Details
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Type:
Epic
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 10.0.0 Major Release
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Labels:None
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Epic Name:Implement r6 Annotations in IGB
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 6.)
- Check the Felix Web Console in your browser (link).
- 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" 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
Reference:
Smoke testing documentation: https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first
Attachments
Activity
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
Smoke testing documentation: https://wiki.bioviz.org/confluence/display/ITD/How+to+test+-+read+this+first
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
- @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}
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
- reverted 'combined commits' commit and made individual commit for each plugin.
- branch that needs to be tested.
PR is merged and installers are built. Get installers from https://bitbucket.org/lorainelab/integrated-genome-browser/downloads as usual.
As of IGBF-3451 we have merged all of the changes from this epic into main-JDK8.
Closing ticket.
'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