Hi Dima, Ok, thanks. I use ctakes some jars pulled from maven central for a couple of projects. I admit that they don't use lvg. However, I simply declare dependencies in a pom and they are pulled down. I then run piper files from ide or cli. For one project I do run simply from command line, but it is using a maven profile. For multiple entry points (development) this is not ideal. I only used mvn exec:java two or three times, but I agree with you that it is one good way to go for development if you are trying to build and run outside an IDE. It is almost as good as writing a script that accepts a main class name. 64 ways to skin a crayola pack of cats.
I think trust James will be able to bring ctakes-lvg into this decade and then you can try using ctakes jars from maven central. Between the FileLocator and possible usable lvg 2016 improvements it shouldn't take too much kludge. Flw. Sean -----Original Message----- From: Dligach, Dmitriy [mailto:ddlig...@luc.edu] Sent: Friday, April 28, 2017 1:52 PM To: dev@ctakes.apache.org Subject: Re: URI is not hierarchical 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_p > rojects_ctakesresources_files_ctakes-2Dresources-2D4.0-2Dbin.zip_downl > oad&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZ > stTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&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/ctake >> s >> - 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=qS4goWBT7poplM69z >> y _ 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=qS4goWBT7poplM69z >> y _ 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= >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>> >>> >>> >>> >> >>
