ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: URI is not hierarchical
Date Tue, 02 May 2017 15:40:28 GMT
Hi James,

I think that your proposed solution is good.  I never use lvg in my workflows as I have yet to see any major impact on performance.  
It would also be less libloat for which I currently use <exclusions> in my project poms.
However, since a lot of people use lvg as part of older default workflows, I understand that there may be some push back against a manual download.

Sean

-----Original Message-----
From: James Masanz [mailto:masanz.james@gmail.com] 
Sent: Tuesday, May 02, 2017 11:14 AM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical

Where I'm at with avoiding "URI is not hierarchical" caused by ctakes-lvg when using ctakes as maven dependency (not installing the convenience
binary)

LVG documentation indicates it needs the LVG HSQLDB to not be in a jar, but something that can be accessed by a java File object.  I'll test that out to make sure, but assuming it can't:

The change I've been working on builds on the existing approach of copying files out of the ctakes-resources jar at runtime

While copying the lvg database out of a jar for the dev environment (running from source) works where 1) it's a dev environment and 2) we have just a subset of the full LVG database outside the jar so you don't have to copy out of the jar unless you want to, it doesn't seem best to copy the full LVG database out of a jar when using ctakes as maven dependencies. The ctakes-resources lvg dependency is >1GB. If we are going to extract files from there, we would want to consider handling what if there's not enough space, plus document that it's going to take a while.  I want to think more about this and also get your input on this alternative:

Documenting that if someone is going to use ctakes as maven dependencies, and if you want to use LVG, then you download the LVG resources yourself and unzip them. And we'd document where to put them.  If the LVG database is not found outside a jar, throw an exception telling user to download (and unzip it)

Going to pick this up again another day (hopefully tomorrow) since there's a workaround for now.

-- James

On Mon, May 1, 2017 at 2:14 PM, Dligach, Dmitriy <ddligach@luc.edu> wrote:

> 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.james@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.james@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 
> >> <ddligach@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://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.or
> >>> g_repos_asf_ctakes_trunk_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J
> >>> ZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Ghi
> >>> qMFcdfSY5XVOI6gn239fc7LcthW2NPL5DPwACnlE&s=3_L6IzktPzjnfttElJ3tr95
> >>> QDQVRkWMK1G1r6NmUj9g&e= 2. git clone 
> >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dm
> >>> itriydligach_ctakes-2Dmisc.git&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKw
> >>> EW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&
> >>> m=GhiqMFcdfSY5XVOI6gn239fc7LcthW2NPL5DPwACnlE&s=i_ETlHnOsuSn9FgrQU
> >>> Jl_qMIN_6Wu9SM46gRUtkWfT4&e=  (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.james@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.james@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://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge
> >>>>> .net_projects_ctakesresources_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xh
> >>>>> KwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4g
> >>>>> Tao&m=GhiqMFcdfSY5XVOI6gn239fc7LcthW2NPL5DPwACnlE&s=BEB_rwa2nG1H
> >>>>> Sa0nDvPUDu6e5Ab5YRTONxnaMIMcJmA&e=
> >>>>> files/ctakes-resources-4.0-bin.zip/download
> >>>>>
> >>>>>
> >>>>> On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy 
> >>>>> <ddligach@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:ddligach@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:ddligach@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:ddligach@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.Finan@childrens.harvard.edu> wrote:
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> Hi Dima,
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> Where did you get that class?  I don't have 
> >>>>>>>>>> UmlsLookupPipeline
> or
> >>>>>> the package org.apache.ctakes.pipelines.
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> If you want to run from command-line I highly recommend 
> >>>>>>>>>> that you
> >>> use
> >>>>>> the PiperFileRunner class in core.pipeline.
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> To run the clinical pipeline use cli parameters:
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> -p DefaultFastPipeline.piper
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> -i {inputDir}
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> --xmiOut {outputDir}
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> --user {umlsUsername}
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> --pass {umlsPassword}
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> If you have the binary installation there is a
> runClinicalPipeline
> >>>>>> script in bin/
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> PiperFileRunner can run other piper files and take other
> >>> parameters
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> #   Runs the pipeline in the piper file specified by -p
> >>> (piperfile)
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> #   with any other provided parameters.  Standard parameters
> are:
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> #     -i , --inputDir {inputDirectory}
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> #     -o , --outputDir {outputDirectory}
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> #     -s , --subDir {subDirectory}  (for i/o)
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> #     --xmiOut {xmiOutputDirectory} (if different from -o)
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> #     -l , --lookupXml {dictionaryConfigFile} (fast only)
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> #     --user {umlsUsername}
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> #     --pass {umlsPassword}
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> #     -? , --help
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> #
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> #   Other parameters may be declared in the piper file using the
> >>> cli
> >>>>>> command:
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> #     cli {parameterName}={singleCharacter}
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> #   For instance, for declaration of ParagraphAnnotator path to
> >>>>>> regex file optional parameter PARAGRAPH_TYPES_PATH,
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> #   in the custom piper file add the line:
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> #     cli PARAGRAPH_TYPES_PATH=t
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> #   and when executing this script use:
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> #      runPiperFile -p path/to/my/custom.piper -t
> >>>>>> path/to/my/custom.bsv  ...
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> The above is a snippet from the runPiperFile script in the 
> >>>>>>>>>> bin/
> >>>>>> directory.
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> I am in the process of writing documentation on piper files 
> >>>>>>>>>> in
> the
> >>>>>> wiki.
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.
> >>>>>>>>>> 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:ddligach@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.proper
> >>>>>> ties
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> 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=https-3A__urldefense.proofpoint&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=GhiqMFcdfSY5XVOI6gn239fc7LcthW2NPL5DPwACnlE&s=IXU30Cq0sFxU4MDRr5IaCEF6_-R_Bhq0BA0dV0RJ_50&e= .
> >>>>>> 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=
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>
> >>>
> >>>
> >>
>
>
Mime
View raw message