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Posted to dev@ctakes.apache.org by "Dligach, Dmitriy" <dd...@luc.edu> on 2016/06/28 14:45:23 UTC
URI is not hierarchical
Dear cTAKES developers,
I am looking for a simple cTAKEs pipeline that can be run from command line to introduce a group of people to cTAKES. This pipeline:
ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
seemed like a good candidate so I gave it a try. It runs fine when in Eclipse, but when I run it from command line:
mvn exec:java -Dexec.mainClass=“org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls”
It begins to run but then crashes. I am including the error messages below. Any clues?
Thank you in advance,
Dima
ava.lang.reflect.InvocationTargetException
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:497)
at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:293)
at java.lang.Thread.run(Thread.java:745)
Caused by: 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:603)
at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
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:123)
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:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
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:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
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:269)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:76)
at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:42)
at org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:68)
... 6 more
Re: URI is not hierarchical
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
Brandon, thank you.
I just did a quick mailing archive search and it looks like this is known issue, which presumably was fixed a while ago:
http://mail-archives.apache.org/mod_mbox/ctakes-dev/201510.mbox/%3CD8F818BA-50FD-4A08-95EA-4E841FF6FBDF@childrens.harvard.edu%3E
Thanks again,
Dima
> On Jun 28, 2016, at 09:50, Geise, Brandon D. <bd...@geisinger.edu> wrote:
>
> Hi Dima,
>
> I believe this is related to the path of LVG. You can try coping the LVG data folder to the same directory (This is at least how I've gotten around it) when running a compiled jar. You can also search the mailing list for additional discussion on this issue.
>
> Thanks,
> Brandon
>
> -----Original Message-----
> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> Sent: Tuesday, June 28, 2016 10:45 AM
> To: cTAKES Developer list <de...@ctakes.apache.org>
> Subject: URI is not hierarchical
>
> Dear cTAKES developers,
>
> I am looking for a simple cTAKEs pipeline that can be run from command line to introduce a group of people to cTAKES. This pipeline:
>
> ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
>
> seemed like a good candidate so I gave it a try. It runs fine when in Eclipse, but when I run it from command line:
>
> mvn exec:java -Dexec.mainClass=“org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls”
>
> It begins to run but then crashes. I am including the error messages below. Any clues?
>
> Thank you in advance,
>
> Dima
>
> ava.lang.reflect.InvocationTargetException
> 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:497)
> at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:293)
> at java.lang.Thread.run(Thread.java:745)
> Caused by: 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:603)
> at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
> at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
> 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:123)
> 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:269)
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
> 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:269)
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
> 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:269)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
> at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:76)
> at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:42)
> at org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:68)
> ... 6 more
>
>
>
>
> IMPORTANT WARNING: The information in this message (and the documents attached to it, if any) is confidential and may be legally privileged. It is intended solely for the addressee. Access to this message by anyone else is unauthorized. If you are not the intended recipient, any disclosure, copying, distribution or any action taken, or omitted to be taken, in reliance on it is prohibited and may be unlawful. If you have received this message in error, please delete all electronic copies of this message (and the documents attached to it, if any), destroy any hard copies you may have created and notify me immediately by replying to this email. Thank you.
>
> Geisinger Health System utilizes an encryption process to safeguard Protected Health Information and other confidential data contained in external e-mail messages. If email is encrypted, the recipient will receive an e-mail instructing them to sign on to the Geisinger Health System Secure E-mail Message Center to retrieve the encrypted e-mail.
RE: URI is not hierarchical
Posted by "Geise, Brandon D." <bd...@geisinger.edu>.
Hi Dima,
I believe this is related to the path of LVG. You can try coping the LVG data folder to the same directory (This is at least how I've gotten around it) when running a compiled jar. You can also search the mailing list for additional discussion on this issue.
Thanks,
Brandon
-----Original Message-----
From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
Sent: Tuesday, June 28, 2016 10:45 AM
To: cTAKES Developer list <de...@ctakes.apache.org>
Subject: URI is not hierarchical
Dear cTAKES developers,
I am looking for a simple cTAKEs pipeline that can be run from command line to introduce a group of people to cTAKES. This pipeline:
ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
seemed like a good candidate so I gave it a try. It runs fine when in Eclipse, but when I run it from command line:
mvn exec:java -Dexec.mainClass=“org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls”
It begins to run but then crashes. I am including the error messages below. Any clues?
Thank you in advance,
Dima
ava.lang.reflect.InvocationTargetException
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:497)
at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:293)
at java.lang.Thread.run(Thread.java:745)
Caused by: 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:603)
at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
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:123)
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:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
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:269)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
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:269)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:76)
at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:42)
at org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:68)
... 6 more
IMPORTANT WARNING: The information in this message (and the documents attached to it, if any) is confidential and may be legally privileged. It is intended solely for the addressee. Access to this message by anyone else is unauthorized. If you are not the intended recipient, any disclosure, copying, distribution or any action taken, or omitted to be taken, in reliance on it is prohibited and may be unlawful. If you have received this message in error, please delete all electronic copies of this message (and the documents attached to it, if any), destroy any hard copies you may have created and notify me immediately by replying to this email. Thank you.
Geisinger Health System utilizes an encryption process to safeguard Protected Health Information and other confidential data contained in external e-mail messages. If email is encrypted, the recipient will receive an e-mail instructing them to sign on to the Geisinger Health System Secure E-mail Message Center to retrieve the encrypted e-mail.
Re: URI is not hierarchical
Posted by "Abramowitsch, Peter" <pa...@hearst.com>.
