Class jalview.ws2.client.slivka.SlivkaWSDiscovererTest

all > jalview.ws2.client.slivka > SlivkaWSDiscovererTest

tests

failures

ignored

0.418s

duration

100%

successful

Tests
Standard error

Test	Duration	Result
getStatusForUrl_exceptionThrown_statusIsInvalid	0.002s	passed
getStatusForUrl_noServicesReturned_statusIsNoServices	0.001s	passed
getStatusForUrl_servicesReturned_statusIsOK	0.023s	passed
testFetchService_clustalFamilyService_containsTwoActions[0](uk.ac.dundee.compbio.slivkaclient.SlivkaService@5e9d8b7c)	0.004s	passed
testFetchService_clustalFamilyService_containsTwoActions[1](uk.ac.dundee.compbio.slivkaclient.SlivkaService@5f28f1e1)	0.001s	passed
testFetchService_clustalFamilyService_containsTwoActions[2](uk.ac.dundee.compbio.slivkaclient.SlivkaService@333a33eb)	0.001s	passed
testFetchServices_RNASecStrPredClassifier_serviceTypeIsRNASecStrPred[0](uk.ac.dundee.compbio.slivkaclient.SlivkaService@20126399)	0.001s	passed
testFetchServices_RNASecStrPredClassifier_serviceTypeIsRNASecStrPred[10](uk.ac.dundee.compbio.slivkaclient.SlivkaService@74999cb9)	0s	passed
testFetchServices_RNASecStrPredClassifier_serviceTypeIsRNASecStrPred[11](uk.ac.dundee.compbio.slivkaclient.SlivkaService@4c44598b)	0s	passed
testFetchServices_RNASecStrPredClassifier_serviceTypeIsRNASecStrPred[1](uk.ac.dundee.compbio.slivkaclient.SlivkaService@1bb03b9b)	0.001s	passed
testFetchServices_RNASecStrPredClassifier_serviceTypeIsRNASecStrPred[2](uk.ac.dundee.compbio.slivkaclient.SlivkaService@39251a8)	0.001s	passed
testFetchServices_RNASecStrPredClassifier_serviceTypeIsRNASecStrPred[3](uk.ac.dundee.compbio.slivkaclient.SlivkaService@3a07caf2)	0.001s	passed
testFetchServices_RNASecStrPredClassifier_serviceTypeIsRNASecStrPred[4](uk.ac.dundee.compbio.slivkaclient.SlivkaService@207a20dc)	0.001s	passed
testFetchServices_RNASecStrPredClassifier_serviceTypeIsRNASecStrPred[5](uk.ac.dundee.compbio.slivkaclient.SlivkaService@6d19eefa)	0.001s	passed
testFetchServices_RNASecStrPredClassifier_serviceTypeIsRNASecStrPred[6](uk.ac.dundee.compbio.slivkaclient.SlivkaService@59d56747)	0s	passed
testFetchServices_RNASecStrPredClassifier_serviceTypeIsRNASecStrPred[7](uk.ac.dundee.compbio.slivkaclient.SlivkaService@6bc1a32c)	0s	passed
testFetchServices_RNASecStrPredClassifier_serviceTypeIsRNASecStrPred[8](uk.ac.dundee.compbio.slivkaclient.SlivkaService@2384644a)	0s	passed
testFetchServices_RNASecStrPredClassifier_serviceTypeIsRNASecStrPred[9](uk.ac.dundee.compbio.slivkaclient.SlivkaService@11b96f5e)	0s	passed
testFetchServices_conservationAnalysisClassifier_serviceTypeIsConservation[0](Operation :: Analysis :: Sequence alignment analysis (conservation))	0.001s	passed
testFetchServices_conservationAnalysisClassifier_serviceTypeIsConservation[1](Operation::Analysis::Sequence alignment analysis (conservation))	0.001s	passed
testFetchServices_conservationAnalysisClassifier_serviceTypeIsConservation[2](Operation :: Analysis :: Sequence alignment analysis (conservation))	0.001s	passed
testFetchServices_conservationAnalysisClassifier_serviceTypeIsConservation[3](Operation :: Analysis :: Sequence analysis :: Sequence alignment analysis (conservation))	0s	passed
testFetchServices_conservationAnalysisClassifier_serviceTypeIsConservation[4](Operation :: Analysis :: Sequence analysis :: Sequence alignment analysis :: Sequence alignment analysis (conservation))	0s	passed
testFetchServices_multipleSequenceAlignmentClassifier_serviceTypeIsMSA[0](Operation :: Analysis :: Multiple sequence alignment)	0.001s	passed
