Attached is a snippet of the console messages
On Sat, Apr 29, 2017 at 9:18 AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Woah, I've never seen that. How did that happen? Is there another bug? > The FileLocator should have logged a very long message saying "I couldn't > find it here or there or the other place ..." and then thrown a > FileNotFoundException. > > > > -----Original Message----- > From: James Masanz [mailto:masanz.ja...@gmail.com] > Sent: Saturday, April 29, 2017 2:00 AM > To: dev@ctakes.apache.org > Subject: Re: URI is not hierarchical > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_re > > pos_asf_ctakes_trunk_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCo > > ppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Lc9XlOnpIxXTTjv > > RKjUkyEK6iZXUXjRQhnbtKubbuQQ&s=ulRVEvEVpyQ8zZjXbCF2pY_ejjjoFaDYOnMk1l0 > > Fez0&e= 2. git clone > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dmitri > > ydligach_ctakes-2Dmisc.git&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMS > > dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Lc9XlOnpIx > > XTTjvRKjUkyEK6iZXUXjRQhnbtKubbuQQ&s=vwWZxpuAYNjunq6khejHsCaw12XBURfSRj > > mZvfbA8TA&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.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. > BackwardsTimeAnnotatorTest): > > > URI is not hierarchical > > > > > > testPipeline(org.apache.ctakes.temporal.ae. > > ContextualModalityAnnotatorTest): > > > URI is not hierarchical > > > testPipeline(org.apache.ctakes.temporal.ae.EventAnnotatorTest): URI > > > is not hierarchical > > > > > > testPipeline(org.apache.ctakes.temporal.ae. > > EventEventRelationAnnotatorTest): > > > URI is not hierarchical > > > > > > testPipeline(org.apache.ctakes.temporal.ae. > > EventTimeRelationAnnotatorTest): > > > 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/ctakesresources/cta > > >> kes- 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.ne > > >> t_projects_ctakesresources_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14 > > >> JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Lc9 > > >> XlOnpIxXTTjvRKjUkyEK6iZXUXjRQhnbtKubbuQQ&s=dKDOAG-k6QNwD3cIsI31U4zH > > >> k2lGmqXzRjKXI4ySz_s&e= 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_ > > 1jVyGOpVo1UHWrMDqjWiVAnk0jfPE&e= > > >>>> > > >>>> > > >>>> > > >>>> But this one succeeds: > > >>>> > > >>>> > > >>>> > > >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github. > > >>> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_ > > >>> org_apache_ctakes_pipelines_BasicPipeline.java&d=DwIGaQ&c= > > >>> qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=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-dpJc0RdnzRfjwQqbNw4gkLwf0SS > > >>> pp0 > > I&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=NWoDwPNChJkDhFseM3j8Gi7KNDdVqz > > i1BFt0onalf9I&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.propertie > > >>> s > > >>>> > > >>>>>> > > >>>> > > >>>>>>> > > >>>> > > >>>>>> > > >>>> > > >>>>>>> 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- > > plugin:1.6.0:java > > >>> (default-cli) on project ctakes-misc: An exception occured while > > executing > > >>> the Java class. URI is not hierarchical -> [Help 1] > > >>>> > > >>>>>> > > >>>> > > >>>>>>> > > >>>> > > >>>>>> > > >>>> > > >>>>>>> [ERROR] > > >>>> > > >>>>>> > > >>>> > > >>>>>>> > > >>>> > > >>>>>> > > >>>> > > >>>>>>> [ERROR] To see the full stack trace of the errors, re-run > > >>>>>>> Maven > > with > > >>> the -e switch. > > >>>> > > >>>>>> > > >>>> > > >>>>>>> > > >>>> > > >>>>>> > > >>>> > > >>>>>>> [ERROR] Re-run Maven using the -X switch to enable full debug > > >>> logging. > > >>>> > > >>>>>> > > >>>> > > >>>>>>> > > >>>> > > >>>>>> > > >>>> > > >>>>>>> [ERROR] > > >>>> > > >>>>>> > > >>>> > > >>>>>>> > > >>>> > > >>>>>> > > >>>> > > >>>>>>> [ERROR] For more information about the errors and possible > > >>> solutions, please read the following articles: > > >>>> > > >>>>>> > > >>>> > > >>>>>>> > > >>>> > > >>>>>> > > >>>> > > >>>>>>> [ERROR] [Help 1] https://urldefense.proofpoint. > com/v2/url?u=https-3A__urldefense.proofpoint&d= > DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m= > Lc9XlOnpIxXTTjvRKjUkyEK6iZXUXjRQhnbtKubbuQQ&s= > qORzTUT4mGAcaxRvrlTVH7hUZDSxp3VJQ6v6oiaYND8&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= > > >>>> > > >>>>>> > > >>>> > > >>>>>> > > >>>> > > >>>>>> > > >>>> > > >>>>> > > >>>> > > >>>> > > >>>> > > >>> > > >>> > > >> > > > > >
29 Apr 2017 01:52:40 INFO LvgAnnotator - URL for lvg.properties =file:/C:/Users/ch192959/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.j ar!/org/apache/ctakes/lvg/data/config/lvg.properties 29 Apr 2017 01:52:41 INFO SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip 29 Apr 2017 01:52:41 INFO TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 29 Apr 2017 01:52:41 INFO ContextDependentTokenizerAnnotator - Finite state machines loaded. 29 Apr 2017 01:52:41 INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip 29 Apr 2017 01:52:41 INFO Chunker - Chunker model file: C:\Users\Dima\Loyola\Workspaces\cTakes\ctakes\ctakes-chunker-res\src\main\resources\org\apache\ctakes\chunker\models\chunker-model.zip 29 Apr 2017 01:52:42 INFO AbstractJCasTermAnnotator - Using dictionary lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence 29 Apr 2017 01:52:42 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 29 Apr 2017 01:52:42 INFO AbstractJCasTermAnnotator - Using minimum term text span: 3 29 Apr 2017 01:52:42 INFO AbstractJCasTermAnnotator - Using Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml 29 Apr 2017 01:52:42 INFO DictionaryDescriptorParser - Parsing dictionary specifications: 29 Apr 2017 01:52:42 INFO UmlsUserApprover - Checking UMLS Account at https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user jamesmasanz: ..29 Apr 2017 01:52:43 INFO UmlsUserApprover - UMLS Account at https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user jamesmasanz has been validated [WARNING] org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: <unknown>) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:407) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:429) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.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.createEngine(AnalysisEngineFactory.java:711) at org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207) at org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLookupPipeline.java:66) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:282) at java.lang.Thread.run(Thread.java:745) Caused by: org.apache.uima.resource.ResourceInitializationException: MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key Could not construct org.apache.ct akes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:131) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266) ... 18 more Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException: MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key Could not construct or g.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:199) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:156) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:128) at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:129) ... 19 more Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:196) ... 22 more 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 [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 7.496 s [INFO] Finished at: 2017-04-29T01:52:43-04:00 [INFO] Final Memory: 168M/439M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.6.0:java (default-cli) on project ctakes-misc: An exception occured while executing the Java class. Initialization of annotator cla ss "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: <unknown>): MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, ke y Could not construct org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary: InvocationTargetException: String index out of range: -7 -> [Help 1]