On second thought... This might be useful
http://stackoverflow.com/questions/18055189/why-my-uri-is-not-hierarchical
On 6/28/16, 9:24 AM, "Abramowitsch, Peter" <pa...@hearst.com>
wrote:
>Dima
>
>Although I'm not an expert, I don't think Ctakes relies on any Environment
>variables a priori, unless you have a Ctakes extensions that has added a
>dependency. Depending on your error you may need to look in AE or
>TypeSystem definition files or in the uimafit types.txt file where search
>paths are defined for locating the TypeSystem files themselves.
>
>But looking specifically at the exception being thrown (URI not
>heirarchical), I'm wondering if there's a path to the LVG resources that
>has accidentally been written with dots as in a Java import, instead of
>slashes. Have you looked at the engine descriptor for LVG?
>
>- p
>
>On 6/28/16, 9:07 AM, "Mattmann, Chris A (3980)"
><ch...@jpl.nasa.gov> wrote:
>
>>Hi Dima,
>>
>>
>>
>>Might be a red herring - I am not 100% positive that there is an env
>>
>>var in cTAKES that you are missing just that in the past when I¹ve
>>
>>had that same bug (in another project), that was the cause. You may
>>
>>try looking for URIs in config file in which the property isn¹t being
>>
>>resolved or it ends up as file://NULL/some/path/that/doesnt/exist
>>
>>
>>
>>Cheers,
>>
>>Chris
>>
>>
>>
>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
>>Chris Mattmann, Ph.D.
>>
>>Chief Architect
>>
>>Instrument Software and Science Data Systems Section (398)
>>
>>NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
>>
>>Office: 168-519, Mailstop: 168-527
>>
>>Email: chris.a.mattmann@nasa.gov
>>
>>WWW:
>>https://urldefense.proofpoint.com/v2/url?u=http-3A__sunset.usc.edu_-7Emat
>>t
>>mann_&d=CwIGaQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4us
>>w
>>NF8BK5Orm10&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=TVAwAlqr2EEEN
>>N
>>3eUKy2N3TmMRYgcGV7BWHoOmQsGQw&e=
>>
>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
>>Director, Information Retrieval and Data Science Group (IRDS)
>>
>>Adjunct Associate Professor, Computer Science Department
>>
>>University of Southern California, Los Angeles, CA 90089 USA
>>
>>WWW:
>>https://urldefense.proofpoint.com/v2/url?u=http-3A__irds.usc.edu_&d=CwIGa
>>Q
>>&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4uswNF8BK5Orm10&m
>>=
>>bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=JEKow6Wp5dTwkernB6S3FhhH1RY
>>X
>>hU7RpzHFREfscxk&e=
>>
>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>On 6/28/16, 9:02 AM, "Dligach, Dmitriy" <dd...@luc.edu> wrote:
>>
>>
>>
>>>Thanks, Chris.
>>
>>>
>>
>>>I didn¹t realize cTAKES was relying on environment variables for
>>>locating resources. Do you know which environment variable might be the
>>>issue?
>>
>>>
>>
>>>Thanks again for your help,
>>
>>>
>>
>>>Dima
>>
>>>
>>
>>>> On Jun 28, 2016, at 10:26, Mattmann, Chris A (3980)
>>>><ch...@jpl.nasa.gov> wrote:
>>
>>>>
>>
>>>> Hi Dima,
>>
>>>>
>>
>>>> In Apache OODT, when we do environment variable replacement on a URI,
>>
>>>> e.g., file://[SOME_ENV]/path, if $SOME_ENV isn¹t defined, you get that
>>
>>>> error like you had below so that was the source of my suggestion sorry
>>
>>>> for not clarifying.
>>
>>>>
>>
>>>> Cheers,
>>
>>>> Chris
>>
>>>>
>>
>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
>>>> Chris Mattmann, Ph.D.
>>
>>>> Chief Architect
>>
>>>> Instrument Software and Science Data Systems Section (398)
>>
>>>> NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
>>
>>>> Office: 168-519, Mailstop: 168-527
>>
>>>> Email: chris.a.mattmann@nasa.gov
>>
>>>> WWW:
>>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__sunset.usc.edu_-7Em
>>>>a
>>>>ttmann_&d=CwIGaQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuV
>>>>F
>>>>4uswNF8BK5Orm10&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=TVAwAlq
>>>>r
>>>>2EEENN3eUKy2N3TmMRYgcGV7BWHoOmQsGQw&e=
>>
>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
>>>> Director, Information Retrieval and Data Science Group (IRDS)
>>
>>>> Adjunct Associate Professor, Computer Science Department
>>
>>>> University of Southern California, Los Angeles, CA 90089 USA
>>
>>>> WWW:
>>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__irds.usc.edu_&d=CwI
>>>>G
>>>>aQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4uswNF8BK5Orm
>>>>1
>>>>0&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=JEKow6Wp5dTwkernB6S3F
>>>>h
>>>>hH1RYXhU7RpzHFREfscxk&e=
>>
>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
>>>>
>>
>>>>
>>
>>>>
>>
>>>>
>>
>>>>
>>
>>>>
>>
>>>>
>>
>>>>
>>
>>>>
>>
>>>>
>>
>>>> On 6/28/16, 8:03 AM, "Dligach, Dmitriy" <dd...@luc.edu> wrote:
>>
>>>>
>>
>>>>> Hi Chris,
>>
>>>>>
>>
>>>>> Sorry, could you please clarify which environment variable I am
>>>>>missing?
>>
>>>>>
>>
>>>>> Thanks,
>>
>>>>>
>>
>>>>> Dima
>>
>>>>>
>>
>>>>>> On Jun 28, 2016, at 09:49, Mattmann, Chris A (3980)
>>>>>><ch...@jpl.nasa.gov> wrote:
>>
>>>>>>
>>
>>>>>> Looks to me like a missing environment variable..
