Details
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Type:
Sub-task
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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:
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Story Points:1.5
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Sprint:Summer 2019 Sprint 8, Summer 2019 Sprint 9, Summer 2019 Sprint 10, Summer 2019 Sprint 11
Description
- Create new repository for ProtAnnot.
- Configure to allow compilation on your local
- Check that you are able to run it within the IGB platform
Once it is finished (to your satisfaction), request to transfer repository ownership to Loraine Lab team for next steps.
Note: Make sure that the build process generates a working bundle and also a working OBR index.
Attachments
Activity
| Workflow | Fall 2019 Workflow Update [ 20236 ] | Revised Fall 2019 Workflow Update [ 22375 ] |
| Workflow | Loraine Lab Workflow [ 18548 ] | Fall 2019 Workflow Update [ 20236 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] | Prutha Kulkarni [ prutha ] |
| Resolution | Done [ 10000 ] | |
| Status | Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Assignee | Shamika Gajanan Kulkarni [ shamika ] |
| Rank | Ranked higher |
| Status | Needs Testing [ 10002 ] | Needs Testing [ 10002 ] |
To test:
- De-activate igbserver app repository
- Install App from Downloads URL of bitbucket repo - https://bitbucket.org/lorainelab/protannot/downloads/
- Launch IGB, select at least one gene model
- Choose Tools > ProtAnnot
- Operate the menu options: Make an image of the view, save data to an XML file, check that you can open it again.
The above functionality may depend on the libraries that have been removed from the project.
| Status | Needs 1st Level Review [ 10005 ] | Needs Testing [ 10002 ] |
I think freehep-graphicsio-svg is being used to creates images, but the code itself (I thought) is coming from the platform. I would say: go ahead and delete it from the POM, but check that you can save an image from the ProtAnnot. Depending on how the wiring is done, you might see class not found errors (OSGi related).
Prof. [~aloraine] I changed the pom as well as the pipeline configuration file of protannot app. I found some dependencies which are not being used by the app. So, I went ahead and commented those dependencies just to check if the app works fine without those dependencies. I tested both apps, the existing one and the latest one which is built using the new repository. Also, I compared the results for InterProScan of both the apps and they are identical. Shall I delete that part of the code? Please let me know.
Below are the artifactIds of the dependencies which are not being used :
freehep-graphicsio-svg
commons-compress
logback-core
logback-classic
guava
| Assignee | Prutha Kulkarni [ prutha ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
I was successfully able to build the JAR file and repository.xml file under the downloads section of the bitbucket. Also, tested the downloads path with IGB platform.
I have transferred the ownership of the repository to 'lorainelab'.
You can check the repository on the following path:
https://bitbucket.org/pkulka10/protannot/src/master/
If you are accessing the repo after accepting the ownership for it then instead of 'pkulka10' you just need to add 'lorainelab'.
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Assignee | Prutha Kulkarni [ prutha ] |
| Status | In Progress [ 3 ] | Open [ 1 ] |
| Assignee | Prutha Kulkarni [ prutha ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Assignee | Prutha Kulkarni [ prutha ] |
| Field | Original Value | New Value |
|---|---|---|
| Assignee | Ann Loraine [ aloraine ] |
The repository for ProtAnnot has been tested successfully. The app is working as expected. Moving to closed.