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sherlok on windows
Raw
sherlok.run.log
,---.| | |
`---.|---.,---.,---.| ,---.|__/
|| ||---'| | | || \
`---'` '`---'` `---'`---'` `
Sherlok Server v. 588d7f1db1
INFO Done loading from local File store (local_repo): 11 bundles, 25 engines, 14 pipelines [o.s.Controller 20:53:47]
== Spark has ignited ...
>> Listening on 0.0.0.0:9600
WARN Could not validate integrity of download from file:/C:/Users/Marco/.m2/repository/ch/epfl/bbp/nlp/bluima_opennlp/1.0.1/bluima_opennlp-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 20:55:47]
WARN Could not validate integrity of download from file:/C:/Users/Marco/.m2/repository/ch/epfl/bbp/nlp/bluima_utils/1.0.1/bluima_utils-1.0.1.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 20:55:55]
WARN Could not validate integrity of download from file:/C:/Users/Marco/.m2/repository/org/apache/xmlbeans/xmlbeans/2.5.0/xmlbeans-2.5.0.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 20:55:56]
WARN Could not validate integrity of download from file:/C:/Users/Marco/.m2/repository/com/googlecode/combinatoricslib/combinatoricslib/2.0/combinatoricslib-2.0.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 20:55:57]
WARN Could not validate integrity of download from file:/C:/Users/Marco/.m2/repository/net/sf/trove4j/trove4j/2.0.2/trove4j-2.0.2.jar: Checksum validation failed, no checksums available [o.e.a.i.i.WarnChecksumPolicy 20:55:57]
INFO could not TEST pipeline '{"name":"bluima.sentence","version":"1.0.1","description":"sentence splitter","domain":"bluima","script":["ENGINE SentenceAnnotator:1.0.1;"],"output":{},"tests":[{"input":"Switzerland is close to Italy, the land of pasta and Michelangelo. Paris is in France. And Madrid in Spain.","expected":{"Sentence":[{"begin":0,"end":66},{"begin":67,"end":86},{"begin":87,"end":107}]},"visible":false,"actual":{"Sentence":[{"begin":0,"end":66},{"begin":67,"end":86},{"begin":87,"end":107}]}}]}' null [o.s.SherlokServer 20:55:59]
org.sherlok.utils.ValidationException: null
at org.sherlok.PipelineLoader.load(PipelineLoader.java:171) ~[sherlok_core-0.1-SNAPSHOT.jar:na]
at org.sherlok.SherlokServer$3.handle(SherlokServer.java:157) ~[sherlok_core-0.1-SNAPSHOT.jar:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_79]
Raw
sherlok.test.log
[INFO] Scanning for projects...
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building Sherlok 0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ sherlok_core ---
[INFO]
[INFO] --- git-commit-id-plugin:2.1.13:revision (default) @ sherlok_core ---
[INFO]
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ sherlok_core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 3 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ sherlok_core ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ sherlok_core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 4 resources
[INFO]
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ sherlok_core ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ sherlok_core ---
[INFO] Surefire report directory: C:\Users\Marco\Desktop\sherlok\target\surefire-reports
-------------------------------------------------------
T E S T S
-------------------------------------------------------
Running org.sherlok.CheckThatTest
Tests run: 24, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.187 sec
Running org.sherlok.config.ConfigVariableManagerTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.094 sec
Running org.sherlok.config.GitConfigVariableTest
Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 24.343 sec
Running org.sherlok.config.HttpConfigVariableTest
Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 9.327 sec
Running org.sherlok.ControllerTest
INFO Done loading from local File store (local_repo): 11 bundles, 25 engines, 14 pipelines [o.s.Controller 20:31:28]
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec
Running org.sherlok.FileBasedTest
Tests run: 8, Failures: 3, Errors: 1, Skipped: 0, Time elapsed: 0.031 sec <<< FAILURE!
test01_GetInexistentFile(org.sherlok.FileBasedTest) Time elapsed: 0.016 sec <<< FAILURE!
java.lang.AssertionError: Expected exception: org.sherlok.utils.ValidationException
at org.junit.internal.runners.statements.ExpectException.evaluate(ExpectException.java:32)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
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$2.evaluate(ParentRunner.java:268)
at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
at org.apache.maven.surefire.booter.ProviderFactory$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)
test04_ListFile(org.sherlok.FileBasedTest) Time elapsed: 0 sec <<< FAILURE!
java.lang.AssertionError
at org.junit.Assert.fail(Assert.java:86)
at org.junit.Assert.assertTrue(Assert.java:41)
at org.junit.Assert.assertTrue(Assert.java:52)
at org.sherlok.FileBasedTest.test04_ListFile(FileBasedTest.java:108)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
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.runners.ParentRunner.runLeaf(ParentRunner.java:325)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
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$2.evaluate(ParentRunner.java:268)
at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
at org.apache.maven.surefire.booter.ProviderFactory$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)
test05_DeleteFile(org.sherlok.FileBasedTest) Time elapsed: 0 sec <<< ERROR!
{
"cause" : null,
"error_value" : "could not delete file 'test/testUploadFile.txt'"
}
at org.sherlok.utils.CheckThat.validateArgument(CheckThat.java:125)
at org.sherlok.FileBased.deleteResource(FileBased.java:353)
at org.sherlok.FileBasedTest.test05_DeleteFile(FileBasedTest.java:113)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
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.runners.ParentRunner.runLeaf(ParentRunner.java:325)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
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$2.evaluate(ParentRunner.java:268)
at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
at org.apache.maven.surefire.booter.ProviderFactory$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)
testReadNonexistentFile(org.sherlok.FileBasedTest) Time elapsed: 0.015 sec <<< FAILURE!
org.junit.ComparisonFailure: expected:<...19-8ff1-b9a8c46c7a1e[]> but was:<...19-8ff1-b9a8c46c7a1e[ (The system cannot find the file specified)]>
at org.junit.Assert.assertEquals(Assert.java:115)
at org.junit.Assert.assertEquals(Assert.java:144)
at org.sherlok.FileBasedTest.testReadNonexistentFile(FileBasedTest.java:126)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
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.runners.ParentRunner.runLeaf(ParentRunner.java:325)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
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$2.evaluate(ParentRunner.java:268)
at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
at org.apache.maven.surefire.booter.ProviderFactory$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.sherlok.integration.AnnotationApiIntegrationTest
,---.| | |
`---.|---.,---.,---.| ,---.|__/
|| ||---'| | | || \
`---'` '`---'` `---'`---'` `
Sherlok Server v. 588d7f1db1
INFO Done loading from local File store (local_repo): 11 bundles, 25 engines, 14 pipelines [o.s.Controller 20:31:29]
== Spark has ignited ...
>> Listening on 0.0.0.0:9605
DEBUG starting test test010_GETAnnotate(org.sherlok.integration.AnnotationApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:29]
WARN Request (GET /annotate/opennlp.ners.en?text=Jack%20Burton%20%28born%20April%2029%2C%201954%20in%20El%20Paso%29%2C%20also%20known%20as%20Jake%20Burton%2C%20is%20an%20American%20snowboarder%20and%20founder%20of%20Burton%20Snowboards.)@1348796900 org.eclipse.jetty.server.Request@506501e4 doesn't contain any value for param version [o.s.SherlokServer 20:31:32]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:43]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:43]
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 1584
Server: Jetty(9.0.2.v20130417)
{
"_context": {
"_types": {
"DocumentAnnotation": {
"_id": "uima.tcas.DocumentAnnotation",
"_feature_types": {
"sofa": "_ref"
}
},
"NamedEntity": {
"_id": "de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity",
"_feature_types": {
"sofa": "_ref"
}
},
"Sofa": {
"_id": "uima.cas.Sofa",
"_feature_types": {
"sofaArray": "_ref"
}
},
"Annotation": {
"_id": "uima.tcas.Annotation",
"_feature_types": {
"sofa": "_ref"
},
"_subtypes": [
"DocumentAnnotation",
"NamedEntity"
]
},
"AnnotationBase": {
"_id": "uima.cas.AnnotationBase",
"_feature_types": {
"sofa": "_ref"
},
"_subtypes": [
"Annotation"
]
},
"TOP": {
"_id": "uima.cas.TOP",
"_subtypes": [
"AnnotationBase",
"Sofa"
]
}
}
},
"_views": {
"_InitialView": {
"DocumentAnnotation": [
{
"sofa": 1,
"begin": 0,
"end": 133,
"language": "en"
}
],
"NamedEntity": [
{
"sofa": 1,
"begin": 0,
"end": 11,
"value": "person"
},
{
"sofa": 1,
"begin": 36,
"end": 43,
"value": "location"
},
{
"sofa": 1,
"begin": 60,
"end": 71,
"value": "person"
}
]
}
},
"_referenced_fss": {
"1": {
"_type": "Sofa",
"sofaNum": 1,
"sofaID": "_InitialView",
"mimeType": "text",
"sofaString": "Jack Burton (born April 29, 1954 in El Paso), also known as Jake Burton, is an American snowboarder and founder of Burton Snowboards."
}
},
"_stats": {
"_pipeline_resolution": 6531,
"_annotation": 4328
}
}
DEBUG starting test test011_POSTAnnotate(org.sherlok.integration.AnnotationApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:43]
WARN Request (POST /annotate/opennlp.ners.en)@518021570 org.eclipse.jetty.server.Request@1ee061c2 doesn't contain any value for param version [o.s.SherlokServer 20:31:44]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:44]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:44]
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 1579
Server: Jetty(9.0.2.v20130417)
{
"_context": {
"_types": {
"DocumentAnnotation": {
"_id": "uima.tcas.DocumentAnnotation",
"_feature_types": {
"sofa": "_ref"
}
},
"NamedEntity": {
"_id": "de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity",
"_feature_types": {
"sofa": "_ref"
}
},
"Sofa": {
"_id": "uima.cas.Sofa",
"_feature_types": {
"sofaArray": "_ref"
}
},
"Annotation": {
"_id": "uima.tcas.Annotation",
"_feature_types": {
"sofa": "_ref"
},
"_subtypes": [
"DocumentAnnotation",
"NamedEntity"
]
},
"AnnotationBase": {
"_id": "uima.cas.AnnotationBase",
"_feature_types": {
"sofa": "_ref"
},
"_subtypes": [
"Annotation"
]
},
"TOP": {
"_id": "uima.cas.TOP",
"_subtypes": [
"AnnotationBase",
"Sofa"
]
}
}
},
"_views": {
"_InitialView": {
"DocumentAnnotation": [
{
"sofa": 1,
"begin": 0,
"end": 133,
"language": "en"
}
],
"NamedEntity": [
{
"sofa": 1,
"begin": 0,
"end": 11,
"value": "person"
},
{
"sofa": 1,
"begin": 36,
"end": 43,
"value": "location"
},
{
"sofa": 1,
"begin": 60,
"end": 71,
"value": "person"
}
]
}
},
"_referenced_fss": {
"1": {
"_type": "Sofa",
"sofaNum": 1,
"sofaID": "_InitialView",
"mimeType": "text",
"sofaString": "Jack Burton (born April 29, 1954 in El Paso), also known as Jake Burton, is an American snowboarder and founder of Burton Snowboards."
}
},
"_stats": {
"_pipeline_resolution": 0,
"_annotation": 94
}
}
WARN Request (POST /annotate/opennlp.ners.en)@1975315281 org.eclipse.jetty.server.Request@75bceb51 doesn't contain any value for param version [o.s.SherlokServer 20:31:44]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:44]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:44]
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 1580
Server: Jetty(9.0.2.v20130417)
{
"_context": {
"_types": {
"DocumentAnnotation": {
"_id": "uima.tcas.DocumentAnnotation",
"_feature_types": {
"sofa": "_ref"
}
},
"NamedEntity": {
"_id": "de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity",
"_feature_types": {
"sofa": "_ref"
}
},
"Sofa": {
"_id": "uima.cas.Sofa",
"_feature_types": {
"sofaArray": "_ref"
}
},
"Annotation": {
"_id": "uima.tcas.Annotation",
"_feature_types": {
"sofa": "_ref"
},
"_subtypes": [
"DocumentAnnotation",
"NamedEntity"
]
},
"AnnotationBase": {
"_id": "uima.cas.AnnotationBase",
"_feature_types": {
"sofa": "_ref"
},
"_subtypes": [
"Annotation"
]
},
"TOP": {
"_id": "uima.cas.TOP",
"_subtypes": [
"AnnotationBase",
"Sofa"
]
}
}
},
"_views": {
"_InitialView": {
"DocumentAnnotation": [
{
"sofa": 1,
"begin": 0,
"end": 133,
"language": "en"
}
],
"NamedEntity": [
{
"sofa": 1,
"begin": 0,
"end": 11,
"value": "person"
},
{
"sofa": 1,
"begin": 36,
"end": 43,
"value": "location"
},
{
"sofa": 1,
"begin": 60,
"end": 71,
"value": "person"
}
]
}
},
"_referenced_fss": {
"1": {
"_type": "Sofa",
"sofaNum": 1,
"sofaID": "_InitialView",
"mimeType": "text",
"sofaString": "Jack Burton (born April 29, 1954 in El Paso), also known as Jake Burton, is an American snowboarder and founder of Burton Snowboards."
}
},
"_stats": {
"_pipeline_resolution": 0,
"_annotation": 109
}
}
DEBUG starting test test011_POSTBodyAnnotate(org.sherlok.integration.AnnotationApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:44]
WARN Request (POST /annotate/opennlp.ners.en)@2008045786 org.eclipse.jetty.server.Request@77b058da doesn't contain any value for param version [o.s.SherlokServer 20:31:44]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:44]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:44]
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 1580
Server: Jetty(9.0.2.v20130417)
{
"_context": {
"_types": {
"DocumentAnnotation": {
"_id": "uima.tcas.DocumentAnnotation",
"_feature_types": {
"sofa": "_ref"
}
},
"NamedEntity": {
"_id": "de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity",
"_feature_types": {
"sofa": "_ref"
}
},
"Sofa": {
"_id": "uima.cas.Sofa",
"_feature_types": {
"sofaArray": "_ref"
}
},
"Annotation": {
"_id": "uima.tcas.Annotation",
"_feature_types": {
"sofa": "_ref"
},
"_subtypes": [
"DocumentAnnotation",
"NamedEntity"
]
},
"AnnotationBase": {
"_id": "uima.cas.AnnotationBase",
"_feature_types": {
"sofa": "_ref"
},
"_subtypes": [
"Annotation"
]
},
"TOP": {
"_id": "uima.cas.TOP",
"_subtypes": [
"AnnotationBase",
"Sofa"
]
}
}
},
"_views": {
"_InitialView": {
"DocumentAnnotation": [
{
"sofa": 1,
"begin": 0,
"end": 133,
"language": "en"
}
],
"NamedEntity": [
{
"sofa": 1,
"begin": 0,
"end": 11,
"value": "person"
},
{
"sofa": 1,
"begin": 36,
"end": 43,
"value": "location"
},
{
"sofa": 1,
"begin": 60,
"end": 71,
"value": "person"
}
]
}
},
"_referenced_fss": {
"1": {
"_type": "Sofa",
"sofaNum": 1,
"sofaID": "_InitialView",
"mimeType": "text",
"sofaString": "Jack Burton (born April 29, 1954 in El Paso), also known as Jake Burton, is an American snowboarder and founder of Burton Snowboards."
}
},
"_stats": {
"_pipeline_resolution": 0,
"_annotation": 125
}
}
WARN Request (POST /annotate/opennlp.ners.en)@1872670430 org.eclipse.jetty.server.Request@6f9eaede doesn't contain any value for param version [o.s.SherlokServer 20:31:44]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:44]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:44]
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 1579
Server: Jetty(9.0.2.v20130417)
{
"_context": {
"_types": {
"DocumentAnnotation": {
"_id": "uima.tcas.DocumentAnnotation",
"_feature_types": {
"sofa": "_ref"
}
},
"NamedEntity": {
"_id": "de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity",
"_feature_types": {
"sofa": "_ref"
}
},
"Sofa": {
"_id": "uima.cas.Sofa",
"_feature_types": {
"sofaArray": "_ref"
}
},
"Annotation": {
"_id": "uima.tcas.Annotation",
"_feature_types": {
"sofa": "_ref"
},
"_subtypes": [
"DocumentAnnotation",
"NamedEntity"
]
},
"AnnotationBase": {
"_id": "uima.cas.AnnotationBase",
"_feature_types": {
"sofa": "_ref"
},
"_subtypes": [
"Annotation"
]
},
"TOP": {
"_id": "uima.cas.TOP",
"_subtypes": [
"AnnotationBase",
"Sofa"
]
}
}
},
"_views": {
"_InitialView": {
"DocumentAnnotation": [
{
"sofa": 1,
"begin": 0,
"end": 133,
"language": "en"
}
],
"NamedEntity": [
{
"sofa": 1,
"begin": 0,
"end": 11,
"value": "person"
},
{
"sofa": 1,
"begin": 36,
"end": 43,
"value": "location"
},
{
"sofa": 1,
"begin": 60,
"end": 71,
"value": "person"
}
]
}
},
"_referenced_fss": {
"1": {
"_type": "Sofa",
"sofaNum": 1,
"sofaID": "_InitialView",
"mimeType": "text",
"sofaString": "Jack Burton (born April 29, 1954 in El Paso), also known as Jake Burton, is an American snowboarder and founder of Burton Snowboards."