>>
>>>>>>
>>
>>>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
>>>>>> Chris Mattmann, Ph.D.
>>
>>>>>> Chief Architect
>>
>>>>>> Instrument Software and Science Data Systems Section (398)
>>
>>>>>> NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
>>
>>>>>> Office: 168-519, Mailstop: 168-527
>>
>>>>>> Email: chris.a.mattmann@nasa.gov
>>
>>>>>> WWW:
>>>>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__sunset.usc.edu_-7
>>>>>>E
>>>>>>mattmann_&d=CwIGaQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjT
>>>>>>j
>>>>>>wuVF4uswNF8BK5Orm10&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=T
>>>>>>V
>>>>>>AwAlqr2EEENN3eUKy2N3TmMRYgcGV7BWHoOmQsGQw&e=
>>
>>>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
>>>>>> Director, Information Retrieval and Data Science Group (IRDS)
>>
>>>>>> Adjunct Associate Professor, Computer Science Department
>>
>>>>>> University of Southern California, Los Angeles, CA 90089 USA
>>
>>>>>> WWW:
>>>>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__irds.usc.edu_&d=C
>>>>>>w
>>>>>>IGaQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4uswNF8BK
>>>>>>5
>>>>>>Orm10&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=JEKow6Wp5dTwker
>>>>>>n
>>>>>>B6S3FhhH1RYXhU7RpzHFREfscxk&e=
>>
>>>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>> On 6/28/16, 7:45 AM, "Dligach, Dmitriy" <dd...@luc.edu> wrote:
>>
>>>>>>
>>
>>>>>>> Dear cTAKES developers,
>>
>>>>>>>
>>
>>>>>>> I am looking for a simple cTAKEs pipeline that can be run from
>>>>>>>command line to introduce a group of people to cTAKES. This
>>>>>>>pipeline:
>>
>>>>>>>
>>
>>>>>>>
>>>>>>>ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpip
>>>>>>>e
>>>>>>>line/ClinicalPipelineWithUmls.java
>>
>>>>>>>
>>
>>>>>>> seemed like a good candidate so I gave it a try. It runs fine when
>>>>>>>in Eclipse, but when I run it from command line:
>>
>>>>>>>
>>
>>>>>>> mvn exec:java
>>>>>>>-Dexec.mainClass=³org.apache.ctakes.clinicalpipeline.ClinicalPipelin
>>>>>>>e
>>>>>>>WithUmls²
>>
>>>>>>>
>>
>>>>>>> It begins to run but then crashes. I am including the error
>>>>>>>messages below. Any clues?
>>
>>>>>>>
>>
>>>>>>> Thank you in advance,
>>
>>>>>>>
>>
>>>>>>> Dima
>>
>>>>>>>
>>
>>>>>>> ava.lang.reflect.InvocationTargetException
>>
>>>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>
>>>>>>> at
>>>>>>>sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl
>>>>>>>.
>>>>>>>java:62)
>>
>>>>>>> at
>>>>>>>sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcce
>>>>>>>s
>>>>>>>sorImpl.java:43)
>>
>>>>>>> at java.lang.reflect.Method.invoke(Method.java:497)
>>
>>>>>>> at
>>>>>>>org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:293)
>>
>>>>>>> at java.lang.Thread.run(Thread.java:745)
>>
>>>>>>> Caused by: java.lang.IllegalArgumentException: URI is not
>>>>>>>hierarchical
>>
>>>>>>> at java.io.File.<init>(File.java:418)
>>
>>>>>>> at
>>>>>>>org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiR
>>>>>>>e
>>>>>>>sourceImpl.java:65)
>>
>>>>>>> at
>>>>>>>org.apache.uima.resource.impl.ResourceManager_impl.registerResource(
>>>>>>>R
>>>>>>>esourceManager_impl.java:603)
>>
>>>>>>> at
>>>>>>>org.apache.uima.resource.impl.ResourceManager_impl.initializeExterna
>>>>>>>l
>>>>>>>Resources(ResourceManager_impl.java:442)
>>
>>>>>>> at
>>>>>>>org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplB
>>>>>>>a
>>>>>>>se.java:153)
>>
>>>>>>> at
>>>>>>>org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initiali
>>>>>>>z
>>>>>>>e(AnalysisEngineImplBase.java:157)
>>
>>>>>>> at
>>>>>>>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.in
>>>>>>>i
>>>>>>>tialize(PrimitiveAnalysisEngine_impl.java:123)
>>
>>>>>>> at
>>>>>>>org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Anal
>>>>>>>y
>>>>>>>sisEngineFactory_impl.java:94)
>>
>>>>>>> at
>>>>>>>org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
>>>>>>>o
>>>>>>>mpositeResourceFactory_impl.java:62)
>>
>>>>>>> at
>>>>>>>org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269
>>>>>>>)
>>
>>>>>>> at
>>>>>>>org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.ja
>>>>>>>v
>>>>>>>a:387)
>>
>>>>>>> at
>>>>>>>org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.jav
>>>>>>>a
>>>>>>>:254)
>>
>>>>>>> at
>>>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.in
>>>>>>>i
>>>>>>>tASB(AggregateAnalysisEngine_impl.java:431)
>>
>>>>>>> at
>>>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.in
>>>>>>>i
>>>>>>>tializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375
>>>>>>>)
>>
>>>>>>> at
>>>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.in
>>>>>>>i
>>>>>>>tialize(AggregateAnalysisEngine_impl.java:185)
>>
>>>>>>> at
>>>>>>>org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Anal
>>>>>>>y
>>>>>>>sisEngineFactory_impl.java:94)
>>
>>>>>>> at
>>>>>>>org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