testFetchServices_multipleSequenceAlignmentClassifier_serviceTypeIsMSA[10](Operation :: Comparison :: Multiple sequence alignment)	0.001s	passed
testFetchServices_multipleSequenceAlignmentClassifier_serviceTypeIsMSA[11](Operation :: Comparison :: Sequence comparison :: Sequence alignment :: Multiple sequence alignment)	0.001s	passed
testFetchServices_multipleSequenceAlignmentClassifier_serviceTypeIsMSA[1](operation :: analysis :: multiple sequence alignment)	0.001s	passed
testFetchServices_multipleSequenceAlignmentClassifier_serviceTypeIsMSA[2](Operation :: Analysis :: Multiple sequence alignment)	0.001s	passed
testFetchServices_multipleSequenceAlignmentClassifier_serviceTypeIsMSA[3](Operation::Analysis::Multiple sequence alignment)	0s	passed
testFetchServices_multipleSequenceAlignmentClassifier_serviceTypeIsMSA[4](Operation :: Analysis :: Multiple Sequence Alignment)	0s	passed
testFetchServices_multipleSequenceAlignmentClassifier_serviceTypeIsMSA[5](OPERATION :: ANALYSIS :: MULTIPLE SEQUENCE ALIGNMENT)	0s	passed
testFetchServices_multipleSequenceAlignmentClassifier_serviceTypeIsMSA[6](Operation :: Analysis :: Sequence alignment :: Multiple sequence alignment)	0s	passed
testFetchServices_multipleSequenceAlignmentClassifier_serviceTypeIsMSA[7](Operation :: Analysis :: Sequence analysis :: Sequence alignment :: Multiple sequence alignment)	0s	passed
testFetchServices_multipleSequenceAlignmentClassifier_serviceTypeIsMSA[8](Operation :: Alignment :: Multiple sequence alignment)	0s	passed
testFetchServices_multipleSequenceAlignmentClassifier_serviceTypeIsMSA[9](Operation :: Alignment :: Sequence alignment :: Multiple sequence alignment)	0.001s	passed
testFetchServices_multipleSequenceAlignmentService_actionTypeIsAlignment[0](uk.ac.dundee.compbio.slivkaclient.SlivkaService@35728aed)	0.001s	passed
testFetchServices_multipleSequenceAlignmentService_actionTypeIsAlignment[1](uk.ac.dundee.compbio.slivkaclient.SlivkaService@5e3ea926)	0s	passed
testFetchServices_multipleSequenceAlignmentService_actionTypeIsAlignment[2](uk.ac.dundee.compbio.slivkaclient.SlivkaService@13c47e34)	0.001s	passed
testFetchServices_multipleSequenceAlignmentService_serviceIsNonInteractive[0](uk.ac.dundee.compbio.slivkaclient.SlivkaService@4f94f80d)	0.001s	passed
testFetchServices_multipleSequenceAlignmentService_serviceIsNonInteractive[1](uk.ac.dundee.compbio.slivkaclient.SlivkaService@75e500b9)	0s	passed
testFetchServices_multipleSequenceAlignmentService_serviceIsNonInteractive[2](uk.ac.dundee.compbio.slivkaclient.SlivkaService@46103782)	0s	passed
testFetchServices_oneService_basicDataMatches	0.190s	passed
testFetchServices_proteinSequenceAnalysisClassifier_serviceTypeIsProtSeqAnalysis[0](Operation :: Analysis :: Sequence analysis :: Protein sequence analysis)	0.002s	passed
testFetchServices_unrecognisedService_noServiceDiscovered[0](uk.ac.dundee.compbio.slivkaclient.SlivkaService@3d5a723d)	0.001s	passed
testGetUrls_noPropEntry_defaultUrlReturned	0.001s	passed
testGetUrls_urlsProperlyParsed[0](http://example.org/, [http://example.org/])	0.001s	passed
testGetUrls_urlsProperlyParsed[1](https://example.org/slivka/, [https://example.org/slivka/])	0.001s	passed
testGetUrls_urlsProperlyParsed[2](https://www.compbio.dundee.ac.uk/,http://www.example.org/, [https://www.compbio.dundee.ac.uk/, http://www.example.org/])	0.152s	passed
testGetUrls_urlsProperlyParsed[3](http://example.org/,, [http://example.org/])	0s	passed
