[
https://issues.apache.org/jira/browse/CTAKES-385?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16834724#comment-16834724
]
Dhruv Rajan edited comment on CTAKES-385 at 5/7/19 12:43 PM:
-------------------------------------------------------------
Is there going to be a fix for this soon?
I am still getting this same issue. I am using ctakes 4.0.0 from sbt in
Intellij, and encounter this error when running example code from the
ctakes-web-api in my own project.
MY CODE: (adapted from
[https://github.com/healthnlp/examples/blob/master/ctakes-web-client/src/main/java/org/apache/ctakes/web/client/servlet/DemoServlet.java])
{code:java}
public static void main(String[] args) throws Exception {
AggregateBuilder aggregateBuilder;
aggregateBuilder = new AggregateBuilder();
aggregateBuilder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
aggregateBuilder.add( AnalysisEngineFactory.createEngineDescription(
DefaultJCasTermAnnotator.class,
AbstractJCasTermAnnotator.PARAM_WINDOW_ANNOT_KEY,
"org.apache.ctakes.typesystem.type.textspan.Sentence",
JCasTermAnnotator.DICTIONARY_DESCRIPTOR_KEY,
//prefix +
"org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml" )
Paths.get("sno_rx_16ab.xml").toAbsolutePath().toString())
);
AnalysisEngine pipeline = aggregateBuilder.createAggregate();
}
{code}
ERROR:
{noformat}
Exception in thread "main" java.lang.IllegalArgumentException: URI is not
hierarchical
at java.base/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.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:708)
at
org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:204)
at Main.main(Main.java:56)
{noformat}
Seems to be exactly the same issue: it's trying to load lvg.properties as a
file, not a stream. Is there a way I could get around this?
was (Author: dhruvrajan):
Is there going to be a fix for this soon?
I am still getting this same issue. I am using ctakes 4.0.0 from sbt in
Intellij, and encounter this error when running example code from the
ctakes-web-api in my own project.
MY CODE: (adapted from
https://github.com/healthnlp/examples/blob/master/ctakes-web-client/src/main/java/org/apache/ctakes/web/client/servlet/DemoServlet.java)
{code:java}
public static void main(String[] args) throws Exception {
AggregateBuilder aggregateBuilder;
LOGGER.info(Paths.get("").toAbsolutePath().toString());
aggregateBuilder = new AggregateBuilder();
aggregateBuilder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
aggregateBuilder.add( AnalysisEngineFactory.createEngineDescription(
DefaultJCasTermAnnotator.class,
AbstractJCasTermAnnotator.PARAM_WINDOW_ANNOT_KEY,
"org.apache.ctakes.typesystem.type.textspan.Sentence",
JCasTermAnnotator.DICTIONARY_DESCRIPTOR_KEY,
//prefix +
"org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml" )
Paths.get("sno_rx_16ab.xml").toAbsolutePath().toString())
);
AnalysisEngine pipeline = aggregateBuilder.createAggregate();
}
{code}
ERROR:
{noformat}
Exception in thread "main" java.lang.IllegalArgumentException: URI is not
hierarchical
at java.base/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.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:708)
at
org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:204)
at Main.main(Main.java:56)
{noformat}
Seems to be exactly the same issue: it's trying to load lvg.properties as a
file, not a stream. Is there a way I could get around this?
> URI is not hierarchical when attempting to obtain lvg.properties within JAR
> ---------------------------------------------------------------------------
>
> Key: CTAKES-385
> URL: https://issues.apache.org/jira/browse/CTAKES-385
> Project: cTAKES
> Issue Type: Improvement
> Components: ctakes-lvg
> Affects Versions: 3.2.2
> Environment: MaxOSX 10.9.5, cTAKES 3.2.3-SNAPSHOT (nightly Wed Oct
> 14th, 2015), Apache Spark 1.5.1 on Apache Hadoop 2.4.0
> Reporter: Lewis John McGibbney
> Priority: Major
> Attachments: CTAKES-385.patch
>
>
> As described in the [accompanying mailing list
> thread|http://www.mail-archive.com/user%40ctakes.apache.org/msg00969.html]
> this issue concerns
> LvgAnnotator.createAnnotatorDescription(LvgAnnotator.java:565) using the
> following syntax
> {code}
> ExternalResourceFactory.createExternalResourceDescription(
> LvgCmdApiResourceImpl.class,
> new File(LvgCmdApiResourceImpl.class.getResource(
>
> "/org/apache/ctakes/lvg/data/config/lvg.properties").toURI()))
> {code}
> Use of LvgCmdApiResourceImpl.class.getResource should be exchanged for
> {code}
> LvgCmdApiResourceImpl.class.getResourceAsStream
> {code}
> Patch coming up.
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