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