Details
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Type:
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:None
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Story Points:2
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Epic Link:
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Sprint:Spring 7, Spring 8, Summer 1
Description
While fixing the Bitbucket pipeline for the "Filter by Score" IGB app and copying the built .jar file to the Downloads section, when attempted to add the Downloads URL as a new app repository in IGB. However, IGB froze upon doing so.
This issue may be related to the fact that we haven’t updated the app code to align with the recent OSGi (Felix) framework changes in IGB. Other apps were recently updated to be compatible with the new framework, and this app may need similar adjustments.
Steps to reproduce:
Clone a copy of the Score Filter App source code from Bitbucket - https://bitbucket.org/lorainelab/filter-by-score
Build the app using mvn clean install command, it generates a target folder.
Start IGB
Select Tools > Open App Manager
Click Manage Repositories... button (opens Plug-in Repositories tab in Preferences window)
Click Add... button (opens Plugin Repository dialog)
Enter a name for your repository (can be anything)
Click Choose local folder button
Select the "target" folder in your filter-by-score project folder.
Once you add "target" as a new local App repository, you should see the Score Filter App added as a new App in the IGB App Manager window but this isn't working as expected.
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-3765 [ 22984 ] |
| Description | When a user uses the SAMtags feature in Color by for one genome and then switches genomes during the same session, the values added in the previous operation is retained. However, triggering a mechanism that clears the values when genomes are changed could be tricky to implement. A Clear All or Delete All button might be a good compromise for this if there's no way to detect when a genome's been changed. |
While fixing the Bitbucket pipeline for the "Filter by Score" IGB app and copying the built .jar file to the Downloads section, when attempted to add the Downloads URL as a new app repository in IGB. However, IGB froze upon doing so.
This issue may be related to the fact that we haven’t updated the app code to align with the recent OSGi (Felix) framework changes in IGB. Other apps were recently updated to be compatible with the new framework, and this app may need similar adjustments. |
| Assignee | Karthik Raveendran [ karthik ] | saideepthi jagarapu [ sjagarap ] |
| Epic Link | IGBF-3765 [ 22984 ] |
| Epic Link | IGBF-1908 [ 17998 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description |
While fixing the Bitbucket pipeline for the "Filter by Score" IGB app and copying the built .jar file to the Downloads section, when attempted to add the Downloads URL as a new app repository in IGB. However, IGB froze upon doing so.
This issue may be related to the fact that we haven’t updated the app code to align with the recent OSGi (Felix) framework changes in IGB. Other apps were recently updated to be compatible with the new framework, and this app may need similar adjustments. |
While fixing the Bitbucket pipeline for the "Filter by Score" IGB app and copying the built .jar file to the Downloads section, when attempted to add the Downloads URL as a new app repository in IGB. However, IGB froze upon doing so.
This issue may be related to the fact that we haven’t updated the app code to align with the recent OSGi (Felix) framework changes in IGB. Other apps were recently updated to be compatible with the new framework, and this app may need similar adjustments. Steps to reproduce: Clone a copy of the Hello World App source code from Bitbucket - https://bitbucket.org/lorainelab/filter-by-score Build the app using mvn clean install command, it generates a target folder. Start IGB Select Tools > Open App Manager Click Manage Repositories... button (opens Plug-in Repositories tab in Preferences window) Click Add... button (opens Plugin Repository dialog) Enter a name for your repository (can be anything) Click Choose local folder button Select the "target" folder in your igb-app-filter-by-score project folder. Once you add "target" as a new local App repository, you should see the Hello World App added as a new App in the IGB App Manager window but this isn't working as expected. |
| Description |
While fixing the Bitbucket pipeline for the "Filter by Score" IGB app and copying the built .jar file to the Downloads section, when attempted to add the Downloads URL as a new app repository in IGB. However, IGB froze upon doing so.
This issue may be related to the fact that we haven’t updated the app code to align with the recent OSGi (Felix) framework changes in IGB. Other apps were recently updated to be compatible with the new framework, and this app may need similar adjustments. Steps to reproduce: Clone a copy of the Hello World App source code from Bitbucket - https://bitbucket.org/lorainelab/filter-by-score Build the app using mvn clean install command, it generates a target folder. Start IGB Select Tools > Open App Manager Click Manage Repositories... button (opens Plug-in Repositories tab in Preferences window) Click Add... button (opens Plugin Repository dialog) Enter a name for your repository (can be anything) Click Choose local folder button Select the "target" folder in your igb-app-filter-by-score project folder. Once you add "target" as a new local App repository, you should see the Hello World App added as a new App in the IGB App Manager window but this isn't working as expected. |
While fixing the Bitbucket pipeline for the "Filter by Score" IGB app and copying the built .jar file to the Downloads section, when attempted to add the Downloads URL as a new app repository in IGB. However, IGB froze upon doing so.
