Running synthea via .jar release with config "physiology.state.enabled=true" throws java.io.FileNotFoundException

[Lauri Methuen]

What happened?

Downloading synthea-with-dependencies.jar and running java -jar ./synthea-with-dependencies.jar --physiology.state.enabled true throws java.io.FileNotFoundException: /physiology/models/circulation/McSharry2003_Synthetic_ECG.xml

Cloning the repository and running ./run_synthea --physiology.state.enabled=true works.

Environment

- OS: macOS 13.3.1
- Java: openjdk 17.0.7

Relevant log output

Loading module modules/epilepsy.json
Loading module modules/female_reproduction.json
Loading module modules/fibromyalgia.json
Loading module modules/food_allergies.json
Loading module modules/gallstones.json
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
java.lang.RuntimeException: java.io.FileNotFoundException: /physiology/models/circulation/McSharry2003_Synthetic_ECG.xml (No such file or directory)
        at org.mitre.synthea.engine.PhysiologySimulator.<init>(PhysiologySimulator.java:202)
        at org.mitre.synthea.engine.State$Physiology.setup(State.java:350)
        at org.mitre.synthea.engine.State$Physiology.initialize(State.java:345)
        at org.mitre.synthea.engine.State.build(State.java:123)
        at org.mitre.synthea.engine.Module.<init>(Module.java:327)
        at org.mitre.synthea.engine.Module.loadFile(Module.java:218)
        at org.mitre.synthea.engine.Module.lambda$walkModuleTree$0(Module.java:141)
        at org.mitre.synthea.engine.Module$ModuleSupplier.get(Module.java:507)
        at org.mitre.synthea.engine.Module.lambda$getModules$4(Module.java:261)
        at java.base/java.util.TreeMap.forEach(TreeMap.java:1282)
        at org.mitre.synthea.engine.Module.getModules(Module.java:257)
        at org.mitre.synthea.engine.Generator.init(Generator.java:276)
        at org.mitre.synthea.engine.Generator.<init>(Generator.java:211)
        at org.mitre.synthea.engine.Generator.<init>(Generator.java:187)
        at App.main(App.java:233)
Caused by: java.io.FileNotFoundException: /physiology/models/circulation/McSharry2003_Synthetic_ECG.xml (No such file or directory)
        at java.base/java.io.FileInputStream.open0(Native Method)
        at java.base/java.io.FileInputStream.open(FileInputStream.java:216)
        at java.base/java.io.FileInputStream.<init>(FileInputStream.java:157)
        at org.sbml.jsbml.xml.stax.SBMLReader.readSBML(SBMLReader.java:302)
        at org.sbml.jsbml.xml.stax.SBMLReader.readSBML(SBMLReader.java:288)
        at org.mitre.synthea.engine.PhysiologySimulator.<init>(PhysiologySimulator.java:200)
        ... 14 more
Exception in thread "main" java.lang.RuntimeException: java.lang.RuntimeException: java.io.FileNotFoundException: /physiology/models/circulation/McSharry2003_Synthetic_ECG.xml (No such file or directory)
        at org.mitre.synthea.engine.Module$ModuleSupplier.get(Module.java:517)
        at org.mitre.synthea.engine.Module.lambda$getModules$4(Module.java:261)
        at java.base/java.util.TreeMap.forEach(TreeMap.java:1282)
        at org.mitre.synthea.engine.Module.getModules(Module.java:257)
        at org.mitre.synthea.engine.Generator.init(Generator.java:276)
        at org.mitre.synthea.engine.Generator.<init>(Generator.java:211)
        at org.mitre.synthea.engine.Generator.<init>(Generator.java:187)
        at App.main(App.java:233)
Caused by: java.lang.RuntimeException: java.io.FileNotFoundException: /physiology/models/circulation/McSharry2003_Synthetic_ECG.xml (No such file or directory)
        at org.mitre.synthea.engine.PhysiologySimulator.<init>(PhysiologySimulator.java:202)
        at org.mitre.synthea.engine.State$Physiology.setup(State.java:350)
        at org.mitre.synthea.engine.State$Physiology.initialize(State.java:345)
        at org.mitre.synthea.engine.State.build(State.java:123)
        at org.mitre.synthea.engine.Module.<init>(Module.java:327)
        at org.mitre.synthea.engine.Module.loadFile(Module.java:218)
        at org.mitre.synthea.engine.Module.lambda$walkModuleTree$0(Module.java:141)
        at org.mitre.synthea.engine.Module$ModuleSupplier.get(Module.java:507)
        ... 7 more
Caused by: java.io.FileNotFoundException: /physiology/models/circulation/McSharry2003_Synthetic_ECG.xml (No such file or directory)
        at java.base/java.io.FileInputStream.open0(Native Method)
        at java.base/java.io.FileInputStream.open(FileInputStream.java:216)
        at java.base/java.io.FileInputStream.<init>(FileInputStream.java:157)
        at org.sbml.jsbml.xml.stax.SBMLReader.readSBML(SBMLReader.java:302)
        at org.sbml.jsbml.xml.stax.SBMLReader.readSBML(SBMLReader.java:288)
        at org.mitre.synthea.engine.PhysiologySimulator.<init>(PhysiologySimulator.java:200)
        ... 14 more