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=
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>
> >>>
> >>>
> >>
>
>

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