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Changes:
[clin] python scripts that are needed for running keras-based CNN
[clin] Enable Convolutional Neural Network for event-time classification. May need further debug.
NeuralEventTimeRelationsEvaluation: will evaluate pre-trained embedding features.
NeuralEventTimeRelationsCNNEvaluation: will write sequece of tokens to feed in to the CNN.
Both above evals will evaluate the test instances within the cleartk framework.
[clin] add syntactic embedding features for classic event-event model
[clin] add syntactic features for classic event-time model
[clin] temporally remove confidence score from classification results for CNN implementation
[clin] modify the way to generate embedding features for CNN
[clin] relax the rule for removing non-contains relations
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Downloading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dependency-parser-res/maven-metadata.xml
Downloaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dependency-parser-res/maven-metadata.xml (405 B at 0.8 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dependency-parser-res/3.2.3-SNAPSHOT/maven-metadata.xml
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dependency-parser-res/3.2.3-SNAPSHOT/maven-metadata.xml (798 B at 0.2 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dependency-parser-res/maven-metadata.xml
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dependency-parser-res/maven-metadata.xml (405 B at 0.1 KB/sec)
[INFO] Deployment in https://repository.apache.org/content/repositories/snapshots (id=apache.snapshots.https,uniqueVersion=true)
Deploying the main artifact ctakes-dictionary-lookup-3.2.3-SNAPSHOT.jar
Downloading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup/3.2.3-SNAPSHOT/maven-metadata.xml
Downloaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup/3.2.3-SNAPSHOT/maven-metadata.xml (794 B at 0.8 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup/3.2.3-SNAPSHOT/ctakes-dictionary-lookup-3.2.3-20160720.133758-92.jar
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup/3.2.3-SNAPSHOT/ctakes-dictionary-lookup-3.2.3-20160720.133758-92.jar (129 KB at 26.0 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup/3.2.3-SNAPSHOT/ctakes-dictionary-lookup-3.2.3-20160720.133758-92.pom
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup/3.2.3-SNAPSHOT/ctakes-dictionary-lookup-3.2.3-20160720.133758-92.pom (3 KB at 3.1 KB/sec)
Downloading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup/maven-metadata.xml
Downloaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup/maven-metadata.xml (401 B at 0.2 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup/3.2.3-SNAPSHOT/maven-metadata.xml
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup/3.2.3-SNAPSHOT/maven-metadata.xml (794 B at 1.0 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup/maven-metadata.xml
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup/maven-metadata.xml (401 B at 0.5 KB/sec)
[INFO] Deployment in https://repository.apache.org/content/repositories/snapshots (id=apache.snapshots.https,uniqueVersion=true)
Deploying the main artifact ctakes-dictionary-lookup-fast-3.2.3-SNAPSHOT.jar
Downloading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast/3.2.3-SNAPSHOT/maven-metadata.xml
Downloaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast/3.2.3-SNAPSHOT/maven-metadata.xml (799 B at 0.7 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast/3.2.3-SNAPSHOT/ctakes-dictionary-lookup-fast-3.2.3-20160720.133813-91.jar
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast/3.2.3-SNAPSHOT/ctakes-dictionary-lookup-fast-3.2.3-20160720.133813-91.jar (118 KB at 85.0 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast/3.2.3-SNAPSHOT/ctakes-dictionary-lookup-fast-3.2.3-20160720.133813-91.pom
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast/3.2.3-SNAPSHOT/ctakes-dictionary-lookup-fast-3.2.3-20160720.133813-91.pom (3 KB at 0.6 KB/sec)
Downloading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast/maven-metadata.xml
Downloaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast/maven-metadata.xml (366 B at 0.7 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast/3.2.3-SNAPSHOT/maven-metadata.xml
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast/3.2.3-SNAPSHOT/maven-metadata.xml (799 B at 1.0 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast/maven-metadata.xml
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast/maven-metadata.xml (366 B at 0.5 KB/sec)
[INFO] Deployment in https://repository.apache.org/content/repositories/snapshots (id=apache.snapshots.https,uniqueVersion=true)
Deploying the main artifact ctakes-dictionary-lookup-fast-res-3.2.3-SNAPSHOT.jar
Downloading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast-res/3.2.3-SNAPSHOT/maven-metadata.xml
Downloaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast-res/3.2.3-SNAPSHOT/maven-metadata.xml (803 B at 1.5 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast-res/3.2.3-SNAPSHOT/ctakes-dictionary-lookup-fast-res-3.2.3-20160720.133824-91.jar