}
},
"_stats": {
"_pipeline_resolution": 0,
"_annotation": 63
}
}
DEBUG starting test test012WrongPipeline(org.sherlok.integration.AnnotationApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:44]
WARN Request (POST /annotate/blablabla)@1100882467 org.eclipse.jetty.server.Request@419e2223 doesn't contain any value for param version [o.s.SherlokServer 20:31:44]
INFO could not annotate text 'Jack Burton (born April 29, 1954 in El Paso), also known as Jake Burton, is an American snowboarder and founder of Burton Snowboards.' null [o.s.SherlokServer 20:31:44]
org.sherlok.utils.ValidationException: null
at org.sherlok.utils.CheckThat.validateNotNull(CheckThat.java:117) ~[classes/:na]
at org.sherlok.PipelineLoader.resolvePipeline(PipelineLoader.java:136) ~[classes/:na]
at org.sherlok.SherlokServer.annotateRequest(SherlokServer.java:497) ~[classes/:na]
at org.sherlok.SherlokServer$2.handle(SherlokServer.java:146) [classes/:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_79]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:44]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:44]
HTTP/1.1 400 Bad Request
Content-Type: application/json
Content-Length: 97
Server: Jetty(9.0.2.v20130417)
{
"message": "could not find Pipeline with Id 'blablabla:0000000000000000000000000000000'"
}
DEBUG starting test test020MissingText(org.sherlok.integration.AnnotationApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:44]
WARN Request (POST /annotate/opennlp.ners.en)@1797290277 org.eclipse.jetty.server.Request@6b207925 doesn't contain any value for param version [o.s.SherlokServer 20:31:44]
WARN Request (POST /annotate/opennlp.ners.en)@1797290277 org.eclipse.jetty.server.Request@6b207925 doesn't contain any value for param text [o.s.SherlokServer 20:31:44]
INFO could not annotate text 'null' null [o.s.SherlokServer 20:31:44]
org.sherlok.utils.ValidationException: null
at org.sherlok.utils.CheckThat.validateNotNull(CheckThat.java:117) ~[classes/:na]
at org.sherlok.SherlokServer.annotateRequest(SherlokServer.java:480) ~[classes/:na]
at org.sherlok.SherlokServer$2.handle(SherlokServer.java:146) [classes/:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_79]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:44]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:44]
HTTP/1.1 400 Bad Request
Content-Type: application/json
Content-Length: 61
Server: Jetty(9.0.2.v20130417)
{
"message": "'text' req parameter should not be null"
}
DEBUG starting test test021EmptyText(org.sherlok.integration.AnnotationApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:44]
WARN Request (POST /annotate/opennlp_en_ners)@1453603077 org.eclipse.jetty.server.Request@56a43905 doesn't contain any value for param version [o.s.SherlokServer 20:31:44]
INFO could not annotate text '' 'text' req parameter should not be empty [o.s.SherlokServer 20:31:44]
org.sherlok.utils.ValidationException: 'text' req parameter should not be empty
at org.sherlok.utils.CheckThat.validateArgument(CheckThat.java:125) ~[classes/:na]
at org.sherlok.SherlokServer.annotateRequest(SherlokServer.java:481) ~[classes/:na]
at org.sherlok.SherlokServer$2.handle(SherlokServer.java:146) [classes/:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_79]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:44]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:44]
HTTP/1.1 400 Bad Request
Content-Type: application/json
Content-Length: 85
Server: Jetty(9.0.2.v20130417)
{
"cause": null,
"error_value": "'text' req parameter should not be empty"
}
>>> Spark shutting down...done
Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 16.434 sec
Running org.sherlok.integration.BundleApiIntegrationTest
INFO Done loading from local File store (local_repo): 11 bundles, 25 engines, 14 pipelines [o.s.Controller 20:31:45]
== Spark has ignited ...
>> Listening on 0.0.0.0:9608
DEBUG starting test test010GetBundles(org.sherlok.integration.BundleApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:46]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:46]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:46]
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 11793
Server: Jetty(9.0.2.v20130417)
[
{
"name": "bluima.preprocessing",
"version": "1.0.1",
"domain": "bluima",
"dependencies": [
{
"value": "ch.epfl.bbp.nlp:bluima_opennlp:1.0.1"
}
],
"engines": [
{
"name": "ChunkAnnotator",
"class": "ch.epfl.bbp.uima.ae.ChunkAnnotator",
"description": "OpenNLP Chunker provides chunks to tokens in IOB format (e.g. B-NP, I-VP)",
"parameters": {
"posTagSetPreference": [
"de.julielab.jules.types.GeniaPOSTag"
],
"modelFile": [
"$bluima/$chunker/Chunker_Genia.bin.gz"
]
}
},
{
"name": "PosTagAnnotator",
"class": "ch.epfl.bbp.uima.ae.PosTagAnnotator",
"description": "OpenNLP Part Of Speech Tagger. This annotator assumes that sentences and tokens have been annotated first.",
"parameters": {
"tagDict": [
"$bluima/$postag/tagdict-genia"
],
"modelFile": [
"$bluima/$postag/Tagger_Genia.bin.gz"
],
"tagset": [
"de.julielab.jules.types.GeniaPOSTag"
],
"caseSensitive": [
"false"
],
"useTagdict": [
"true"
]
}
},
{
"name": "SentenceAnnotator",
"class": "ch.epfl.bbp.uima.ae.SentenceAnnotator",
"description": "Sentence splitter, based on OpenNLP's MaxEnt SentenceDetector, and trained on biomedical corpora (PennBio or Genia corpora).",
"parameters": {
"modelFile": [
"$bluima/opennlp/sentence/SentDetectGenia.bin.gz"
]
}
},
{
"name": "TokenAnnotator",
"class": "ch.epfl.bbp.uima.ae.TokenAnnotator",
"description": "OpenNLP Tokenizer. This engine assumes that sentences have been annotated first.",
"parameters": {
"modelFile": [
"$bluima/opennlp/token/TokenizerGenia.bin.gz"
]
}
}
],
"config": {
"bluima": {
"type": "git",
"url": "https://github.com/BlueBrain/bluima_resources.git",
"ref": "master"
},
"chunker": {
"value": "opennlp/chunker"
},
"postag": {
"type": "text",
"value": "opennlp/postag"
}
}
},
{
"name": "bluima.commons",
"version": "1.0.1",
"domain": "bluima",
"dependencies": [
{
"value": "ch.epfl.bbp.nlp:bluima_commons:1.0.1"
}
],
"engines": [
{
"name": "BlueBioLemmatizer",
"class": "ch.epfl.bbp.uima.ae.BlueBioLemmatizer"
},
{
"name": "LinnaeusAnnotator",
"class": "ch.epfl.bbp.uima.ae.LinnaeusAnnotator",
"parameters": {
"CONFIG_FILE": [
"$bluima/linnaeus/properties.conf"
]
}
}
],
"config": {
"bluima": {
"type": "git",
"url": "https://github.com/BlueBrain/bluima_resources.git",
"ref": "master"
}
}
},
{
"name": "dkpro.opennlp.en",
"version": "1.7.0",
"description": "all opennlp engines and models for English",
"domain": "dkpro",
"dependencies": [
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.stanfordnlp-gpl:1.7.0"
},
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.opennlp-asl:1.7.0"
},
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.opennlp-model-ner-en-person:20130624.1"
},
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.opennlp-model-ner-en-organization:20100907.0"
},
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.opennlp-model-ner-en-location:20100907.0"
}
],
"repositories": {
"dkpro": "http://zoidberg.ukp.informatik.tu-darmstadt.de/artifactory/public-model-releases-local/"
},
"engines": [
{
"name": "opennlp.ner.location.en",
"class": "de.tudarmstadt.ukp.dkpro.core.opennlp.OpenNlpNameFinder",
"parameters": {
"language": [
"en"
],
"modelVariant": [
"location"
]
}
},
{
"name": "opennlp.ner.person.en",
"class": "de.tudarmstadt.ukp.dkpro.core.opennlp.OpenNlpNameFinder",
"parameters": {
"language": [
"en"
],
"modelVariant": [
"person"
]
}
},
{
"name": "opennlp.pos.en",
"class": "de.tudarmstadt.ukp.dkpro.core.opennlp.OpenNlpPosTagger",
"parameters": {
"language": [
"en"
]
}
},
{
"name": "opennlp.segmenter.en",
"class": "de.tudarmstadt.ukp.dkpro.core.opennlp.OpenNlpSegmenter",
"parameters": {
"language": [
"en"
]
}
}
]
},
{
"name": "dkpro.berkeleyparser.en",
"version": "1.7.0",
"description": "Berkeleyparser sm6 English",
"domain": "dkpro",
"dependencies": [
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.berkeleyparser-gpl:1.7.0"
},
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.berkeleyparser-upstream-parser-en-sm6:20100819"
}
],
"repositories": {
"dkpro": "http://zoidberg.ukp.informatik.tu-darmstadt.de/artifactory/public-model-releases-local/"
},
"engines": [
{
"name": "berkeleyparser.en",
"class": "de.tudarmstadt.ukp.dkpro.core.berkeleyparser.BerkeleyParser",
"parameters": {
"language": [
"en"
],
"modelVariant": [
"sm6"
],
"writePennTree": [
"true"
]
}
}
]
},
{
"name": "dkpro.mallet",
"version": "1.7.0",
"domain": "dkpro",
"dependencies": [
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.mallet-asl:1.7.0"
}
],
"engines": [
{
"name": "MalletTopicModelEstimator",
"class": "de.tudarmstadt.ukp.dkpro.core.mallet.topicmodel.MalletTopicModelEstimator",
"parameters": {
"typeName": [
"de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token"
],
"nTopics": [
"10"
],
"nIterations": [
"1000"
],
"useLemma": [
"false"
],
"optimizeInterval": [
"50"
],
"displayNTopicWords": [
"7"
],
"targetLocation": [
"TODO"
],
"nThreads": [
"1"
]
}
},
{
"name": "MalletTopicModelInferencer",
"class": "de.tudarmstadt.ukp.dkpro.core.mallet.topicmodel.MalletTopicModelInferencer",
"parameters": {
"nIterations": [
"10"
],
"typeName": [
"de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token"
],
"thinning": [
"5"
],
"modelLocation": [
"TODO"
],
"useLemma": [
"false"
],
"burnIn": [
"1"
]
}
}
]
},
{
"name": "dkpro.stanford.preprocessing.en",
"version": "1.7.0",
"description": "TODO Stanford NLP preprocessing English",
"domain": "stanford",
"dependencies": [
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.stanfordnlp-model-parser-en-rnn:20140104"
}
],
"repositories": {
"dkpro": "http://zoidberg.ukp.informatik.tu-darmstadt.de/artifactory/public-model-releases-local/"
}
},
{
"name": "dkpro.stanfordparser.rnn.en",
"version": "1.7.0",
"description": "Stanford RNN parser English. TODO",
"domain": "dkpro",
"dependencies": [
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.stanfordnlp-model-parser-en-rnn:20140104"
}
],
"repositories": {
"dkpro": "http://zoidberg.ukp.informatik.tu-darmstadt.de/artifactory/public-model-releases-local/"
},
"engines": [
{
"name": "stanfordparser.rnn.en",
"class": "TODO",
"parameters": {
"language": [
"en"
],
"modelVariant": [
"linear"
]
}
}
]
},
{
"name": "dkpro.maltparser.en",
"version": "1.7.0",
"description": "all engines and models for Malt parser English",
"domain": "dkpro",
"dependencies": [
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.maltparser-asl:1.7.0"
},
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.maltparser-upstream-parser-en-linear:20120312"
}
],
"repositories": {
"dkpro": "http://zoidberg.ukp.informatik.tu-darmstadt.de/artifactory/public-model-releases-local/"
},
"engines": [
{
"name": "maltparser.en",
"class": "de.tudarmstadt.ukp.dkpro.core.maltparser.MaltParser",
"parameters": {
"language": [
"en"
],
"modelVariant": [
"linear"
]
}
}
]
},
{
"name": "sherlok.mallet",
"version": "0.1",
"dependencies": [
{
"value": "org.sherlok:sherlok_mallet:0.0.1-SNAPSHOT"
}
],
"engines": [
{
"name": "NaiveBayesClassifier",
"class": "org.sherlok.NaiveBayesClassifier.NaiveBayesClassifier",
"parameters": {
"annotationClass": [
"org.sherlok.types.Category"
],
"featureName": [
"categoryType"
]
}
}
]
},
{
"name": "dkpro.langdetect",
"version": "1.7.0",
"domain": "dkpro",
"dependencies": [
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.langdetect-asl:1.7.0"
},
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.langdetect-model-languageidentifier-any-wikipedia:20141013.1"
},
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.langdetect-model-languageidentifier-any-socialmedia:20141013.1"
}
],
"repositories": {
"dkpro": "http://zoidberg.ukp.informatik.tu-darmstadt.de/artifactory/public-model-releases-local/"
},
"engines": [
{
"name": "languageidentifier",
"class": "de.tudarmstadt.ukp.dkpro.core.langdetect.LangDetectLanguageIdentifier",
"parameters": {
"modelVariant": [
"wikipedia"
]
}
},
{
"name": "languageidentifier.socialmedia",
"class": "de.tudarmstadt.ukp.dkpro.core.langdetect.LangDetectLanguageIdentifier",
"parameters": {
"modelVariant": [
"socialmedia"
]
}
}
]
},
{
"name": "bluima_regions",
"version": "1.0.1",
"domain": "bluima",
"dependencies": [
{
"value": "ch.epfl.bbp.nlp:bluima_regions:1.0.1"
},
{
"value": "ch.epfl.bbp.nlp:bluima_utils:1.0.1"
},
{
"value": "ch.epfl.bbp.nlp:bluima_units:1.0.1"
},
{
"value": "ch.epfl.bbp.nlp:bluima_jsre:1.0.1"
}
],
"engines": [
{
"name": "BrainRegionAnnotator",
"class": "ch.epfl.bbp.uima.ae.BrainRegionAnnotator",
"parameters": {
"modelFile": [
"$bluima/regions/20131116_BrainRegion.model"
],
"mode": [
"infer"
]
}
},
{
"name": "MeasureRegexAnnotator",
"class": "ch.epfl.bbp.uima.ae.RegExAnnotator",
"parameters": {
"ConceptFiles": [
"$bluima/regex_concepts/concentrations.xml",
"$bluima/regex_concepts/measures.xml"
]
}
},
{
"name": "PruneMeasuresAnnotator",
"class": "ch.epfl.bbp.uima.ae.KeepLargestAnnotationAnnotator",
"parameters": {
"annotationClass": [
"ch.epfl.bbp.uima.types.Measure"
]
}
},
{
"name": "KeepLargestBrainRegionAnnotator",
"class": "ch.epfl.bbp.uima.ae.KeepLargestAnnotationAnnotator",
"parameters": {
"annotationClass": [
"ch.epfl.bbp.uima.types.BrainRegion"
]
}
},
{
"name": "KeepLargestCooccurrenceAnnotator",
"class": "ch.epfl.bbp.uima.ae.KeepLargestAnnotationAnnotator",
"parameters": {
"annotationClass": [
"ch.epfl.bbp.uima.types.Cooccurrence"
]
}
},
{
"name": "ExtractSameBrainRegionCoocurrences",
"class": "ch.epfl.bbp.uima.ae.relations.ExtractSameCoocurrences",
"parameters": {
"annot1": [
"ch.epfl.bbp.uima.types.BrainRegion"
],
"annot2": [
"ch.epfl.bbp.uima.types.BrainRegion"
]
}
},
{
"name": "JsreBrainRegionFilterAnnotator",
"class": "ch.epfl.bbp.uima.jsre.JsreFilterAnnotator",
"parameters": {
"annotationClass": [
"ch.epfl.bbp.uima.types.BrainRegion"
]
}
}
],
"config": {
"bluima": {
"type": "git",
"url": "https://github.com/BlueBrain/bluima_resources.git",
"ref": "master"
}
}
}
]
DEBUG starting test test020GetBundle(org.sherlok.integration.BundleApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:46]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:46]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:46]
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 1699
Server: Jetty(9.0.2.v20130417)
{
"name": "dkpro.opennlp.en",
"version": "1.7.0",
"description": "all opennlp engines and models for English",
"domain": "dkpro",
"dependencies": [
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.stanfordnlp-gpl:1.7.0"
},
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.opennlp-asl:1.7.0"
},
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.opennlp-model-ner-en-person:20130624.1"
},
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.opennlp-model-ner-en-organization:20100907.0"
},
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.opennlp-model-ner-en-location:20100907.0"
}
],
"repositories": {