>>>>>>>o
>>>>>>>mpositeResourceFactory_impl.java:62)
>>
>>>>>>> at
>>>>>>>org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269
>>>>>>>)
>>
>>>>>>> at
>>>>>>>org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.ja
>>>>>>>v
>>>>>>>a:387)
>>
>>>>>>> at
>>>>>>>org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.jav
>>>>>>>a
>>>>>>>:254)
>>
>>>>>>> at
>>>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.in
>>>>>>>i
>>>>>>>tASB(AggregateAnalysisEngine_impl.java:431)
>>
>>>>>>> at
>>>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.in
>>>>>>>i
>>>>>>>tializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375
>>>>>>>)
>>
>>>>>>> at
>>>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.in
>>>>>>>i
>>>>>>>tialize(AggregateAnalysisEngine_impl.java:185)
>>
>>>>>>> at
>>>>>>>org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Anal
>>>>>>>y
>>>>>>>sisEngineFactory_impl.java:94)
>>
>>>>>>> at
>>>>>>>org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C
>>>>>>>o
>>>>>>>mpositeResourceFactory_impl.java:62)
>>
>>>>>>> at
>>>>>>>org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269
>>>>>>>)
>>
>>>>>>> at
>>>>>>>org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314
>>>>>>>)
>>
>>>>>>> at
>>>>>>>org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.ja
>>>>>>>v
>>>>>>>a:425)
>>
>>>>>>> at
>>>>>>>org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java
>>>>>>>:
>>>>>>>76)
>>
>>>>>>> at
>>>>>>>org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java
>>>>>>>:
>>>>>>>42)
>>
>>>>>>> at
>>>>>>>org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(Cli
>>>>>>>n
>>>>>>>icalPipelineWithUmls.java:68)
>>
>>>>>>> ... 6 more
>>
>>>>>>>
>>
>>>>>>>
>>
>>>>>
>>
>>>
>>
>
Re: URI is not hierarchical
Posted by "Abramowitsch, Peter" <pa...@hearst.com>.
Dima
Although I'm not an expert, I don't think Ctakes relies on any Environment
variables a priori, unless you have a Ctakes extensions that has added a
dependency. Depending on your error you may need to look in AE or
TypeSystem definition files or in the uimafit types.txt file where search
paths are defined for locating the TypeSystem files themselves.
But looking specifically at the exception being thrown (URI not
heirarchical), I'm wondering if there's a path to the LVG resources that
has accidentally been written with dots as in a Java import, instead of
slashes. Have you looked at the engine descriptor for LVG?
- p
On 6/28/16, 9:07 AM, "Mattmann, Chris A (3980)"
<ch...@jpl.nasa.gov> wrote:
>Hi Dima,
>
>
>
>Might be a red herring - I am not 100% positive that there is an env
>
>var in cTAKES that you are missing just that in the past when I¹ve
>
>had that same bug (in another project), that was the cause. You may
>
>try looking for URIs in config file in which the property isn¹t being
>
>resolved or it ends up as file://NULL/some/path/that/doesnt/exist
>
>
>
>Cheers,
>
>Chris
>
>
>
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>Chris Mattmann, Ph.D.
>
>Chief Architect
>
>Instrument Software and Science Data Systems Section (398)
>
>NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
>
>Office: 168-519, Mailstop: 168-527
>
>Email: chris.a.mattmann@nasa.gov
>
>WWW:
>https://urldefense.proofpoint.com/v2/url?u=http-3A__sunset.usc.edu_-7Ematt
>mann_&d=CwIGaQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4usw
>NF8BK5Orm10&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=TVAwAlqr2EEENN
>3eUKy2N3TmMRYgcGV7BWHoOmQsGQw&e=
>
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>Director, Information Retrieval and Data Science Group (IRDS)
>
>Adjunct Associate Professor, Computer Science Department
>
>University of Southern California, Los Angeles, CA 90089 USA
>
>WWW:
>https://urldefense.proofpoint.com/v2/url?u=http-3A__irds.usc.edu_&d=CwIGaQ
>&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4uswNF8BK5Orm10&m=
>bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=JEKow6Wp5dTwkernB6S3FhhH1RYX
>hU7RpzHFREfscxk&e=
>
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>On 6/28/16, 9:02 AM, "Dligach, Dmitriy" <dd...@luc.edu> wrote:
>
>
>
>>Thanks, Chris.
>
>>
>
>>I didn¹t realize cTAKES was relying on environment variables for
>>locating resources. Do you know which environment variable might be the
>>issue?
>
>>
>
>>Thanks again for your help,
>
>>
>
>>Dima
>
>>
>
>>> On Jun 28, 2016, at 10:26, Mattmann, Chris A (3980)
>>><ch...@jpl.nasa.gov> wrote:
>
>>>
>
>>> Hi Dima,
>
>>>
>
>>> In Apache OODT, when we do environment variable replacement on a URI,
>
>>> e.g., file://[SOME_ENV]/path, if $SOME_ENV isn¹t defined, you get that
>
>>> error like you had below so that was the source of my suggestion sorry
>
>>> for not clarifying.
>
>>>
>
>>> Cheers,
>
>>> Chris
>
>>>
>
>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>>> Chris Mattmann, Ph.D.
