Going back to your original email, I notice cTAKES is referencing
lvg.properties
as being within a jar
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
But I also see in LvgCmdApiResourceImpl.java the following code, which is
trying to handle it as a File, not a stream. :(
File configFile = new File(dr.getUri());
configFileName = configFile.getPath();
At first glance, looks like LvgCmdApiResourceImpl needs updating.
As a workaround, you could try extracting the lvg subdirectory from
ctakes-resources-4.0-bin.zip that's on sourceforge [1] into something on
the classpath so the lvg.propertiesfile appears under
org/apache/ctakes/lvg/data/config/lvg.properties
You might also need to have the rest of the files and directories under
org/apache/ctakes/lvg/data to also be outside the jar, not sure offhand.
I can try that out this afternoon.
[1]
https://sourceforge.net/projects/ctakesresources/files/ctakes-resources-4.0-bin.zip/download
On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy <ddlig...@luc.edu> wrote:
> Hi Sean,
>
> First of all, a huge thank you for taking time to debug this issue. I
> really appreciate your help.
>
> Second, I think my main message somehow got lost in translation (sorry, I
> should’ve included it for clarity with my recent emails). I never had any
> trouble running this pipeline in Eclipse. The “URI is not hierarchical”
> error only happens when I run it from command line.
>
> I run it using the following maven command:
>
> mvn exec:java
> -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
> -Dexec.args="" -Dctakes.umlsuser=<my umls login name> -Dctakes.umlspw=<my
> umls password>
>
> As I said in my previous email, the other pipeline (that does not have
> dictionary lookup) runs fine at command line. The error only happens when I
> run pipelines containing dictionary lookup.
>
> Dima
>
>
>
> > On Apr 26, 2017, at 13:36, Finan, Sean <sean.fi...@childrens.harvard.edu>
> wrote:
> >
> > Hi Dima,
> >
> > Good news: no uri hierarchical error.
> >
> > All that I did was import your ctakes-misc pom as a maven project in
> intellij. Then I created a run configuration with my sandbox as the
> working directory, ctakes-misc as the classpath module, and my umls
> credentials in the environment.
> > All database files were found, the pipeline ran, and I got output:
> > total 2448
> > drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
> > drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
> > -rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19
> GenSurg_UmbilicalHernia_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19
> OBGYN_Gen_Abscess_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19
> OBGYN_HysterectomyAndBSO_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
> OBGYN_IUD_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19
> OBGYN_LaborProgressNote_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19
> OBGYN_MVAPrego_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19
> OBGYN_PROMCheck_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19
> Peds_Dysphagia_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19
> Peds_FebrileSez_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19
> Peds_RoutBirthNote_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19
> VascSurg_AAA_Leak_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19
> VascSurg_FollowUp_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19
> VascSurg_PVD_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19
> VascSurg_RO-AAA_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19
> VascSurg_RO-DVT.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19
> VascSurg_RO-DVT_1.rtf.xmi
> >
> >
> >
> >
> > Bad news: it looks like the hsqldb port of lvg2008 is not working.
> >
> > Caused by: org.hsqldb.HsqlException: error in script file line: 61
> C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\
> org\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read
> beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX '3198299
> 60557 3198299 53129 0 0 0 0 1210464']
> >
> > Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException:
> read beyond end of file
> >
> >
> > At any rate, the code works but I think that something is missing from
> your configuration.
> > Since it is a personal development environment you are kind of on your
> own.
> > Good luck,
> > Sean
> >
> > P.S. Get rid of the ctakes-resources-umls2011ab artifact in your pom.
> It isn't doing anything.
> >
> >
> >
> > -----Original Message-----
> > From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
> > Sent: Wednesday, April 26, 2017 12:46 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: URI is not hierarchical
> >
> > I am definitely still seeing the “URI is not hierarchical” issue. Here’s
> a piece of information that might help you figure out what the problem is:
> >
> >
> >
> > It only happens if the pipeline includes dictionary lookup. For
> instance, this one fails:
> >
> >
> >
> > 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=Cv-_Ac9CLY7wNnflevRAn-
> a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_1jVyGOpVo1UHWrMDqjWiVAnk0jfPE&e=
> >
> >
> >
> > But this one succeeds:
> >
> >
> >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_
> java_org_apache_ctakes_pipelines_BasicPipeline.java&
> d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-
> a92vTj9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
> >
> >
> >
> > (it’s the same as the first one, but the dictionary lookup part is
> removed).
