Hi Pei, I was finally able to get around to testing this. I am running into the same issue that Tim has encountered.
Thanks for making the fix and logging the ticket for the xdl.xsd issue. Kim Ebert 1.801.669.7342 Perfect Search Corp http://www.perfectsearchcorp.com/ On 08/26/2014 12:30 AM, Tim O'Connell wrote: > Hi Pei, > > Yes, I was able to get as far as it looks like you did - until I ran into > the same error with ytex: > 2014-08-25 22:43:09,596 WARN org.apache.ctakes.ytex.umls.dao.UMLSDaoTest > - sql exception - mrconso probably doesn't exist, check error > > However, earlier in the ytex tests, I did get another error: > Running org.apache.ctakes.jdl.data.xml.ValidationTest > org.xml.sax.SAXParseException; schema_reference.4: Failed to read schema > document > 'file:/C:/Users/oconnell/workspace/cTakes%20Projects/ctakes/ctakes-ytex/file:/C:/Users/oconnell/workspace/cTakes%2520Projects/ctakes/ctakes-ytex-res/target/ctakes-ytex-res-3.2.1-SNAPSHOT.jar!/org/apache/ctakes/jdl/xdl.xsd', > because 1) could not find the document; 2) the document could not be read; > 3) the root element of the document is not <xsd:schema>. > at > com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:198) > ... > Caused by: java.io.FileNotFoundException: > C:\Users\oconnell\workspace\cTakes > Projects\ctakes\ctakes-ytex\file:\C:\Users\oconnell\workspace\cTakes%20Projects\ctakes\ctakes-ytex-res\target\ctakes-ytex-res-3.2.1-SNAPSHOT.jar!\org\apache\ctakes\jdl\xdl.xsd > (The filename, directory name, or volume label syntax is incorrect) > ... > Tests run: 3, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.624 sec > <<< FAILURE! > > It then goes on to keep running tests, and finds the ytex UMLS/SQL error > above, but at the end of that error dump, it says: > Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.539 sec > > Results : > > Tests in error: > setSchema(org.apache.ctakes.jdl.data.xml.ValidationTest) > > Tests run: 36, Failures: 0, Errors: 1, Skipped: 4 > > Which seems to point towards the earlier test error as being what is > stopping the build. Any thoughts? > > Tim > > > > On Mon, Aug 25, 2014 at 8:52 AM, Chen, Pei <pei.c...@childrens.harvard.edu> > wrote: > >> Tim/Kim, >> After a quick debug, it looks like the DependencyParser Tests looks okay, >> however, the test pipeline uses LVG. And during maven 'install', these >> files are inside a jar which LVG explicitly needs a File or Directory. I >> just committed a step in the pom.xml to unpack the lvg-res. This should be >> fine for the junit test; but also keep that in mind when configuring for a >> production environment. >> If you have a chance, could you try trunk? It should solve the parser >> issue (and any other test components that depend on lvg-res), but not sure >> about potentially other test errors. >> >> --Pei >> >>> -----Original Message----- >>> From: Tim O'Connell [mailto:tim.oconn...@gmail.com] >>> Sent: Monday, August 25, 2014 12:38 AM >>> To: dev@ctakes.apache.org >>> Subject: Re: managing ctakes resources on classpath >>> >>> Thanks Kim & Pei. If it helps any, I'm getting the same error in >> Eclipse. >>> I just checked out the code this morning from SVN. >>> >>> Using -DskipTests=true I was able to get it to build from the command >> line. >>> Tim >>> >>> >>> >>> >>> On Wed, Aug 20, 2014 at 12:41 PM, Kim Ebert >>> <kim.eb...@perfectsearchcorp.com >>>> wrote: >>>> I've added issue 307. >>>> >>>> https://issues.apache.org/jira/browse/CTAKES-307 >>>> >>>> Kim Ebert >>>> 1.801.669.7342 >>>> Perfect Search Corp >>>> http://www.perfectsearchcorp.com/ >>>> >>>> On 08/20/2014 11:52 AM, Chen, Pei wrote: >>>>> Thanks Kim- would you mind opening up a Jira to track this? >>>>> The cTAKES ClearNLP Dependency Parser and/or Test Cases most likely >>>>> need >>>> to be updated to enable resources to be picked up from the jar. >>>>>> -----Original Message----- >>>>>> From: Kim Ebert [mailto:kim.eb...@perfectsearchcorp.com] >>>>>> Sent: Wednesday, August 20, 2014 1:39 PM >>>>>> To: dev@ctakes.apache.org >>>>>> Subject: Re: managing ctakes resources on classpath >>>>>> >>>>>> I'm just using exactly what came out of SVN, so I haven't modified >>>>>> the default classpath yet. >>>>>> >>>>>> Kim Ebert >>>>>> 1.801.669.7342 >>>>>> Perfect Search Corp >>>>>> http://www.perfectsearchcorp.com/ >>>>>> >>>>>> On 08/20/2014 11:28 AM, Chen, Pei wrote: >>>>>>> Do you happen to have both jars and unpacked in your cp? >>>>>>> Temp workaround: -DskipTests=true? >>>>>>> >>>>>>> Sent from my iPhone >>>>>>> >>>>>>>> On Aug 20, 2014, at 1:25 PM, "Kim Ebert" >>>>>> <kim.eb...