testGetUrls_urlsProperlyParsed[4](,http://example.org, [http://example.org])	0s	passed
testGetUrls_urlsProperlyParsed[5](, [])	0s	passed
testGetUrls_urlsProperlyParsed[6](,, [])	0s	passed
testGetUrls_urlsProperlyParsed[7](example.org, [])	0s	passed
testGetUrls_urlsProperlyParsed[8](example.org,http://example.org, [http://example.org])	0s	passed
testServiceParameter_slivkaParameterMappedToJalviewParameter[0](uk.ac.dundee.compbio.slivkaclient.Parameter$IntegerParameter@51db881d, class jalview.ws.params.simple.IntegerParameter)	0.002s	passed
testServiceParameter_slivkaParameterMappedToJalviewParameter[1](uk.ac.dundee.compbio.slivkaclient.Parameter$DecimalParameter@4566050d, class jalview.ws.params.simple.DoubleParameter)	0.001s	passed
testServiceParameter_slivkaParameterMappedToJalviewParameter[2](uk.ac.dundee.compbio.slivkaclient.Parameter$TextParameter@56bb08f6, class jalview.ws.params.simple.StringParameter)	0.001s	passed
testServiceParameter_slivkaParameterMappedToJalviewParameter[3](uk.ac.dundee.compbio.slivkaclient.Parameter$FlagParameter@6fb2924b, class jalview.ws.params.simple.BooleanOption)	0.001s	passed
testServiceParameter_slivkaParameterMappedToJalviewParameter[4](uk.ac.dundee.compbio.slivkaclient.Parameter$ChoiceParameter@443f9a14, class jalview.ws.params.simple.StringParameter)	0s	passed
testServiceParameters_testBasicParameterProperties[0](uk.ac.dundee.compbio.slivkaclient.Parameter$IntegerParameter@5c559902, (hasProperty("name", "param1") and hasProperty("label", "Parameter 1") and hasProperty("description", "Description of parameter 1") and hasProperty("required", is <true>) and hasProperty("value", null)))	0.006s	passed
testServiceParameters_testBasicParameterProperties[1](uk.ac.dundee.compbio.slivkaclient.Parameter$IntegerParameter@58465241, (hasProperty("name", "param2") and hasProperty("label", "param2") and hasProperty("description", null) and hasProperty("required", is <true>) and hasProperty("value", null)))	0s	passed
testServiceParameters_testBasicParameterProperties[2](uk.ac.dundee.compbio.slivkaclient.Parameter$IntegerParameter@59a5a9c, (hasProperty("name", "param3") and hasProperty("label", "Parameter 3") and hasProperty("description", "") and hasProperty("required", is <false>) and hasProperty("value", "12")))	0.001s	passed
testServiceParameters_testIntegerProperties[0](uk.ac.dundee.compbio.slivkaclient.Parameter$IntegerParameter@24553e1b, hasProperty("validValue", hasProperty("type", is <Integer>)))	0.002s	passed
testServiceParameters_testIntegerProperties[1](uk.ac.dundee.compbio.slivkaclient.Parameter$IntegerParameter@4a79218e, hasProperty("validValue", (hasProperty("min", null) and hasProperty("max", null))))	0.001s	passed
testServiceParameters_testIntegerProperties[2](uk.ac.dundee.compbio.slivkaclient.Parameter$IntegerParameter@31424101, hasProperty("validValue", (hasProperty("min", is <-12>) and hasProperty("max", is <42>))))	0.001s	passed
testSetUrls_emptyList_propertyReset	0.001s	passed
testSetUrls_null_propertyReset	0.001s	passed
testSetUrls_urlsPropertySet[0]([http://example.org], http://example.org)	0.001s	passed
testSetUrls_urlsPropertySet[1]([http://example.org/], http://example.org/)	0.001s	passed
testSetUrls_urlsPropertySet[2]([http://example.org/slivka/], http://example.org/slivka/)	0s	passed
testSetUrls_urlsPropertySet[3]([https://www.compbio.dundee.ac.uk/slivka/, http://example.org], https://www.compbio.dundee.ac.uk/slivka/,http://example.org)	0s	passed

