Hi James, Thank you so much for looking into this!
Your general setup matches mine. I also do: 1. svn co https://svn.apache.org/repos/asf/ctakes/trunk/ 2. git clone https://github.com/dmitriydligach/ctakes-misc.git (in trunk/) 3. mvn clean compile (in trunk/) 4. mvn clean compile (in ctakes-misc/) BTW, I just discovered that it’s not necessary to check out a fresh copy of ctakes-misc into a subdirectory in trunk. It will build no matter where it is on your system as long as you first do an ‘mvn clean compile’ in trunk/ (without it, ctakes-misc/ will not build). Thanks again, James. Dima > On Apr 28, 2017, at 16:30, James Masanz <masanz.ja...@gmail.com> wrote: > > 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= >>>> >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> >>>>> >>>> >>>> >>>> >>> >>> >>
