Errors in comp flattening routine (cannot register compartment, cannot register parameter)

[matthiaskoenig]

When trying to flatten some simple comp models I get errors for the following files:
comp.zip

Flattening is performed via

doc = SBMLReader.read(file);
CompFlatteningConverter compFlatteningConverter = new CompFlatteningConverter();
docFlat = compFlatteningConverter.flatten(doc);

E.g. for test10.xml one gets

May 19, 2020 2:53:12 PM org.sbml.jsbml.ext.comp.util.CompFlatteningConverter initSubModels
INFO: No model definition found in sub1.
May 19, 2020 2:53:12 PM org.sbml.jsbml.ext.comp.util.CompFlatteningConverter initSubModels
INFO: No model definition found in sub1.
ERROR (Model.java:4687) - An element of type compartment with the id "moddef1C" is already present in this model. The new element of type compartment will not have it's id set. In some cases, the new element will not be added to the model.

java.lang.IllegalArgumentException: Cannot register compartment.

	at org.sbml.jsbml.AbstractSBase.registerChild(AbstractSBase.java:2220)
	at org.sbml.jsbml.ListOf.add(ListOf.java:444)
	at org.sbml.jsbml.Model.addCompartment(Model.java:351)
	at org.sbml.jsbml.ext.comp.util.CompFlatteningConverter.mergeListsOfModels(CompFlatteningConverter.java:385)
	at org.sbml.jsbml.ext.comp.util.CompFlatteningConverter.mergeModels(CompFlatteningConverter.java:347)
	at org.sbml.jsbml.ext.comp.util.CompFlatteningConverter.flattenAndMergeModels(CompFlatteningConverter.java:304)
	at org.sbml.jsbml.ext.comp.util.CompFlatteningConverter.flattenAndMergeModels(CompFlatteningConverter.java:299)
	at org.sbml.jsbml.ext.comp.util.CompFlatteningConverter.initSubModels(CompFlatteningConverter.java:284)
	at org.sbml.jsbml.ext.comp.util.CompFlatteningConverter.initSubModels(CompFlatteningConverter.java:277)
	at org.sbml.jsbml.ext.comp.util.CompFlatteningConverter.instantiateSubModels(CompFlatteningConverter.java:153)
	at org.sbml.jsbml.ext.comp.util.CompFlatteningConverter.flatten(CompFlatteningConverter.java:115)
	at org.simulator.comp.CompSimulator.<init>(CompSimulator.java:43)
	at org.simulator.comp.CompSimulatorTest.testComp(CompSimulatorTest.java:45)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
	at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
	at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
	at org.junit.runners.Suite.runChild(Suite.java:127)
	at org.junit.runners.Suite.runChild(Suite.java:26)
	at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
	at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
	at org.junit.runners.Suite.runChild(Suite.java:127)
	at org.junit.runners.Suite.runChild(Suite.java:26)
	at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
	at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
	at org.junit.runner.JUnitCore.run(JUnitCore.java:160)
	at com.intellij.junit4.JUnit4IdeaTestRunner.startRunnerWithArgs(JUnit4IdeaTestRunner.java:68)
	at com.intellij.rt.execution.junit.IdeaTestRunner$Repeater.startRunnerWithArgs(IdeaTestRunner.java:47)
	at com.intellij.rt.execution.junit.JUnitStarter.prepareStreamsAndStart(JUnitStarter.java:242)
	at com.intellij.rt.execution.junit.JUnitStarter.main(JUnitStarter.java:70)

For test6.xml one gets

ERROR (Model.java:4687) - An element of type parameter with the id "Mod1subparam2" is already present in this model. The new element of type parameter will not have it's id set. In some cases, the new element will not be added to the model.

java.lang.IllegalArgumentException: Cannot register parameter.

