[IGBF-3411] Implement r6 Annotations in IGB - JIRA UNCC

Nowlan Freese created issue - 16/Aug/23 1:38 PM

Nowlan Freese made changes - 16/Aug/23 1:39 PM

Field	Original Value	New Value
Epic Child		~~IGBF-3379~~ [ 22402 ]

Nowlan Freese made changes - 16/Aug/23 1:39 PM

Summary

stub

Implement r6 Annotations in IGB

Nowlan Freese made changes - 16/Aug/23 1:40 PM

Description

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Nowlan Freese made changes - 16/Aug/23 1:47 PM

Description

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

Workflow:
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
# If any test fails, make a new ticket, do not commit changes to branch.
# Start IGB, check log/standard output for any warnings/errors. If there are relevant warnings/errors make a new ticket, do not commit changes to branch.
# Check the Felix Web Console in your browser (http://localhost:7080/system/console/bundles#). If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch.
# Click on the Arabidopsis genome.
# Test the individual module functionality.
# Reset preferences to default when closing IGB.
# Commit change for that specific module using the following example: Update annotations for Plugin - Graph Tab
# Push commit to your branch

Nowlan Freese made changes - 16/Aug/23 1:47 PM

Description

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

Workflow:
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
# If any test fails, make a new ticket, do not commit changes to branch.
# Start IGB, check log/standard output for any warnings/errors. If there are relevant warnings/errors make a new ticket, do not commit changes to branch.
# Check the Felix Web Console in your browser (http://localhost:7080/system/console/bundles#). If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch.
# Click on the Arabidopsis genome.
# Test the individual module functionality.
# Reset preferences to default when closing IGB.
# Commit change for that specific module using the following example: Update annotations for Plugin - Graph Tab
# Push commit to your branch

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

Workflow:
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
# If any test fails, make a new ticket, do not commit changes to branch.
# Start IGB, check log/standard output for any warnings/errors. If there are relevant warnings/errors make a new ticket, do not commit changes to branch.
# Check the Felix Web Console in your browser (http://localhost:7080/system/console/bundles#). If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch.
# Click on the Arabidopsis genome.
# Test the individual module functionality.
# Reset preferences to default when closing IGB.
# Commit change for that specific module using the following example: Update annotations for Plugin - Graph Tab
# Push commit to your branch.
# Mark the module as completed below.

Nowlan Freese made changes - 16/Aug/23 1:52 PM

Description

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

Workflow:
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
# If any test fails, make a new ticket, do not commit changes to branch.
# Start IGB, check log/standard output for any warnings/errors. If there are relevant warnings/errors make a new ticket, do not commit changes to branch.
# Check the Felix Web Console in your browser (http://localhost:7080/system/console/bundles#). If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch.
# Click on the Arabidopsis genome.
# Test the individual module functionality.
# Reset preferences to default when closing IGB.
# Commit change for that specific module using the following example: Update annotations for Plugin - Graph Tab
# Push commit to your branch.
# Mark the module as completed below.

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

Workflow:
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
## If any test fails, make a new ticket, do not commit changes to branch.
# Start IGB, check log/standard output for any warnings/errors.
## If there are relevant warnings/errors make a new ticket, do not commit changes to branch.
# Check the Felix Web Console in your browser (http://localhost:7080/system/console/bundles#).
## If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch.
# Click on the Arabidopsis genome.
# Test the individual module functionality.
## If unclear as to how to test module functionality, ask Dr. Loraine.
## If module functionality appears to be broken, make a new ticket, do not commit changes to branch.
# Reset preferences to default when closing IGB.
# Commit change for that specific module using the following example: Update annotations for Plugin - Graph Tab
# Push commit to your branch.
# Mark the module as completed below.