"dkpro": "http://zoidberg.ukp.informatik.tu-darmstadt.de/artifactory/public-model-releases-local/"
},
"engines": [
{
"name": "opennlp.ner.location.en",
"class": "de.tudarmstadt.ukp.dkpro.core.opennlp.OpenNlpNameFinder",
"parameters": {
"language": [
"en"
],
"modelVariant": [
"location"
]
}
},
{
"name": "opennlp.ner.person.en",
"class": "de.tudarmstadt.ukp.dkpro.core.opennlp.OpenNlpNameFinder",
"parameters": {
"language": [
"en"
],
"modelVariant": [
"person"
]
}
},
{
"name": "opennlp.pos.en",
"class": "de.tudarmstadt.ukp.dkpro.core.opennlp.OpenNlpPosTagger",
"parameters": {
"language": [
"en"
]
}
},
{
"name": "opennlp.segmenter.en",
"class": "de.tudarmstadt.ukp.dkpro.core.opennlp.OpenNlpSegmenter",
"parameters": {
"language": [
"en"
]
}
}
]
}
DEBUG starting test test030PostBundle(org.sherlok.integration.BundleApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:48]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:48]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:48]
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 57
Server: Jetty(9.0.2.v20130417)
{
"status": "created",
"bundle_id": "test:172"
}
DEBUG starting test test031PostFaultyBundle(org.sherlok.integration.BundleApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:48]
INFO could not POST bundle 'blah' com.fasterxml.jackson.core.JsonParseException: Unrecognized token 'blah': was expecting ('true', 'false' or 'null')
at [Source: blah; line: 1, column: 9] [o.s.SherlokServer 20:31:48]
org.sherlok.utils.ValidationException: com.fasterxml.jackson.core.JsonParseException: Unrecognized token 'blah': was expecting ('true', 'false' or 'null')
at [Source: blah; line: 1, column: 9]
at org.sherlok.FileBased.putBundle(FileBased.java:120) ~[classes/:na]
at org.sherlok.Controller.putBundle(Controller.java:171) ~[classes/:na]
at org.sherlok.SherlokServer$12.handle(SherlokServer.java:358) ~[classes/:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_79]
Caused by: com.fasterxml.jackson.core.JsonParseException: Unrecognized token 'blah': was expecting ('true', 'false' or 'null')
at [Source: blah; line: 1, column: 9]
at com.fasterxml.jackson.core.JsonParser._constructError(JsonParser.java:1419) ~[jackson-core-2.4.2.jar:2.4.2]
at com.fasterxml.jackson.core.base.ParserMinimalBase._reportError(ParserMinimalBase.java:508) ~[jackson-core-2.4.2.jar:2.4.2]
at com.fasterxml.jackson.core.json.ReaderBasedJsonParser._reportInvalidToken(ReaderBasedJsonParser.java:2300) ~[jackson-core-2.4.2.jar:2.4.2]
at com.fasterxml.jackson.core.json.ReaderBasedJsonParser._handleOddValue(ReaderBasedJsonParser.java:1459) ~[jackson-core-2.4.2.jar:2.4.2]
at com.fasterxml.jackson.core.json.ReaderBasedJsonParser.nextToken(ReaderBasedJsonParser.java:683) ~[jackson-core-2.4.2.jar:2.4.2]
at com.fasterxml.jackson.databind.ObjectMapper._initForReading(ObjectMapper.java:3090) ~[jackson-databind-2.4.2.jar:2.4.2]
at com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:3036) ~[jackson-databind-2.4.2.jar:2.4.2]
at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:2146) ~[jackson-databind-2.4.2.jar:2.4.2]
at org.sherlok.FileBased.putBundle(FileBased.java:116) ~[classes/:na]
... 15 common frames omitted
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:48]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:48]
HTTP/1.1 400 Bad Request
Content-Type: application/json
Content-Length: 5802
Server: Jetty(9.0.2.v20130417)
{
"cause": {
"cause": null,
"localizedMessage": "Unrecognized token 'blah': was expecting ('true', 'false' or 'null')\n at [Source: blah; line: 1, column: 9]",
"location": {
"byteOffset": -1,
"charOffset": 8,
"columnNr": 9,
"lineNr": 1,
"sourceRef": "blah"
},
"message": "Unrecognized token 'blah': was expecting ('true', 'false' or 'null')\n at [Source: blah; line: 1, column: 9]",
"originalMessage": "Unrecognized token 'blah': was expecting ('true', 'false' or 'null')",
"stackTrace": [
{
"className": "com.fasterxml.jackson.core.JsonParser",
"fileName": "JsonParser.java",
"lineNumber": 1419,
"methodName": "_constructError",
"nativeMethod": false
},
{
"className": "com.fasterxml.jackson.core.base.ParserMinimalBase",
"fileName": "ParserMinimalBase.java",
"lineNumber": 508,
"methodName": "_reportError",
"nativeMethod": false
},
{
"className": "com.fasterxml.jackson.core.json.ReaderBasedJsonParser",
"fileName": "ReaderBasedJsonParser.java",
"lineNumber": 2300,
"methodName": "_reportInvalidToken",
"nativeMethod": false
},
{
"className": "com.fasterxml.jackson.core.json.ReaderBasedJsonParser",
"fileName": "ReaderBasedJsonParser.java",
"lineNumber": 1459,
"methodName": "_handleOddValue",
"nativeMethod": false
},
{
"className": "com.fasterxml.jackson.core.json.ReaderBasedJsonParser",
"fileName": "ReaderBasedJsonParser.java",
"lineNumber": 683,
"methodName": "nextToken",
"nativeMethod": false
},
{
"className": "com.fasterxml.jackson.databind.ObjectMapper",
"fileName": "ObjectMapper.java",
"lineNumber": 3090,
"methodName": "_initForReading",
"nativeMethod": false
},
{
"className": "com.fasterxml.jackson.databind.ObjectMapper",
"fileName": "ObjectMapper.java",
"lineNumber": 3036,
"methodName": "_readMapAndClose",
"nativeMethod": false
},
{
"className": "com.fasterxml.jackson.databind.ObjectMapper",
"fileName": "ObjectMapper.java",
"lineNumber": 2146,
"methodName": "readValue",
"nativeMethod": false
},
{
"className": "org.sherlok.FileBased",
"fileName": "FileBased.java",
"lineNumber": 116,
"methodName": "putBundle",
"nativeMethod": false
},
{
"className": "org.sherlok.Controller",
"fileName": "Controller.java",
"lineNumber": 171,
"methodName": "putBundle",
"nativeMethod": false
},
{
"className": "org.sherlok.SherlokServer$12",
"fileName": "SherlokServer.java",
"lineNumber": 358,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "spark.webserver.MatcherFilter",
"fileName": "MatcherFilter.java",
"lineNumber": 139,
"methodName": "doFilter",
"nativeMethod": false
},
{
"className": "spark.webserver.JettyHandler",
"fileName": "JettyHandler.java",
"lineNumber": 54,
"methodName": "doHandle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.session.SessionHandler",
"fileName": "SessionHandler.java",
"lineNumber": 179,
"methodName": "doScope",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.handler.ScopedHandler",
"fileName": "ScopedHandler.java",
"lineNumber": 136,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.handler.HandlerList",
"fileName": "HandlerList.java",
"lineNumber": 52,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.handler.HandlerWrapper",
"fileName": "HandlerWrapper.java",
"lineNumber": 97,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.Server",
"fileName": "Server.java",
"lineNumber": 451,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.HttpChannel",
"fileName": "HttpChannel.java",
"lineNumber": 252,
"methodName": "run",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.HttpConnection",
"fileName": "HttpConnection.java",
"lineNumber": 266,
"methodName": "onFillable",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.io.AbstractConnection$ReadCallback",
"fileName": "AbstractConnection.java",
"lineNumber": 240,
"methodName": "run",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.util.thread.QueuedThreadPool",
"fileName": "QueuedThreadPool.java",
"lineNumber": 596,
"methodName": "runJob",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.util.thread.QueuedThreadPool$3",
"fileName": "QueuedThreadPool.java",
"lineNumber": 527,
"methodName": "run",
"nativeMethod": false
},
{
"className": "java.lang.Thread",
"fileName": "Thread.java",
"lineNumber": 745,
"methodName": "run",
"nativeMethod": false
}
],
"suppressed": [
]
},
"error_value": "com.fasterxml.jackson.core.JsonParseException: Unrecognized token 'blah': was expecting ('true', 'false' or 'null')\n at [Source: blah; line: 1, column: 9]"
}
DEBUG starting test test032PostFaultyBundle(org.sherlok.integration.BundleApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:48]
INFO could not POST bundle '{ "name" : "blabla"}' {
"cause" : null,
"error_value" : "blabla:null 'version' : cannot be empty or null"
} [o.s.SherlokServer 20:31:48]
org.sherlok.utils.ValidationException: {
"cause" : null,
"error_value" : "blabla:null 'version' : cannot be empty or null"
}
at org.sherlok.FileBased.putBundle(FileBased.java:120) ~[classes/:na]
at org.sherlok.Controller.putBundle(Controller.java:171) ~[classes/:na]
at org.sherlok.SherlokServer$12.handle(SherlokServer.java:358) ~[classes/:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_79]
Caused by: org.sherlok.utils.ValidationException: blabla:null 'version' : cannot be empty or null
at org.sherlok.utils.CheckThat.checkOnlyAlphanumDotUnderscore(CheckThat.java:44) ~[classes/:na]
at org.sherlok.mappings.Def.validate(Def.java:116) ~[classes/:na]
at org.sherlok.mappings.BundleDef.validate(BundleDef.java:327) ~[classes/:na]
at org.sherlok.FileBased.writeBundle(FileBased.java:202) ~[classes/:na]
at org.sherlok.FileBased.putBundle(FileBased.java:117) ~[classes/:na]
... 15 common frames omitted
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:48]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:48]
HTTP/1.1 400 Bad Request
Content-Type: application/json
Content-Length: 4384
Server: Jetty(9.0.2.v20130417)
{
"cause": {
"cause": null,
"localizedMessage": "blabla:null 'version' : cannot be empty or null",
"map": null,
"message": "blabla:null 'version' : cannot be empty or null",
"stackTrace": [
{
"className": "org.sherlok.utils.CheckThat",
"fileName": "CheckThat.java",
"lineNumber": 44,
"methodName": "checkOnlyAlphanumDotUnderscore",
"nativeMethod": false
},
{
"className": "org.sherlok.mappings.Def",
"fileName": "Def.java",
"lineNumber": 116,
"methodName": "validate",
"nativeMethod": false
},
{
"className": "org.sherlok.mappings.BundleDef",
"fileName": "BundleDef.java",
"lineNumber": 327,
"methodName": "validate",
"nativeMethod": false
},
{
"className": "org.sherlok.FileBased",
"fileName": "FileBased.java",
"lineNumber": 202,
"methodName": "writeBundle",
"nativeMethod": false
},
{
"className": "org.sherlok.FileBased",
"fileName": "FileBased.java",
"lineNumber": 117,
"methodName": "putBundle",
"nativeMethod": false
},
{
"className": "org.sherlok.Controller",
"fileName": "Controller.java",
"lineNumber": 171,
"methodName": "putBundle",
"nativeMethod": false
},
{
"className": "org.sherlok.SherlokServer$12",
"fileName": "SherlokServer.java",
"lineNumber": 358,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "spark.webserver.MatcherFilter",
"fileName": "MatcherFilter.java",
"lineNumber": 139,
"methodName": "doFilter",
"nativeMethod": false
},
{
"className": "spark.webserver.JettyHandler",
"fileName": "JettyHandler.java",
"lineNumber": 54,
"methodName": "doHandle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.session.SessionHandler",
"fileName": "SessionHandler.java",
"lineNumber": 179,
"methodName": "doScope",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.handler.ScopedHandler",
"fileName": "ScopedHandler.java",
"lineNumber": 136,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.handler.HandlerList",
"fileName": "HandlerList.java",
"lineNumber": 52,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.handler.HandlerWrapper",
"fileName": "HandlerWrapper.java",
"lineNumber": 97,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.Server",
"fileName": "Server.java",
"lineNumber": 451,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.HttpChannel",
"fileName": "HttpChannel.java",
"lineNumber": 252,
"methodName": "run",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.HttpConnection",
"fileName": "HttpConnection.java",
"lineNumber": 266,
"methodName": "onFillable",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.io.AbstractConnection$ReadCallback",
"fileName": "AbstractConnection.java",
"lineNumber": 240,
"methodName": "run",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.util.thread.QueuedThreadPool",
"fileName": "QueuedThreadPool.java",
"lineNumber": 596,
"methodName": "runJob",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.util.thread.QueuedThreadPool$3",
"fileName": "QueuedThreadPool.java",
"lineNumber": 527,
"methodName": "run",
"nativeMethod": false
},
{
"className": "java.lang.Thread",
"fileName": "Thread.java",
"lineNumber": 745,
"methodName": "run",
"nativeMethod": false
}
],
"suppressed": [
]
},
"error_value": "{\r\n \"cause\" : null,\r\n \"error_value\" : \"blabla:null 'version' : cannot be empty or null\"\r\n}"
}
DEBUG starting test test040GetTestBundle(org.sherlok.integration.BundleApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:48]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:48]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:48]
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 223
Server: Jetty(9.0.2.v20130417)
{
"name": "test",
"version": "172",
"dependencies": [
{
"value": "de.tudarmstadt.ukp.dkpro.core:de.tudarmstadt.ukp.dkpro.core.stanfordnlp-gpl:1.7.0"
}
],
"engines": [
{
"name": "myE"
}
]
}
DEBUG starting test test041GetFaultyTestBundle(org.sherlok.integration.BundleApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:48]
INFO could not GET bundle 'test' null [o.s.SherlokServer 20:31:48]
org.sherlok.utils.ValidationException: null
at org.sherlok.SherlokServer$11.handle(SherlokServer.java:344) ~[classes/:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_79]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:48]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:48]
HTTP/1.1 400 Bad Request
Content-Type: application/json
Content-Length: 73
Server: Jetty(9.0.2.v20130417)
{
"message": "bundle id",
"not_found": "test:1000000000198198"
}
DEBUG starting test test050DeleteBundle(org.sherlok.integration.BundleApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:48]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:48]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:48]
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 57
Server: Jetty(9.0.2.v20130417)
{
"status": "deleted",
"bundle_id": "test:172"
}
DEBUG starting test test060GetTestBundleGone(org.sherlok.integration.BundleApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:48]
INFO could not GET bundle 'test' null [o.s.SherlokServer 20:31:48]
org.sherlok.utils.ValidationException: null
at org.sherlok.SherlokServer$11.handle(SherlokServer.java:344) ~[classes/:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_79]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:48]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:48]
HTTP/1.1 400 Bad Request
Content-Type: application/json
Content-Length: 60
Server: Jetty(9.0.2.v20130417)
{
"message": "bundle id",
"not_found": "test:172"
}
>>> Spark shutting down...done
Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.04 sec
Running org.sherlok.integration.PipelineApiIntegrationTest
INFO Done loading from local File store (local_repo): 11 bundles, 25 engines, 14 pipelines [o.s.Controller 20:31:49]
== Spark has ignited ...
