Failing export to svg from pdmap converted to sbml
I exported pdmap from https://pdmap.uni.lu/minerva/# to CD and then ran convert to SBML and exported to SVG (fails also with other graphical formats). Got the following exception
lcsb.mapviewer.converter.InvalidInputDataExecption: lcsb.mapviewer.common.exception.InvalidArgumentException: Line undefined for element sa10632 in reaction re5091__re5091_1163
at lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionParser.mergeLayout(SbmlReactionParser.java:208)
at lcsb.mapviewer.converter.model.sbml.SbmlParser.createModel(SbmlParser.java:99)
at lcsb.mapviewer.api.convert.ConvertRestImpl.converToImage(ConvertRestImpl.java:61)
at lcsb.mapviewer.api.convert.ConvertRestImpl.converToImage(ConvertRestImpl.java:75)
at lcsb.mapviewer.api.convert.ConvertRestImpl$$FastClassBySpringCGLIB$$c6591b50.invoke(<generated>)
at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:736)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:671)
at lcsb.mapviewer.api.convert.ConvertRestImpl$$EnhancerBySpringCGLIB$$b33cf2fc.converToImage(<generated>)
at lcsb.mapviewer.api.convert.ConvertRestImplTest.testCelDesigner2Sbml2SvgPD(ConvertRestImplTest.java:375)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:50)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:47)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.springframework.test.context.junit4.statements.RunBeforeTestMethodCallbacks.evaluate(RunBeforeTestMethodCallbacks.java:75)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
at org.springframework.test.context.junit4.statements.RunAfterTestMethodCallbacks.evaluate(RunAfterTestMethodCallbacks.java:86)
at org.springframework.test.context.junit4.statements.SpringRepeat.evaluate(SpringRepeat.java:84)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
at org.springframework.test.context.junit4.SpringJUnit4ClassRunner.runChild(SpringJUnit4ClassRunner.java:252)
at org.springframework.test.context.junit4.SpringJUnit4ClassRunner.runChild(SpringJUnit4ClassRunner.java:94)
at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
at org.springframework.test.context.junit4.statements.RunBeforeTestClassCallbacks.evaluate(RunBeforeTestClassCallbacks.java:61)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
at org.springframework.test.context.junit4.statements.RunAfterTestClassCallbacks.evaluate(RunAfterTestClassCallbacks.java:70)
at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
at org.springframework.test.context.junit4.SpringJUnit4ClassRunner.run(SpringJUnit4ClassRunner.java:191)
at org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:86)
at org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:538)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:760)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:460)
at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:206)
Caused by: lcsb.mapviewer.common.exception.InvalidArgumentException: Line undefined for element sa10632 in reaction re5091__re5091_1163
at lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionParser.mergeLayout(SbmlReactionParser.java:146)
... 46 more
I created a failing test for that in conversion-rest-api-scaling -> rest-api/src/test/java/lcsb/mapviewer/api/convert/ConvertRestImplTest.java -> testCelDesigner2Sbml2SvgPD. The test pdmap file is in the branch as well.