RE: Command line invocation
It does look like that class has hardcoded paths. There may be another pipeline that is appropriate -- what kind of output are you looking to get from your documents? Tim From: Abraham Tom [a...@practicefusion.com] Sent: Tuesday, April 15, 2014 12:08 AM To: dev@ctakes.apache.org Subject: RE: Command line invocation Update java -cp $CTAKES_HOME/lib/*:$CTAKES_HOME/desc/:$CTAKES_HOME/resources/ -Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx1024M org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls /opt/cTAKES-3.1.1/data/test01.txt /opt/cTAKES-3.1.1/data_out/ Exception in thread "main" org.apache.uima.resource.ResourceInitializationException at org.cleartk.util.cr.FilesCollectionReader.initialize(FilesCollectionReader.java:251) at org.uimafit.component.JCasCollectionReader_ImplBase.initialize(JCasCollectionReader_ImplBase.java:57) at org.apache.uima.collection.CollectionReader_ImplBase.initialize(CollectionReader_ImplBase.java:71) at org.apache.uima.impl.CollectionReaderFactory_impl.produceResource(CollectionReaderFactory_impl.java:103) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceCollectionReader(UIMAFramework.java:711) at org.uimafit.factory.CollectionReaderFactory.createCollectionReader(CollectionReaderFactory.java:171) at org.cleartk.util.cr.FilesCollectionReader.getCollectionReader(FilesCollectionReader.java:88) at org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:56) Caused by: java.io.IOException: file or directory /sharp-home/assertion/data/ActiveLearning/plaintext does not exist ... 10 more file or directory /sharp-home/assertion/data/ActiveLearning/plaintext does this mean I cannot pass a directory and file in and I have to use the expected directory? Best regards, Abraham Tom Abraham Tom -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Sunday, April 13, 2014 5:32 AM To: 'dev@ctakes.apache.org' Subject: RE: Command line invocation Yes, that's possible. You need more things on your classpath - you can take a look at the classpath within runctakesCVD.bat Or if you are open to using groovy, take a look at the scripts directory within ctakes-core -Original Message- From: Abraham Tom [mailto:a...@practicefusion.com] Sent: Saturday, April 12, 2014 10:55 AM To: dev@ctakes.apache.org Subject: Command line invocation I am not a core java developer, I am a Hadoop data guy We are experimenting with using cTakes and we have no Java developers in house I am trying to invoke ClinicalPipelineWithUmls on a server where I installed the developer cTakes. This invocation is done via the following command line java -verbose -cp "/opt/cTAKES-3.1.1/ctakes-clinical-pipeline/target/classes;/home/mapr/.m2/repository/org/cleartk/cleartk-util/0.9.2/cleartk-util-0.9.2.jar" org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls but I am getting a Class not found error I would like to invoke via command line so that I can wrap a shell script around it and automate the processing of various docs. This should be possible shouldn't it? Best regards, Abraham Tom
suggestion for default pipelines
The discussion in the other thread with Abraham Tom gave me an idea I wanted to float to the list. We have been using some UIMAFit pipeline builders in the temporal project that maybe could be moved into clinical-pipeline. For example, look to this file: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java?view=markup with the static methods getPreprocessorAggregateBuilder() and getLightweightPreprocessorAggregateBuilder() [no umls]. So my idea would be to create a class in clinical-pipeline (CTakesPipelines) with static methods for some standard pipelines (to return AnalysisEngineDescriptions instead of AggregateBuilders?): getStandardUMLSPipeline() -- builds pipeline currently in AggregatePlaintextUMLSProcessor.xml getFullPipeline() -- same as above but with SRL, constituency parsing, etc., every component in ctakes We could then potentially merge our entry points -- I think Abraham's experience points out that this is currently confusing, as well as probably not implemented optimally. For example, either ClinicalPipelineWithUmls or BagOfCUIsGenerator would use that static method to run a uimafit-style pipeline. Maybe we can slowly deprecate our xml descriptors too unless people feel strongly about keeping those around. Another benefit is that the cTAKES API is then trivial -- if you import ctakes into your pom file getting a UIMA pipeline is one UimaFit call: builder.add(CTAKESPipelines.getStandardUMLSPipeline()); I think this would actually be pretty easy to implement, but hoping to get some feedback on whether this is a good direction. Tim