>> Listening on 0.0.0.0:9606
DEBUG starting test test010GetPipelines(org.sherlok.integration.PipelineApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:50]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
HTTP/1.1 200 OK
Content-Type: application/json
Transfer-Encoding: chunked
Server: Jetty(9.0.2.v20130417)
[
{
"name": "02.ruta.annotate.countries",
"version": "1",
"description": "Example that annotates countries",
"domain": "examples",
"script": [
"WORDLIST CountriesList = 'countries.txt';",
"DECLARE Country;",
"Document{-> MARKFAST(Country, CountriesList)};"
],
"output": {
"include_annotations": [
"org.sherlok.ruta.Country"
]
},
"tests": [
{
"input": "Switzerland is close to Italy, the land of pasta and Michelangelo. Paris is in France. And Madrid in Spain.",
"expected": {
"Country": [
{
"begin": 0,
"end": 11
},
{
"begin": 24,
"end": 29
},
{
"begin": 79,
"end": 85
},
{
"begin": 101,
"end": 106
}
]
}
},
{
"input": "China's GDP has taken over the United States.",
"expected": {
"Country": [
{
"begin": 0,
"end": 5
},
{
"begin": 31,
"end": 44
}
]
}
}
]
},
{
"name": "langdetect",
"version": "1.7.0",
"description": "Detects language",
"domain": "dkpro",
"script": [
"ENGINE languageidentifier:1.7.0;"
],
"output": {
},
"tests": [
{
"input": "Ce mod\u00c3\u00a8le sert \u00c3\u00a0 d\u00c3\u00a9tecter la langue d'un document."
}
]
},
{
"name": "01.ruta.annotate.dog",
"version": "1",
"description": "Example that annotates 'dog' as an Animal",
"domain": "examples",
"script": [
"DECLARE Dog;",
"W{REGEXP(\"dog\") -> MARK(Dog)};"
],
"output": {
"include_annotations": [
"org.sherlok.ruta.Dog"
]
},
"tests": [
{
"input": "This is a very good dog!",
"expected": {
"Dog": [
{
"begin": 20,
"end": 23
}
]
},
"comparison": "exact"
}
]
},
{
"name": "berkeleyparser.en",
"version": "1.7.0",
"description": "Parses syntactic tree using the Berkeley parser",
"domain": "dkpro",
"script": [
"ENGINE opennlp.segmenter.en:1.7.0;",
"ENGINE opennlp.pos.en:1.7.0;",
"ENGINE berkeleyparser.en:1.7.0;"
],
"output": {
"include_annotations": [
"de.tudarmstadt.ukp.dkpro.core.api.syntax.type.constituent.*",
"de.tudarmstadt.ukp.dkpro.core.api.syntax.type.PennTree"
]
},
"tests": [
{
"input": "The blue house of my childhood was bought: what a pity!"
}
]
},
{
"name": "bluima.regions",
"version": "1.0.1",
"description": "annotate brain regions",
"domain": "bluima",
"script": [
"ENGINE SentenceAnnotator:1.0.1;",
"ENGINE TokenAnnotator:1.0.1;",
"ENGINE PosTagAnnotator:1.0.1;",
"ENGINE BlueBioLemmatizer:1.0.1;",
"ENGINE MeasureRegexAnnotator:1.0.1;",
"ENGINE PruneMeasuresAnnotator:1.0.1;",
"ENGINE LinnaeusAnnotator:1.0.1;",
"ENGINE BrainRegionAnnotator:1.0.1;",
"ENGINE KeepLargestBrainRegionAnnotator:1.0.1;",
"ENGINE ExtractSameBrainRegionCoocurrences:1.0.1;",
"ENGINE JsreBrainRegionFilterAnnotator:1.0.1;",
"ENGINE KeepLargestCooccurrenceAnnotator:1.0.1;"
],
"output": {
},
"tests": [
{
"input": "Sex differences in the gross size of the rat neocortex.",
"expected": {
"BrainRegion": [
{
"begin": 45,
"end": 54
}
]
}
}
]
},
{
"name": "bluima.token",
"version": "1.0.1",
"description": "tokenizer",
"domain": "bluima",
"script": [
"ENGINE TokenAnnotator:1.0.1;"
],
"output": {
},
"tests": [
{
"input": "Switzerland is close to Italy, the land of pasta and Michelangelo. Paris is in France. And Madrid in Spain.",
"expected": {
"Token": [
{
"begin": 0,
"end": 11
},
{
"begin": 12,
"end": 14
},
{
"begin": 15,
"end": 20
},
{
"begin": 21,
"end": 23
},
{
"begin": 24,
"end": 29
},
{
"begin": 29,
"end": 30
},
{
"begin": 31,
"end": 34
},
{
"begin": 35,
"end": 39
},
{
"begin": 40,
"end": 42
},
{
"begin": 43,
"end": 48
},
{
"begin": 49,
"end": 52
},
{
"begin": 53,
"end": 65
},
{
"begin": 65,
"end": 66
},
{
"begin": 67,
"end": 72
},
{
"begin": 73,
"end": 75
},
{
"begin": 76,
"end": 78
},
{
"begin": 79,
"end": 85
},
{
"begin": 85,
"end": 86
},
{
"begin": 87,
"end": 90
},
{
"begin": 91,
"end": 97
},
{
"begin": 98,
"end": 100
},
{
"begin": 101,
"end": 106
},
{
"begin": 106,
"end": 107
}
]
}
}
]
},
{
"name": "maltparser.en",
"version": "1.7.0",
"description": "Parses syntactic tree using Malt parser, see http://www.maltparser.org",
"domain": "dkpro",
"script": [
"ENGINE opennlp.segmenter.en:1.7.0;",
"ENGINE opennlp.pos.en:1.7.0;",
"ENGINE maltparser.en:1.7.0;"
],
"output": {
"include_annotations": [
"de.tudarmstadt.ukp.dkpro.core.api.syntax.type.dependency.Dependency"
]
},
"tests": [
{
"input": "The blue house of my childhood was bought: what a pity!"
}
]
},
{
"name": "opennlp.ners.en",
"version": "1.7.0",
"description": "annotates English persons and locations using OpenNLP models",
"domain": "dkpro",
"script": [
"ENGINE opennlp.segmenter.en:1.7.0;",
"ENGINE opennlp.pos.en:1.7.0;",
"ENGINE opennlp.ner.person.en:1.7.0;",
"ENGINE opennlp.ner.location.en:1.7.0;"
],
"output": {
"include_annotations": [
"de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity"
]
},
"tests": [
{
"input": "Jack Burton (born April 29, 1954 in El Paso), also known as Jake Burton, is an American snowboarder and founder of Burton Snowboards.",
"expected": {
"NamedEntity": [
{
"begin": 0,
"end": 11,
"properties": {
"value": "person"
}
},
{
"begin": 60,
"end": 71,
"properties": {
"value": "person"
}
},
{
"begin": 36,
"end": 43,
"properties": {
"value": "location"
}
}
]
}
}
]
},
{
"name": "bluima.sentence",
"version": "1.0.1",
"description": "sentence splitter",
"domain": "bluima",
"script": [
"ENGINE SentenceAnnotator:1.0.1;"
],
"output": {
},
"tests": [
{
"input": "Switzerland is close to Italy, the land of pasta and Michelangelo. Paris is in France. And Madrid in Spain.",
"expected": {
"Sentence": [
{
"begin": 0,
"end": 66
},
{
"begin": 67,
"end": 86
},
{
"begin": 87,
"end": 107
}
]
}
}
]
},
{
"name": "neuroner",
"version": "0.1",
"description": "named entity recognizer for neuronal cells, based on UIMA Ruta rules",
"domain": "bluima/neuroner",
"script": [
"PACKAGE neuroner;",
"",
"Document{-> RETAINTYPE(BREAK)};",
"",
"DECLARE NeuronTrigger, NeuronProperty; // acts as a trigger",
"DECLARE NeuronProperty Function;",
"DECLARE NeuronProperty Morphology;",
"DECLARE NeuronProperty BrainRegionProp; // so as not to be confused w/ other BrainRegion",
"DECLARE ProteinName; // is further aggregated below",
"",
"",
"// DEVELOPMENTAL STAGES",
"WORDTABLE developmentalWt = '$bluima/neuroner/hbp_developmental_ontology.csv';",
"DECLARE NeuronProperty Developmental(STRING name, STRING ontologyId); ",
"Document{-> MARKTABLE(Developmental, 1, developmentalWt, true, 2, \"\", 2, \"ontologyId\" = 2)};",
"",
"// NEUROTRANSMITTER",
"WORDTABLE neurotransmitterWt = '$bluima/neuroner/hbp_neurotransmitter_ontology.csv';",
"DECLARE NeuronProperty NeurotransmitterProp(STRING name, STRING ontologyId);",
"Document{-> MARKTABLE(NeurotransmitterProp, 1, neurotransmitterWt, true, 2, \"\", 2, \"ontologyId\" = 2)};",
"",
"// LAYER",
"//\"[Ll]ayers? ([1-6][AaBb]?([/-][1-6][AaBb]?)?|[iIvV]+([/-][iIvV]+)?)\" -> Layer;",
"WORDTABLE layerWt = '$bluima/neuroner/hbp_layer_ontology.csv';",
"DECLARE NeuronProperty Layer(STRING name, STRING ontologyId);",
"Document{-> MARKTABLE(Layer, 1, layerWt, true, 2, \"\", 2, \"ontologyId\" = 2)};",
"",
"// SPECIES",
"WORDTABLE speciesWt = '$bluima/neuroner/ncbi_species_top1000.csv';",
"DECLARE NeuronProperty Species(STRING name, STRING ontologyId);",
"Document{-> MARKTABLE(Species, 1, speciesWt, true, 2, \"\", 2, \"ontologyId\" = 2)};",
"",
"",
"",
"// ORIENTATION",
"DECLARE NeuronProperty Orientation;",
"\"(?i)inverted|horizontal|descending|upper|lower\" -> Orientation;",
"",
"// SIZE",
"DECLARE NeuronProperty Size;",
"\"(?i)large|medium|small|narrow|giant\" -> Size;",
"",
"// ELECTROPYHSIOLOGY",
"DECLARE NeuronProperty Electrophysiology;",
"\"(?i)((continu(ally|ous)?|delayed) )?(((ir)?regular|fast|late|burst(ing)?|classical|delayed)[ -])?((non[- ]?)?(accomm?odating|adapting|spiking|firing|irregular|stuttering))\" -> Electrophysiology;",
"",
"",
"// DICTIONARY MATCHING",
"// we use a single compiled trie to match word lists (found in resources folder)",
"WORDLIST generated = '$bluima/neuroner/generated.mtwl';",
"Document{->TRIE(",
"\"neuron_triggers.txt\" = NeuronTrigger,",
"\"functions.txt\" = Function,",
"\"morphology.txt\" = Morphology,",
"\"proteins_ns_dan.txt\" = ProteinName,",
"\"proteins_obo_pro.txt\" = ProteinName,",
"\"regions_adverbs_al.txt\" = BrainRegionProp,",
"\"regions_adverbs_ic.txt\" = BrainRegionProp,",
"\"regions_lfrench.txt\" = BrainRegionProp,",
"\"regions.txt\" = BrainRegionProp,",
"generated, true, 4, false, 0, \"\")}; // case ignored if word length > 4; edit distance deactivated",
"",
"",
"// PROTEIN",
"// aggregate protein names (as it was matched above) with a trigger ",
"DECLARE ProteinTrigger;",
"\"(?i)expressing|principal|containing|immuno(nega|posi|reac)tive|positive\" -> ProteinTrigger;",
"DECLARE NeuronProperty ProteinProp;",
"(ProteinName \"-\"? ProteinTrigger){-> MARK(ProteinProp)};",
"(ProteinTrigger ProteinName (COMMA ProteinName)?){-> MARK(ProteinProp)};",
"//TODO (ProteinTrigger){-> MARK(ProteinProp, 1, 2)} (\"-\"? ProteinName);",
"",
"",
"(NeuronTrigger \"and\" NeuronTrigger){-> SHIFT(NeuronTrigger)};",
"",
"//////////////////////////////////////////////////////////",
"",
"DECLARE Neuron;",
"// gather NeuronProperty occurring around Neuron",
"(NeuronProperty* NeuronTrigger NeuronProperty*) {-> MARK(Neuron)} ;",
"(NeuronProperty+ (COMMA | \"and\" | (COMMA \"and\")))* {-> MARK(Neuron, 1, 3)} NeuronProperty+ NeuronTrigger;",
"",
"// remove single isolated Neuron, unless \"cell\"",
"NeuronTrigger{NOT(REGEXP(\"[Cc]ells?\")) -> MARK(Neuron, 1, 1)}; ",
"",
"Neuron{CONTAINS(BREAK) -> DEL};",
"// keep only longest Neuron",
"Neuron{PARTOF(Neuron) -> DEL};",
"// TODO remove cells without NeuronProperty",
"",
"// Find up to 3 unmatched words preceding a Neuron to see what is still missing",
"// DECLARE Sentence; PERIOD #{-> MARK(Sentence)} PERIOD;",
"DECLARE Missing, InBetweenMissing;",
"NeuronProperty (ANY{-PARTOF(NeuronProperty)}) {-> MARK(Missing, 2, 2)}(Neuron|NeuronTrigger);",
"NeuronProperty (ANY{-PARTOF(NeuronProperty)} ANY{-PARTOF(NeuronProperty)}) {-> MARK(Missing, 2, 2)}(Neuron|NeuronTrigger);",
"NeuronProperty (ANY{-PARTOF(NeuronProperty)} ANY{-PARTOF(NeuronProperty)} ANY{-PARTOF(NeuronProperty)}) {-> MARK(Missing, 2, 2)}(Neuron|NeuronTrigger);"
],
"output": {
"include_annotations": [
"neuroner.*"
]
},
"tests": [
{
"input": "layer V and layer iii large pyramidal neurons",
"expected": {
"Layer": [
{
"begin": 0,
"end": 7,
"properties": {
"ontologyId": "HBP_LAYER:0000005"
}
},
{
"begin": 12,
"end": 21,
"properties": {
"ontologyId": "HBP_LAYER:0000003"
}
}
],
"Size": [
{
"begin": 22,
"end": 27
}
],
"BrainRegionProp": [
{
"begin": 0,
"end": 7
},
{
"begin": 12,
"end": 21
}
],
"Neuron": [
{
"begin": 0,
"end": 45
}
]
}
},
{
"input": "slowly adapting stretch receptor neuron",
"expected": {
"Function": [
{
"begin": 0,
"end": 23
},
{
"begin": 24,
"end": 32
}
],
"Neuron": [
{
"begin": 0,
"end": 39
}
]
}
}
],
"config": {
"bluima": {
"type": "git",
"url": "https://github.com/BlueBrain/bluima_resources.git",
"ref": "master",
"mode": "ruta"
}
}
},
{
"name": "bluima.lemma",
"version": "1.0.1",
"description": "lemmatizer",
"domain": "bluima",
"script": [
"ENGINE TokenAnnotator:1.0.1;",
"ENGINE BlueBioLemmatizer:1.0.1;"
],
"output": {
},
"tests": [
{
"input": "long form pressure hydrocephalus (NPH) be classify. Thalamic conditioned acoustic areas houses",
"expected": {
"Token": [
{
"begin": 0,
"end": 4,
"properties": {
"lemmaStr": "long"
}
},
{
"begin": 5,
"end": 9,
"properties": {
"lemmaStr": "form"
}
},
{
"begin": 10,
"end": 18,
"properties": {
"lemmaStr": "pressure"
}
},
{
"begin": 19,
"end": 32,
"properties": {
"lemmaStr": "hydrocephalus"
}
},
{
"begin": 33,
"end": 34,
"properties": {
"lemmaStr": "("
}
},
{
"begin": 34,
"end": 37,
"properties": {
"lemmaStr": "NPH"
}
},
{
"begin": 37,
"end": 38,
"properties": {
"lemmaStr": ")"
}
},
{
"begin": 39,
"end": 41,
"properties": {
"lemmaStr": "be"
}
},
{
"begin": 42,
"end": 50,
"properties": {
"lemmaStr": "classify"
}
},
{
"begin": 50,
"end": 51,
"properties": {
"lemmaStr": "."