Nowlan Freese made changes - 16/Aug/23 1:52 PM

Description

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

Workflow:
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
## If any test fails, make a new ticket, do not commit changes to branch.
# Start IGB, check log/standard output for any warnings/errors.
## If there are relevant warnings/errors make a new ticket, do not commit changes to branch.
# Check the Felix Web Console in your browser (http://localhost:7080/system/console/bundles#).
## If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch.
# Click on the Arabidopsis genome.
# Test the individual module functionality.
## If unclear as to how to test module functionality, ask Dr. Loraine.
## If module functionality appears to be broken, make a new ticket, do not commit changes to branch.
# Reset preferences to default when closing IGB.
# Commit change for that specific module using the following example: Update annotations for Plugin - Graph Tab
# Push commit to your branch.
# Mark the module as completed below.

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

Workflow:
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
## If any test fails, make a new ticket, do not commit changes to branch.
# Start IGB, check log/standard output for any warnings/errors.
## If there are relevant warnings/errors make a new ticket, do not commit changes to branch.
# Check the Felix Web Console in your browser ([link|http://localhost:7080/system/console/bundles#]).
## If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch.
# Click on the Arabidopsis genome.
# Test the individual module functionality.
## If unclear as to how to test module functionality, ask Dr. Loraine.
## If module functionality appears to be broken, make a new ticket, do not commit changes to branch.
# Reset preferences to default when closing IGB.
# Commit change for that specific module using the following example: Update annotations for Plugin - Graph Tab
# Push commit to your branch.
# Mark the module as completed below.

Nowlan Freese made changes - 16/Aug/23 1:53 PM

Description

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

Workflow:
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
## If any test fails, make a new ticket, do not commit changes to branch.
# Start IGB, check log/standard output for any warnings/errors.
## If there are relevant warnings/errors make a new ticket, do not commit changes to branch.
# Check the Felix Web Console in your browser ([link|http://localhost:7080/system/console/bundles#]).
## If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch.
# Click on the Arabidopsis genome.
# Test the individual module functionality.
## If unclear as to how to test module functionality, ask Dr. Loraine.
## If module functionality appears to be broken, make a new ticket, do not commit changes to branch.
# Reset preferences to default when closing IGB.
# Commit change for that specific module using the following example: Update annotations for Plugin - Graph Tab
# Push commit to your branch.
# Mark the module as completed below.

Nowlan Freese made changes - 16/Aug/23 1:56 PM

Description

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

Workflow:
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
## If any test fails, make a new ticket, do not commit changes to branch.
# Start IGB, check log/standard output for any warnings/errors.
## If there are relevant warnings/errors make a new ticket, do not commit changes to branch.
# Check the Felix Web Console in your browser ([link|http://localhost:7080/system/console/bundles#]).
## If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch.
# Click on the Arabidopsis genome.
# Test the individual module functionality.
## If unclear as to how to test module functionality, ask Dr. Loraine.
## If module functionality appears to be broken, make a new ticket, do not commit changes to branch.
# Reset preferences to default when closing IGB.
# Commit change for that specific module using the following example: Update annotations for Plugin - Graph Tab
# Push commit to your branch.
# Mark the module as completed below.

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

Workflow:
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
## If any test fails, make a new ticket, do not commit changes to branch.
# Start IGB, check log/standard output for any warnings/errors.
## If there are relevant warnings/errors make a new ticket, do not commit changes to branch.
# Check the Felix Web Console in your browser ([link|http://localhost:7080/system/console/bundles#]).
## If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch.
# Click on the Arabidopsis genome.
# Test the individual module functionality.
## If unclear as to how to test module functionality, ask Dr. Loraine.
## If module functionality appears to be broken, make a new ticket, do not commit changes to branch.
# Reset preferences to default when closing IGB.
# Commit change for that specific module using the following example: Update annotations for Plugin - Graph Tab
# Push commit to your branch.
# Mark the module as completed below.

