Errors are detected when running some SBMLTestSuite case.

[tyzerrr]

I'd love to use sbscl.v.2.1, so I wrote the wrapper class for SBMLTestSuite using org.testsuite.SBMLTestSuiteRunnerWrapper.
But in some SBMLTestSuite cases, the same error has been detected. Specifically, the case numbers are here.

Failed cases with same error: [00182 00184 00531 00532 00534 00535 00539 00540 00541 00542 00543 00545 00546 00549 00550 00551 00552 00553 00554 00555 00556 00557 00558 00559 00560 00561 00562 00563 00564 00565 00566 00567 00568 00569 00570 00571 00572 00573 00574 0057600613 00614 00615 00628 00629 00630 00658 00659 00660 00661 00662 00665 00666 00673 00674 00675 00687 00695 00696 00705 00760 00761 00762 00778 00779 00780 00876 00983 01054 01481 01502 01503 01539 01567 01793 01820 01821]

The error content is below.

java.lang.NullPointerException: Cannot invoke "java.util.Map.size()" because "m" is null
	at java.base/java.util.HashMap.putMapEntries(HashMap.java:495)
	at java.base/java.util.HashMap.putAll(HashMap.java:783)
	at org.sbml.jsbml.AbstractTreeNode.<init>(AbstractTreeNode.java:172)
	at org.sbml.jsbml.ASTNode.<init>(ASTNode.java:1639)
	at org.sbml.jsbml.ASTNode.clone(ASTNode.java:1914)
	at org.sbml.jsbml.ASTNode.<init>(ASTNode.java:1645)
	at org.sbml.jsbml.ASTNode.clone(ASTNode.java:1914)
	at org.simulator.sbml.AlgebraicRuleConverter.getAssignmentRules(AlgebraicRuleConverter.java:408)
	at org.simulator.sbml.EquationSystem.evaluateAlgebraicRules(EquationSystem.java:1216)
	at org.simulator.sbml.EquationSystem.init(EquationSystem.java:634)
	at org.simulator.sbml.SBMLinterpreter.init(SBMLinterpreter.java:442)
	at org.simulator.sbml.SBMLinterpreter.<init>(SBMLinterpreter.java:130)
	at org.testsuite.SBMLTestSuiteRunnerWrapper.runSBMLSimulation(SBMLTestSuiteRunnerWrapper.java:272)
	at org.testsuite.SBMLTestSuiteRunnerWrapper.main(SBMLTestSuiteRunnerWrapper.java:156)
	at main.CD5.Main.main(Unknown Source)

And also, I tried to use sbscl v.1.4, the error was not detected.
If the wrapper shell scripts which I wrote are necessary, I'll share you.
Any help, please.

[draeger]

@TlexCypher Thanks for raising and closing this issue. What solved the problem?

[tyzerrr]

Sorry, this problem is not solved, but this issues raised by jsbml. I'm going on solving this, so reopen this issue.

[draeger]

Thanks for this clarification. May I ask you to link the corresponding JSBML issue here? Thanks a lot!

[tyzerrr]

I wrote the error log in previous statement. But probably, JSBML' s previous version has not been revised that ASTNode Constructor.

SBSCL v.2.1 uses jsbml-v.1.6.1, but I think that in this version, ASTNode Constructor has been already revised.
I checked the release-log of jsbml then, probably, in jsbml-1.0-beta-1, the resource of Problem, ASTNode constructor was implemented. And SBSCL uses maven to get jsbml-1.6.1.
By my thinking, maven got jsbml-1.0-beta1, instead of jsbml-1.6.1. But I can't find out what is the resource of this problem.
I'll try to revise this! Thank you for great help!

[draeger]

Thanks! I created a new issue in JSBML, see sbmlteam/jsbml#258. What is needed is a new release of this library in Maven.

[tyzerrr]

I checked new issue of jsbml. I'm gonna try to make PR to new issue of jsbml! Thank you!

[tyzerrr]

@draeger This problem is raised only in case of using jsbml-1.6.1-newASTNode-with-dependencies.jar.
Maven is not related. Sorry for my miss understanding.
So, in conclusion, I changed jsbml jar file from jsbml-1.6.1-newASTNode-with-dependencies.jar to jsbml-1.6.1-with-dependencies.jar, this problem was not raised. So, this problem is detected only in case of using jsbml-1.6.1-newASTNode-with-dependencies.jar.

[tyzerrr]

Is it necessary to note this to sbmlteam/jsbml#258 ?

[dyrpsf]

Hi @draeger,

I’ve opened PR sbmlteam/jsbml#271 which fixes the NPE in AbstractTreeNode/ASTNode.

Locally, I built JSBML from that PR as a 1.7-SNAPSHOT and pointed SBSCL 2.1.1 to it.
With this setup, I was able to run at least these SBMLTestSuite semantic cases without the previous NPE:

• 00001
• 00981

So from SBSCL’s perspective, the issue appears resolved when using the fixed JSBML.
Once a new JSBML release containing this fix is available and SBSCL updates its dependency, this issue can probably be closed.