}
},
{
"begin": 52,
"end": 60,
"properties": {
"lemmaStr": "thalamic"
}
},
{
"begin": 61,
"end": 72,
"properties": {
"lemmaStr": "condition"
}
},
{
"begin": 73,
"end": 81,
"properties": {
"lemmaStr": "acoustic"
}
},
{
"begin": 82,
"end": 87,
"properties": {
"lemmaStr": "area"
}
},
{
"begin": 88,
"end": 94,
"properties": {
"lemmaStr": "house"
}
}
]
}
}
]
},
{
"name": "bluima.pos",
"version": "1.0.1",
"description": "PoS Tagger",
"domain": "bluima",
"script": [
"ENGINE SentenceAnnotator:1.0.1;",
"ENGINE TokenAnnotator:1.0.1;",
"ENGINE PosTagAnnotator:1.0.1;"
],
"output": {
},
"tests": [
{
"input": "Switzerland is close to Italy, the land of pasta and Michelangelo. Paris is in France. And Madrid in Spain.",
"expected": {
"Sentence": [
{
"begin": 0,
"end": 66
},
{
"begin": 67,
"end": 86
},
{
"begin": 87,
"end": 107
}
],
"Token": [
{
"begin": 0,
"end": 11,
"properties": {
"posTag": 792,
"pos": "NN"
}
},
{
"begin": 12,
"end": 14,
"properties": {
"posTag": 804,
"pos": "VBZ"
}
},
{
"begin": 15,
"end": 20,
"properties": {
"posTag": 816,
"pos": "JJ"
}
},
{
"begin": 21,
"end": 23,
"properties": {
"posTag": 828,
"pos": "TO"
}
},
{
"begin": 24,
"end": 29,
"properties": {
"posTag": 840,
"pos": "RB"
}
},
{
"begin": 29,
"end": 30,
"properties": {
"posTag": 852,
"pos": ","
}
},
{
"begin": 31,
"end": 34,
"properties": {
"posTag": 864,
"pos": "DT"
}
},
{
"begin": 35,
"end": 39,
"properties": {
"posTag": 876,
"pos": "NN"
}
},
{
"begin": 40,
"end": 42,
"properties": {
"posTag": 888,
"pos": "IN"
}
},
{
"begin": 43,
"end": 48,
"properties": {
"posTag": 900,
"pos": "NN"
}
},
{
"begin": 49,
"end": 52,
"properties": {
"posTag": 912,
"pos": "CC"
}
},
{
"begin": 53,
"end": 65,
"properties": {
"posTag": 924,
"pos": "NN"
}
},
{
"begin": 65,
"end": 66,
"properties": {
"posTag": 936,
"pos": "."
}
},
{
"begin": 67,
"end": 72,
"properties": {
"posTag": 948,
"pos": "NN"
}
},
{
"begin": 73,
"end": 75,
"properties": {
"posTag": 960,
"pos": "VBZ"
}
},
{
"begin": 76,
"end": 78,
"properties": {
"posTag": 972,
"pos": "IN"
}
},
{
"begin": 79,
"end": 85,
"properties": {
"posTag": 984,
"pos": "NN"
}
},
{
"begin": 85,
"end": 86,
"properties": {
"posTag": 996,
"pos": "."
}
},
{
"begin": 87,
"end": 90,
"properties": {
"posTag": 1008,
"pos": "CC"
}
},
{
"begin": 91,
"end": 97,
"properties": {
"posTag": 1020,
"pos": "NN"
}
},
{
"begin": 98,
"end": 100,
"properties": {
"posTag": 1032,
"pos": "IN"
}
},
{
"begin": 101,
"end": 106,
"properties": {
"posTag": 1044,
"pos": "NN"
}
},
{
"begin": 106,
"end": 107,
"properties": {
"posTag": 1056,
"pos": "."
}
}
]
}
}
]
},
{
"name": "bluima.chunk",
"version": "1.0.1",
"description": "chunker",
"domain": "bluima",
"script": [
"ENGINE SentenceAnnotator:1.0.1;",
"ENGINE TokenAnnotator:1.0.1;",
"ENGINE PosTagAnnotator:1.0.1;",
"ENGINE ChunkAnnotator:1.0.1;"
],
"output": {
},
"tests": [
{
"input": "Switzerland is close to Italy, the land of pasta and Michelangelo. Paris is in France. And Madrid in Spain.",
"expected": {
"ChunkADJP": [
{
"begin": 15,
"end": 20
}
],
"ChunkNP": [
{
"begin": 0,
"end": 11
},
{
"begin": 24,
"end": 29
},
{
"begin": 31,
"end": 39
},
{
"begin": 43,
"end": 48
},
{
"begin": 53,
"end": 65
},
{
"begin": 67,
"end": 72
},
{
"begin": 79,
"end": 85
},
{
"begin": 91,
"end": 97
},
{
"begin": 101,
"end": 106
}
],
"ChunkPP": [
{
"begin": 21,
"end": 23
},
{
"begin": 40,
"end": 42
},
{
"begin": 76,
"end": 78
},
{
"begin": 98,
"end": 100
}
],
"ChunkVP": [
{
"begin": 12,
"end": 14
},
{
"begin": 73,
"end": 75
}
],
"Sentence": [
{
"begin": 0,
"end": 66
},
{
"begin": 67,
"end": 86
},
{
"begin": 87,
"end": 107
}
],
"Token": [
{
"begin": 0,
"end": 11,
"properties": {
"posTag": 792,
"pos": "NN"
}
},
{
"begin": 12,
"end": 14,
"properties": {
"posTag": 804,
"pos": "VBZ"
}
},
{
"begin": 15,
"end": 20,
"properties": {
"posTag": 816,
"pos": "JJ"
}
},
{
"begin": 21,
"end": 23,
"properties": {
"posTag": 828,
"pos": "TO"
}
},
{
"begin": 24,
"end": 29,
"properties": {
"posTag": 840,
"pos": "RB"
}
},
{
"begin": 29,
"end": 30,
"properties": {
"posTag": 852,
"pos": ","
}
},
{
"begin": 31,
"end": 34,
"properties": {
"posTag": 864,
"pos": "DT"
}
},
{
"begin": 35,
"end": 39,
"properties": {
"posTag": 876,
"pos": "NN"
}
},
{
"begin": 40,
"end": 42,
"properties": {
"posTag": 888,
"pos": "IN"
}
},
{
"begin": 43,
"end": 48,
"properties": {
"posTag": 900,
"pos": "NN"
}
},
{
"begin": 49,
"end": 52,
"properties": {
"posTag": 912,
"pos": "CC"
}
},
{
"begin": 53,
"end": 65,
"properties": {
"posTag": 924,
"pos": "NN"
}
},
{
"begin": 65,
"end": 66,
"properties": {
"posTag": 936,
"pos": "."
}
},
{
"begin": 67,
"end": 72,
"properties": {
"posTag": 948,
"pos": "NN"
}
},
{
"begin": 73,
"end": 75,
"properties": {
"posTag": 960,
"pos": "VBZ"
}
},
{
"begin": 76,
"end": 78,
"properties": {
"posTag": 972,
"pos": "IN"
}
},
{
"begin": 79,
"end": 85,
"properties": {
"posTag": 984,
"pos": "NN"
}
},
{
"begin": 85,
"end": 86,
"properties": {
"posTag": 996,
"pos": "."
}
},
{
"begin": 87,
"end": 90,
"properties": {
"posTag": 1008,
"pos": "CC"
}
},
{
"begin": 91,
"end": 97,
"properties": {
"posTag": 1020,
"pos": "NN"
}
},
{
"begin": 98,
"end": 100,
"properties": {
"posTag": 1032,
"pos": "IN"
}
},
{
"begin": 101,
"end": 106,
"properties": {
"posTag": 1044,
"pos": "NN"
}
},
{
"begin": 106,
"end": 107,
"properties": {
"posTag": 1056,
"pos": "."
}
}
]
}
}
]
},
{
"name": "bluima.linnaeus",
"version": "1.0.1",
"description": "linnaeus",
"domain": "bluima",
"script": [
"ENGINE LinnaeusAnnotator:1.0.1;"
],
"output": {
},
"tests": [
{
"input": "bla bla rat bla bla",
"expected": {
"LinnaeusSpecies": [
{
"begin": 8,
"end": 11,
"properties": {
"mostProbableSpeciesId": "species:ncbi:10116",
"ambigous": false,
"allIdsString": "species:ncbi:10116"
}
}
]
}
}
]
}
]
DEBUG starting test test020GetPipeline(org.sherlok.integration.PipelineApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:50]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 1049
Server: Jetty(9.0.2.v20130417)
{
"name": "opennlp.ners.en",
"version": "1.7.0",
"description": "annotates English persons and locations using OpenNLP models",
"domain": "dkpro",
"script": [
"ENGINE opennlp.segmenter.en:1.7.0;",
"ENGINE opennlp.pos.en:1.7.0;",
"ENGINE opennlp.ner.person.en:1.7.0;",
"ENGINE opennlp.ner.location.en:1.7.0;"
],
"output": {
"include_annotations": [
"de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity"
]
},
"tests": [
{
"input": "Jack Burton (born April 29, 1954 in El Paso), also known as Jake Burton, is an American snowboarder and founder of Burton Snowboards.",
"expected": {
"NamedEntity": [
{
"begin": 0,
"end": 11,
"properties": {
"value": "person"
}
},
{
"begin": 60,
"end": 71,
"properties": {
"value": "person"
}
},
{
"begin": 36,
"end": 43,
"properties": {
"value": "location"
}
}
]
}
}
]
}
DEBUG starting test test030PostPipeline(org.sherlok.integration.PipelineApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:50]
WARN no tests for pipeline 'test:1' [o.s.mappings.Def 20:31:50]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 57
Server: Jetty(9.0.2.v20130417)
{
"pipeline_id": "test:1",
"status": "created"
}
DEBUG starting test test031PostFaultyPipeline(org.sherlok.integration.PipelineApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:50]
INFO could not POST pipeline 'blah' com.fasterxml.jackson.core.JsonParseException: Unrecognized token 'blah': was expecting ('true', 'false' or 'null')
at [Source: blah; line: 1, column: 9] [o.s.SherlokServer 20:31:50]
org.sherlok.utils.ValidationException: com.fasterxml.jackson.core.JsonParseException: Unrecognized token 'blah': was expecting ('true', 'false' or 'null')
at [Source: blah; line: 1, column: 9]
at org.sherlok.FileBased.putPipeline(FileBased.java:142) ~[classes/:na]
at org.sherlok.Controller.putPipeline(Controller.java:183) ~[classes/:na]
at org.sherlok.SherlokServer$8.handle(SherlokServer.java:286) ~[classes/:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_79]
Caused by: com.fasterxml.jackson.core.JsonParseException: Unrecognized token 'blah': was expecting ('true', 'false' or 'null')
at [Source: blah; line: 1, column: 9]
at com.fasterxml.jackson.core.JsonParser._constructError(JsonParser.java:1419) ~[jackson-core-2.4.2.jar:2.4.2]
at com.fasterxml.jackson.core.base.ParserMinimalBase._reportError(ParserMinimalBase.java:508) ~[jackson-core-2.4.2.jar:2.4.2]
at com.fasterxml.jackson.core.json.ReaderBasedJsonParser._reportInvalidToken(ReaderBasedJsonParser.java:2300) ~[jackson-core-2.4.2.jar:2.4.2]
at com.fasterxml.jackson.core.json.ReaderBasedJsonParser._handleOddValue(ReaderBasedJsonParser.java:1459) ~[jackson-core-2.4.2.jar:2.4.2]
at com.fasterxml.jackson.core.json.ReaderBasedJsonParser.nextToken(ReaderBasedJsonParser.java:683) ~[jackson-core-2.4.2.jar:2.4.2]
at com.fasterxml.jackson.databind.ObjectMapper._initForReading(ObjectMapper.java:3090) ~[jackson-databind-2.4.2.jar:2.4.2]
at com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:3036) ~[jackson-databind-2.4.2.jar:2.4.2]
at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:2146) ~[jackson-databind-2.4.2.jar:2.4.2]
at org.sherlok.FileBased.parsePipeline(FileBased.java:174) ~[classes/:na]
at org.sherlok.FileBased.putPipeline(FileBased.java:137) ~[classes/:na]
... 15 common frames omitted
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
HTTP/1.1 400 Bad Request
Content-Type: application/json
Content-Length: 5995
Server: Jetty(9.0.2.v20130417)
{
"cause": {
"cause": null,
"localizedMessage": "Unrecognized token 'blah': was expecting ('true', 'false' or 'null')\n at [Source: blah; line: 1, column: 9]",
"location": {
"byteOffset": -1,
"charOffset": 8,
"columnNr": 9,
"lineNr": 1,
"sourceRef": "blah"
},
"message": "Unrecognized token 'blah': was expecting ('true', 'false' or 'null')\n at [Source: blah; line: 1, column: 9]",
"originalMessage": "Unrecognized token 'blah': was expecting ('true', 'false' or 'null')",
"stackTrace": [
{
"className": "com.fasterxml.jackson.core.JsonParser",
"fileName": "JsonParser.java",
"lineNumber": 1419,
"methodName": "_constructError",
"nativeMethod": false
},
{
"className": "com.fasterxml.jackson.core.base.ParserMinimalBase",
"fileName": "ParserMinimalBase.java",
"lineNumber": 508,
"methodName": "_reportError",
"nativeMethod": false
},
{
"className": "com.fasterxml.jackson.core.json.ReaderBasedJsonParser",
"fileName": "ReaderBasedJsonParser.java",
"lineNumber": 2300,
"methodName": "_reportInvalidToken",
"nativeMethod": false
},
{
"className": "com.fasterxml.jackson.core.json.ReaderBasedJsonParser",
"fileName": "ReaderBasedJsonParser.java",
"lineNumber": 1459,
"methodName": "_handleOddValue",
"nativeMethod": false
},
{
"className": "com.fasterxml.jackson.core.json.ReaderBasedJsonParser",
"fileName": "ReaderBasedJsonParser.java",
"lineNumber": 683,
"methodName": "nextToken",
"nativeMethod": false
},
{
"className": "com.fasterxml.jackson.databind.ObjectMapper",
"fileName": "ObjectMapper.java",
"lineNumber": 3090,
"methodName": "_initForReading",
"nativeMethod": false
},
{
"className": "com.fasterxml.jackson.databind.ObjectMapper",
"fileName": "ObjectMapper.java",
"lineNumber": 3036,
"methodName": "_readMapAndClose",
"nativeMethod": false
},
{
"className": "com.fasterxml.jackson.databind.ObjectMapper",
"fileName": "ObjectMapper.java",
"lineNumber": 2146,
"methodName": "readValue",
"nativeMethod": false
},
{
"className": "org.sherlok.FileBased",
"fileName": "FileBased.java",
"lineNumber": 174,
"methodName": "parsePipeline",
"nativeMethod": false
},
{
"className": "org.sherlok.FileBased",
"fileName": "FileBased.java",
"lineNumber": 137,
"methodName": "putPipeline",
"nativeMethod": false
},
{
"className": "org.sherlok.Controller",
"fileName": "Controller.java",
"lineNumber": 183,
"methodName": "putPipeline",
"nativeMethod": false
},
{
"className": "org.sherlok.SherlokServer$8",
"fileName": "SherlokServer.java",
"lineNumber": 286,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "spark.webserver.MatcherFilter",
"fileName": "MatcherFilter.java",
"lineNumber": 139,
"methodName": "doFilter",
"nativeMethod": false
},
{
"className": "spark.webserver.JettyHandler",
"fileName": "JettyHandler.java",
"lineNumber": 54,
"methodName": "doHandle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.session.SessionHandler",
"fileName": "SessionHandler.java",
"lineNumber": 179,
"methodName": "doScope",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.handler.ScopedHandler",
"fileName": "ScopedHandler.java",
"lineNumber": 136,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.handler.HandlerList",
"fileName": "HandlerList.java",
"lineNumber": 52,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.handler.HandlerWrapper",
"fileName": "HandlerWrapper.java",
"lineNumber": 97,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.Server",
"fileName": "Server.java",
"lineNumber": 451,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.HttpChannel",
"fileName": "HttpChannel.java",
"lineNumber": 252,
"methodName": "run",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.HttpConnection",
"fileName": "HttpConnection.java",
"lineNumber": 266,
"methodName": "onFillable",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.io.AbstractConnection$ReadCallback",
"fileName": "AbstractConnection.java",
"lineNumber": 240,
"methodName": "run",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.util.thread.QueuedThreadPool",
"fileName": "QueuedThreadPool.java",
"lineNumber": 596,
"methodName": "runJob",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.util.thread.QueuedThreadPool$3",
"fileName": "QueuedThreadPool.java",
"lineNumber": 527,
"methodName": "run",
"nativeMethod": false
},
{
"className": "java.lang.Thread",
"fileName": "Thread.java",
"lineNumber": 745,
"methodName": "run",
"nativeMethod": false
}
],
"suppressed": [
]
},
"error_value": "com.fasterxml.jackson.core.JsonParseException: Unrecognized token 'blah': was expecting ('true', 'false' or 'null')\n at [Source: blah; line: 1, column: 9]"
}
DEBUG starting test test032PostFaultyPipeline(org.sherlok.integration.PipelineApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:50]
INFO could not POST pipeline '{
"name" : "test_1431541910635",
"version" : "1",
"script" : [
"ENGINE nonexisting.engine:1431541910635"
],
"output" : { },
"tests" : [ ]
}' {
"not_found" : "nonexisting.engine:1431541910635",
"error_value" : "engine declared in pipeline 'test_1431541910635:1' but not found"
} [o.s.SherlokServer 20:31:50]
org.sherlok.utils.ValidationException: {
"not_found" : "nonexisting.engine:1431541910635",
"error_value" : "engine declared in pipeline 'test_1431541910635:1' but not found"
}
at org.sherlok.FileBased.putPipeline(FileBased.java:142) ~[classes/:na]
at org.sherlok.Controller.putPipeline(Controller.java:183) ~[classes/:na]
at org.sherlok.SherlokServer$8.handle(SherlokServer.java:286) ~[classes/:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_79]
Caused by: org.sherlok.utils.ValidationException: null
at org.sherlok.mappings.PipelineDef.validateEngines(PipelineDef.java:263) ~[classes/:na]
at org.sherlok.FileBased.putPipeline(FileBased.java:138) ~[classes/:na]
... 15 common frames omitted
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
HTTP/1.1 400 Bad Request
Content-Type: application/json
Content-Length: 3930
Server: Jetty(9.0.2.v20130417)
{
"cause": {
"cause": null,
"localizedMessage": null,
"map": {
"not_found": "nonexisting.engine:1431541910635",
"error_value": "engine declared in pipeline 'test_1431541910635:1' but not found"
},
"message": null,
