Hi James, With a glance at LvgCmdApiResource ... good gods, do we still need this? Given that we updated to lvg 2016 it looks like half of lvg-res should be completely revamped and we can probably get rid of the hacky references. 4.1 ?
Sean -----Original Message----- From: James Masanz [mailto:masanz.ja...@gmail.com] Sent: Friday, April 28, 2017 12:28 PM To: dev@ctakes.apache.org Subject: Re: URI is not hierarchical 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://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D4.0-2Dbin.zip_download&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ra9HfnuMGpOujoaSUtQA9mL4u6gpme6fd--2pbUGohc&s=fqcKKFIrMw69bxvC7tXm0ZWex5PvIsP32HivEqbJZrc&e= 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=https-3A__urldefense.proofpoint&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ra9HfnuMGpOujoaSUtQA9mL4u6gpme6fd--2pbUGohc&s=YQ9ZF9smiNYo-O3hS6Q5Ig98tZLemJD5aRphQazqOkI&e= > >>>> . > 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= > > > >>> > > > >>> > > > >>> > > > >> > > > > > > > >
