[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.

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Nowlan Freese added a comment - 16/Aug/23 1:41 PM

@Component
- provide :: service
@Reference
- 'multiple = true, optional = true' :: cardinality = ReferenceCardinality.MULTIPLE
  'multiple = true, optional = false' :: cardinality = ReferenceCardinality.AT_LEAST_ONE
  'multiple=false & optional = true' :: cardinality = ReferenceCardinality.OPTIONAL
  'multiple = true' :: cardinality = ReferenceCardinality.AT_LEAST_ONE
  'optional=false' :: cardinality = ReferenceCardinality.MANDATORY
  'dynamic = true' :: policy = ReferencePolicy.DYNAMIC

Show

Nowlan Freese added a comment - 16/Aug/23 1:41 PM @Component provide :: service @Reference 'multiple = true, optional = true' :: cardinality = ReferenceCardinality.MULTIPLE 'multiple = true, optional = false' :: cardinality = ReferenceCardinality.AT_LEAST_ONE 'multiple=false & optional = true' :: cardinality = ReferenceCardinality.OPTIONAL 'multiple = true' :: cardinality = ReferenceCardinality.AT_LEAST_ONE 'optional=false' :: cardinality = ReferenceCardinality.MANDATORY 'dynamic = true' :: policy = ReferencePolicy.DYNAMIC

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.

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Nowlan Freese added a comment - 16/Aug/23 1:48 PM - edited

Core - Heatmap Editor
Core - Affymetrix Common
(Fails test, may be due to not handling spaces in file/path names) Core - Genometry (Data Models)
Core - IGB
Core - IGB Swing Extensions
Core - IGB Services API
Core - Window Service
Core - Bundle wrapper, deployer
Core - Logging Config
Core - Genoviz Extensions
Core - Preferences
Core - Web Links
Core - Quickload (data source)
(Fails test on Mac) Core - DAS (data source)
Core - Frame Manager
Core - Synonym Lookup
Core - JavaFX Utilities
Core - Menu API
Core - Context Menu Service
Plugin - Apollo Library
(COMPLETE) Plugin - Annotation Tab
(COMPLETE) Plugin - Console Tab
Plugin - Track Operations API, GUI
Plugin - Bigbed data format handler
Plugin - Bigwig data format handler
Plugin - Bookmarks and REST API
Plugin - External View
(COMPLETE) Plugin - Graph Tab
Plugin - Script handler
Plugin - Keyword Search
Plugin - NCBI Blast
(COMPLETE) Plugin - Selection Info tab
(COMPLETE) Plugin - Restriction Sites tab
Plugin - Search Id or Props
(COMPLETE) Plugin - Advanced Search Tab
Plugin - Sequence Viewer GUI
Plugin - Survey GUI
Plugin - Graph thresholding visual analytics
Plugin - Update
Plugin - App Manager GUI
Plugin - Paired-end Read Preprocessor
(COMPLETE) Plugin - Save Image GUI
(COMPLETE) Plugin - Save Session Manager
Plugin - Toolbar Preferences GUI
Plugin - Data caching GUI
Plugin - Data caching API
Plugin - Feedback
Plugin - Sorting API and Impl
Plugin - Narrowpeak data format handler
Plugin - File Handler - Genotyping Results
Plugin - BED file format handler
Plugin - BAM data format handler
Plugin - BAI index visualization handler
Plugin - App Store REST API

Show

Nowlan Freese added a comment - 16/Aug/23 1:48 PM - edited Core - Heatmap Editor Core - Affymetrix Common (Fails test, may be due to not handling spaces in file/path names) Core - Genometry (Data Models) Core - IGB Core - IGB Swing Extensions Core - IGB Services API Core - Window Service Core - Bundle wrapper, deployer Core - Logging Config Core - Genoviz Extensions Core - Preferences Core - Web Links Core - Quickload (data source) (Fails test on Mac) Core - DAS (data source) Core - Frame Manager Core - Synonym Lookup Core - JavaFX Utilities Core - Menu API Core - Context Menu Service Plugin - Apollo Library (COMPLETE) Plugin - Annotation Tab (COMPLETE) Plugin - Console Tab Plugin - Track Operations API, GUI Plugin - Bigbed data format handler Plugin - Bigwig data format handler Plugin - Bookmarks and REST API Plugin - External View (COMPLETE) Plugin - Graph Tab Plugin - Script handler Plugin - Keyword Search Plugin - NCBI Blast (COMPLETE) Plugin - Selection Info tab (COMPLETE) Plugin - Restriction Sites tab Plugin - Search Id or Props (COMPLETE) Plugin - Advanced Search Tab Plugin - Sequence Viewer GUI Plugin - Survey GUI Plugin - Graph thresholding visual analytics Plugin - Update Plugin - App Manager GUI Plugin - Paired-end Read Preprocessor (COMPLETE) Plugin - Save Image GUI (COMPLETE) Plugin - Save Session Manager Plugin - Toolbar Preferences GUI Plugin - Data caching GUI Plugin - Data caching API Plugin - Feedback Plugin - Sorting API and Impl Plugin - Narrowpeak data format handler Plugin - File Handler - Genotyping Results Plugin - BED file format handler Plugin - BAM data format handler Plugin - BAI index visualization handler Plugin - App Store REST API

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]

Hide

Permalink

Nowlan Freese added a comment - 16/Aug/23 4:14 PM

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

Show

Nowlan Freese added a comment - 16/Aug/23 4:14 PM Smoke testing documentation: https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first

