UD-3169: new app to open cytoscape-web from desktop

[sreuland]

• * Refactor cytoscape-web launch to be performed in task runner.
• * Add top toolbar menu icon to be enabled/disabled only one network open and launches same cytoscape web import url
• * Add properties under opencyweb group for web config and network validation parameters.

this is how the toolbar looks with the new icon positioned at farthest left next to the other buttons that are related to open/save networks. It's the cytoscape web 'graph' logo.

properties editor:

network validation error message:

[Copilot]

Pull request overview

Refactors the “Open in Cytoscape Web” launch flow so that opening the Cytoscape Web import URL is executed via a Cytoscape task, and adjusts app initialization timing via an OSGi startup event listener.

Changes:

• Introduces a new DoTask to open the Cytoscape Web import URL in the default browser and adds unit tests for it.
• Refactors OpenInCytoscapeWebTaskFactoryImpl to return a real task iterator (removing the previous no-op task).
• Updates OSGi activation to register services after AppsFinishedStartingEvent, and adds app-api dependency to support the listener.

Reviewed changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
src/test/java/edu/ucsd/idekerlab/opencyweb/DoTaskTest.java	Adds unit tests for browser-launch task behavior (success + invalid URL).
src/test/java/edu/ucsd/idekerlab/opencyweb/DoNothingTaskTest.java	Removes tests for the deleted no-op task.
src/main/java/edu/ucsd/idekerlab/opencyweb/util/Constants.java	Removes unused constants class.
src/main/java/edu/ucsd/idekerlab/opencyweb/query/OpenInCytoscapeWebTaskFactoryImpl.java	Refactors task factory to build and return DoTask rather than running logic inline.
src/main/java/edu/ucsd/idekerlab/opencyweb/DoTask.java	Adds task implementation that opens Cytoscape Web import URL via Desktop.browse.
src/main/java/edu/ucsd/idekerlab/opencyweb/DoNothingTask.java	Removes no-op task previously used as placeholder.
src/main/java/edu/ucsd/idekerlab/opencyweb/CyActivator.java	Defers service registration until apps finished starting (adds listener + initialization method).
pom.xml	Adds org.cytoscape:app-api dependency (provided scope).
Makefile	Simplifies help/coverage/docs targets and removes browser-opening helpers.

Comments suppressed due to low confidence (1)

src/main/java/edu/ucsd/idekerlab/opencyweb/query/OpenInCytoscapeWebTaskFactoryImpl.java:23

• The class-level Javadoc refers to implementing NetworkViewTaskFactory/AbstractNodeViewTaskFactory and sending node members to iQuery, but this class currently implements NetworkCollectionTaskFactory and launches Cytoscape Web. Please update the Javadoc to match the current behavior and remove stale iQuery/node-task references.

/**
 * Implementation of {@link NetworkViewTaskFactory} and
 * {@link AbstractNodeViewTaskFactory} to send members of specified
 * node to iQuery
 *

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[sreuland]

@coleslaw481 , this is ready for re-review if you have a moment, I've added network size validations via properties as discussed. Thanks!

[coleslaw481]

This is great. One wish list item, instead of adding a rest.port property under opencyweb, just use rest.port property value under cytoscape 3 properties

[sreuland]

This is great. One wish list item, instead of adding a rest.port property under opencyweb, just use rest.port property value under cytoscape 3 properties

great suggestion, done.

I created the publishing docs also:

Tutorial
FAQ
User Manual