"stackTrace": [
{
"className": "org.sherlok.mappings.PipelineDef",
"fileName": "PipelineDef.java",
"lineNumber": 263,
"methodName": "validateEngines",
"nativeMethod": false
},
{
"className": "org.sherlok.FileBased",
"fileName": "FileBased.java",
"lineNumber": 138,
"methodName": "putPipeline",
"nativeMethod": false
},
{
"className": "org.sherlok.Controller",
"fileName": "Controller.java",
"lineNumber": 183,
"methodName": "putPipeline",
"nativeMethod": false
},
{
"className": "org.sherlok.SherlokServer$8",
"fileName": "SherlokServer.java",
"lineNumber": 286,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "spark.webserver.MatcherFilter",
"fileName": "MatcherFilter.java",
"lineNumber": 139,
"methodName": "doFilter",
"nativeMethod": false
},
{
"className": "spark.webserver.JettyHandler",
"fileName": "JettyHandler.java",
"lineNumber": 54,
"methodName": "doHandle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.session.SessionHandler",
"fileName": "SessionHandler.java",
"lineNumber": 179,
"methodName": "doScope",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.handler.ScopedHandler",
"fileName": "ScopedHandler.java",
"lineNumber": 136,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.handler.HandlerList",
"fileName": "HandlerList.java",
"lineNumber": 52,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.handler.HandlerWrapper",
"fileName": "HandlerWrapper.java",
"lineNumber": 97,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.Server",
"fileName": "Server.java",
"lineNumber": 451,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.HttpChannel",
"fileName": "HttpChannel.java",
"lineNumber": 252,
"methodName": "run",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.HttpConnection",
"fileName": "HttpConnection.java",
"lineNumber": 266,
"methodName": "onFillable",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.io.AbstractConnection$ReadCallback",
"fileName": "AbstractConnection.java",
"lineNumber": 240,
"methodName": "run",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.util.thread.QueuedThreadPool",
"fileName": "QueuedThreadPool.java",
"lineNumber": 596,
"methodName": "runJob",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.util.thread.QueuedThreadPool$3",
"fileName": "QueuedThreadPool.java",
"lineNumber": 527,
"methodName": "run",
"nativeMethod": false
},
{
"className": "java.lang.Thread",
"fileName": "Thread.java",
"lineNumber": 745,
"methodName": "run",
"nativeMethod": false
}
],
"suppressed": [
]
},
"error_value": "{\r\n \"not_found\" : \"nonexisting.engine:1431541910635\",\r\n \"error_value\" : \"engine declared in pipeline 'test_1431541910635:1' but not found\"\r\n}"
}
DEBUG starting test test033PostFaultyPipeline(org.sherlok.integration.PipelineApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:50]
INFO could not POST pipeline '{ "name" : "opennlp.ners.en"}' {
"cause" : null,
"error_value" : "opennlp.ners.en:null 'version' : cannot be empty or null"
} [o.s.SherlokServer 20:31:50]
org.sherlok.utils.ValidationException: {
"cause" : null,
"error_value" : "opennlp.ners.en:null 'version' : cannot be empty or null"
}
at org.sherlok.FileBased.putPipeline(FileBased.java:142) ~[classes/:na]
at org.sherlok.Controller.putPipeline(Controller.java:183) ~[classes/:na]
at org.sherlok.SherlokServer$8.handle(SherlokServer.java:286) ~[classes/:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_79]
Caused by: org.sherlok.utils.ValidationException: opennlp.ners.en:null 'version' : cannot be empty or null
at org.sherlok.utils.CheckThat.checkOnlyAlphanumDotUnderscore(CheckThat.java:44) ~[classes/:na]
at org.sherlok.mappings.Def.validate(Def.java:116) ~[classes/:na]
at org.sherlok.mappings.PipelineDef.validate(PipelineDef.java:214) ~[classes/:na]
at org.sherlok.FileBased.writePipeline(FileBased.java:209) ~[classes/:na]
at org.sherlok.FileBased.putPipeline(FileBased.java:139) ~[classes/:na]
... 15 common frames omitted
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
HTTP/1.1 400 Bad Request
Content-Type: application/json
Content-Length: 4420
Server: Jetty(9.0.2.v20130417)
{
"cause": {
"cause": null,
"localizedMessage": "opennlp.ners.en:null 'version' : cannot be empty or null",
"map": null,
"message": "opennlp.ners.en:null 'version' : cannot be empty or null",
"stackTrace": [
{
"className": "org.sherlok.utils.CheckThat",
"fileName": "CheckThat.java",
"lineNumber": 44,
"methodName": "checkOnlyAlphanumDotUnderscore",
"nativeMethod": false
},
{
"className": "org.sherlok.mappings.Def",
"fileName": "Def.java",
"lineNumber": 116,
"methodName": "validate",
"nativeMethod": false
},
{
"className": "org.sherlok.mappings.PipelineDef",
"fileName": "PipelineDef.java",
"lineNumber": 214,
"methodName": "validate",
"nativeMethod": false
},
{
"className": "org.sherlok.FileBased",
"fileName": "FileBased.java",
"lineNumber": 209,
"methodName": "writePipeline",
"nativeMethod": false
},
{
"className": "org.sherlok.FileBased",
"fileName": "FileBased.java",
"lineNumber": 139,
"methodName": "putPipeline",
"nativeMethod": false
},
{
"className": "org.sherlok.Controller",
"fileName": "Controller.java",
"lineNumber": 183,
"methodName": "putPipeline",
"nativeMethod": false
},
{
"className": "org.sherlok.SherlokServer$8",
"fileName": "SherlokServer.java",
"lineNumber": 286,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "spark.webserver.MatcherFilter",
"fileName": "MatcherFilter.java",
"lineNumber": 139,
"methodName": "doFilter",
"nativeMethod": false
},
{
"className": "spark.webserver.JettyHandler",
"fileName": "JettyHandler.java",
"lineNumber": 54,
"methodName": "doHandle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.session.SessionHandler",
"fileName": "SessionHandler.java",
"lineNumber": 179,
"methodName": "doScope",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.handler.ScopedHandler",
"fileName": "ScopedHandler.java",
"lineNumber": 136,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.handler.HandlerList",
"fileName": "HandlerList.java",
"lineNumber": 52,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.handler.HandlerWrapper",
"fileName": "HandlerWrapper.java",
"lineNumber": 97,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.Server",
"fileName": "Server.java",
"lineNumber": 451,
"methodName": "handle",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.HttpChannel",
"fileName": "HttpChannel.java",
"lineNumber": 252,
"methodName": "run",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.server.HttpConnection",
"fileName": "HttpConnection.java",
"lineNumber": 266,
"methodName": "onFillable",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.io.AbstractConnection$ReadCallback",
"fileName": "AbstractConnection.java",
"lineNumber": 240,
"methodName": "run",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.util.thread.QueuedThreadPool",
"fileName": "QueuedThreadPool.java",
"lineNumber": 596,
"methodName": "runJob",
"nativeMethod": false
},
{
"className": "org.eclipse.jetty.util.thread.QueuedThreadPool$3",
"fileName": "QueuedThreadPool.java",
"lineNumber": 527,
"methodName": "run",
"nativeMethod": false
},
{
"className": "java.lang.Thread",
"fileName": "Thread.java",
"lineNumber": 745,
"methodName": "run",
"nativeMethod": false
}
],
"suppressed": [
]
},
"error_value": "{\r\n \"cause\" : null,\r\n \"error_value\" : \"opennlp.ners.en:null 'version' : cannot be empty or null\"\r\n}"
}
DEBUG starting test test040GetTestPipeline(org.sherlok.integration.PipelineApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:50]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 157
Server: Jetty(9.0.2.v20130417)
{
"name": "test",
"version": "1",
"domain": "test",
"script": [
"ENGINE languageidentifier:1.7.0"
],
"output": {
},
"tests": [
]
}
DEBUG starting test test041GetFaultyTestPipeline(org.sherlok.integration.PipelineApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:50]
INFO could not GET pipeline 'test' null [o.s.SherlokServer 20:31:50]
org.sherlok.utils.ValidationException: null
at org.sherlok.SherlokServer$7.handle(SherlokServer.java:273) ~[classes/:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_79]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
HTTP/1.1 400 Bad Request
Content-Type: application/json
Content-Length: 75
Server: Jetty(9.0.2.v20130417)
{
"message": "pipeline id",
"not_found": "test:1000000000198198"
}
DEBUG starting test test050DeletePipeline(org.sherlok.integration.PipelineApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:50]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 57
Server: Jetty(9.0.2.v20130417)
{
"pipeline_id": "test:1",
"status": "deleted"
}
DEBUG starting test test060GetTestPipelineGone(org.sherlok.integration.PipelineApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:50]
INFO could not GET pipeline 'test' null [o.s.SherlokServer 20:31:50]
org.sherlok.utils.ValidationException: null
at org.sherlok.SherlokServer$7.handle(SherlokServer.java:273) ~[classes/:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_79]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:50]
HTTP/1.1 400 Bad Request
Content-Type: application/json
Content-Length: 60
Server: Jetty(9.0.2.v20130417)
{
"message": "pipeline id",
"not_found": "test:1"
}
>>> Spark shutting down...done
Tests run: 10, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.852 sec
Running org.sherlok.integration.PipelineLoaderIntegrationTest
DEBUG starting test testResolve(org.sherlok.integration.PipelineLoaderIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:51]
INFO Done loading from local File store (local_repo): 11 bundles, 25 engines, 14 pipelines [o.s.Controller 20:31:51]
DEBUG {"_context" : {
"_types" : {
"DocumentAnnotation" : {"_id" : "uima.tcas.DocumentAnnotation",
"_feature_types" : {"sofa" : "_ref" } },
"NamedEntity" : {"_id" : "de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity",
"_feature_types" : {"sofa" : "_ref" } },
"Sofa" : {"_id" : "uima.cas.Sofa",
"_feature_types" : {"sofaArray" : "_ref" } },
"Annotation" : {"_id" : "uima.tcas.Annotation",
"_feature_types" : {"sofa" : "_ref" },
"_subtypes" : ["DocumentAnnotation", "NamedEntity" ] },
"AnnotationBase" : {"_id" : "uima.cas.AnnotationBase",
"_feature_types" : {"sofa" : "_ref" },
"_subtypes" : ["Annotation" ] },
"TOP" : {"_id" : "uima.cas.TOP",
"_subtypes" : ["AnnotationBase", "Sofa" ] } } },
"_views" : {
"_InitialView" : {
"DocumentAnnotation" : [
{"sofa" : 1, "begin" : 0, "end" : 133, "language" : "en" } ],
"NamedEntity" : [
{"sofa" : 1, "begin" : 0, "end" : 11, "value" : "person" },
{"sofa" : 1, "begin" : 36, "end" : 43, "value" : "location" },
{"sofa" : 1, "begin" : 60, "end" : 71, "value" : "person" } ] } },
"_referenced_fss" : {
"1" : {"_type" : "Sofa", "sofaNum" : 1, "sofaID" : "_InitialView", "mimeType" : "text", "sofaString" : "Jack Burton (born April 29, 1954 in El Paso), also known as Jake Burton, is an American snowboarder and founder of Burton Snowboards." } } } [o.s.i.PipelineLoaderIntegrationTest 20:31:58]
DEBUG starting test testNaturalOrdering(org.sherlok.integration.PipelineLoaderIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:58]
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.453 sec
Running org.sherlok.integration.ResourcesApiIntegrationTest
INFO Done loading from local File store (local_repo): 11 bundles, 25 engines, 14 pipelines [o.s.Controller 20:31:58]
== Spark has ignited ...
>> Listening on 0.0.0.0:9610
DEBUG starting test test010GetResources(org.sherlok.integration.ResourcesApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:59]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:59]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:59]
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 80
Server: Jetty(9.0.2.v20130417)
[
"countries.txt",
"test\\test030PostResource.txt",
"test\\testUploadFile.txt"
]
DEBUG starting test test020GetResource(org.sherlok.integration.ResourcesApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:59]
DEBUG Parsing response as: application/octet-stream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:59]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:59]
HTTP/1.1 200 OK
Content-Type: application/octet-stream
Content-Disposition: attachment; filename="countries.txt"
Content-Length: 1843
Server: Jetty(9.0.2.v20130417)
Afghanistan
Albania
Algeria
Andorra
Angola
Antigua & Deps
Argentina
Armenia
Australia
Austria
Azerbaijan
Bahamas
Bahrain
Bangladesh
Barbados
Belarus
Belgium
Belize
Benin
Bhutan
Bolivia
Bosnia Herzegovina
Botswana
Brazil
Brunei
Bulgaria
Burkina
Burundi
Cambodia
Cameroon
Canada
Cape Verde
Central African Rep
Chad
Chile
China
Colombia
Comoros
Congo
Congo {Democratic Rep}
Costa Rica
Croatia
Cuba
Cyprus
Czech Republic
Denmark
Djibouti
Dominica
Dominican Republic
East Timor
Ecuador
Egypt
El Salvador
Equatorial Guinea
Eritrea
Estonia
Ethiopia
Fiji
Finland
France
Gabon
Gambia
Georgia
Germany
Ghana
Greece
Grenada
Guatemala
Guinea
Guinea-Bissau
Guyana
Haiti
Honduras
Hungary
Iceland
India
Indonesia
Iran
Iraq
Ireland {Republic}
Israel
Italy
Ivory Coast
Jamaica
Japan
Jordan
Kazakhstan
Kenya
Kiribati
Korea North
Korea South
Kosovo
Kuwait
Kyrgyzstan
Laos
Latvia
Lebanon
Lesotho
Liberia
Libya
Liechtenstein
Lithuania
Luxembourg
Macedonia
Madagascar
Malawi
Malaysia
Maldives
Mali
Malta
Marshall Islands
Mauritania
Mauritius
Mexico
Micronesia
Moldova
Monaco
Mongolia
Montenegro
Morocco
Mozambique
Myanmar, {Burma}
Namibia
Nauru
Nepal
Netherlands
New Zealand
Nicaragua
Niger
Nigeria
Norway
Oman
Pakistan
Palau
Panama
Papua New Guinea
Paraguay
Peru
Philippines
Poland
Portugal
Qatar
Romania
Russian Federation
Rwanda
St Kitts & Nevis
St Lucia
Saint Vincent & the Grenadines
Samoa
San Marino
Sao Tome & Principe
Saudi Arabia
Senegal
Serbia
Seychelles
Sierra Leone
Singapore
Slovakia
Slovenia
Solomon Islands
Somalia
South Africa
South Sudan
Spain
Sri Lanka
Sudan
Suriname
Swaziland
Sweden
Switzerland
Syria
Taiwan
Tajikistan
Tanzania
Thailand
Togo
Tonga
Trinidad & Tobago
Tunisia
Turkey
Turkmenistan
Tuvalu
Uganda
Ukraine
United Arab Emirates
United Kingdom
United States
Uruguay
Uzbekistan
Vanuatu
Vatican City
Venezuela
Vietnam
Yemen
Zambia
Zimbabwe
DEBUG starting test test030PostTestResource(org.sherlok.integration.ResourcesApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:59]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:59]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:59]
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 81
Server: Jetty(9.0.2.v20130417)
{
"resource_path": "test/test030PostResource.txt",
"status": "created"
}
DEBUG starting test test031PostWrongTestResourceWithDots(org.sherlok.integration.ResourcesApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:59]
INFO could not POST resource '' path cannot contain '..' [o.s.SherlokServer 20:31:59]
org.sherlok.utils.ValidationException: path cannot contain '..'
at org.sherlok.utils.CheckThat.validateArgument(CheckThat.java:125) ~[classes/:na]
at org.sherlok.FileBased.putResource(FileBased.java:157) ~[classes/:na]
at org.sherlok.Controller.putResource(Controller.java:189) ~[classes/:na]
at org.sherlok.SherlokServer$16.handle(SherlokServer.java:442) ~[classes/:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_79]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:59]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:31:59]
HTTP/1.1 400 Bad Request
Content-Type: application/json
Content-Length: 69
Server: Jetty(9.0.2.v20130417)
{
"cause": null,
"error_value": "path cannot contain '..'"