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

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Kaushik Gopu added a comment - 17/Aug/23 11:22 AM - edited

created a subtask to work on the following plugins:
Plugin - Toolbar Preferences GUI
Plugin - Data caching GUI
Plugin - Data caching API
Plugin - Feedback
Plugin - Sorting API and Impl
Plugin - Narrowpeak data format handler
Plugin - File Handler - Genotyping Results
Plugin - BED file format handler
Plugin - BAM data format handler
Plugin - BAI index visualization handler
Plugin - App Store REST API

Show

Kaushik Gopu added a comment - 17/Aug/23 11:22 AM - edited created a subtask to work on the following plugins: Plugin - Toolbar Preferences GUI Plugin - Data caching GUI Plugin - Data caching API Plugin - Feedback Plugin - Sorting API and Impl Plugin - Narrowpeak data format handler Plugin - File Handler - Genotyping Results Plugin - BED file format handler Plugin - BAM data format handler Plugin - BAI index visualization handler Plugin - App Store REST API

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Kaushik Gopu added a comment - 18/Aug/23 4:07 PM - edited

@Component
provide :: service
@Reference
'multiple = true, optional = true' :: cardinality = ReferenceCardinality.MULTIPLE
'multiple = true, optional = false' :: cardinality = ReferenceCardinality.AT_LEAST_ONE
'multiple=false & optional = true' :: cardinality = ReferenceCardinality.OPTIONAL
'multiple = true' :: cardinality = ReferenceCardinality.AT_LEAST_ONE
'optional=false' :: cardinality = ReferenceCardinality.MANDATORY
'dynamic = true' :: policy = ReferencePolicy.DYNAMIC
properties = "name=" + ThresholdingAction.COMPONENT_NAME :: property = {"name=" + ThresholdingAction.COMPONENT_NAME}

Show

Kaushik Gopu added a comment - 18/Aug/23 4:07 PM - edited @Component provide :: service @Reference 'multiple = true, optional = true' :: cardinality = ReferenceCardinality.MULTIPLE 'multiple = true, optional = false' :: cardinality = ReferenceCardinality.AT_LEAST_ONE 'multiple=false & optional = true' :: cardinality = ReferenceCardinality.OPTIONAL 'multiple = true' :: cardinality = ReferenceCardinality.AT_LEAST_ONE 'optional=false' :: cardinality = ReferenceCardinality.MANDATORY 'dynamic = true' :: policy = ReferencePolicy.DYNAMIC properties = "name=" + ThresholdingAction.COMPONENT_NAME :: property = {"name=" + ThresholdingAction.COMPONENT_NAME}

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Kaushik Gopu added a comment - 21/Aug/23 2:59 PM - edited

List of plugins using new OSGI v6 annotations:
Plugin - Graph thresholding visual analytics
Plugin - Track Operations API, GUI
Plugin - App Manager GUI
Plugin - Save Image GUI
Plugin - Save Session Manager
Plugin - Advanced Search Tab
Plugin - Selection Info tab
Plugin - Graph Tab
Plugin - Selection Info tab
Plugin - BAM data format handler
Plugin - Restriction Sites tab
Plugin - Bigbed data format handler
Plugin - Bigwig data format handler
Plugin - Annotation Tab
Plugin - App Store REST API
Plugin - BAI index visualization handler
Plugin - Console Tab
Plugin - Sorting API and Impl
Plugin - BED file format handler
Plugin - Feedback
Plugin - Bookmarks and REST API
Plugin - Data caching GUI
Plugin - Toolbar Preferences GUI
Plugin - Keyword Search
Plugin - Data caching API
Plugin - External View
Plugin - Sequence Viewer GUI
Plugin - File Handler - Genotyping Results
Plugin - Script handler
Plugin - Paired-end Read Preprocessor
Plugin - Search Id or Props

Show

Kaushik Gopu added a comment - 21/Aug/23 2:59 PM - edited List of plugins using new OSGI v6 annotations: Plugin - Graph thresholding visual analytics Plugin - Track Operations API, GUI Plugin - App Manager GUI Plugin - Save Image GUI Plugin - Save Session Manager Plugin - Advanced Search Tab Plugin - Selection Info tab Plugin - Graph Tab Plugin - Selection Info tab Plugin - BAM data format handler Plugin - Restriction Sites tab Plugin - Bigbed data format handler Plugin - Bigwig data format handler Plugin - Annotation Tab Plugin - App Store REST API Plugin - BAI index visualization handler Plugin - Console Tab Plugin - Sorting API and Impl Plugin - BED file format handler Plugin - Feedback Plugin - Bookmarks and REST API Plugin - Data caching GUI Plugin - Toolbar Preferences GUI Plugin - Keyword Search Plugin - Data caching API Plugin - External View Plugin - Sequence Viewer GUI Plugin - File Handler - Genotyping Results Plugin - Script handler Plugin - Paired-end Read Preprocessor Plugin - Search Id or Props

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 ]

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Kaushik Gopu added a comment - 31/Aug/23 11:51 AM

reverted 'combined commits' commit and made individual commit for each plugin.
branch that needs to be tested.

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Kaushik Gopu added a comment - 31/Aug/23 11:51 AM reverted 'combined commits' commit and made individual commit for each plugin. branch that needs to be tested.

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Kaushik Gopu added a comment - 31/Aug/23 12:10 PM

pull request submitted.

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Kaushik Gopu added a comment - 31/Aug/23 12:10 PM pull request submitted .

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Ann Loraine added a comment - 31/Aug/23 2:12 PM

PR is merged and installers are built. Get installers from https://bitbucket.org/lorainelab/integrated-genome-browser/downloads as usual.

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Ann Loraine added a comment - 31/Aug/23 2:12 PM PR is merged and installers are built. Get installers from https://bitbucket.org/lorainelab/integrated-genome-browser/downloads as usual.

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 ]