>
>>> Chief Architect
>
>>> Instrument Software and Science Data Systems Section (398)
>
>>> NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
>
>>> Office: 168-519, Mailstop: 168-527
>
>>> Email: chris.a.mattmann@nasa.gov
>
>>> WWW:
>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__sunset.usc.edu_-7Ema
>>>ttmann_&d=CwIGaQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF
>>>4uswNF8BK5Orm10&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=TVAwAlqr
>>>2EEENN3eUKy2N3TmMRYgcGV7BWHoOmQsGQw&e=
>
>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>>> Director, Information Retrieval and Data Science Group (IRDS)
>
>>> Adjunct Associate Professor, Computer Science Department
>
>>> University of Southern California, Los Angeles, CA 90089 USA
>
>>> WWW:
>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__irds.usc.edu_&d=CwIG
>>>aQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4uswNF8BK5Orm1
>>>0&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=JEKow6Wp5dTwkernB6S3Fh
>>>hH1RYXhU7RpzHFREfscxk&e=
>
>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>>>
>
>>>
>
>>>
>
>>>
>
>>>
>
>>>
>
>>>
>
>>>
>
>>>
>
>>>
>
>>> On 6/28/16, 8:03 AM, "Dligach, Dmitriy" <dd...@luc.edu> wrote:
>
>>>
>
>>>> Hi Chris,
>
>>>>
>
>>>> Sorry, could you please clarify which environment variable I am
>>>>missing?
>
>>>>
>
>>>> Thanks,
>
>>>>
>
>>>> Dima
>
>>>>
>
>>>>> On Jun 28, 2016, at 09:49, Mattmann, Chris A (3980)
>>>>><ch...@jpl.nasa.gov> wrote:
>
>>>>>
>
>>>>> Looks to me like a missing environment variable..
>
>>>>>
>
>>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>>>>> Chris Mattmann, Ph.D.
>
>>>>> Chief Architect
>
>>>>> Instrument Software and Science Data Systems Section (398)
>
>>>>> NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
>
>>>>> Office: 168-519, Mailstop: 168-527
>
>>>>> Email: chris.a.mattmann@nasa.gov
>
>>>>> WWW:
>>>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__sunset.usc.edu_-7E
>>>>>mattmann_&d=CwIGaQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTj
>>>>>wuVF4uswNF8BK5Orm10&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=TV
>>>>>AwAlqr2EEENN3eUKy2N3TmMRYgcGV7BWHoOmQsGQw&e=
>
>>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>>>>> Director, Information Retrieval and Data Science Group (IRDS)
>
>>>>> Adjunct Associate Professor, Computer Science Department
>
>>>>> University of Southern California, Los Angeles, CA 90089 USA
>
>>>>> WWW:
>>>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__irds.usc.edu_&d=Cw
>>>>>IGaQ&c=B73tqXN8Ec0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4uswNF8BK5
>>>>>Orm10&m=bvlKRI-5MIbkVQ3lsFgkt-cv5zWqLUPBPBLWfqf96rY&s=JEKow6Wp5dTwkern
>>>>>B6S3FhhH1RYXhU7RpzHFREfscxk&e=
>
>>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> On 6/28/16, 7:45 AM, "Dligach, Dmitriy" <dd...@luc.edu> wrote:
>
>>>>>
>
>>>>>> Dear cTAKES developers,
>
>>>>>>
>
>>>>>> I am looking for a simple cTAKEs pipeline that can be run from
>>>>>>command line to introduce a group of people to cTAKES. This pipeline:
>
>>>>>>
>
>>>>>>
>>>>>>ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipe
>>>>>>line/ClinicalPipelineWithUmls.java
>
>>>>>>
>
>>>>>> seemed like a good candidate so I gave it a try. It runs fine when
>>>>>>in Eclipse, but when I run it from command line:
>
>>>>>>
>
>>>>>> mvn exec:java
>>>>>>-Dexec.mainClass=³org.apache.ctakes.clinicalpipeline.ClinicalPipeline
>>>>>>WithUmls²
>
>>>>>>
>
>>>>>> It begins to run but then crashes. I am including the error
>>>>>>messages below. Any clues?
>
>>>>>>
>
>>>>>> Thank you in advance,
>
>>>>>>
>
>>>>>> Dima
>
>>>>>>
>
>>>>>> ava.lang.reflect.InvocationTargetException
>
>>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>
>>>>>> at
>>>>>>sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.