Git:
Branch: https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6
Once you have completed the above workflow steps for a module(s), create a pull request from your branch to [main-JDK8-r6|https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6]

Nowlan Freese made changes - 16/Aug/23 1:59 PM

Description

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

Workflow:
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
## If any test fails, make a new ticket, do not commit changes to branch.
# Start IGB, check log/standard output for any warnings/errors.
## If there are relevant warnings/errors make a new ticket, do not commit changes to branch.
# Check the Felix Web Console in your browser ([link|http://localhost:7080/system/console/bundles#]).
## If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch.
# Click on the Arabidopsis genome.
# Test the individual module functionality.
## If unclear as to how to test module functionality, ask Dr. Loraine.
## If module functionality appears to be broken, make a new ticket, do not commit changes to branch.
# Reset preferences to default when closing IGB.
# Commit change for that specific module using the following example: Update annotations for Plugin - Graph Tab
# Push commit to your branch.
# Mark the module as completed below.

Git:
Branch: https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6
Once you have completed the above workflow steps for a module(s), create a pull request from your branch to [main-JDK8-r6|https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6]

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

Workflow:
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
## If any test fails, make a new ticket, do not commit changes to branch.
# Start IGB, check log/standard output for any warnings/errors.
## If there are relevant warnings/errors make a new ticket, do not commit changes to branch.
# Check the Felix Web Console in your browser ([link|http://localhost:7080/system/console/bundles#]).
## If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch.
# Click on the Arabidopsis genome.
# Test the individual module functionality.
## If unclear as to how to test module functionality, ask Dr. Loraine.
## If module functionality appears to be broken, make a new ticket, do not commit changes to branch.
# Reset preferences to default when closing IGB.
# Commit change for that specific module using the following example: Update annotations for Plugin - Graph Tab
# Push commit to your branch.
# Mark the module as completed below.

Git:
Branch: https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6
Create a pull request from your branch to [main-JDK8-r6|https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6]

Karthik Raveendran made changes - 16/Aug/23 10:54 PM

Epic Child

~~IGBF-3412~~ [ 22435 ]

Karthik Raveendran made changes - 16/Aug/23 10:58 PM

Epic Child

~~IGBF-3413~~ [ 22436 ]

Karthik Raveendran made changes - 16/Aug/23 11:03 PM

Epic Child

~~IGBF-3414~~ [ 22437 ]

Ann Loraine made changes - 17/Aug/23 10:18 AM

Description

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

Workflow:
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
## If any test fails, make a new ticket, do not commit changes to branch.
# Start IGB, check log/standard output for any warnings/errors.
## If there are relevant warnings/errors make a new ticket, do not commit changes to branch.
# Check the Felix Web Console in your browser ([link|http://localhost:7080/system/console/bundles#]).
## If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch.
# Click on the Arabidopsis genome.
# Test the individual module functionality.
## If unclear as to how to test module functionality, ask Dr. Loraine.
## If module functionality appears to be broken, make a new ticket, do not commit changes to branch.
# Reset preferences to default when closing IGB.
# Commit change for that specific module using the following example: Update annotations for Plugin - Graph Tab
# Push commit to your branch.
# Mark the module as completed below.

Git:
Branch: https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6
Create a pull request from your branch to [main-JDK8-r6|https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6]

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

Workflow:
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
## If any test fails, make a new ticket, do not commit changes to branch.
# Start IGB, check log/standard output for any warnings/errors.
## If there are relevant warnings/errors make a new ticket, do not commit changes to branch.
# Check the Felix Web Console in your browser ([link|http://localhost:7080/system/console/bundles#]).
## If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch.
# Click on the Arabidopsis genome.
# Test the individual module functionality.
## If unclear as to how to test module functionality, ask Dr. Loraine.
## If module functionality appears to be broken, make a new ticket, do not commit changes to branch.
# Reset preferences to default when closing IGB.
# Commit change for that specific module using the following example: Update annotations for Plugin - Graph Tab
# Push commit to your branch.
# Mark the module as completed below.