ERROR - slivka could not retrieve services from http://example.org
java.io.IOException: null
	at jalview.ws2.client.slivka.SlivkaWSDiscoverer.getStatusForUrl(SlivkaWSDiscoverer.java:66) ~[clover-classes/:?]
	at jalview.ws2.client.slivka.SlivkaWSDiscovererTest.__CLR4_4_1sqlabt40ue(SlivkaWSDiscovererTest.java:91) ~[clover-test-classes/:?]
	at jalview.ws2.client.slivka.SlivkaWSDiscovererTest.getStatusForUrl_exceptionThrown_statusIsInvalid(SlivkaWSDiscovererTest.java:86) ~[clover-test-classes/:?]
	at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]
	at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?]
	at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
	at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139) ~[testng-7.7.0.jar:7.7.0]
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677) ~[testng-7.7.0.jar:7.7.0]
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221) ~[testng-7.7.0.jar:7.7.0]
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50) ~[testng-7.7.0.jar:7.7.0]
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969) ~[testng-7.7.0.jar:7.7.0]
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194) ~[testng-7.7.0.jar:7.7.0]
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148) ~[testng-7.7.0.jar:7.7.0]
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128) ~[testng-7.7.0.jar:7.7.0]
	at java.util.ArrayList.forEach(ArrayList.java:1541) [?:?]
	at org.testng.TestRunner.privateRun(TestRunner.java:829) [testng-7.7.0.jar:7.7.0]
	at org.testng.TestRunner.run(TestRunner.java:602) [testng-7.7.0.jar:7.7.0]
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437) [testng-7.7.0.jar:7.7.0]
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431) [testng-7.7.0.jar:7.7.0]
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391) [testng-7.7.0.jar:7.7.0]
	at org.testng.SuiteRunner.run(SuiteRunner.java:330) [testng-7.7.0.jar:7.7.0]
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) [testng-7.7.0.jar:7.7.0]
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95) [testng-7.7.0.jar:7.7.0]
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256) [testng-7.7.0.jar:7.7.0]
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176) [testng-7.7.0.jar:7.7.0]
	at org.testng.TestNG.runSuites(TestNG.java:1099) [testng-7.7.0.jar:7.7.0]
	at org.testng.TestNG.run(TestNG.java:1067) [testng-7.7.0.jar:7.7.0]
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:141) [gradle-testing-jvm-7.4.2.jar:7.4.2]
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:90) [gradle-testing-jvm-7.4.2.jar:7.4.2]
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) [gradle-testing-base-7.4.2.jar:7.4.2]
	at jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]
	at jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?]
	at jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
	at java.lang.reflect.Method.invoke(Method.java:566) ~[?:?]
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36) [gradle-messaging-7.4.2.jar:7.4.2]
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) [gradle-messaging-7.4.2.jar:7.4.2]
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33) [gradle-messaging-7.4.2.jar:7.4.2]
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94) [gradle-messaging-7.4.2.jar:7.4.2]
	at com.sun.proxy.$Proxy2.stop(Unknown Source) [?:?]
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:193) [gradle-testing-base-7.4.2.jar:7.4.2]
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:129) [gradle-testing-base-7.4.2.jar:7.4.2]
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:100) [gradle-testing-base-7.4.2.jar:7.4.2]
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:60) [gradle-testing-base-7.4.2.jar:7.4.2]
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56) [gradle-worker-processes-7.4.2.jar:7.4.2]
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:133) [gradle-worker-processes-7.4.2.jar:7.4.2]
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:71) [gradle-worker-processes-7.4.2.jar:7.4.2]
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69) [gradle-worker.jar:?]
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74) [gradle-worker.jar:?]
WARN - Problem whilst trying to make a URL from ''. This was probably due to malformed comma-separated-list in the SLIVKAHOSTURLS entry of ${HOME}/.jalview-properties
WARN - Problem whilst trying to make a URL from ''. This was probably due to malformed comma-separated-list in the SLIVKAHOSTURLS entry of ${HOME}/.jalview-properties
WARN - Problem whilst trying to make a URL from 'example.org'. This was probably due to malformed comma-separated-list in the SLIVKAHOSTURLS entry of ${HOME}/.jalview-properties
WARN - Problem whilst trying to make a URL from 'example.org'. This was probably due to malformed comma-separated-list in the SLIVKAHOSTURLS entry of ${HOME}/.jalview-properties