Hmmm, sorry. Instead of copying from %CTAKES_HOME%/resources, try checking out a copy of the lvg resources from sourceforge svn checkout svn:// svn.code.sf.net/p/ctakesresources/code/trunk/ctakes-resources-lvg2008/src/main/resources/org/apache/ctakes/lvg/
-- James On Sat, Apr 29, 2017 at 2:23 PM, Dligach, Dmitriy <ddlig...@luc.edu> wrote: > Hi James, > > > Copy the lvg directory that's in > > > > %CTAKES_HOME%/resources/org/apache/ctakes/ > > Sorry, in my case, I am only seeing one directory here called > ‘dictionary’. Is that the one or should there be something called ‘lvg’? > > Dima > > > > to be under the target/classes/org/apache/ctakes directory that's > within > > your local copy of ctakes-misc > > > > so for example, on my system, after the copy, I see > > C:\from.svn\ctakes-misc.git\trunk\target\classes\org\ > > apache\ctakes\lvg\data\config\lvg.properties > > > > (For anyone else reading this, that resources directory will show up when > > you do mvn clean install of cTAKES) > > > > If you want lvg to use the actual lvg resources, you can't just copy the > > lvg.properties file for this workaround, you have to copy the entire > > subtree, or it will create an empty lvg database. > > > > > > I'll check out the StringIndexOutOfBoundsException on Monday unless > someone > > else beats me to it before then. > > > > > > FYI, to test this workaround, before I did the copy, I was seeing > > > > 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) > > > > After I copied that lvg directory, I was then able see output in the > > outputDirectory > > defined by UmlsLookupPipeline.java > > > > FYI #2, I'm using Win 7 Pro. This workaround should work for linux/mac > but > > was not tested there. > > > > FYI #3, this was using your idea of not having ctakes-misc be under > ctakes. > > thanks for that tip! keeps things nicely separated - no need to update > > the parent pom at all. > > > > > > > > On Sat, Apr 29, 2017 at 2:00 AM, James Masanz <masanz.ja...@gmail.com> > > wrote: > > > >> Hi Dima, > >> > >> what revision of trunk are you using? I'm getting an error you weren't > >> seeing so I'm guessing it's because I checked out ctakes just today. > >> > >> Caused by: java.lang.StringIndexOutOfBoundsException: String index out > of > >> range: -7 > >> at java.lang.String.substring(String.java:1967) > >> at org.apache.ctakes.dictionary.lookup2.util. > >> JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:110) > >> at org.apache.ctakes.dictionary.lookup2.util. > >> JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:63) > >> at org.apache.ctakes.dictionary.lookup2.dictionary. > >> JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91) > >> at org.apache.ctakes.dictionary.lookup2.dictionary. > >> JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72) > >> at org.apache.ctakes.dictionary.lookup2.dictionary. > >> UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31) > >> ... 27 more > >> > >> FYI, I created the directories needed by UmlsLookupPipeline.java for > >> chunker-model.zip and inputDirectory and outputDirectory, and I > get > >> the above regardless of whether I use text input file containing just > "pain > >> in left knee started on Wednesday." or if I use > >> GenSurg_UmbilicalHernia_1.rtf as the input file instead. > >> > >> > >> On Fri, Apr 28, 2017 at 5:48 PM, Dligach, Dmitriy <ddlig...@luc.edu> > >> wrote: > >> > >>> 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.BackwardsTimeAnno > >>> tatorTest): > >>>> URI is not hierarchical > >>>> > >>>> testPipeline(org.apache.ctakes.temporal.ae.ContextualModalit > >>> yAnnotatorTest): > >>>> URI is not hierarchical > >>>> testPipeline(org.apache.ctakes.temporal.ae.EventAnnotatorTest): URI > is > >>>> not hierarchical > >>>> > >>>> testPipeline(org.apache.ctakes.temporal.ae.EventEventRelatio > >>> nAnnotatorTest): > >>>> URI is not hierarchical > >>>> > >>>> testPipeline(org.apache.ctakes.temporal.ae.EventTimeRelation > >>> AnnotatorTest): > >>>> 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/ctakesresour > >>> ces/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_1jVyGOpVo1UHWrMDqjW > >>> iVAnk0jfPE&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-dpJc0RdnzRfjwQqbNw4gk > >>> Lwf0SSpp0I&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=NWoDwPNChJkDhFseM3j8Gi7KNDdVqzi1B > >>> Ft0onalf9I&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-p > >>> lugin: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= > >>>>>>> > >>>>>>>>> > >>>>>>> > >>>>>>>>> > >>>>>>> > >>>>>>>>> > >>>>>>> > >>>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>> > >>>>>> > >>>>> > >>> > >>> > >> > >