>>>>>>java:62)
>
>>>>>> at
>>>>>>sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
>>>>>>sorImpl.java:43)
>
>>>>>> at java.lang.reflect.Method.invoke(Method.java:497)
>
>>>>>> at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:293)
>
>>>>>> at java.lang.Thread.run(Thread.java:745)
>
>>>>>> Caused by: java.lang.IllegalArgumentException: URI is not
>>>>>>hierarchical
>
>>>>>> at java.io.File.<init>(File.java:418)
>
>>>>>> at
>>>>>>org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiRe
>>>>>>sourceImpl.java:65)
>
>>>>>> at
>>>>>>org.apache.uima.resource.impl.ResourceManager_impl.registerResource(R
>>>>>>esourceManager_impl.java:603)
>
>>>>>> at
>>>>>>org.apache.uima.resource.impl.ResourceManager_impl.initializeExternal
>>>>>>Resources(ResourceManager_impl.java:442)
>
>>>>>> at
>>>>>>org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBa
>>>>>>se.java:153)
>
>>>>>> at
>>>>>>org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initializ
>>>>>>e(AnalysisEngineImplBase.java:157)
>
>>>>>> at
>>>>>>org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.ini
>>>>>>tialize(PrimitiveAnalysisEngine_impl.java:123)
>
>>>>>> at
>>>>>>org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy
>>>>>>sisEngineFactory_impl.java:94)
>
>>>>>> at
>>>>>>org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co
>>>>>>mpositeResourceFactory_impl.java:62)
>
>>>>>> at
>>>>>>org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>
>>>>>> at
>>>>>>org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.jav
>>>>>>a:387)
>
>>>>>> at
>>>>>>org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java
>>>>>>:254)
>
>>>>>> at
>>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
>>>>>>tASB(AggregateAnalysisEngine_impl.java:431)
>
>>>>>> at
>>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
>>>>>>tializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>
>>>>>> at
>>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
>>>>>>tialize(AggregateAnalysisEngine_impl.java:185)
>
>>>>>> at
>>>>>>org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy
>>>>>>sisEngineFactory_impl.java:94)
>
>>>>>> at
>>>>>>org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co
>>>>>>mpositeResourceFactory_impl.java:62)
>
>>>>>> at
>>>>>>org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>
>>>>>> at
>>>>>>org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.jav
>>>>>>a:387)
>
>>>>>> at
>>>>>>org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java
>>>>>>:254)
>
>>>>>> at
>>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
>>>>>>tASB(AggregateAnalysisEngine_impl.java:431)
>
>>>>>> at
>>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
>>>>>>tializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>
>>>>>> at
>>>>>>org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.ini
>>>>>>tialize(AggregateAnalysisEngine_impl.java:185)
>
>>>>>> at
>>>>>>org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analy
>>>>>>sisEngineFactory_impl.java:94)
>
>>>>>> at
>>>>>>org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Co
>>>>>>mpositeResourceFactory_impl.java:62)
>
>>>>>> at
>>>>>>org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>
>>>>>> at
>>>>>>org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
>
>>>>>> at
>>>>>>org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.jav
>>>>>>a:425)
>
>>>>>> at
>>>>>>org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:
>>>>>>76)
>
>>>>>> at
>>>>>>org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:
>>>>>>42)
>
>>>>>> at
>>>>>>org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(Clin
>>>>>>icalPipelineWithUmls.java:68)
>
>>>>>> ... 6 more
>
>>>>>>
>
>>>>>>
>
>>>>
>
>>
>
Re: URI is not hierarchical
Posted by "Mattmann, Chris A (3980)" <ch...@jpl.nasa.gov>.
Hi Dima,
Might be a red herring - I am not 100% positive that there is an env
var in cTAKES that you are missing just that in the past when I’ve
had that same bug (in another project), that was the cause. You may
try looking for URIs in config file in which the property isn’t being
resolved or it ends up as file://NULL/some/path/that/doesnt/exist
Cheers,
Chris
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Chris Mattmann, Ph.D.
Chief Architect
Instrument Software and Science Data Systems Section (398)
NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
Office: 168-519, Mailstop: 168-527
Email: chris.a.mattmann@nasa.gov
WWW: http://sunset.usc.edu/~mattmann/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Director, Information Retrieval and Data Science Group (IRDS)
Adjunct Associate Professor, Computer Science Department
University of Southern California, Los Angeles, CA 90089 USA
WWW: http://irds.usc.edu/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
On 6/28/16, 9:02 AM, "Dligach, Dmitriy" <dd...@luc.edu> wrote:
>Thanks, Chris.
>
>I didn’t realize cTAKES was relying on environment variables for locating resources. Do you know which environment variable might be the issue?
>
>Thanks again for your help,
>
>Dima
>
>> On Jun 28, 2016, at 10:26, Mattmann, Chris A (3980) <ch...@jpl.nasa.gov> wrote:
>>
>> Hi Dima,
>>
>> In Apache OODT, when we do environment variable replacement on a URI,
>> e.g., file://[SOME_ENV]/path, if $SOME_ENV isn’t defined, you get that
>> error like you had below so that was the source of my suggestion sorry
>> for not clarifying.
>>
>> Cheers,
>> Chris
>>
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> Chris Mattmann, Ph.D.
>> Chief Architect
>> Instrument Software and Science Data Systems Section (398)
>> NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
>> Office: 168-519, Mailstop: 168-527
>> Email: chris.a.mattmann@nasa.gov
>> WWW: http://sunset.usc.edu/~mattmann/
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> Director, Information Retrieval and Data Science Group (IRDS)
>> Adjunct Associate Professor, Computer Science Department
>> University of Southern California, Los Angeles, CA 90089 USA
>> WWW: http://irds.usc.edu/
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On 6/28/16, 8:03 AM, "Dligach, Dmitriy" <dd...@luc.edu> wrote:
>>
>>> Hi Chris,
>>>
>>> Sorry, could you please clarify which environment variable I am missing?
>>>
>>> Thanks,
>>>
>>> Dima
>>>
>>>> On Jun 28, 2016, at 09:49, Mattmann, Chris A (3980) <ch...@jpl.nasa.gov> wrote:
>>>>
>>>> Looks to me like a missing environment variable..
>>>>
>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>> Chris Mattmann, Ph.D.
>>>> Chief Architect
>>>> Instrument Software and Science Data Systems Section (398)
>>>> NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
>>>> Office: 168-519, Mailstop: 168-527
>>>> Email: chris.a.mattmann@nasa.gov
>>>> WWW: http://sunset.usc.edu/~mattmann/
>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>> Director, Information Retrieval and Data Science Group (IRDS)
>>>> Adjunct Associate Professor, Computer Science Department
>>>> University of Southern California, Los Angeles, CA 90089 USA
>>>> WWW: http://irds.usc.edu/
>>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 6/28/16, 7:45 AM, "Dligach, Dmitriy" <dd...@luc.edu> wrote:
>>>>
>>>>> Dear cTAKES developers,
>>>>>
>>>>> I am looking for a simple cTAKEs pipeline that can be run from command line to introduce a group of people to cTAKES. This pipeline:
>>>>>
>>>>> ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
>>>>>
>>>>> seemed like a good candidate so I gave it a try. It runs fine when in Eclipse, but when I run it from command line:
>>>>>
>>>>> mvn exec:java -Dexec.mainClass=“org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls”
>>>>>
>>>>> It begins to run but then crashes. I am including the error messages below. Any clues?