This issue may be related to the fact that we haven’t updated the app code to align with the recent OSGi (Felix) framework changes in IGB. Other apps were recently updated to be compatible with the new framework, and this app may need similar adjustments. Steps to reproduce: Clone a copy of the Score Filter App source code from Bitbucket - https://bitbucket.org/lorainelab/filter-by-score Build the app using mvn clean install command, it generates a target folder. Start IGB Select Tools > Open App Manager Click Manage Repositories... button (opens Plug-in Repositories tab in Preferences window) Click Add... button (opens Plugin Repository dialog) Enter a name for your repository (can be anything) Click Choose local folder button Select the "target" folder in your igb-app-filter-by-score project folder. Once you add "target" as a new local App repository, you should see the Score Filter App added as a new App in the IGB App Manager window but this isn't working as expected. |
| Description |
While fixing the Bitbucket pipeline for the "Filter by Score" IGB app and copying the built .jar file to the Downloads section, when attempted to add the Downloads URL as a new app repository in IGB. However, IGB froze upon doing so.
This issue may be related to the fact that we haven’t updated the app code to align with the recent OSGi (Felix) framework changes in IGB. Other apps were recently updated to be compatible with the new framework, and this app may need similar adjustments. Steps to reproduce: Clone a copy of the Score Filter App source code from Bitbucket - https://bitbucket.org/lorainelab/filter-by-score Build the app using mvn clean install command, it generates a target folder. Start IGB Select Tools > Open App Manager Click Manage Repositories... button (opens Plug-in Repositories tab in Preferences window) Click Add... button (opens Plugin Repository dialog) Enter a name for your repository (can be anything) Click Choose local folder button Select the "target" folder in your igb-app-filter-by-score project folder. Once you add "target" as a new local App repository, you should see the Score Filter App added as a new App in the IGB App Manager window but this isn't working as expected. |
While fixing the Bitbucket pipeline for the "Filter by Score" IGB app and copying the built .jar file to the Downloads section, when attempted to add the Downloads URL as a new app repository in IGB. However, IGB froze upon doing so.
This issue may be related to the fact that we haven’t updated the app code to align with the recent OSGi (Felix) framework changes in IGB. Other apps were recently updated to be compatible with the new framework, and this app may need similar adjustments. Steps to reproduce: Clone a copy of the Score Filter App source code from Bitbucket - https://bitbucket.org/lorainelab/filter-by-score Build the app using mvn clean install command, it generates a target folder. Start IGB Select Tools > Open App Manager Click Manage Repositories... button (opens Plug-in Repositories tab in Preferences window) Click Add... button (opens Plugin Repository dialog) Enter a name for your repository (can be anything) Click Choose local folder button Select the "target" folder in your filter-by-score project folder. Once you add "target" as a new local App repository, you should see the Score Filter App added as a new App in the IGB App Manager window but this isn't working as expected. |
Score Filter works in IGB version 9 but not in recent versions like 10, 11
Handled issues in the ticket:
1. IGB version is updated from 9 to 10 in pom.xml
2. Upgraded jdk 1.8 to 21
3. Updated dependency with Annotations.
For testing IGB version 11:
Change the IGB version i.e., change the version in all the poms in igb project to 11.0.0 (you can do this simply by using the Replace in Files option in IntelliJ) and try to add the app for that version too.
Branch - https://bitbucket.org/lorainelab-deepthi/filter-by-score/branch/IGBF-4226
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | saideepthi jagarapu [ sjagarap ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
I have a question about this file that is included in the commit: src/main/resources/git.properties
Was this included by accident, or does it have a purpose?
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | saideepthi jagarapu [ sjagarap ] |
It doesn't need to be in PR, will remove it and update the PR
| Assignee | saideepthi jagarapu [ sjagarap ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Thanks saideepthi jagarapu!
Please submit PR when ready.
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | saideepthi jagarapu [ sjagarap ] |
Request for saideepthi jagarapu: Please add a link to the PR as a comment and I will work on merging it.
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | saideepthi jagarapu [ sjagarap ] |
PR is merged.
New jar file and new repository.xml files are created. Ready for testing.
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Tested changes, app is getting added in the app manager.
Moving this ticket to done.
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | saideepthi jagarapu [ sjagarap ] |
When you create a new version of the App, be sure to change its version and also be sure to define the version of IGB it needs.