}
DEBUG starting test test032PostWrongEmptyTestResource(org.sherlok.integration.ResourcesApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:31:59]
INFO could not POST resource '' path cannot contain '..' [o.s.SherlokServer 20:32:00]
org.sherlok.utils.ValidationException: path cannot contain '..'
at org.sherlok.utils.CheckThat.validateArgument(CheckThat.java:125) ~[classes/:na]
at org.sherlok.FileBased.putResource(FileBased.java:157) ~[classes/:na]
at org.sherlok.Controller.putResource(Controller.java:189) ~[classes/:na]
at org.sherlok.SherlokServer$16.handle(SherlokServer.java:442) ~[classes/:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_79]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:32:00]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:32:00]
HTTP/1.1 400 Bad Request
Content-Type: application/json
Content-Length: 69
Server: Jetty(9.0.2.v20130417)
{
"cause": null,
"error_value": "path cannot contain '..'"
}
DEBUG starting test test033PostWrongNoTestResource(org.sherlok.integration.ResourcesApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:32:00]
INFO could not POST resource: Invalid part 'file' null [o.s.SherlokServer 20:32:00]
org.sherlok.utils.ValidationException: null
at org.sherlok.SherlokServer$16.handle(SherlokServer.java:437) [classes/:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_79]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:32:00]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:32:00]
HTTP/1.1 400 Bad Request
Content-Type: application/json
Content-Length: 55
Server: Jetty(9.0.2.v20130417)
{
"error": "Content-Type != multipart/form-data"
}
DEBUG starting test test040GetTestResource(org.sherlok.integration.ResourcesApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:32:00]
DEBUG Parsing response as: application/octet-stream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:32:00]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:32:00]
HTTP/1.1 200 OK
Content-Type: application/octet-stream
Content-Disposition: attachment; filename="/test030PostResource.txt"
Content-Length: 11
Server: Jetty(9.0.2.v20130417)
hello world
DEBUG starting test test050DeleteResource(org.sherlok.integration.ResourcesApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:32:00]
INFO could not DELETE resource '' could not delete file 'test/test030PostResource.txt' [o.s.SherlokServer 20:32:00]
org.sherlok.utils.ValidationException: could not delete file 'test/test030PostResource.txt'
at org.sherlok.utils.CheckThat.validateArgument(CheckThat.java:125) ~[classes/:na]
at org.sherlok.FileBased.deleteResource(FileBased.java:353) ~[classes/:na]
at org.sherlok.Controller.deleteResource(Controller.java:213) ~[classes/:na]
at org.sherlok.SherlokServer$17.handle(SherlokServer.java:458) ~[classes/:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_79]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:32:00]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:32:00]
HTTP/1.1 400 Bad Request
Content-Type: application/json
Content-Length: 97
Server: Jetty(9.0.2.v20130417)
{
"cause": null,
"error_value": "could not delete file 'test/test030PostResource.txt'"
}
DEBUG starting test test060ResourceShouldBeGone(org.sherlok.integration.ResourcesApiIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:32:00]
DEBUG Parsing response as: application/octet-stream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:32:00]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:32:00]
HTTP/1.1 200 OK
Content-Type: application/octet-stream
Content-Disposition: attachment; filename="/test030PostResource.txt"
Content-Length: 11
Server: Jetty(9.0.2.v20130417)
hello world
>>> Spark shutting down...done
Tests run: 9, Failures: 2, Errors: 0, Skipped: 0, Time elapsed: 2.196 sec <<< FAILURE!
test050DeleteResource(org.sherlok.integration.ResourcesApiIntegrationTest) Time elapsed: 0.063 sec <<< FAILURE!
java.lang.AssertionError: Expected status code <200> doesn't match actual status code <400>.
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:77)
at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:102)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:57)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:182)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:190)
at com.jayway.restassured.internal.ResponseSpecificationImpl$HamcrestAssertionClosure.validate(ResponseSpecificationImpl.groovy:572)
at com.jayway.restassured.internal.ResponseSpecificationImpl$HamcrestAssertionClosure$validate$1.call(Unknown Source)
at com.jayway.restassured.internal.ResponseSpecificationImpl.validateResponseIfRequired(ResponseSpecificationImpl.groovy:731)
at com.jayway.restassured.internal.ResponseSpecificationImpl.this$2$validateResponseIfRequired(ResponseSpecificationImpl.groovy)
at com.jayway.restassured.internal.ResponseSpecificationImpl$this$2$validateResponseIfRequired$1.callCurrent(Unknown Source)
at com.jayway.restassured.internal.ResponseSpecificationImpl.statusCode(ResponseSpecificationImpl.groovy:106)
at com.jayway.restassured.specification.ResponseSpecification$statusCode$0.callCurrent(Unknown Source)
at com.jayway.restassured.internal.ResponseSpecificationImpl.statusCode(ResponseSpecificationImpl.groovy:114)
at com.jayway.restassured.internal.ValidatableResponseOptionsImpl.statusCode(ValidatableResponseOptionsImpl.java:114)
at org.sherlok.integration.ResourcesApiIntegrationTest.test050DeleteResource(ResourcesApiIntegrationTest.java:139)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
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.rules.TestWatcher$1.evaluate(TestWatcher.java:55)
at org.junit.rules.RunRules.evaluate(RunRules.java:20)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
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$2.evaluate(ParentRunner.java:268)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
at org.apache.maven.surefire.booter.ProviderFactory$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)
test060ResourceShouldBeGone(org.sherlok.integration.ResourcesApiIntegrationTest) Time elapsed: 0.015 sec <<< FAILURE!
java.lang.AssertionError: Expected status code <404> doesn't match actual status code <200>.
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:77)
at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:102)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:190)
at com.jayway.restassured.internal.ResponseSpecificationImpl$HamcrestAssertionClosure.validate(ResponseSpecificationImpl.groovy:572)
at com.jayway.restassured.internal.ResponseSpecificationImpl$HamcrestAssertionClosure$validate$1.call(Unknown Source)
at com.jayway.restassured.internal.ResponseSpecificationImpl.validateResponseIfRequired(ResponseSpecificationImpl.groovy:731)
at com.jayway.restassured.internal.ResponseSpecificationImpl.this$2$validateResponseIfRequired(ResponseSpecificationImpl.groovy)
at com.jayway.restassured.internal.ResponseSpecificationImpl$this$2$validateResponseIfRequired$1.callCurrent(Unknown Source)
at com.jayway.restassured.internal.ResponseSpecificationImpl.statusCode(ResponseSpecificationImpl.groovy:106)
at com.jayway.restassured.specification.ResponseSpecification$statusCode$0.callCurrent(Unknown Source)
at com.jayway.restassured.internal.ResponseSpecificationImpl.statusCode(ResponseSpecificationImpl.groovy:114)
at com.jayway.restassured.internal.ValidatableResponseOptionsImpl.statusCode(ValidatableResponseOptionsImpl.java:114)
at org.sherlok.integration.ResourcesApiIntegrationTest.test060ResourceShouldBeGone(ResourcesApiIntegrationTest.java:145)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
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.rules.TestWatcher$1.evaluate(TestWatcher.java:55)
at org.junit.rules.RunRules.evaluate(RunRules.java:20)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
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$2.evaluate(ParentRunner.java:268)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
at org.apache.maven.surefire.booter.ProviderFactory$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.sherlok.integration.RutaIntegrationTest
DEBUG starting test test010_NeuronerAnnotate(org.sherlok.integration.RutaIntegrationTest) [o.s.i.MethodNameLoggerWatcher 20:32:00]
INFO Done loading from local File store (local_repo): 11 bundles, 25 engines, 14 pipelines [o.s.Controller 20:32:00]
== Spark has ignited ...
>> Listening on 0.0.0.0:9609
WARN Request (GET /annotate/neuroner?text=Layer%20V%20and%20layer%20iii%20large%20pyramidal%20neurons.%20slowly%20adapting%20stretch%20receptor%20neuron)@1120499783 org.eclipse.jetty.server.Request@42c97847 doesn't contain any value for param version [o.s.SherlokServer 20:32:01]
INFO Error in line 13, "c9dbab29": expected SEMI, but found Identifier
Error in line 13, "/": expected SEMI, but found SLASH
[o.s.UimaPipeline 20:32:16]
ERROR Error in line 13, "c9dbab29": expected SEMI, but found Identifier
Error in line 13, "/": expected SEMI, but found SLASH
[o.s.UimaPipeline 20:32:16]
INFO could not annotate text 'Layer V and layer iii large pyramidal neurons. slowly adapting stretch receptor neuron' null [o.s.SherlokServer 20:32:16]
org.sherlok.utils.ValidationException: null
at org.sherlok.UimaPipeline.initEngines(UimaPipeline.java:244) ~[classes/:na]
at org.sherlok.UimaPipeline.<init>(UimaPipeline.java:122) ~[classes/:na]
at org.sherlok.PipelineLoader.load(PipelineLoader.java:183) ~[classes/:na]
at org.sherlok.PipelineLoader.resolvePipeline(PipelineLoader.java:139) ~[classes/:na]
at org.sherlok.SherlokServer.annotateRequest(SherlokServer.java:497) ~[classes/:na]
at org.sherlok.SherlokServer$1.handle(SherlokServer.java:140) [classes/:na]
at spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139) [spark-core-1.1.1.jar:na]
at spark.webserver.JettyHandler.doHandle(JettyHandler.java:54) [spark-core-1.1.1.jar:na]
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.Server.handle(Server.java:451) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266) [jetty-server-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240) [jetty-io-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527) [jetty-util-9.0.2.v20130417.jar:9.0.2.v20130417]
at java.lang.Thread.run(Thread.java:745) [na:1.7.0_79]
DEBUG Parsing response as: application/json [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:32:16]
DEBUG Parsed data to instance of: class org.apache.http.conn.EofSensorInputStream [c.j.r.i.RequestSpecificationImpl$RestAssuredHttpBuilder 20:32:16]
HTTP/1.1 400 Bad Request
Content-Type: application/json
Content-Length: 3263
Server: Jetty(9.0.2.v20130417)
{
"message": "Ruta script error",
"error_value": "java.lang.ClassCastException: org.apache.uima.ruta.expression.resource.ReferenceWordTableExpression cannot be cast to java.lang.String\r\n\tat org.apache.uima.ruta.RutaEnvironment.getLiteralValue(RutaEnvironment.java:724)\r\n\tat org.apache.uima.ruta.parser.RutaParser.setValue(RutaParser.java:394)\r\n\tat org.apache.uima.ruta.parser.RutaParser.variableDeclaration(RutaParser.java:1511)\r\n\tat org.apache.uima.ruta.parser.RutaParser.statement(RutaParser.java:910)\r\n\tat org.apache.uima.ruta.parser.RutaParser.statements(RutaParser.java:678)\r\n\tat org.apache.uima.ruta.parser.RutaParser.file_input(RutaParser.java:586)\r\n\tat org.apache.uima.ruta.engine.RutaEngine.loadScript(RutaEngine.java:933)\r\n\tat org.apache.uima.ruta.engine.RutaEngine.initializeScript(RutaEngine.java:685)\r\n\tat org.apache.uima.ruta.engine.RutaEngine.initialize(RutaEngine.java:466)\r\n\tat org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:262)\r\n\tat org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:169)\r\n\tat org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)\r\n\tat org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)\r\n\tat org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279)\r\n\tat org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:331)\r\n\tat org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:448)\r\n\tat org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:205)\r\n\tat org.sherlok.UimaPipeline.createEngines(UimaPipeline.java:270)\r\n\tat org.sherlok.UimaPipeline.initEngines(UimaPipeline.java:228)\r\n\tat org.sherlok.UimaPipeline.<init>(UimaPipeline.java:122)\r\n\tat org.sherlok.PipelineLoader.load(PipelineLoader.java:183)\r\n\tat org.sherlok.PipelineLoader.resolvePipeline(PipelineLoader.java:139)\r\n\tat org.sherlok.SherlokServer.annotateRequest(SherlokServer.java:497)\r\n\tat org.sherlok.SherlokServer$1.handle(SherlokServer.java:140)\r\n\tat spark.webserver.MatcherFilter.doFilter(MatcherFilter.java:139)\r\n\tat spark.webserver.JettyHandler.doHandle(JettyHandler.java:54)\r\n\tat org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:179)\r\n\tat org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136)\r\n\tat org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52)\r\n\tat org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97)\r\n\tat org.eclipse.jetty.server.Server.handle(Server.java:451)\r\n\tat org.eclipse.jetty.server.HttpChannel.run(HttpChannel.java:252)\r\n\tat org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:266)\r\n\tat org.eclipse.jetty.io.AbstractConnection$ReadCallback.run(AbstractConnection.java:240)\r\n\tat org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:596)\r\n\tat org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:527)\r\n\tat java.lang.Thread.run(Thread.java:745)\r\n"
}
Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 15.764 sec <<< FAILURE!
test010_NeuronerAnnotate(org.sherlok.integration.RutaIntegrationTest) Time elapsed: 15.764 sec <<< FAILURE!
java.lang.AssertionError: Expected status code <200> doesn't match actual status code <400>.
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:77)
at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:102)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:190)
at com.jayway.restassured.internal.ResponseSpecificationImpl$HamcrestAssertionClosure.validate(ResponseSpecificationImpl.groovy:572)
at com.jayway.restassured.internal.ResponseSpecificationImpl$HamcrestAssertionClosure$validate$1.call(Unknown Source)
at com.jayway.restassured.internal.ResponseSpecificationImpl.validateResponseIfRequired(ResponseSpecificationImpl.groovy:731)
at com.jayway.restassured.internal.ResponseSpecificationImpl.this$2$validateResponseIfRequired(ResponseSpecificationImpl.groovy)
at com.jayway.restassured.internal.ResponseSpecificationImpl$this$2$validateResponseIfRequired$1.callCurrent(Unknown Source)
at com.jayway.restassured.internal.ResponseSpecificationImpl.statusCode(ResponseSpecificationImpl.groovy:106)
at com.jayway.restassured.specification.ResponseSpecification$statusCode$0.callCurrent(Unknown Source)
at com.jayway.restassured.internal.ResponseSpecificationImpl.statusCode(ResponseSpecificationImpl.groovy:114)
at com.jayway.restassured.internal.ValidatableResponseOptionsImpl.statusCode(ValidatableResponseOptionsImpl.java:114)
at org.sherlok.integration.RutaIntegrationTest.test010_NeuronerAnnotate(RutaIntegrationTest.java:68)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
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.rules.TestWatcher$1.evaluate(TestWatcher.java:55)
at org.junit.rules.RunRules.evaluate(RunRules.java:20)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
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$2.evaluate(ParentRunner.java:268)
at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
at org.apache.maven.surefire.booter.ProviderFactory$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.sherlok.integration.SlaveModeIntegrationTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 1, Time elapsed: 0 sec
Running org.sherlok.integration.TestApiIntegrationTest
INFO Done loading from local File store (local_repo): 11 bundles, 25 engines, 14 pipelines [o.s.Controller 20:32:16]
>>> Spark shutting down...done
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.939 sec <<< FAILURE!
org.sherlok.integration.TestApiIntegrationTest Time elapsed: 0.939 sec <<< ERROR!
