned above in the comments.
Merged and ready for testing.
I have tested the ticket with all the file types in SmokeTesting Folder such as ( bedgraph, bai, bam, tz, gz, bigWig, broadPeak, narrowPeak, wig) and other file types as well. IGB is loading the updated foreground, background and genome versions correctly.
But, If the file name has a space for example (BigBed_Homo Sapien.bigbed) IGB fails to load the file, it shows the following error message.
WARNING: Error reading file header for https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/BigBed_Homo Sapien.bigbed
java.lang.RuntimeException: Error reading file header for https://data.cyverse.org/dav-anon/iplant/home/nowlanf/SmokeTesting/H_sapiens_Dec_2013/BigBed_Homo Sapien.bigbed
However, the above version is a Legacy issue which is also present in the previous versions.
The CyVerse metadata bridge has been implemented with shortcomings. At the IGB loaded initially, the metadata is sent to IGB when the View In IGB button is clicked,however the foreground and background colors are not rendered then. On clicking it a second time, the colors are rendered when chromosomes are changed. The same happens when User preferences are rest. This happens because the lamda function at line 284 of BookmarkUnibrowControlServlet is skipped. The colors are not rendered when the function, BookmarkController.applyProperties(igbService, seq, parameters, feature, combos), is not rendered, which happens when IGB is initially loaded and when preferences are reset. Further investigation required in this regard.