Hi Dima,
Where did you get that class? I don't have UmlsLookupPipeline or the package
org.apache.ctakes.pipelines.
If you want to run from command-line I highly recommend that you use the
PiperFileRunner class in core.pipeline.
To run the clinical pipeline use cli parameters:
-p DefaultFastPipeline.piper
-i {inputDir}
--xmiOut {outputDir}
--user {umlsUsername}
--pass {umlsPassword}
If you have the binary installation there is a runClinicalPipeline script in
bin/
PiperFileRunner can run other piper files and take other parameters
# Runs the pipeline in the piper file specified by -p (piperfile)
# with any other provided parameters. Standard parameters are:
# -i , --inputDir {inputDirectory}
# -o , --outputDir {outputDirectory}
# -s , --subDir {subDirectory} (for i/o)
# --xmiOut {xmiOutputDirectory} (if different from -o)
# -l , --lookupXml {dictionaryConfigFile} (fast only)
# --user {umlsUsername}
# --pass {umlsPassword}
# -? , --help
#
# Other parameters may be declared in the piper file using the cli command:
# cli {parameterName}={singleCharacter}
# For instance, for declaration of ParagraphAnnotator path to regex file
optional parameter PARAGRAPH_TYPES_PATH,
# in the custom piper file add the line:
# cli PARAGRAPH_TYPES_PATH=t
# and when executing this script use:
# runPiperFile -p path/to/my/custom.piper -t path/to/my/custom.bsv ...
The above is a snippet from the runPiperFile script in the bin/ directory.
I am in the process of writing documentation on piper files in the wiki.
https://cwiki.apache.org/confluence/display/CTAKES/Piper+Files
-----Original Message-----
From: Dligach, Dmitriy [mailto:[email protected]]
Sent: Friday, April 14, 2017 12:17 PM
To: cTAKES Developer list
Subject: URI is not hierarchical
Dear cTAKES developers,
I am trying to run a simple pipeline that involves dictionary lookup:
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_org_apache_ctakes_pipelines_UmlsLookupPipeline.java&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=NWoDwPNChJkDhFseM3j8Gi7KNDdVqzi1BFt0onalf9I&e=
from command line as follows:
mvn exec:java -Dexec.mainClass=“org.apache.ctakes.pipelines.UmlsLookupPipeline”
It runs fine if the dictionary lookup related fragmented is commented out, but
it fails with “URI is not hierarchical” when the dictionary lookup is enabled.
I believe this is an old issue, so are there any plans for fixing it in the new
release? In the meantime, are there any workarounds?
Many thanks!
The full error is below.
Dima
14 Apr 2017 11:04:24 INFO LvgAnnotator - URL for lvg.properties
=file:/home/dima/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
14 Apr 2017 11:04:24 INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
14 Apr 2017 11:04:24 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
14 Apr 2017 11:04:24 INFO ContextDependentTokenizerAnnotator - Finite state
machines loaded.
14 Apr 2017 11:04:24 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
14 Apr 2017 11:04:24 INFO Chunker - Chunker model file:
/home/dima/cTakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/models/chunker-model.zip
14 Apr 2017 11:04:26 INFO AbstractJCasTermAnnotator - Using dictionary lookup
window type: org.apache.ctakes.typesystem.type.textspan.Sentence
14 Apr 2017 11:04:26 INFO AbstractJCasTermAnnotator - Exclusion tagset loaded:
CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN VBP VBZ WDT
WP WPS WRB
14 Apr 2017 11:04:26 INFO AbstractJCasTermAnnotator - Using minimum term text
span: 3
14 Apr 2017 11:04:26 INFO AbstractJCasTermAnnotator - Using Dictionary
Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
14 Apr 2017 11:04:26 INFO DictionaryDescriptorParser - Parsing dictionary
specifications:
14 Apr 2017 11:04:26 INFO UmlsUserApprover - Checking UMLS Account at
https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=k4vvKW_sfiLO__5LyOVbw7jMlmz2h1urVXde-7hEzg8&e=
for user dmitriydligach:
.14 Apr 2017 11:04:26 INFO UmlsUserApprover - UMLS Account at
https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=k4vvKW_sfiLO__5LyOVbw7jMlmz2h1urVXde-7hEzg8&e=
for user dmitriydligach has been validated
14 Apr 2017 11:04:26 INFO JdbcConnectionFactory - Connecting to
jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab:
14 Apr 2017 11:04:26 INFO ENGINE - open start - state not modified
.................
14 Apr 2017 11:04:32 INFO JdbcConnectionFactory - Database connected
14 Apr 2017 11:04:32 INFO JdbcRareWordDictionary - Connected to cui and term
table CUI_TERMS
14 Apr 2017 11:04:32 INFO JdbcConceptFactory - Connected to concept table TUI
with class TUI
14 Apr 2017 11:04:32 INFO JdbcConceptFactory - Connected to concept table
RXNORM with class LONG
14 Apr 2017 11:04:32 INFO JdbcConceptFactory - Connected to concept table
PREFTERM with class PREFTERM
14 Apr 2017 11:04:32 INFO JdbcConceptFactory - Connected to concept table
SNOMEDCT_US with class LONG
[WARNING]
java.lang.IllegalArgumentException: URI is not hierarchical
at java.io.File.<init>(File.java:418)
at
org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiResourceImpl.java:65)
at
org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:628)
at
org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:464)
at
org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:193)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:131)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:407)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:429)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:373)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:186)
at
org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:711)
at
org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207)
at
org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLookupPipeline.java:66)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:282)
at java.lang.Thread.run(Thread.java:745)
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 9.900 s
[INFO] Finished at: 2017-04-14T11:04:32-05:00
[INFO] Final Memory: 510M/1455M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.6.0:java
(default-cli) on project ctakes-misc: An exception occured while executing the
Java class. URI is not hierarchical -> [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]
https://urldefense.proofpoint.com/v2/url?u=http-3A__cwiki.apache.org_confluence_display_MAVEN_MojoExecutionException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=JfA-JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e=