java.lang.IllegalStateException: This must be done before route mapping has begun
at spark.Spark.throwBeforeRouteMappingException(Spark.java:320)
at spark.Spark.setPort(Spark.java:97)
at org.sherlok.SherlokServer.init(SherlokServer.java:129)
at org.sherlok.integration.TestApiIntegrationTest.beforeClass(TestApiIntegrationTest.java:64)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:50)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:47)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
at org.apache.maven.surefire.booter.ProviderFactory$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.sherlok.mappings.BundleDefTest
Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec
Running org.sherlok.mappings.JsonAnnotationTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec
Running org.sherlok.mappings.PipelineDefTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec
Running org.sherlok.mappings.SherlokResultTest
Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec
Running org.sherlok.MavenPomTest
INFO Done loading from local File store (local_repo): 11 bundles, 25 engines, 14 pipelines [o.s.Controller 20:32:17]
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 sec
Running org.sherlok.RutaHelperTest
Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec
Running org.sherlok.SherlokServerArgsTest
Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec
Running org.sherlok.UimaPipelineTest
INFO Done loading from local File store (local_repo): 11 bundles, 25 engines, 14 pipelines [o.s.Controller 20:32:17]
DEBUG {"_context" : {
"_types" : {
"DocumentAnnotation" : {"_id" : "uima.tcas.DocumentAnnotation",
"_feature_types" : {"sofa" : "_ref" } },
"Dog" : {"_id" : "org.sherlok.ruta.Dog",
"_feature_types" : {"sofa" : "_ref" } },
"Sofa" : {"_id" : "uima.cas.Sofa",
"_feature_types" : {"sofaArray" : "_ref" } },
"Annotation" : {"_id" : "uima.tcas.Annotation",
"_feature_types" : {"sofa" : "_ref" },
"_subtypes" : ["DocumentAnnotation", "Dog" ] },
"AnnotationBase" : {"_id" : "uima.cas.AnnotationBase",
"_feature_types" : {"sofa" : "_ref" },
"_subtypes" : ["Annotation" ] },
"TOP" : {"_id" : "uima.cas.TOP",
"_subtypes" : ["AnnotationBase", "Sofa" ] } } },
"_views" : {
"_InitialView" : {
"DocumentAnnotation" : [
{"sofa" : 1, "begin" : 0, "end" : 3, "language" : "en" } ],
"Dog" : [
{"sofa" : 1, "begin" : 0, "end" : 3 } ] } },
"_referenced_fss" : {
"1" : {"_type" : "Sofa", "sofaNum" : 1, "sofaID" : "_InitialView", "mimeType" : "text", "sofaString" : "dog" } } } [o.s.UimaPipelineTest 20:32:18]
INFO Done loading from local File store (local_repo): 11 bundles, 25 engines, 14 pipelines [o.s.Controller 20:32:18]
INFO Done loading from local File store (local_repo): 11 bundles, 25 engines, 14 pipelines [o.s.Controller 20:32:22]
WARN no tests for pipeline 'testUseUimaEngines:0.1' [o.s.mappings.Def 20:32:22]
WARN failed to add feature 'uima.cas.NonEmptyFSList:head' to type 'uima.cas.NonEmptyFSList': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.cas.NonEmptyFSList:tail' to type 'uima.cas.NonEmptyFSList': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.cas.NonEmptyFloatList:head' to type 'uima.cas.NonEmptyFloatList': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.cas.NonEmptyFloatList:tail' to type 'uima.cas.NonEmptyFloatList': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.cas.NonEmptyIntegerList:head' to type 'uima.cas.NonEmptyIntegerList': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.cas.NonEmptyIntegerList:tail' to type 'uima.cas.NonEmptyIntegerList': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.cas.NonEmptyStringList:head' to type 'uima.cas.NonEmptyStringList': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.cas.NonEmptyStringList:tail' to type 'uima.cas.NonEmptyStringList': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.cas.Sofa:sofaNum' to type 'uima.cas.Sofa': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.cas.Sofa:sofaID' to type 'uima.cas.Sofa': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.cas.Sofa:mimeType' to type 'uima.cas.Sofa': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.cas.Sofa:sofaArray' to type 'uima.cas.Sofa': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.cas.Sofa:sofaString' to type 'uima.cas.Sofa': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.cas.Sofa:sofaURI' to type 'uima.cas.Sofa': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.cas.AnnotationBase:sofa' to type 'uima.cas.AnnotationBase': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.cas.AnnotationBase:sofa' to type 'uima.tcas.Annotation': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.tcas.Annotation:begin' to type 'uima.tcas.Annotation': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.tcas.Annotation:end' to type 'uima.tcas.Annotation': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.cas.AnnotationBase:sofa' to type 'uima.tcas.DocumentAnnotation': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.tcas.Annotation:begin' to type 'uima.tcas.DocumentAnnotation': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.tcas.Annotation:end' to type 'uima.tcas.DocumentAnnotation': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
WARN failed to add feature 'uima.tcas.DocumentAnnotation:language' to type 'uima.tcas.DocumentAnnotation': null [o.a.u.c.i.FilteringTypeSystem 20:32:23]
DEBUG {"_context" : {
"_types" : {
"ART" : {"_id" : "de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.ART",
"_feature_types" : {"sofa" : "_ref" } },
"DocumentAnnotation" : {"_id" : "uima.tcas.DocumentAnnotation",
"_feature_types" : {"sofa" : "_ref" } },
"FSArray" : {"_id" : "uima.cas.FSArray" },
"NN" : {"_id" : "de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.NN",
"_feature_types" : {"sofa" : "_ref" } },
"PUNC" : {"_id" : "de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.PUNC",
"_feature_types" : {"sofa" : "_ref" } },
"Sentence" : {"_id" : "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Sentence",
"_feature_types" : {"sofa" : "_ref" } },
"Sofa" : {"_id" : "uima.cas.Sofa",
"_feature_types" : {"sofaArray" : "_ref" } },
"TagsetDescription" : {"_id" : "de.tudarmstadt.ukp.dkpro.core.api.metadata.type.TagsetDescription",
"_feature_types" : {"sofa" : "_ref", "tags" : "_ref" } },
"Token" : {"_id" : "de.tudarmstadt.ukp.dkpro.core.api.segmentation.type.Token",
"_feature_types" : {"sofa" : "_ref", "parent" : "_ref", "lemma" : "_ref", "stem" : "_ref", "pos" : "_ref", "morph" : "_ref" } },
"POS" : {"_id" : "de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS",
"_feature_types" : {"sofa" : "_ref" },
"_subtypes" : ["ART", "N", "PUNC" ] },
"Annotation" : {"_id" : "uima.tcas.Annotation",
"_feature_types" : {"sofa" : "_ref" },
"_subtypes" : ["POS", "DocumentAnnotation", "Sentence", "TagsetDescription", "Token" ] },
"AnnotationBase" : {"_id" : "uima.cas.AnnotationBase",
"_feature_types" : {"sofa" : "_ref" },
"_subtypes" : ["Annotation" ] },
"TOP" : {"_id" : "uima.cas.TOP",
"_subtypes" : ["AnnotationBase", "ArrayBase", "Sofa" ] },
"ArrayBase" : {"_id" : "uima.cas.ArrayBase",
"_subtypes" : ["FSArray" ] },
"N" : {"_id" : "de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.N",
"_feature_types" : {"sofa" : "_ref" },
"_subtypes" : ["NN" ] } } },
"_views" : {
"_InitialView" : {
"DocumentAnnotation" : [
{"sofa" : 1, "begin" : 0, "end" : 18, "language" : "en" } ],
"PUNC" : [274 ],
"TagsetDescription" : [
{"sofa" : 1, "begin" : 0, "end" : 18, "layer" : "de.tudarmstadt.ukp.dkpro.core.api.lexmorph.type.pos.POS", "name" : "ptb", "tags" : [
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" },
{"_type" : "TagDescription" } ] } ],
"Sentence" : [
{"sofa" : 1, "begin" : 0, "end" : 18 } ],
"Token" : [
{"sofa" : 1, "begin" : 0, "end" : 1, "pos" : 259 },
{"sofa" : 1, "begin" : 2, "end" : 8, "pos" : 264 },
{"sofa" : 1, "begin" : 9, "end" : 17, "pos" : 269 },
{"sofa" : 1, "begin" : 17, "end" : 18, "pos" : 274 } ],
"ART" : [259 ],
"NN" : [264, 269 ] } },
"_referenced_fss" : {
"1" : {"_type" : "Sofa", "sofaNum" : 1, "sofaID" : "_InitialView", "mimeType" : "text", "sofaString" : "A sample sentence." },
"259" : {"_type" : "ART", "sofa" : 1, "begin" : 0, "end" : 1, "PosValue" : "DT" },
"264" : {"_type" : "NN", "sofa" : 1, "begin" : 2, "end" : 8, "PosValue" : "NN" },
"269" : {"_type" : "NN", "sofa" : 1, "begin" : 9, "end" : 17, "PosValue" : "NN" },
"274" : {"_type" : "PUNC", "sofa" : 1, "begin" : 17, "end" : 18, "PosValue" : "." } } } [o.s.UimaPipelineTest 20:32:24]
INFO Done loading from local File store (local_repo): 11 bundles, 25 engines, 14 pipelines [o.s.Controller 20:32:24]
DEBUG {"_referenced_fss":{"1":{"begin":0,"end":0,"properties":{"sofaString":"The dog walks on the lake.","_type":"Sofa","sofaID":"_InitialView","sofaNum":1,"mimeType":"text"}}},"_views":{"_InitialView":{"DocumentAnnotation":[{"sofa":1,"begin":0,"end":26,"language":"en"}],"Dependency":[{"sofa":1,"begin":0,"end":3,"Governor":{"_type":"Token","sofa":1,"begin":4,"end":7},"Dependent":{"_type":"Token","sofa":1,"begin":0,"end":3},"DependencyType":"det"},{"sofa":1,"begin":4,"end":7,"Governor":{"_type":"Token","sofa":1,"begin":8,"end":13},"Dependent":{"_type":"Token","sofa":1,"begin":4,"end":7},"DependencyType":"nsubj"},{"sofa":1,"begin":14,"end":16,"Governor":{"_type":"Token","sofa":1,"begin":8,"end":13},"Dependent":{"_type":"Token","sofa":1,"begin":14,"end":16},"DependencyType":"prep"},{"sofa":1,"begin":17,"end":20,"Governor":{"_type":"Token","sofa":1,"begin":21,"end":25},"Dependent":{"_type":"Token","sofa":1,"begin":17,"end":20},"DependencyType":"det"},{"sofa":1,"begin":21,"end":25,"Governor":{"_type":"Token","sofa":1,"begin":14,"end":16},"Dependent":{"_type":"Token","sofa":1,"begin":21,"end":25},"DependencyType":"pobj"},{"sofa":1,"begin":25,"end":26,"Governor":{"_type":"Token","sofa":1,"begin":8,"end":13},"Dependent":{"_type":"Token","sofa":1,"begin":25,"end":26},"DependencyType":"punct"}]}},"_context":{"_types":{"Dependency":{"_id":"de.tudarmstadt.ukp.dkpro.core.api.syntax.type.dependency.Dependency","_feature_types":{"sofa":"_ref","Governor":"_ref","Dependent":"_ref"}},"DocumentAnnotation":{"_id":"uima.tcas.DocumentAnnotation","_feature_types":{"sofa":"_ref"}},"Sofa":{"_id":"uima.cas.Sofa","_feature_types":{"sofaArray":"_ref"}},"Annotation":{"_id":"uima.tcas.Annotation","_feature_types":{"sofa":"_ref"},"_subtypes":["Dependency","DocumentAnnotation"]},"AnnotationBase":{"_id":"uima.cas.AnnotationBase","_feature_types":{"sofa":"_ref"},"_subtypes":["Annotation"]},"TOP":{"_id":"uima.cas.TOP","_subtypes":["AnnotationBase","Sofa"]}}},"_stats":null,"_types":null} [o.s.UimaPipelineTest 20:32:37]
INFO Done loading from local File store (local_repo): 11 bundles, 25 engines, 14 pipelines [o.s.Controller 20:32:37]
DEBUG {"_context" : {
"_types" : {
"Country" : {"_id" : "org.sherlok.ruta.Country",
"_feature_types" : {"sofa" : "_ref" } },
"DocumentAnnotation" : {"_id" : "uima.tcas.DocumentAnnotation",
"_feature_types" : {"sofa" : "_ref" } },
"Sofa" : {"_id" : "uima.cas.Sofa",
"_feature_types" : {"sofaArray" : "_ref" } },
"Annotation" : {"_id" : "uima.tcas.Annotation",
"_feature_types" : {"sofa" : "_ref" },
"_subtypes" : ["Country", "DocumentAnnotation" ] },
"AnnotationBase" : {"_id" : "uima.cas.AnnotationBase",
"_feature_types" : {"sofa" : "_ref" },
"_subtypes" : ["Annotation" ] },
"TOP" : {"_id" : "uima.cas.TOP",
"_subtypes" : ["AnnotationBase", "Sofa" ] } } },
"_views" : {
"_InitialView" : {
"DocumentAnnotation" : [
{"sofa" : 1, "begin" : 0, "end" : 11, "language" : "en" } ],
"Country" : [
{"sofa" : 1, "begin" : 0, "end" : 11 } ] } },
"_referenced_fss" : {
"1" : {"_type" : "Sofa", "sofaNum" : 1, "sofaID" : "_InitialView", "mimeType" : "text", "sofaString" : "Switzerland" } } } [o.s.UimaPipelineTest 20:32:39]
Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 20.437 sec
Running org.sherlok.utils.ConfigurationFieldParserTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 sec
Running org.sherlok.utils.SherlokTestsTest
DEBUG starting test testAllPipelines(org.sherlok.utils.SherlokTestsTest) [o.s.i.MethodNameLoggerWatcher 20:32:39]
INFO Done loading from local File store (local_repo): 11 bundles, 25 engines, 14 pipelines [o.s.Controller 20:32:39]
DEBUG testing bluima.chunk:1.0.1 [o.s.u.SherlokTestsTest 20:32:39]
DEBUG starting test testAnnotateDogs(org.sherlok.utils.SherlokTestsTest) [o.s.i.MethodNameLoggerWatcher 20:32:41]
INFO Done loading from local File store (local_repo): 11 bundles, 25 engines, 14 pipelines [o.s.Controller 20:32:41]
Tests run: 3, Failures: 0, Errors: 1, Skipped: 1, Time elapsed: 2.813 sec <<< FAILURE!
testAllPipelines(org.sherlok.utils.SherlokTestsTest) Time elapsed: 2.156 sec <<< ERROR!
{
"message" : "Failed to load pipeline: Could not find artifact de.jules:jules-utilities:jar:2.1.1 in local_default (file:/C:/Users/Marco/.m2/repository/)",
"error_value" : "bluima.chunk:1.0.1"
}
at org.sherlok.PipelineLoader.load(PipelineLoader.java:171)
at org.sherlok.PipelineLoader.resolvePipeline(PipelineLoader.java:139)
at org.sherlok.utils.SherlokTestsTest.testAllPipelines(SherlokTestsTest.java:78)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
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.rules.TestWatcher$1.evaluate(TestWatcher.java:55)
at org.junit.rules.RunRules.evaluate(RunRules.java:20)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
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$2.evaluate(ParentRunner.java:268)
at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:252)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:141)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:112)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189)
at org.apache.maven.surefire.booter.ProviderFactory$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)
Results :
Failed tests: test01_GetInexistentFile(org.sherlok.FileBasedTest): Expected exception: org.sherlok.utils.ValidationException
test04_ListFile(org.sherlok.FileBasedTest)
testReadNonexistentFile(org.sherlok.FileBasedTest): expected:<...19-8ff1-b9a8c46c7a1e[]> but was:<...19-8ff1-b9a8c46c7a1e[ (The system cannot find the file specified)]>
test050DeleteResource(org.sherlok.integration.ResourcesApiIntegrationTest): Expected status code <200> doesn't match actual status code <400>.(..)
test060ResourceShouldBeGone(org.sherlok.integration.ResourcesApiIntegrationTest): Expected status code <404> doesn't match actual status code <200>.(..)
test010_NeuronerAnnotate(org.sherlok.integration.RutaIntegrationTest): Expected status code <200> doesn't match actual status code <400>.(..)
Tests in error:
test05_DeleteFile(org.sherlok.FileBasedTest): could not delete file 'test/testUploadFile.txt'
org.sherlok.integration.TestApiIntegrationTest: This must be done before route mapping has begun
testAllPipelines(org.sherlok.utils.SherlokTestsTest)
Tests run: 119, Failures: 6, Errors: 3, Skipped: 2
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 02:01 min
[INFO] Finished at: 2015-05-13T20:32:42+02:00
[INFO] Final Memory: 15M/41M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.12.4:test (default-test) on project sherlok_core: There are test failures.
[ERROR]
[ERROR] Please refer to C:\Users\Marco\Desktop\sherlok\target\surefire-reports for the individual test results.
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException
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