RE: suggestion for default pipelines
+1 I think that a factory is a great idea. I (personally) dislike the descriptor schema, but I think that deprecation is the way to go until a replacement comes along. -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Tuesday, April 15, 2014 9:54 AM To: dev@ctakes.apache.org Subject: suggestion for default pipelines The discussion in the other thread with Abraham Tom gave me an idea I wanted to float to the list. We have been using some UIMAFit pipeline builders in the temporal project that maybe could be moved into clinical-pipeline. For example, look to this file: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java?view=markup with the static methods getPreprocessorAggregateBuilder() and getLightweightPreprocessorAggregateBuilder() [no umls]. So my idea would be to create a class in clinical-pipeline (CTakesPipelines) with static methods for some standard pipelines (to return AnalysisEngineDescriptions instead of AggregateBuilders?): getStandardUMLSPipeline() -- builds pipeline currently in AggregatePlaintextUMLSProcessor.xml getFullPipeline() -- same as above but with SRL, constituency parsing, etc., every component in ctakes We could then potentially merge our entry points -- I think Abraham's experience points out that this is currently confusing, as well as probably not implemented optimally. For example, either ClinicalPipelineWithUmls or BagOfCUIsGenerator would use that static method to run a uimafit-style pipeline. Maybe we can slowly deprecate our xml descriptors too unless people feel strongly about keeping those around. Another benefit is that the cTAKES API is then trivial -- if you import ctakes into your pom file getting a UIMA pipeline is one UimaFit call: builder.add(CTAKESPipelines.getStandardUMLSPipeline()); I think this would actually be pretty easy to implement, but hoping to get some feedback on whether this is a good direction. Tim
RE: suggestion for default pipelines
+1 -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Tuesday, April 15, 2014 9:05 AM To: dev@ctakes.apache.org Subject: RE: suggestion for default pipelines +1 I think that a factory is a great idea. I (personally) dislike the descriptor schema, but I think that deprecation is the way to go until a replacement comes along. -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Tuesday, April 15, 2014 9:54 AM To: dev@ctakes.apache.org Subject: suggestion for default pipelines The discussion in the other thread with Abraham Tom gave me an idea I wanted to float to the list. We have been using some UIMAFit pipeline builders in the temporal project that maybe could be moved into clinical-pipeline. For example, look to this file: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java?view=markup with the static methods getPreprocessorAggregateBuilder() and getLightweightPreprocessorAggregateBuilder() [no umls]. So my idea would be to create a class in clinical-pipeline (CTakesPipelines) with static methods for some standard pipelines (to return AnalysisEngineDescriptions instead of AggregateBuilders?): getStandardUMLSPipeline() -- builds pipeline currently in AggregatePlaintextUMLSProcessor.xml getFullPipeline() -- same as above but with SRL, constituency parsing, etc., every component in ctakes We could then potentially merge our entry points -- I think Abraham's experience points out that this is currently confusing, as well as probably not implemented optimally. For example, either ClinicalPipelineWithUmls or BagOfCUIsGenerator would use that static method to run a uimafit-style pipeline. Maybe we can slowly deprecate our xml descriptors too unless people feel strongly about keeping those around. Another benefit is that the cTAKES API is then trivial -- if you import ctakes into your pom file getting a UIMA pipeline is one UimaFit call: builder.add(CTAKESPipelines.getStandardUMLSPipeline()); I think this would actually be pretty easy to implement, but hoping to get some feedback on whether this is a good direction. Tim
RE: suggestion for default pipelines