@perfectsearchcorp.com> wrote: >>>>>>>> I am encountering this same issue when I try to run mvn install >>>>>>>> from the command line. Is there a way to get mvn install to work? >>>>>>>> >>>>>>>> ------------------------------------------------------- >>>>>>>> T E S T S >>>>>>>> ------------------------------------------------------- >>>>>>>> Running >>>>>>>> org.apache.ctakes.dependency.parser.ae.util.TestClearNLPAnalysisE >>>>>>>> ngin >>>>>>>> es >>>>>>>> log4j: reset attribute= "false". >>>>>>>> log4j: Threshold ="null". >>>>>>>> log4j: Level value for root is [INFO]. >>>>>>>> log4j: root level set to INFO >>>>>>>> log4j: Class name: [org.apache.log4j.ConsoleAppender] >>>>>>>> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout" >>>>>>>> log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy >>>>>>>> HH:mm:ss} %5p %c{1} - %m%n]. >>>>>>>> log4j: Adding appender named [consoleAppender] to category >>> [root]. >>>>>>>> Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: >>>>>>>> 1.397 sec <<< FAILURE! >>>>>>>> >>>>>>>> Results : >>>>>>>> >>>>>>>> Tests in error: >>>>>>>> >>>>>>>> >>>>>> TestClearNLPPipeLine(org.apache.ctakes.dependency.parser.ae.util.Te >>>>>> stCle >>>>>> arNLPAnalysisEngines): >>>>>>>> URI is not hierarchical >>>>>>>> >>>>>>>> Kim Ebert >>>>>>>> 1.801.669.7342 >>>>>>>> Perfect Search Corp >>>>>>>> http://www.perfectsearchcorp.com/ >>>>>>>> >>>>>>>>> On 09/10/2013 07:33 AM, Pei Chen wrote: >>>>>>>>> Hi Steve, >>>>>>>>> The URI is not hierarchical is most likely caused by the code >>>>>>>>> trying to use the resources/models, but they are inside a jar >>>>>>>>> instead of >>>>>> unpacked. >>>>>>>>> -Which version of cTAKES are you using? >>>>>>>>> -Do you happen to have the resource file name that caused the >>> above? >>>>>>>>> --Pei >>>>>>>>> >>>>>>>>> >>>>>>>>>> On Mon, Sep 9, 2013 at 9:48 PM, Steve Hookway >>>>>> <shook...@cra.com> wrote: >>>>>>>>>> Hi all, >>>>>>>>>> >>>>>>>>>> I'm trying to integrate ctakes into a webapp and am running >>>>>>>>>> into issues getting the resources to load correctly. In a >>>>>>>>>> standalone version of the app, if I add the resources folder to >>>>>>>>>> the buildpath (as described in the install directions) >>>>>>>>>> everything works as expected. However, if I add the folder to >>>>>>>>>> the project classpath instead, I get a URI is not hierarchical >>>>>>>>>> exception from >>>>>> FileResourceImpl.load: >>>>>>>>>> java.lang.IllegalArgumentException: URI is not hierarchical >>>>>>>>>> at java.io.File.<init>(File.java:392) >>>>>>>>>> at >>>>>>>>>> >>>> org.apache.ctakes.core.resource.FileResourceImpl.load(FileResourceImpl >>>> .ja >>>>>> va:44) >>>>>>>>>> at >>>>>>>>>> >>> org.apache.uima.resource.impl.ResourceManager_impl.registerResource >>>>>>>>>> (ResourceManager_impl.java:603) >>>>>>>>>> >>>>>>>>>> Similarly if I try and run from a webapp - setting up tomcat's >>>>>>>>>> classpath to include the ctakes resource folder, I get the same >>>>>>>>>> URI is not hierarchical error. I found this bug report: >>>>>>>>>> https://issues.apache.org/jira/browse/CTAKES-89 but it >>>>>>>>>> suggests adding the resource folder to my classpath, which >>>>>>>>>> isn't doing the >>>> trick. >>>>>>>>>> If you can steer me in the right direction, I'd really >>>>>>>>>> appreciate >>>> it. >>>>>>>>>> Thanks, >>>>>>>>>> Steve >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> THIS MESSAGE IS INTENDED FOR THE USE OF THE PERSON TO >>> WHOM IT >>>>>> IS >>>>>>>>>> ADDRESSED. IT MAY CONTAIN INFORMATION THAT IS PRIVILEGED, >>>>>>>>>> CONFIDENTIAL AND EXEMPT FROM DISCLOSURE UNDER >>> APPLICABLE >>>>>> LAW. If >>>>>>>>>> you are not the intended recipient, your use of this message >>>>>>>>>> for any >>>>>> purpose is strictly prohibited. >>>>>>>>>> If you have received this communication in error, please delete >>>>>>>>>> the message and notify the sender so that we may correct our >>> records. >>>>