Git:
Branch: https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6
Create a pull request from your branch to [main-JDK8-r6|https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6]

**Reference:**

Smoke testing documentation: https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first

Ann Loraine made changes - 17/Aug/23 10:18 AM

Description

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

Workflow:
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
## If any test fails, make a new ticket, do not commit changes to branch.
# Start IGB, check log/standard output for any warnings/errors.
## If there are relevant warnings/errors make a new ticket, do not commit changes to branch.
# Check the Felix Web Console in your browser ([link|http://localhost:7080/system/console/bundles#]).
## If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch.
# Click on the Arabidopsis genome.
# Test the individual module functionality.
## If unclear as to how to test module functionality, ask Dr. Loraine.
## If module functionality appears to be broken, make a new ticket, do not commit changes to branch.
# Reset preferences to default when closing IGB.
# Commit change for that specific module using the following example: Update annotations for Plugin - Graph Tab
# Push commit to your branch.
# Mark the module as completed below.

Git:
Branch: https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6
Create a pull request from your branch to [main-JDK8-r6|https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6]

**Reference:**

Smoke testing documentation: https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

Workflow:
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
## If any test fails, make a new ticket, do not commit changes to branch.
# Start IGB, check log/standard output for any warnings/errors.
## If there are relevant warnings/errors make a new ticket, do not commit changes to branch.
# Check the Felix Web Console in your browser ([link|http://localhost:7080/system/console/bundles#]).
## If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch.
# Click on the Arabidopsis genome.
# Test the individual module functionality.
## If unclear as to how to test module functionality, ask Dr. Loraine.
## If module functionality appears to be broken, make a new ticket, do not commit changes to branch.
# Reset preferences to default when closing IGB.
# Commit change for that specific module using the following example: Update annotations for Plugin - Graph Tab
# Push commit to your branch.
# Mark the module as completed below.

Git:
Branch: https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6
Create a pull request from your branch to [main-JDK8-r6|https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6]

*Reference:*

Smoke testing documentation: https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first

Ann Loraine made changes - 17/Aug/23 10:41 AM

Description

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

Workflow:
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
## If any test fails, make a new ticket, do not commit changes to branch.
# Start IGB, check log/standard output for any warnings/errors.
## If there are relevant warnings/errors make a new ticket, do not commit changes to branch.
# Check the Felix Web Console in your browser ([link|http://localhost:7080/system/console/bundles#]).
## If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch.
# Click on the Arabidopsis genome.
# Test the individual module functionality.
## If unclear as to how to test module functionality, ask Dr. Loraine.
## If module functionality appears to be broken, make a new ticket, do not commit changes to branch.
# Reset preferences to default when closing IGB.
# Commit change for that specific module using the following example: Update annotations for Plugin - Graph Tab
# Push commit to your branch.
# Mark the module as completed below.

Git:
Branch: https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6
Create a pull request from your branch to [main-JDK8-r6|https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6]

*Reference:*

Smoke testing documentation: https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

* Development Workflow:*
# Make or pick a ticket representing work on updating a module or set of modules. Assign it to yourself.
# Branch from the latest tip of main-JDK8-r6 (as usual) to create a topic branch for this task.
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
## If any test fails, do not commit changes to any branch. Instead, (1) create a new ticket documenting the error and (2) discard the changes on your local system. Later either you or someone else will attempt investigate.
# Start IGB, check log/standard output for any warnings/errors.
## If there are relevant warnings/errors make a new ticket, do not commit changes to branch. (See previous instruction.)
# Check the Felix Web Console in your browser ([link|http://localhost:7080/system/console/bundles#]).
## If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch. (See previous instruction.)
# Click on the Arabidopsis genome.
# Test the individual module functionality. (See "[smoke testing documentation|https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first]" for how to test a module.)
## If unclear as to how to test module functionality, ask Dr. Loraine.
## If module functionality appears to be broken, make a new ticket, do not commit changes to branch. (See previous instruction.)
# Reset preferences to default; doing this will quit IGB.
# Commit change for that specific module to your topic branch. Format your commit message following this example: Update annotations for Plugin - Graph Tab. Each module should be modified in a single commit.
# Push branch to your fork.
# Mark the module as completed below.