> >
> >
> >
> > Dima
> >
> >
> >
> >
> >
> >
> >
> >> On Apr 26, 2017, at 11:37, Finan, Sean <Sean.Finan@childrens.harvard.
> edu> wrote:
> >
> >>
> >
> >> Hi again Dima,
> >
> >>
> >
> >> The piper files are not meant to replace uimafit. Uimafit is great for
> many purposes.
> >
> >>
> >
> >> As for that annoying old "URI is not hierarchical" bug, a while back I
> checked in a fix that worked for me. Since then I cannot duplicate it.
> >
> >>
> >
> >> Sean
> >
> >>
> >
> >> -----Original Message-----
> >
> >> From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
> >
> >> Sent: Wednesday, April 26, 2017 12:18 PM
> >
> >> To: dev@ctakes.apache.org
> >
> >> Subject: Re: URI is not hierarchical
> >
> >>
> >
> >> As I said in my previous email, the piper approach looks very
> promising. However many of us probably still have lots of existing uimaFIT
> pipelines and it would be nice to be able to run them from command line.
> >
> >>
> >
> >> So, are there any plans to finally fix this old “URI is not
> hierarchical” problem? Do we at least know what’s causing it?
> >
> >>
> >
> >> Dima
> >
> >>
> >
> >>
> >
> >>
> >
> >>> On Apr 14, 2017, at 12:14, Finan, Sean <Sean.Finan@childrens.harvard.
> edu> wrote:
> >
> >>>
> >
> >>> Ok, thanks. For your original question:
> >
> >>>
> >
> >>>> 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?
> >
> >>>
> >
> >>> I thought that I had already fixed it. So much for my thorough
> testing.
> >
> >>>
> >
> >>> Let me know what happens with the piper approach.
> >
> >>> Sean
> >
> >>>
> >
> >>>
> >
> >>> -----Original Message-----
> >
> >>> From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
> >
> >>> Sent: Friday, April 14, 2017 12:47 PM
> >
> >>> To: dev@ctakes.apache.org
> >
> >>> Subject: Re: URI is not hierarchical
> >
> >>>
> >
> >>> Hi Sean,
> >
> >>>
> >
> >>>
> >
> >>>
> >
> >>> The pipeline I am trying to run is this:
> >
> >>>
> >
> >>>
> >
> >>>
> >
> >>> 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=
> xe6RaWm66aSyUeXjU20x8dEc3xfYTHbadlwhgSdrIsw&s=ixO9vX_WJ7p-
> dpJc0RdnzRfjwQqbNw4gkLwf0SSpp0I&e=
> >
> >>>
> >
> >>>
> >
> >>>
> >
> >>> (This is the UmlsLookupPipeline class).
> >
> >>>
> >
> >>>
> >
> >>>
> >
> >>> It runs fine in Eclipse but fails when I run from command line.
> >
> >>>
> >
> >>>
> >
> >>>
> >
> >>> I will look into the solution you are suggesting (thanks!).
> >
> >>>
> >
> >>>
> >
> >>>
> >
> >>> Dima
> >
> >>>
> >
> >>>
> >
> >>>
> >
> >>>
> >
> >>>
> >
> >>>
> >
> >>>
> >
> >>>> On Apr 14, 2017, at 11:35, Finan, Sean <Sean.Finan@childrens.harvard.
> edu> wrote:
> >
> >>>
> >
> >>>>
> >
> >>>
> >
> >>>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.
> apache.org_confluence_display_CTAKES_Piper-2BFiles&d=DwIGaQ&
> c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> xe6RaWm66aSyUeXjU20x8dEc3xfYTHbadlwhgSdrIsw&s=
> pNVLJSOBMk5orJZ4Oy4ZwtpkPp0tU48-g1qxtpIBucw&e=
> >
> >>>
> >
> >>>>
> >
> >>>
> >
> >>>>
> >
> >>>
> >
> >>>> -----Original Message-----
> >
> >>>
> >
> >>>> From: Dligach, Dmitriy [mailto:ddlig...@luc.edu]
> >
> >>>
> >
> >>>> 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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&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.initializeAggregateAnalysisEng
> ine(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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=JfA-
> JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e=
> >
> >>>
> >
> >>>
> >
> >>>
> >
> >>
> >
> >
> >
>
>
