Btw. the full stacktrace is as follows:
19 Aug 2021 13:11:20 INFO LvgAnnotator - URL for lvg.properties
=file:/Users/myuser/.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
19 Aug 2021 13:11:20 INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
19 Aug 2021 13:11:20 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
[WARNING]
java.lang.IllegalArgumentException: URI is not hierarchical
at java.io.File.<init> (File.java:420)
at org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load
(LvgCmdApiResourceImpl.java:65)
at org.apache.uima.resource.impl.ResourceManager_impl.registerResource
(ResourceManager_impl.java:753)
at
org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources
(ResourceManager_impl.java:597)
at org.apache.uima.resource.Resource_ImplBase.initialize
(Resource_ImplBase.java:210)
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:136)
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:435)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine
(AggregateAnalysisEngine_impl.java:379)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize
(AggregateAnalysisEngine_impl.java:192)
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:435)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine
(AggregateAnalysisEngine_impl.java:379)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize
(AggregateAnalysisEngine_impl.java:192)
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:435)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine
(AggregateAnalysisEngine_impl.java:379)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize
(AggregateAnalysisEngine_impl.java:192)
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.produceResource
(UIMAFramework.java:331)
at org.apache.uima.UIMAFramework.produceAnalysisEngine
(UIMAFramework.java:448)
at org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine
(AnalysisEngineFactory.java:206)
at org.apache.uima.fit.pipeline.SimplePipeline.runPipeline
(SimplePipeline.java:296)
at org.apache.uima.fit.pipeline.SimplePipeline.runPipeline
(SimplePipeline.java:329)
at com.careindexing.app.HelloWorldAggregatePipeline.main
(HelloWorldAggregatePipeline.java:64)
at org.codehaus.mojo.exec.ExecJavaMojo$1.run (ExecJavaMojo.java:254)
at java.lang.Thread.run (Thread.java:748)
[INFO]
------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO]
------------------------------------------------------------------------
[INFO] Total time: 1.874 s
[INFO] Finished at: 2021-08-19T13:11:20+02:00
On Thu, Aug 19, 2021 at 11:38 AM Benjamin hansen <benjaminkakke...@gmail.com>
wrote:
> Thanks for the input.
> So I am trying to use
> the ClinicalPipelineFactory.getTokenProcessingPipeline which includes the
> LVG which seems to be having the issue. But you say i can just replace the
> LVG part with the DependencyParser in that pipeline? Can you elaborate a
> bit on where I can find the DependencyParser?
>
>
> On Wed, Aug 18, 2021 at 5:56 PM Peter Abramowitsch <
> pabramowit...@gmail.com> wrote:
>
>> Hi Benjamin,
>>
>> If what you're looking for are the lemmas of tokens, just use the
>> DependencyParser instead of LVG
>> I had another problem with LVG as well, but I think that it might be
>> simply
>> that all the needed resources are not being copied into the right place.
>> This was done without the lvg
>>
>> {
>> "_type": "ConllDependencyNode",
>> "sofa": 1,
>> "begin": 3,
>> "end": 10,
>> "id": 2,
>> "form": "decided",
>> "lemma": "decide",
>> "cpostag": "VBD",
>> "postag": "VBD",
>> "feats": "_",
>> "head": 137,
>> "deprel": "root",
>> "pdeprel": "_"
>> }
>>
>> On Wed, Aug 18, 2021 at 7:29 AM Finan, Sean <
>> sean.fi...@childrens.harvard.edu> wrote:
>>
>> > Hi Benjamin,
>> >
>> > My first question is: what pipeline are you trying to run?
>> >
>> > My second question is: Do you really need to use LVG?
>> >
>> > Sean
>> > ________________________________________
>> > From: Benjamin hansen <benjaminkakke...@gmail.com>
>> > Sent: Wednesday, August 18, 2021 3:07 AM
>> > To: dev@ctakes.apache.org
>> > Subject: An exception occured while executing the Java class. URI is not
>> > hierarchical [EXTERNAL]
>> >
>> > * External Email - Caution *
>> >
>> >
>> > While working at a simple pipeline example I got this error:
>> >
>> > *java.lang.IllegalArgumentException*: *URI is not hierarchical*
>> >
>> > *at* java.io.File.<init> (*File.java:420*)
>> >
>> > *at* org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load (
>> > *LvgCmdApiResourceImpl.java:65*)
>> >
>> >
>> > I found that this issue has already been reported 4 years ago here
>> >
>> >
>> https://urldefense.com/v3/__https://issues.apache.org/jira/browse/CTAKES-445__;!!NZvER7FxgEiBAiR_!9HBmXkq30TUdwnSpuHc8_7iEVkoMAiJ3p_rSTXE5d90TARHEdioOMNukOUaL6eB5CboTRBMsOYI$
>> >
>> >
>> > I am on MacOS which the workaround patched proposed in that thread does
>> not
>> > fix... And like the last comment in the thread says - the patch likely
>> also
>> > does not work on linux.
>> >
>> >
>> > This seems to be quite a serious bug since both mac and linux would be
>> > serious development and production platforms for ctakes users.
>> >
>> >
>> > Is there no fix for this after 4 years?
>> >
>>
>
