James, I was able to get around the “URI not hierarchical” issue by doing what you suggested!
I checked out lvg from svn.code.sf.net/p/ctakesresources/code/trunk/ctakes-resources-lvg2008/src/main/resources/org/apache/ctakes/lvg/ and put it in target/classes/org/apache/ctakes/. Thank you so much, you made my day today :) Dima > On Apr 29, 2017, at 01:57, James Masanz <masanz.ja...@gmail.com> wrote: > > Hi Dima, > > I modified my local copy of FileLocator to avoid the > StringIndexOutOfBoundsException I was seeing using HEAD, and here's the > workaround for the problem you were seeing until the code change is made to > LvgCmdApiResourceImpl: > > Copy the lvg directory that's in > > %CTAKES_HOME%/resources/org/apache/ctakes/ > > 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= >>>>>>> >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> >>>>>>>>> >>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> >>> >>> >>
