Hi Dima, Just to let you know I am taking a look at this. More later, if not today, then tomorrow. FYI here is where I'm at so far.
I checked out a fresh copy of ctakes trunk and put files from your ctakes-misc into a subdirectory called ctakes-misc, and I updated my local copy of the main pom.xml for ctakes to include ctakes-misc. I am able to reproduce getting URI is not hierarchical just by letting tests run during "mvn clean install": Tests in error: testPipeline(org.apache.ctakes.temporal.ae.BackwardsTimeAnnotatorTest): URI is not hierarchical testPipeline(org.apache.ctakes.temporal.ae.ContextualModalityAnnotatorTest): URI is not hierarchical testPipeline(org.apache.ctakes.temporal.ae.EventAnnotatorTest): URI is not hierarchical testPipeline(org.apache.ctakes.temporal.ae.EventEventRelationAnnotatorTest): URI is not hierarchical testPipeline(org.apache.ctakes.temporal.ae.EventTimeRelationAnnotatorTest): URI is not hierarchical On Fri, Apr 28, 2017 at 12:27 PM, James Masanz <masanz.ja...@gmail.com> wrote: > > 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.c >> takes.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.Finan@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\o >> rg\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=fs67G >> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevR >> An-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=fs67GvlGZstTpy >> IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-a92vTj >> 9x79u08OjKfQ9U4&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=fs67G >> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20 >> x8dEc3xfYTHbadlwhgSdrIsw&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.fi...@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.a >> pache.org_confluence_display_CTAKES_Piper-2BFiles&d=DwIGaQ&c >> =qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp >> yIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20x8dEc3xf >> YTHbadlwhgSdrIsw&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=fs67G >> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf >> _qgdQj3HYIeLCeKr9Q303b0Q&s=NWoDwPNChJkDhFseM3j8Gi7KNDdVqzi1BFt0onalf9I&e= >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> from command line as follows: >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> mvn exec:java -Dexec.mainClass=“org.apache.c >> takes.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/ctakesresour >> ces/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/resource >> s/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.t >> ype.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/l >> ookup/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-2Dw >> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po >> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP >> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30 >> 3b0Q&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-2Dw >> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po >> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP >> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30 >> 3b0Q&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/look >> up/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(Lv >> gCmdApiResourceImpl.java:65) >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> at org.apache.uima.resource.impl.ResourceManager_impl.registerR >> esource(ResourceManager_impl.java:628) >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> at org.apache.uima.resource.impl.ResourceManager_impl.initializ >> eExternalResources(ResourceManager_impl.java:464) >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> at org.apache.uima.resource.Resource_ImplBase.initialize(Resour >> ce_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.produceResou >> rce(AnalysisEngineFactory_impl.java:94) >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe >> source(CompositeResourceFactory_impl.java:62) >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework. >> java:279) >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram >> ework.java:407) >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_ >> impl.java:256) >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine >> _impl.initASB(AggregateAnalysisEngine_impl.java:429) >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine >> _impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl. >> java:373) >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine >> _impl.initialize(AggregateAnalysisEngine_impl.java:186) >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> at org.apache.uima.fit.factory.AnalysisEngineFactory.createEngi >> ne(AnalysisEngineFactory.java:711) >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> at org.apache.uima.fit.factory.AggregateBuilder.createAggregate >> (AggregateBuilder.java:207) >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> at org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLook >> upPipeline.java:66) >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAcce >> ssorImpl.java:62) >> > >> >>> >> > >> >>>> >> > >> >>> >> > >> >>>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMe >> thodAccessorImpl.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_MA >> VEN_MojoExecutionException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3x >> hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4 >> f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s= >> JfA-JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e= >> > >> >>> >> > >> >>> >> > >> >>> >> > >> >> >> > >> > >> > >> >> >