Git:
Branch: https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6
Create a pull request from your branch to [main-JDK8-r6|https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6]

*Reference:*
Smoke testing documentation: https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first

Ann Loraine made changes - 17/Aug/23 10:41 AM

Description

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

* Development Workflow:*
# Make or pick a ticket representing work on updating a module or set of modules. Assign it to yourself.
# Branch from the latest tip of main-JDK8-r6 (as usual) to create a topic branch for this task.
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
## If any test fails, do not commit changes to any branch. Instead, (1) create a new ticket documenting the error and (2) discard the changes on your local system. Later either you or someone else will attempt investigate.
# Start IGB, check log/standard output for any warnings/errors.
## If there are relevant warnings/errors make a new ticket, do not commit changes to branch. (See previous instruction.)
# Check the Felix Web Console in your browser ([link|http://localhost:7080/system/console/bundles#]).
## If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch. (See previous instruction.)
# Click on the Arabidopsis genome.
# Test the individual module functionality. (See "[smoke testing documentation|https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first]" for how to test a module.)
## If unclear as to how to test module functionality, ask Dr. Loraine.
## If module functionality appears to be broken, make a new ticket, do not commit changes to branch. (See previous instruction.)
# Reset preferences to default; doing this will quit IGB.
# Commit change for that specific module to your topic branch. Format your commit message following this example: Update annotations for Plugin - Graph Tab. Each module should be modified in a single commit.
# Push branch to your fork.
# Mark the module as completed below.

Git:
Branch: https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6
Create a pull request from your branch to [main-JDK8-r6|https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6]

*Reference:*
Smoke testing documentation: https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

*Development Workflow:*
# Make or pick a ticket representing work on updating a module or set of modules. Assign it to yourself.
# Branch from the latest tip of main-JDK8-r6 (as usual) to create a topic branch for this task.
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
## If any test fails, do not commit changes to any branch. Instead, (1) create a new ticket documenting the error and (2) discard the changes on your local system. Later either you or someone else will attempt investigate.
# Start IGB, check log/standard output for any warnings/errors.
## If there are relevant warnings/errors make a new ticket, do not commit changes to branch. (See previous instruction.)
# Check the Felix Web Console in your browser ([link|http://localhost:7080/system/console/bundles#]).
## If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch. (See previous instruction.)
# Click on the Arabidopsis genome.
# Test the individual module functionality. (See "[smoke testing documentation|https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first]" for how to test a module.)
## If unclear as to how to test module functionality, ask Dr. Loraine.
## If module functionality appears to be broken, make a new ticket, do not commit changes to branch. (See previous instruction.)
# Reset preferences to default; doing this will quit IGB.
# Commit change for that specific module to your topic branch. Format your commit message following this example: Update annotations for Plugin - Graph Tab. Each module should be modified in a single commit.
# Push branch to your fork.
# Mark the module as completed below.

Git:
Branch: https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6
Create a pull request from your branch to [main-JDK8-r6|https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6]

*Reference:*
Smoke testing documentation: https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first

Ann Loraine made changes - 17/Aug/23 10:42 AM

Description

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

*Development Workflow:*
# Make or pick a ticket representing work on updating a module or set of modules. Assign it to yourself.
# Branch from the latest tip of main-JDK8-r6 (as usual) to create a topic branch for this task.
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
## If any test fails, do not commit changes to any branch. Instead, (1) create a new ticket documenting the error and (2) discard the changes on your local system. Later either you or someone else will attempt investigate.
# Start IGB, check log/standard output for any warnings/errors.
## If there are relevant warnings/errors make a new ticket, do not commit changes to branch. (See previous instruction.)
# Check the Felix Web Console in your browser ([link|http://localhost:7080/system/console/bundles#]).
## If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch. (See previous instruction.)
# Click on the Arabidopsis genome.
# Test the individual module functionality. (See "[smoke testing documentation|https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first]" for how to test a module.)
## If unclear as to how to test module functionality, ask Dr. Loraine.
## If module functionality appears to be broken, make a new ticket, do not commit changes to branch. (See previous instruction.)
# Reset preferences to default; doing this will quit IGB.
# Commit change for that specific module to your topic branch. Format your commit message following this example: Update annotations for Plugin - Graph Tab. Each module should be modified in a single commit.
# Push branch to your fork.
# Mark the module as completed below.

