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CIDARLAB / Cello-v2

Cello v2 is the continuation of the Cello genetic circuit design software.
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Fix Broken Tests #46

Open georgemjohnson11 opened 2 years ago

georgemjohnson11 commented 2 years ago

Upon running mvn clean package I get the following tests as failures and have to use the flag -DskipTests to skip tests. 

 org.cellocad.v2.common.file.dot.utils.DotUtilsTest
  org.cellocad.v2.common.target.data.data.LookupTableFunctionTest
  org.cellocad.v2.common.target.data.data.UnivariateLookupTableFunctionTest
  org.cellocad.v2.common.target.data.TargetDataTest
  org.cellocad.v2.common.target.data.TargetDataInstanceTest

 T E S T S
-------------------------------------------------------
Running org.cellocad.v2.common.file.dot.utils.DotUtilsTest
java.io.IOException: Cannot run program "dot": error=2, No such file or directory
        at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)
        at java.lang.Runtime.exec(Runtime.java:620)
        at java.lang.Runtime.exec(Runtime.java:485)
        at org.cellocad.v2.common.ExecCommand.<init>(ExecCommand.java:146)
        at org.cellocad.v2.common.Utils.executeAndWaitForCommand(Utils.java:288)
        at org.cellocad.v2.common.file.dot.utils.DotUtils.dot2any(DotUtils.java:56)
        at org.cellocad.v2.common.file.dot.utils.DotUtils.dot2pdf(DotUtils.java:73)
        at org.cellocad.v2.common.file.dot.utils.DotUtilsTest.test(DotUtilsTest.java:48)
        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:45)
        at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
        at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:42)
        at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20)
        at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:263)
        at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:68)
        at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:47)
        at org.junit.runners.ParentRunner$3.run(ParentRunner.java:231)
        at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:60)
        at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:229)
        at org.junit.runners.ParentRunner.access$000(ParentRunner.java:50)
        at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:222)
        at org.junit.runners.ParentRunner.run(ParentRunner.java:300)
        at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
        at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
        at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
        at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:165)
        at org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:85)
        at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:115)
        at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:75)
Caused by: java.io.IOException: error=2, No such file or directory
        at java.lang.UNIXProcess.forkAndExec(Native Method)
        at java.lang.UNIXProcess.<init>(UNIXProcess.java:247)
        at java.lang.ProcessImpl.start(ProcessImpl.java:134)
        at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)
        ... 36 more
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.411 sec <<< FAILURE!
test(org.cellocad.v2.common.file.dot.utils.DotUtilsTest)  Time elapsed: 0.372 sec  <<< ERROR!
java.lang.NullPointerException
        at org.cellocad.v2.common.ExecCommand.getError(ExecCommand.java:180)
        at org.cellocad.v2.common.file.dot.utils.DotUtils.dot2any(DotUtils.java:57)
        at org.cellocad.v2.common.file.dot.utils.DotUtils.dot2pdf(DotUtils.java:73)
        at org.cellocad.v2.common.file.dot.utils.DotUtilsTest.test(DotUtilsTest.java:48)
        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:45)
        at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
        at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:42)
        at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20)
        at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:263)
        at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:68)
        at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:47)
        at org.junit.runners.ParentRunner$3.run(ParentRunner.java:231)
        at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:60)
        at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:229)
        at org.junit.runners.ParentRunner.access$000(ParentRunner.java:50)
        at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:222)
        at org.junit.runners.ParentRunner.run(ParentRunner.java:300)
        at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
        at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
        at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
        at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:165)
        at org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:85)
        at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:115)
        at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:75)

Running org.cellocad.v2.common.target.data.data.CircuitRulesTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.442 sec
Running org.cellocad.v2.common.target.data.data.LookupTableFunctionTest
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.015 sec <<< FAILURE!
org.cellocad.v2.common.target.data.data.LookupTableFunctionTest  Time elapsed: 0.015 sec  <<< ERROR!
java.lang.NullPointerException
        at org.cellocad.v2.common.Utils.getResourceAsString(Utils.java:103)
        at org.cellocad.v2.common.target.data.data.LookupTableFunctionTest.init(LookupTableFunctionTest.java:63)
        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$1.runReflectiveCall(FrameworkMethod.java:45)
        at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
        at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:42)
        at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:27)
        at org.junit.runners.ParentRunner.run(ParentRunner.java:300)
        at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
        at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
        at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
        at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:165)
        at org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:85)
        at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:115)
        at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:75)

Running org.cellocad.v2.common.target.data.data.UnivariateLookupTableFunctionTest
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.002 sec <<< FAILURE!
org.cellocad.v2.common.target.data.data.UnivariateLookupTableFunctionTest  Time elapsed: 0.001 sec  <<< ERROR!
java.lang.NullPointerException
        at org.cellocad.v2.common.Utils.getResourceAsString(Utils.java:103)
        at org.cellocad.v2.common.target.data.data.UnivariateLookupTableFunctionTest.init(UnivariateLookupTableFunctionTest.java:63)
        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$1.runReflectiveCall(FrameworkMethod.java:45)
        at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
        at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:42)
        at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:27)
        at org.junit.runners.ParentRunner.run(ParentRunner.java:300)
        at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
        at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
        at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
        at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:165)
        at org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:85)
        at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:115)
        at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:75)