>>>>>
>>>>> Thank you in advance,
>>>>>
>>>>> Dima
>>>>>
>>>>> ava.lang.reflect.InvocationTargetException
>>>>> 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:497)
>>>>> at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:293)
>>>>> at java.lang.Thread.run(Thread.java:745)
>>>>> Caused by: 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:603)
>>>>> at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
>>>>> at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
>>>>> 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:123)
>>>>> 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:269)
>>>>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
>>>>> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
>>>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
>>>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>>>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>>>>> 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:269)
>>>>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
>>>>> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
>>>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
>>>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>>>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>>>>> 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:269)
>>>>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
>>>>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
>>>>> at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:76)
>>>>> at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:42)
>>>>> at org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:68)
>>>>> ... 6 more
>>>>>
>>>>>
>>>
>
Re: URI is not hierarchical
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
Thanks, Chris.
I didn’t realize cTAKES was relying on environment variables for locating resources. Do you know which environment variable might be the issue?
Thanks again for your help,
Dima
> On Jun 28, 2016, at 10:26, Mattmann, Chris A (3980) <ch...@jpl.nasa.gov> wrote:
>
> Hi Dima,
>
> In Apache OODT, when we do environment variable replacement on a URI,
> e.g., file://[SOME_ENV]/path, if $SOME_ENV isn’t defined, you get that
> error like you had below so that was the source of my suggestion sorry
> for not clarifying.
>
> Cheers,
> Chris
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Chris Mattmann, Ph.D.
> Chief Architect
> Instrument Software and Science Data Systems Section (398)
> NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
> Office: 168-519, Mailstop: 168-527
> Email: chris.a.mattmann@nasa.gov
> WWW: http://sunset.usc.edu/~mattmann/
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Director, Information Retrieval and Data Science Group (IRDS)
> Adjunct Associate Professor, Computer Science Department
> University of Southern California, Los Angeles, CA 90089 USA
> WWW: http://irds.usc.edu/
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
>
>
>
>
>
>
>
> On 6/28/16, 8:03 AM, "Dligach, Dmitriy" <dd...@luc.edu> wrote:
>
>> Hi Chris,
>>
>> Sorry, could you please clarify which environment variable I am missing?
>>
>> Thanks,
>>
>> Dima
>>
>>> On Jun 28, 2016, at 09:49, Mattmann, Chris A (3980) <ch...@jpl.nasa.gov> wrote:
>>>
>>> Looks to me like a missing environment variable..
>>>
>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>> Chris Mattmann, Ph.D.
>>> Chief Architect
>>> Instrument Software and Science Data Systems Section (398)
>>> NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
>>> Office: 168-519, Mailstop: 168-527
>>> Email: chris.a.mattmann@nasa.gov
>>> WWW: http://sunset.usc.edu/~mattmann/
>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>> Director, Information Retrieval and Data Science Group (IRDS)
>>> Adjunct Associate Professor, Computer Science Department
>>> University of Southern California, Los Angeles, CA 90089 USA
>>> WWW: http://irds.usc.edu/
>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 6/28/16, 7:45 AM, "Dligach, Dmitriy" <dd...@luc.edu> wrote:
>>>
>>>> Dear cTAKES developers,
>>>>
>>>> I am looking for a simple cTAKEs pipeline that can be run from command line to introduce a group of people to cTAKES. This pipeline:
>>>>
>>>> ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
>>>>
>>>> seemed like a good candidate so I gave it a try. It runs fine when in Eclipse, but when I run it from command line:
>>>>
>>>> mvn exec:java -Dexec.mainClass=“org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls”
>>>>
>>>> It begins to run but then crashes. I am including the error messages below. Any clues?
>>>>
>>>> Thank you in advance,
>>>>
>>>> Dima
>>>>
>>>> ava.lang.reflect.InvocationTargetException
>>>> 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:497)
>>>> at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:293)
>>>> at java.lang.Thread.run(Thread.java:745)
>>>> Caused by: 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:603)
>>>> at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
>>>> at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
>>>> 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:123)
>>>> 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:269)
>>>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
>>>> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
>>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
>>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>>>> 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:269)
>>>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
>>>> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
>>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
>>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>>>> 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:269)
>>>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
>>>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
>>>> at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:76)
>>>> at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:42)
>>>> at org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:68)
>>>> ... 6 more
>>>>
>>>>
>>
Re: URI is not hierarchical
Posted by "Mattmann, Chris A (3980)" <ch...@jpl.nasa.gov>.
Hi Dima,
In Apache OODT, when we do environment variable replacement on a URI,
e.g., file://[SOME_ENV]/path, if $SOME_ENV isn’t defined, you get that
error like you had below so that was the source of my suggestion sorry
for not clarifying.
Cheers,
Chris
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Chris Mattmann, Ph.D.
Chief Architect
Instrument Software and Science Data Systems Section (398)
NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
Office: 168-519, Mailstop: 168-527
Email: chris.a.mattmann@nasa.gov
WWW: http://sunset.usc.edu/~mattmann/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Director, Information Retrieval and Data Science Group (IRDS)
Adjunct Associate Professor, Computer Science Department
University of Southern California, Los Angeles, CA 90089 USA
WWW: http://irds.usc.edu/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
On 6/28/16, 8:03 AM, "Dligach, Dmitriy" <dd...@luc.edu> wrote:
>Hi Chris,
>
>Sorry, could you please clarify which environment variable I am missing?