+1 Best regards, Abraham Tom Abraham Tom Data Warehouse Engineer 415.757.4674 (p) | 415.356.0950 (f) a...@practicefusion.com http://www.practicefusion.com www.facebook.com/practicefusion The contents of this message, together with any attachments, are intended only for the use of the individual or entity to which they are addressed and may contain information that is legally privileged, confidential and exempt from disclosure. If you are not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this message, or any attachment, is strictly prohibited. If you have received this message in error, please notify the original sender or contact Practice Fusion at 415.346.7700 ext 4 immediately by telephone or by return E-mail and delete this message, along with any attachments, from your computer. Thank you -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Tuesday, April 15, 2014 7:05 AM To: dev@ctakes.apache.org Subject: RE: suggestion for default pipelines +1 I think that a factory is a great idea. I (personally) dislike the descriptor schema, but I think that deprecation is the way to go until a replacement comes along. -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Tuesday, April 15, 2014 9:54 AM To: dev@ctakes.apache.org Subject: suggestion for default pipelines The discussion in the other thread with Abraham Tom gave me an idea I wanted to float to the list. We have been using some UIMAFit pipeline builders in the temporal project that maybe could be moved into clinical-pipeline. For example, look to this file: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java?view=markup with the static methods getPreprocessorAggregateBuilder() and getLightweightPreprocessorAggregateBuilder() [no umls]. So my idea would be to create a class in clinical-pipeline (CTakesPipelines) with static methods for some standard pipelines (to return AnalysisEngineDescriptions instead of AggregateBuilders?): getStandardUMLSPipeline() -- builds pipeline currently in AggregatePlaintextUMLSProcessor.xml getFullPipeline() -- same as above but with SRL, constituency parsing, etc., every component in ctakes We could then potentially merge our entry points -- I think Abraham's experience points out that this is currently confusing, as well as probably not implemented optimally. For example, either ClinicalPipelineWithUmls or BagOfCUIsGenerator would use that static method to run a uimafit-style pipeline. Maybe we can slowly deprecate our xml descriptors too unless people feel strongly about keeping those around. Another benefit is that the cTAKES API is then trivial -- if you import ctakes into your pom file getting a UIMA pipeline is one UimaFit call: builder.add(CTAKESPipelines.getStandardUMLSPipeline()); I think this would actually be pretty easy to implement, but hoping to get some feedback on whether this is a good direction. Tim
Re: suggestion for default pipelines
+1. And note that once you have a descriptor, you can generate the XML, so we should arrange to replace the current XML descriptors with ones generated automatically from the uimaFIT code. That should reduce some synchronization problems when the Java code was changed but the XML descriptor was not. Steve On Tue, Apr 15, 2014 at 8:52 AM, Miller, Timothy wrote: > The discussion in the other thread with Abraham Tom gave me an idea I > wanted to float to the list. We have been using some UIMAFit pipeline > builders in the temporal project that maybe could be moved into > clinical-pipeline. For example, look to this file: > > http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java?view=markup > > with the static methods getPreprocessorAggregateBuilder() and > getLightweightPreprocessorAggregateBuilder() [no umls]. > > So my idea would be to create a class in clinical-pipeline > (CTakesPipelines) with static methods for some standard pipelines (to > return AnalysisEngineDescriptions instead of AggregateBuilders?): > > getStandardUMLSPipeline() -- builds pipeline currently in > AggregatePlaintextUMLSProcessor.xml > getFullPipeline() -- same as above but with SRL, constituency parsing, > etc., every component in ctakes > > We could then potentially merge our entry points -- I think Abraham's > experience points out that this is currently confusing, as well as > probably not implemented optimally. For example, either > ClinicalPipelineWithUmls or BagOfCUIsGenerator would use that static > method to run a uimafit-style pipeline. Maybe we can slowly deprecate > our xml descriptors too unless people feel strongly about keeping those > around. > > Another benefit is that the cTAKES API is then trivial -- if you import > ctakes into your pom file getting a UIMA pipeline is one UimaFit call: > > builder.add(CTAKESPipelines.getStandardUMLSPipeline()); > > > I think this would actually be pretty easy to implement, but hoping to > get some feedback on whether this is a good direction. > > Tim > > >
