Event queue cleanup, categorization & tests (JAMESII-423)

[JAMESII-426] Support factory filtering of event queues by their way of handling event identity and event ordering Created: 15/Nov/13  Updated: 25/Sep/14

Status: In Progress
Project: James II
Component/s: Core
Affects Version/s: None
Fix Version/s: James II 0.9.8
Security Level: public (Visible to EVERYONE.)

Type: Sub-task Priority: Major
Reporter: Anonymous Assignee: Unassigned
Resolution: Unresolved Votes: 0
Labels: event-queue, plugnsimulate
Remaining Estimate: Not Specified
Time Spent: Not Specified
Original Estimate: Not Specified


 Description   

This should resolve issues (1) and (2) in JAMESII-423, as the properties of each event queue are explicit.






Invalid parameterization of text-based species-reactions models (depending on context) (JAMESII-302)

[JAMESII-303] Parameters for an {{SRModel}} can only be provided within an "initialState" parameter {{Map}}, containing itself parameters of type {{SRModelParameter}} Created: 11/Jan/13  Updated: 25/Sep/14

Status: Open
Project: James II
Component/s: SR
Affects Version/s: James II 0.8.8, James II 0.9, James II 0.9.1
Fix Version/s: James II 0.9.8
Security Level: public (Visible to EVERYONE.)

Type: Technical task Priority: Minor
Reporter: Stefan Rybacki Assignee: Unassigned
Resolution: Unresolved Votes: 0
Labels: None
Remaining Estimate: 0 minutes
Time Spent: Not Specified
Original Estimate: 0 minutes


 Description   

This makes it hard, to correctly provide parameters provided by ExperimentVariables as there is no structure producing this data structure from a parameter tree for example.






[JAMESII-357] Unhandled exception during registry initialization can cause deadlock in parallel task runner Created: 11/Jun/13  Updated: 25/Sep/14

Status: Open
Project: James II
Component/s: Core
Affects Version/s: James II 0.9.2
Fix Version/s: James II 0.9.8
Security Level: public (Visible to EVERYONE.)

Type: Bug Priority: Minor
Reporter: Anonymous Assignee: Stefan Rybacki
Resolution: Unresolved Votes: 0
Labels: deadlock, stability
Remaining Estimate: Not Specified
Time Spent: Not Specified
Original Estimate: Not Specified


 Description   

This happend in a recent SESSL build, where the plugin folder did not exist and hence the registry threw an exception (which is OK), and the ParallelTaskRunner crashed (not OK):

Jun 11, 2013 5:11:37 PM org.jamesii.core.experiments.taskrunner.parallel.ParallelComputationTaskRunner executeConfiguration (Line: 264)
SEVERE: Plug-in dir /home/jenkins/workspace/SESSL/sessl-integration/target/classes not found!
org.jamesii.core.plugins.PluginLoadException: Plug-in dir /home/jenkins/workspace/SESSL/sessl-integration/target/classes not found!
	at org.jamesii.core.plugins.install.DiscPlugInFinder.parseDirectory(DiscPlugInFinder.java:107)
	at org.jamesii.core.plugins.install.DiscPlugInFinder.parseDirectory(DiscPlugInFinder.java:91)
	at org.jamesii.core.Registry.initBySearch(Registry.java:924)
	at org.jamesii.core.Registry.initPlugins(Registry.java:981)
	at org.jamesii.SimSystem.initializeAndSetRegistry(SimSystem.java:258)
	at org.jamesii.SimSystem.createRegistry(SimSystem.java:220)
	at org.jamesii.SimSystem.getRegistry(SimSystem.java:199)
	at org.jamesii.core.experiments.taskrunner.parallel.ParallelComputationTaskRunner.initModelReader(ParallelComputationTaskRunner.java:344)
	at org.jamesii.core.experiments.taskrunner.parallel.ParallelComputationTaskRunner.setupTaskConfig(ParallelComputationTaskRunner.java:285)
	at org.jamesii.core.experiments.taskrunner.parallel.ParallelComputationTaskRunner.executeConfiguration(ParallelComputationTaskRunner.java:261)
	at org.jamesii.core.experiments.taskrunner.AbstractTaskRunner.run(AbstractTaskRunner.java:106)
	at java.lang.Thread.run(Thread.java:722)





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