Details
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Type:
New Feature
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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:4
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Epic Link:
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Sprint:Summer 2018 Part 2, Summer 2018 Part 3, Fall 2018 1, Summer 2019 Sprint 10, Summer 2019 Sprint 11, Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3
Description
A potential App developer asks:
"can I extract from IGB values for selected/all loaded lines for selected genomic region? For example, I have two tracks for ChIP-seq against two different transcription factors and I want to know what is their average score for selected region e.q. 1kb or 10kb. Can I have also information about which genes (mRNA) are present in this region or values for any other line?"
Investigate:
- How does an App find out what tracks are loaded (or selected) in IGB?
- How does an App access the loaded data for a region?
Tip:
- Look at how track filters and operators work.
*EDIT*: Instead of documenting, let's create a demo App that shows how these things can be done. For spec, see June 2019 comments from Dr. Loraine.
Attachments
Issue Links
Activity
To review:
- Look at the code. Developer should be able to read the code and know (1) how to build it (2) how to run and test the App in IGB
- Run the code. Developer should be able to install the App and try it out in IGB.
Please make comments here for SK.
Goal: This App is meant to serve as an example for how an App developer can get access to items in the IGB display. Developers (e.g., people like us) are the target audience for this App.
Shamika Gajanan Kulkarni, I have reviewed the code for the Demo App. It is very easy to understand.
IGB service is used to get sequence map view. After that a for loop is ran on the sequence map to get selected syms. And for each score entry for the sym, you have calculated average.
When I was reviewing your code, I have noticed that the target folder is accidentally pushed to the app repository which shouldn't be there. Along with that there is git.properties file in the resource directory of the source folder which also should be removed from the repository.
Other than that, everything is fine. Even the message popup that you are showing on click of Tools>"Get Average Score" is perfect.
Moving the ticket to TO DO. Once you're done removing this folder/file from the repository, let me know so that I can move it forward to Ready for pull request.
Thanks.
I am sorry I overlooked this fact and I have made the necessary changes.
Also, Dr. Loraine suggested a few changes:
1) To add a new AppDecription.md file that will be visible in the App Manager and provide instructions to the user on how to use the app.
2) To modify the existing README.md file providing the user with instructions on how to install the app. The README.md file will only be visible on bitbucket. The App Manager should show the AppDescription.md data.
The changes have been implemented and usability testing has been conducted for the same.
Kindly check the link below and let me know if you observe any more changes that need to be done. Thank you for the review.
https://bitbucket.org/skulka2710/get-average-score/src/master/
Shamika Gajanan Kulkarni, I have checked both markdown files, the one after adding plugin to the IGB app manager which is AppDescription as well as the one which is displayed on the bitbucket i.e. README.
Moving the ticket forward. You can now submit a PR for the same.
Thank you for the reviews.
Since the repository is a separate one for the Demo App - Get Average Score, the ownership to the repo is transferred to LoraineLabs. Moving the ticket to PR Submitted. Kindly review.
This is closely related to
IGBF-1351.Review the comments there.
Most importantly:
draft documentation:
https://docs.google.com/document/d/1qYb0MSAV3kiKmv0EZdfS2hqImDMb3FRGG09h-WmkrQI