feat: throw runtime error for dimensional check failures

[sanjayankur31]

No description provided.

[sanjayankur31]

All the LEMS examples in the NeuroML2 repo passed, but it'll be good to check if any of our existing models fail because of this (and correct them?).

[sanjayankur31]

@pgleeson : just ran into this fall out from the dimensional fixes while re-building the java stack in experimental: python getNeuroML.py experimental:

[ERROR] Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.965 s <<< FAILURE! -- in org.neuroml.importer.test.SBMLImporterTest
[ERROR] org.neuroml.importer.test.SBMLImporterTest.testIzhikevich -- Time elapsed: 0.038 s <<< ERROR!
org.lemsml.jlems.core.expression.ParseError:
Error checking equations of ComponentType: ComponentType, name=Izhikevicha (none)
b (none)
c (none)
d (none)
Vthresh (none)
i_amp (none)
i_del (none)
tscale (per_time)  = 1per_s
cell (none)  = 1.0

(Dimension mismatch in the equation: time = 1. Residual dimension: ExprDimensional[t=1]
Dimension of time: Dimension[none dimensionless], multiplier=Dimension[per_time t=-1], left=Dimension[ t=-1], rhs=ExprDimensional[dimensionless]
All:{vv=Dimension[none dimensionless], a=Dimension[none dimensionless], i_del=Dimension[none dimensionless], b=Dimension[none dimensionless], c=Dimension[none dimensionless], tscale=Dimension[per_time t=-1], d=Dimension[none dimensionless], i=Dimension[none dimensionless], Vthresh=Dimension[none dimensionless], cell=Dimension[none dimensionless], t=ExprDimensional[t=1], U=Dimension[none dimensionless], i_amp=Dimension[none dimensionless], time=Dimension[none dimensionless]})
        at org.lemsml.jlems.core.type.Lems.resolve(Lems.java:176)
        at org.neuroml.importer.test.SBMLImporterTest.convertSBMLtoLEMSFile(SBMLImporterTest.java:83)
        at org.neuroml.importer.test.SBMLImporterTest.testIzhikevich(SBMLImporterTest.java:40)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:568)
        at junit.framework.TestCase.runTest(TestCase.java:177)
        at junit.framework.TestCase.runBare(TestCase.java:142)
        at junit.framework.TestResult$1.protect(TestResult.java:122)
        at junit.framework.TestResult.runProtected(TestResult.java:142)
        at junit.framework.TestResult.run(TestResult.java:125)
        at junit.framework.TestCase.run(TestCase.java:130)
        at junit.framework.TestSuite.runTest(TestSuite.java:241)
        at junit.framework.TestSuite.run(TestSuite.java:236)
        at org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:90)
        at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:316)
        at org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:240)
        at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:214)
        at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:155)
        at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
        at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
        at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
        at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: org.lemsml.jlems.core.sim.ContentError: Dimension mismatch in the equation: time = 1. Residual dimension: ExprDimensional[t=1]
Dimension of time: Dimension[none dimensionless], multiplier=Dimension[per_time t=-1], left=Dimension[ t=-1], rhs=ExprDimensional[dimensionless]
All:{vv=Dimension[none dimensionless], a=Dimension[none dimensionless], i_del=Dimension[none dimensionless], b=Dimension[none dimensionless], c=Dimension[none dimensionless], tscale=Dimension[per_time t=-1], d=Dimension[none dimensionless], i=Dimension[none dimensionless], Vthresh=Dimension[none dimensionless], cell=Dimension[none dimensionless], t=ExprDimensional[t=1], U=Dimension[none dimensionless], i_amp=Dimension[none dimensionless], time=Dimension[none dimensionless]}
        at org.lemsml.jlems.core.type.dynamics.AbstractStateChange.checkDimensions(AbstractStateChange.java:98)
        at org.lemsml.jlems.core.type.dynamics.Dynamics.checkEquations(Dynamics.java:578)
        at org.lemsml.jlems.core.type.ComponentType.checkEquations(ComponentType.java:682)
        at org.lemsml.jlems.core.type.Lems.resolve(Lems.java:173)
        ... 23 more

[INFO]
[INFO] Results:
[INFO]
[ERROR] Errors:
[ERROR]   SBMLImporterTest.testIzhikevich:40->convertSBMLtoLEMSFile:83 » Parse Error checking equations of ComponentType: ComponentType, name=Izhikevicha (none)
b (none)
c (none)
d (none)
Vthresh (none)
i_amp (none)
i_del (none)
tscale (per_time)  = 1per_s
cell (none)  = 1.0

(Dimension mismatch in the equation: time = 1. Residual dimension: ExprDimensional[t=1]
Dimension of time: Dimension[none dimensionless], multiplier=Dimension[per_time t=-1], left=Dimension[ t=-1], rhs=ExprDimensional[dimensionless]
All:{vv=Dimension[none dimensionless], a=Dimension[none dimensionless], i_del=Dimension[none dimensionless], b=Dimension[none dimensionless], c=Dimension[none dimensionless], tscale=Dimension[per_time t=-1], d=Dimension[none dimensionless], i=Dimension[none dimensionless], Vthresh=Dimension[none dimensionless], cell=Dimension[none dimensionless], t=ExprDimensional[t=1], U=Dimension[none dimensionless], i_amp=Dimension[none dimensionless], time=Dimension[none dimensionless]})
[INFO]
[ERROR] Tests run: 8, Failures: 0, Errors: 1, Skipped: 0
 

Still debugging to see what's causing it.

Edit: added complete traceback

[sanjayankur31]

Here's the LEMS file that is generated that it doesn't like:

Izhikevich_LEMS.xml.txt

[sanjayankur31]

This is the dynamics block:

        <Dynamics simultaneous="false">
            <StateVariable name="i" dimension="none" exposure="i"/>
            <StateVariable name="vv" dimension="none" exposure="vv"/>
            <StateVariable name="U" dimension="none" exposure="U"/>
            <StateVariable name="time" dimension="none"/>
            <TimeDerivative variable="i" value="tscale * 0"/>
            <TimeDerivative variable="vv" value="tscale * ((((((0.04 * (vv ^ 2.0)) + (5.0 * vv)) + 140.0) - U) + i))"/>
            <TimeDerivative variable="U" value="tscale * ((a * ((b * vv) - U)))"/>
            <TimeDerivative variable="time" value="1"/>
            <OnStart>
                <StateAssignment variable="i" value="0.0"/>
                <StateAssignment variable="vv" value="-70.0"/>
                <StateAssignment variable="U" value="-14.0"/>
            </OnStart>
            <OnCondition test="vv .gt. Vthresh">
                <StateAssignment variable="vv" value="c"/>
                <StateAssignment variable="U" value="(U + d)"/>
            </OnCondition>
            <OnCondition test="(t * tscale)  .gt. i_del">
                <StateAssignment variable="i" value="i_amp"/>
            </OnCondition>
        </Dynamics>
        <Constant name="tscale" value="1per_s" dimension="per_time"/>
        <Constant name="cell" value="1.0" dimension="none"/>

the error is pointing to this line:

            <TimeDerivative variable="time" value="1"/>

I think the RHS needs to be value = "tscale * 1" perhaps?

[pgleeson]

@sanjayankur31 Yes, probably that's the issue. Note the age of those files though, they predate the sbml showcase and probably izh in nml2... If it's a quick fix then fix it, otherwise they're not needed...

[sanjayankur31]

Cool, wasn't too hard to figure out luckily, opened a one line PR here: NeuroML/org.neuroml.import#24