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast-res/3.2.3-SNAPSHOT/ctakes-dictionary-lookup-fast-res-3.2.3-20160720.133824-91.jar (8 KB at 6.0 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast-res/3.2.3-SNAPSHOT/ctakes-dictionary-lookup-fast-res-3.2.3-20160720.133824-91.pom
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast-res/3.2.3-SNAPSHOT/ctakes-dictionary-lookup-fast-res-3.2.3-20160720.133824-91.pom (4 KB at 0.0 KB/sec)
Downloading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast-res/maven-metadata.xml
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Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast-res/3.2.3-SNAPSHOT/maven-metadata.xml
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Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast-res/maven-metadata.xml
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-fast-res/maven-metadata.xml (370 B at 0.1 KB/sec)
[INFO] Deployment in https://repository.apache.org/content/repositories/snapshots (id=apache.snapshots.https,uniqueVersion=true)
Deploying the main artifact ctakes-dictionary-lookup-res-3.2.3-SNAPSHOT.jar
Downloading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-res/3.2.3-SNAPSHOT/maven-metadata.xml
Downloaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-res/3.2.3-SNAPSHOT/maven-metadata.xml (798 B at 0.0 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-res/3.2.3-SNAPSHOT/ctakes-dictionary-lookup-res-3.2.3-20160720.140951-91.jar
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-res/3.2.3-SNAPSHOT/ctakes-dictionary-lookup-res-3.2.3-20160720.140951-91.jar (11 KB at 3.3 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-res/3.2.3-SNAPSHOT/ctakes-dictionary-lookup-res-3.2.3-20160720.140951-91.pom
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-res/3.2.3-SNAPSHOT/ctakes-dictionary-lookup-res-3.2.3-20160720.140951-91.pom (4 KB at 0.3 KB/sec)
Downloading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-res/maven-metadata.xml
Downloaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-res/maven-metadata.xml (405 B at 0.0 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-res/3.2.3-SNAPSHOT/maven-metadata.xml
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-res/3.2.3-SNAPSHOT/maven-metadata.xml (798 B at 0.0 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-res/maven-metadata.xml
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-dictionary-lookup-res/maven-metadata.xml (405 B at 0.0 KB/sec)
[INFO] Deployment in https://repository.apache.org/content/repositories/snapshots (id=apache.snapshots.https,uniqueVersion=true)
Deploying the main artifact ctakes-distribution-3.2.3-SNAPSHOT.pom
Downloading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-distribution/3.2.3-SNAPSHOT/maven-metadata.xml
Downloaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-distribution/3.2.3-SNAPSHOT/maven-metadata.xml (2 KB at 0.2 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-distribution/3.2.3-SNAPSHOT/ctakes-distribution-3.2.3-20160720.141100-82.pom
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-distribution/3.2.3-SNAPSHOT/ctakes-distribution-3.2.3-20160720.141100-82.pom (7 KB at 0.2 KB/sec)
Downloading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-distribution/maven-metadata.xml
Downloaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-distribution/maven-metadata.xml (407 B at 0.1 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-distribution/3.2.3-SNAPSHOT/maven-metadata.xml
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-distribution/3.2.3-SNAPSHOT/maven-metadata.xml (2 KB at 0.1 KB/sec)
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-distribution/maven-metadata.xml
Uploaded: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-distribution/maven-metadata.xml (407 B at 0.0 KB/sec)
Deploying the main artifact ctakes-distribution-3.2.3-SNAPSHOT-bin.tar.gz
Uploading: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-distribution/3.2.3-SNAPSHOT/ctakes-distribution-3.2.3-20160720.141100-82-bin.tar.gz
ERROR: Failed to deploy artifacts: Could not transfer artifact org.apache.ctakes:ctakes-distribution:tar.gz:bin:3.2.3-20160720.141100-82 from/to apache.snapshots.https (https://repository.apache.org/content/repositories/snapshots): Failed to transfer file: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-distribution/3.2.3-SNAPSHOT/ctakes-distribution-3.2.3-20160720.141100-82-bin.tar.gz. Return code is: 504, ReasonPhrase: Gateway Timeout.
org.apache.maven.artifact.deployer.ArtifactDeploymentException: Failed to deploy artifacts: Could not transfer artifact org.apache.ctakes:ctakes-distribution:tar.gz:bin:3.2.3-20160720.141100-82 from/to apache.snapshots.https (https://repository.apache.org/content/repositories/snapshots): Failed to transfer file: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-distribution/3.2.3-SNAPSHOT/ctakes-distribution-3.2.3-20160720.141100-82-bin.tar.gz. Return code is: 504, ReasonPhrase: Gateway Timeout.
