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:2
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Epic Link:
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Sprint:Spring 2 : 20 Jan to 31 Jan
Description
There are several older Apps in repository https://bitbucket.org/lorainelab/experimental-apps-for-igb/ that demonstrate aspects of the IGB API but are not hooking into IGB's extensions points in the right way.
Specifically, the older Apps pre-date our migration to using dependency injection annotations "Component" and "Reference."
For this task, add these annotations to OverlapAnnotationOperator to ensure that the Operator will get properly added to the Annotation tab.
Suggestions: Consult with Shamika Gajanan Kulkarni, who has worked on this type of thing. Also, look at the existing Apps and existing Operators that are part of the IGB core code base.
Attachments
Activity
Merged and ready for testing.
Hi Dr. [~aloraine]
The above is working fine.
https://bitbucket.org/srishtitiwari/experimental-apps-for-igb/downloads/
PR submitted -
https://bitbucket.org/lorainelab/experimental-apps-for-igb/pull-requests/7/igbf-2229/diff
Srishti Tiwari please configure your fork to build the apps via bitbucket pipelines to confirm that
- the project can build
- an IGB user can use the Downloads folder to install the Apps from your fork
If that works, submit a PR.
Hi Dr. [~aloraine], I removed extra entries in the pom and tested it again.
Please have a look.
https://bitbucket.org/srishtitiwari/experimental-apps-for-igb/commits/41c73ca
Srishti Tiwari - pleases see questions in the comments on your branch
Hello ,
I have done required changes for this task.
Changes made:
1. Deleted the activator class
2. Ensured the required plugins were present in the parent pom.
3. Added annotation to the newly added service.
Please find the commit below for first level review:
https://bitbucket.org/srishtitiwari/experimental-apps-for-igb/commits/6548325
To test:
1. Clone this branch and run "mvn package" for OverlapAnnotationOperator to build this app.
2. Add the target folder (of OverlapAnnotationOperator) as a plugin/app repository in the Integrated Genome Browser.
3. Select two tracks in IGB for any genome.
4. In the Annotations tab, a new operator (subset by overlap) should be visible under Multi-track Operations.
Please let me know if the above steps are not clear.
Refer to the code for Merge Annotation Operator app to check how the menu entry for Merge option gets added. This can help to infer how and where OverlapAnnotation adds an option.
Other suggestion:
Read OSGi declarative services specification: https://osgi.org/specification/osgi.cmpn/7.0.0/service.component.html
Quoting from above:
"The service component model uses a declarative model for publishing, finding and binding to OSGi services. This model simplifies the task of authoring OSGi services by performing the work of registering the service and handling service dependencies. This minimizes the amount of code a programmer has to write; it also allows service components to be loaded only when they are needed. As a result, bundles need not provide a BundleActivator class to collaborate with others through the service registry."
Tested the ticket. I was able to install the app and could see the option 'Subset by overlap' in Multi menu under Annotation Tab when I selected two tracks. Moving to closed.