>
>Thanks,
>
>Dima
>
>> On Jun 28, 2016, at 09:49, Mattmann, Chris A (3980) <ch...@jpl.nasa.gov> wrote:
>>
>> Looks to me like a missing environment variable..
>>
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> Chris Mattmann, Ph.D.
>> Chief Architect
>> Instrument Software and Science Data Systems Section (398)
>> NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
>> Office: 168-519, Mailstop: 168-527
>> Email: chris.a.mattmann@nasa.gov
>> WWW: http://sunset.usc.edu/~mattmann/
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> Director, Information Retrieval and Data Science Group (IRDS)
>> Adjunct Associate Professor, Computer Science Department
>> University of Southern California, Los Angeles, CA 90089 USA
>> WWW: http://irds.usc.edu/
>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On 6/28/16, 7:45 AM, "Dligach, Dmitriy" <dd...@luc.edu> wrote:
>>
>>> Dear cTAKES developers,
>>>
>>> I am looking for a simple cTAKEs pipeline that can be run from command line to introduce a group of people to cTAKES. This pipeline:
>>>
>>> ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
>>>
>>> seemed like a good candidate so I gave it a try. It runs fine when in Eclipse, but when I run it from command line:
>>>
>>> mvn exec:java -Dexec.mainClass=“org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls”
>>>
>>> It begins to run but then crashes. I am including the error messages below. Any clues?
>>>
>>> Thank you in advance,
>>>
>>> Dima
>>>
>>> ava.lang.reflect.InvocationTargetException
>>> 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:497)
>>> at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:293)
>>> at java.lang.Thread.run(Thread.java:745)
>>> Caused by: 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:603)
>>> at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
>>> at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
>>> 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:123)
>>> 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:269)
>>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
>>> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>>> 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:269)
>>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
>>> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>>> 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:269)
>>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
>>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
>>> at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:76)
>>> at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:42)
>>> at org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:68)
>>> ... 6 more
>>>
>>>
>
Re: URI is not hierarchical
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
Hi Chris,
Sorry, could you please clarify which environment variable I am missing?
Thanks,
Dima
> On Jun 28, 2016, at 09:49, Mattmann, Chris A (3980) <ch...@jpl.nasa.gov> wrote:
>
> Looks to me like a missing environment variable..
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Chris Mattmann, Ph.D.
> Chief Architect
> Instrument Software and Science Data Systems Section (398)
> NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
> Office: 168-519, Mailstop: 168-527
> Email: chris.a.mattmann@nasa.gov
> WWW: http://sunset.usc.edu/~mattmann/
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Director, Information Retrieval and Data Science Group (IRDS)
> Adjunct Associate Professor, Computer Science Department
> University of Southern California, Los Angeles, CA 90089 USA
> WWW: http://irds.usc.edu/
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
>
>
>
>
>
>
>
> On 6/28/16, 7:45 AM, "Dligach, Dmitriy" <dd...@luc.edu> wrote:
>
>> Dear cTAKES developers,
>>
>> I am looking for a simple cTAKEs pipeline that can be run from command line to introduce a group of people to cTAKES. This pipeline:
>>
>> ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
>>
>> seemed like a good candidate so I gave it a try. It runs fine when in Eclipse, but when I run it from command line:
>>
>> mvn exec:java -Dexec.mainClass=“org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls”
>>
>> It begins to run but then crashes. I am including the error messages below. Any clues?
>>
>> Thank you in advance,
>>
>> Dima
>>
>> ava.lang.reflect.InvocationTargetException
>> 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:497)
>> at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:293)
>> at java.lang.Thread.run(Thread.java:745)
>> Caused by: 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:603)
>> at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
>> at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
>> 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:123)
>> 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:269)
>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
>> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>> 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:269)
>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
>> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>> 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:269)
>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
>> at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:76)
>> at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:42)
>> at org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:68)
>> ... 6 more
>>
>>
Re: URI is not hierarchical
Posted by "Mattmann, Chris A (3980)" <ch...@jpl.nasa.gov>.
Looks to me like a missing environment variable..
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Chris Mattmann, Ph.D.
Chief Architect
Instrument Software and Science Data Systems Section (398)
NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
Office: 168-519, Mailstop: 168-527
Email: chris.a.mattmann@nasa.gov
WWW: http://sunset.usc.edu/~mattmann/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Director, Information Retrieval and Data Science Group (IRDS)
Adjunct Associate Professor, Computer Science Department
University of Southern California, Los Angeles, CA 90089 USA
WWW: http://irds.usc.edu/
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
On 6/28/16, 7:45 AM, "Dligach, Dmitriy" <dd...@luc.edu> wrote:
>Dear cTAKES developers,
>
>I am looking for a simple cTAKEs pipeline that can be run from command line to introduce a group of people to cTAKES. This pipeline:
>
>ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
>
>seemed like a good candidate so I gave it a try. It runs fine when in Eclipse, but when I run it from command line:
>
>mvn exec:java -Dexec.mainClass=“org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls”
>
>It begins to run but then crashes. I am including the error messages below. Any clues?
>
>Thank you in advance,
>
>Dima
>
>ava.lang.reflect.InvocationTargetException
> 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:497)
> at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:293)
> at java.lang.Thread.run(Thread.java:745)
>Caused by: 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:603)
> at org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
> at org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
> 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:123)
> 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:269)
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
> 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:269)
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
> 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:269)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
> at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:76)
> at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:42)
> at org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:68)
> ... 6 more
>
>