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: 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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- Closed
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Activity
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.
PR is merged and new code is deployed to "early access" section of the Bioviz.org Web site.
Testing main branch installer on Mac.
I am able to use the Color by... and Filter... options by right-clicking on the track name and selecting Property > property and then selecting from the expanded list of options present in files from UCSC REST. The color and filter options appear to work correctly. If I select multiple files at the same time then only the properties that are shared are available as options.
Closing ticket.
Note: Both Kaushik and Sravani did a significant amount of work on this ticket. As Kaushik did the initial work I am assigning the completed ticket to him.
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.