at org.apache.maven.artifact.deployer.DefaultArtifactDeployer.deploy(DefaultArtifactDeployer.java:143)
at hudson.maven.reporters.MavenArtifactRecord.deploy(MavenArtifactRecord.java:208)
at hudson.maven.RedeployPublisher.perform(RedeployPublisher.java:176)
at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20)
at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:782)
at hudson.model.AbstractBuild$AbstractBuildExecution.performAllBuildSteps(AbstractBuild.java:723)
at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.post2(MavenModuleSetBuild.java:1047)
at hudson.model.AbstractBuild$AbstractBuildExecution.post(AbstractBuild.java:668)
at hudson.model.Run.execute(Run.java:1763)
at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:531)
at hudson.model.ResourceController.execute(ResourceController.java:98)
at hudson.model.Executor.run(Executor.java:410)
Caused by: org.eclipse.aether.deployment.DeploymentException: Failed to deploy artifacts: Could not transfer artifact org.apache.ctakes:ctakes-distribution:tar.gz:bin:3.2.3-20160720.141100-82 from/to apache.snapshots.https (https://repository.apache.org/content/repositories/snapshots): Failed to transfer file: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-distribution/3.2.3-SNAPSHOT/ctakes-distribution-3.2.3-20160720.141100-82-bin.tar.gz. Return code is: 504, ReasonPhrase: Gateway Timeout.
at org.eclipse.aether.internal.impl.DefaultDeployer.deploy(DefaultDeployer.java:341)
at org.eclipse.aether.internal.impl.DefaultDeployer.deploy(DefaultDeployer.java:269)
at org.eclipse.aether.internal.impl.DefaultRepositorySystem.deploy(DefaultRepositorySystem.java:413)
at org.apache.maven.artifact.deployer.DefaultArtifactDeployer.deploy(DefaultArtifactDeployer.java:139)
... 11 more
Caused by: org.eclipse.aether.transfer.ArtifactTransferException: Could not transfer artifact org.apache.ctakes:ctakes-distribution:tar.gz:bin:3.2.3-20160720.141100-82 from/to apache.snapshots.https (https://repository.apache.org/content/repositories/snapshots): Failed to transfer file: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-distribution/3.2.3-SNAPSHOT/ctakes-distribution-3.2.3-20160720.141100-82-bin.tar.gz. Return code is: 504, ReasonPhrase: Gateway Timeout.
at org.eclipse.aether.connector.wagon.WagonRepositoryConnector$6.wrap(WagonRepositoryConnector.java:1016)
at org.eclipse.aether.connector.wagon.WagonRepositoryConnector$6.wrap(WagonRepositoryConnector.java:1004)
at org.eclipse.aether.connector.wagon.WagonRepositoryConnector$PutTask.run(WagonRepositoryConnector.java:895)
at org.eclipse.aether.connector.wagon.WagonRepositoryConnector.put(WagonRepositoryConnector.java:522)
at org.eclipse.aether.internal.impl.DefaultDeployer.deploy(DefaultDeployer.java:335)
... 14 more
Caused by: org.apache.maven.wagon.TransferFailedException: Failed to transfer file: https://repository.apache.org/content/repositories/snapshots/org/apache/ctakes/ctakes-distribution/3.2.3-SNAPSHOT/ctakes-distribution-3.2.3-20160720.141100-82-bin.tar.gz. Return code is: 504, ReasonPhrase: Gateway Timeout.
at org.apache.maven.wagon.shared.http4.AbstractHttpClientWagon.put(AbstractHttpClientWagon.java:626)
at org.apache.maven.wagon.shared.http4.AbstractHttpClientWagon.put(AbstractHttpClientWagon.java:524)
at org.apache.maven.wagon.shared.http4.AbstractHttpClientWagon.put(AbstractHttpClientWagon.java:505)
at org.apache.maven.wagon.shared.http4.AbstractHttpClientWagon.put(AbstractHttpClientWagon.java:485)
at org.eclipse.aether.connector.wagon.WagonRepositoryConnector$PutTask.run(WagonRepositoryConnector.java:871)
... 16 more
[INFO] Deployment failed after 2 hr 8 min
Build step 'Deploy artifacts to Maven repository' changed build result to FAILURE