Details
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Type:
Improvement
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Status: Reviewing Pull Request (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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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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Epic Link:
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Sprint:Spring 5, Spring 6, Spring 7, Spring 8, Spring 9, Spring 10
Description
Situation: Many of the files provided by the UCSC REST API (see IGBF-3129) include additional coumns (see comments in IGBF-3598). These additional columns are added as "props" and can contain many different types of information.
In IGB, if you right-click on a track there are options to "Color by..." or "Filter...". Some of the current options include values for Length, RGB, Score, Property. However, the values stored in the "props" are not included.
Task: Investigate the possibility of enabling a user to use the "Color by..." or "Filter..." on the "props" values.
Attachments
Issue Links
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IGBF-3660 Include schema of UCSC data in the properties field of the dataset.
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- Merged Needs Testing
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Activity
Development is completed and the props are populated in the properties dropdown for both color by and filter by, need to test one more scenario. once that is done will move the ticket to review. Updated code is at branch: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3640
Merged all the other code changes and did a few fixes. Updated code is available at: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3640. Tested the code and it is working as expected. Below are screenshots:
Selected single track with extra properties:
Selected single track without extra properties:
Selected two tracks, both have similar extra properties:
Selected two tracks, one has similar extra properties and the other one doesn't have:
To Test:
- Build the jar file for the branch.
- Start the application in debug mode, select any species, and select any one of the ucsc rest tracks that has extra properties (bed, bigBed, bedDetail, and bigGenePRed track types have extra properties).
- Now while loading the empty track, an API call is made and the featureProps are loaded.
- Load data for the track and right-click on the track name to see the options menu
- Click on Color by option and select property from the dropdown items
- Now, in the property dropdown list, you should be able to see the extra properties that are present in that track
Built and tested Sravani's branch locally on my Mac.
Following the testing above, the additional properties show up for the appropriate files from UCSC REST. I am able to filter and color the data appropriately. If multiple tracks are selected, only the shared/common properties appear.
Did code review with Sravani.
Ready for pull request.
Created a single Pull request for both tickets, https://jira.bioviz.org/browse/IGBF-3660 and https://jira.bioviz.org/browse/IGBF-3640. Nowlan Freese already reviewed it, Kaushik Gopu Please review it and let me know if find any issues. Added the test case fix for windows as well in the commit and added a try catch block as per Kaushik Gopu suggestion. Here is the updated PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1008
IGB was built without skipping test cases; all test cases passed on Windows, and no issues occurred during the build process.
Jaya Sravani Sirigineedi incorporated suggested changes in the code.
Example:
Open the most recent chicken genome (G_gallus_Mar_2018).
Navigate to 1:79,200,818-79,317,139
Under UCSC REST in the Data Access tab under Available Data, select cpgIslandExt
Load Data
Select one of the data points and look at the Selection Info tab, you should see props such as "perCpg"
For the example above you will either need to be on Sravani's branch, or wait until we merge her changes into the Loraine Lab repo.