Git:
Branch: https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6
Create a pull request from your branch to [main-JDK8-r6|https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6]

*Reference:*
Smoke testing documentation: https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first

Situation: In order to update the maven-bundle-plugin update to be compatible with JDK 11 we need to implement the new r6 declarative service component annotations in IGB.

Task: Update each module (core/plugin) in IGB to use the new annotations (see comments below). Each updated module should be its own commit.

*Development Workflow:*
# Make or pick a ticket representing work on updating a module or set of modules. Assign it to yourself.
# Branch from the latest tip of main-JDK8-r6 (as usual) to create a topic branch for this task.
# Make code changes to new OSGI annotations.
# Delete the .m2 folder
# Delete the .igb folder (appData/igb folder on Windows).
# Run mvn clean install (Do not skip tests).
## If any test fails, do not commit changes to any branch. Instead, (1) create a new ticket documenting the error and (2) discard the changes on your local system. Later either you or someone else will attempt investigate.
# Start IGB, check log/standard output for any warnings/errors.
## If there are relevant warnings/errors make a new ticket, do not commit changes to branch. (See 6.)
# Check the Felix Web Console in your browser ([link|http://localhost:7080/system/console/bundles#]).
## If any bundles are listed as fragments/installed then make a new ticket, do not commit changes to branch. (See 6.)
# Click on the Arabidopsis genome.
# Test the individual module functionality. See "[smoke testing documentation|https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first]" for how to test a module.
## If unclear as to how to test module functionality, ask Dr. Loraine.
## If module functionality appears to be broken, make a new ticket, do not commit changes to branch. (See 6.)
# Reset preferences to default; doing this will quit IGB.
# Commit change for that specific module to your topic branch. Format your commit message following this example: Update annotations for Plugin - Graph Tab. Each module should be modified in a single commit.
# Push branch to your fork.
# Mark the module as completed below.

Git:
Branch: https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6
Create a pull request from your branch to [main-JDK8-r6|https://bitbucket.org/lorainelab/integrated-genome-browser/commits/branch/main-JDK8-r6]

*Reference:*
Smoke testing documentation: https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first

Kaushik Gopu made changes - 24/Aug/23 10:38 AM

Epic Child

~~IGBF-3417~~ [ 22440 ]

Kaushik Gopu made changes - 24/Aug/23 10:44 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Kaushik Gopu made changes - 24/Aug/23 10:44 AM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Kaushik Gopu made changes - 28/Aug/23 2:39 PM

Epic Child

~~IGBF-3422~~ [ 22523 ]

Nowlan Freese made changes - 29/Aug/23 9:18 AM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Nowlan Freese made changes - 29/Aug/23 9:18 AM

Status

First Level Review in Progress [ 10301 ]

To-Do [ 10305 ]

Nowlan Freese made changes - 29/Aug/23 9:20 AM

Epic Child

~~IGBF-3416~~ [ 22439 ]

Nowlan Freese made changes - 29/Aug/23 9:21 AM

Comment

[ Moving to first level review.
pull [this|https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/branch/IGBF-3411] branch in order to test. ]

Nowlan Freese made changes - 31/Aug/23 10:42 AM

Epic Child

~~IGBF-3422~~ [ 22523 ]

Karthik Raveendran made changes - 05/Sep/23 10:21 AM

Epic Child

~~IGBF-3430~~ [ 22532 ]

Karthik Raveendran made changes - 05/Sep/23 10:23 AM

Epic Child

~~IGBF-3431~~ [ 22533 ]

Nowlan Freese made changes - 07/Sep/23 10:34 AM

Epic Child

~~IGBF-3433~~ [ 22535 ]

Nowlan Freese made changes - 20/Sep/23 9:40 AM

Epic Child

~~IGBF-3451~~ [ 22553 ]

Nowlan Freese made changes - 25/Sep/23 11:19 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Nowlan Freese made changes - 25/Sep/23 11:19 AM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]