Hi Sean, My goal is just to run the pipelines in ctakes-misc on a remote server. I only have SSH access to this server, so I’d like to run these pipelines from command line. I will not need to modify ctakes code.
I have not been able yet to get ctakes-misc to compile without a ctakes installation, but I am working on it (I started a separate email thread related to this and you had some suggestions which I’m trying now). Dima > On Apr 28, 2017, at 11:54, Finan, Sean <sean.fi...@childrens.harvard.edu> > wrote: > > Hi Dima, > I have a question: > > Are you running ctakes-misc directly or do you have a master pom (like > misc_pom.xml) that includes ctakes-misc(-master) as a dependency along with > other ctakes modules? > In other words, are you trying to run using ctakes source code/resources or > ctakes jars? To put it another way, do you have a need to modify ctakes code > as you develop -misc? > > If you are running with ctakes "as an api" then I think that I may have > misunderstood your entire goal here ... > > -----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= >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>> >>> >>> >>> >> >>