	at org.sbml.jsbml.AbstractSBase.registerChild(AbstractSBase.java:2220)
	at org.sbml.jsbml.ListOf.add(ListOf.java:444)
	at org.sbml.jsbml.Model.addParameter(Model.java:434)
	at org.sbml.jsbml.ext.comp.util.CompFlatteningConverter.mergeListsOfModels(CompFlatteningConverter.java:451)
	at org.sbml.jsbml.ext.comp.util.CompFlatteningConverter.mergeModels(CompFlatteningConverter.java:354)
	at org.sbml.jsbml.ext.comp.util.CompFlatteningConverter.flattenAndMergeModels(CompFlatteningConverter.java:304)
	at org.sbml.jsbml.ext.comp.util.CompFlatteningConverter.initSubModels(CompFlatteningConverter.java:284)
	at org.sbml.jsbml.ext.comp.util.CompFlatteningConverter.instantiateSubModels(CompFlatteningConverter.java:153)
	at org.sbml.jsbml.ext.comp.util.CompFlatteningConverter.flatten(CompFlatteningConverter.java:115)
	at org.simulator.comp.CompSimulator.<init>(CompSimulator.java:43)
	at org.simulator.comp.CompSimulatorTest.testComp(CompSimulatorTest.java:45)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
	at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
	at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
	at org.junit.runners.Suite.runChild(Suite.java:127)
	at org.junit.runners.Suite.runChild(Suite.java:26)
	at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
	at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
	at org.junit.runners.Suite.runChild(Suite.java:127)
	at org.junit.runners.Suite.runChild(Suite.java:26)
	at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
	at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
	at org.junit.runner.JUnitCore.run(JUnitCore.java:160)
	at com.intellij.junit4.JUnit4IdeaTestRunner.startRunnerWithArgs(JUnit4IdeaTestRunner.java:68)
	at com.intellij.rt.execution.junit.IdeaTestRunner$Repeater.startRunnerWithArgs(IdeaTestRunner.java:47)
	at com.intellij.rt.execution.junit.JUnitStarter.prepareStreamsAndStart(JUnitStarter.java:242)
	at com.intellij.rt.execution.junit.JUnitStarter.main(JUnitStarter.java:70)

[matthiaskoenig]

Hi all,

does anybody know what is going on here? This worked in earlier versions of JSBML and should be picked up by regression tests. When we worked 1-2 years ago with Shalin on the CompSimulation in SBSCL all these models flattened just fine.

What changed in the Comp flattening since then?

[niko-rodrigue]

a student worked on loading external model definition from all possible ways. He might have broken something for the flattening. There might not have been integrated tests for the comp flattening at the moment, so this went unnoticed.

…

On Thu, 28 May 2020 at 15:58, Matthias König ***@***.***> wrote: Hi all, does anybody know what is going on here? This worked in earlier versions of JSBML and should be picked up by regression tests. When we worked 1-2 years ago with Shalin on the CompSimulation in SBSCL all these models flattened just fine. What changed in the Comp flattening since then? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#213 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAMVB4L3BGYJ4LIZXJHDEEDRTZ3XXANCNFSM4NFA5XOA> .

[matthiaskoenig]

Hi all,
I will tackle this issue.

There are many test models in the repository, the failures were just not very obvious (2 failing tests). After creating some better tests (parametrized tests instead of one test running all test models) 54/60 comp test models cannot be flattened.
If anybody gives me commit access to the repository I can push my changes in a branch and work on fixing the flattening issues.

Best Matthias

[niko-rodrigue]

Hi Matthias, good to hear. Andreas should be able to give you access if needed. But you can also fork the repo and do some push requests afterwards.

…

On Tue, 14 Jul 2020 at 20:18, Matthias König ***@***.***> wrote: Hi all, I will tackle this issue. There are many test models in the repository, the failures were just not very obvious (2 failing tests). After creating some better tests (parametrized tests instead of one test running all test models) 54/60 comp test models cannot be flattened. If anybody gives me commit access to the repository I can push my changes in a branch and work on fixing the flattening issues. Best Matthias — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#213 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAMVB4KW7P2KEXSMXCMOARDR3SVP5ANCNFSM4NFA5XOA> .

[draeger]

@matthiaskoenig has been invited as a collaborator with write permission. Thanks, @niko-rodrigue and @matthiaskoenig!