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 <[email protected]> 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:[email protected]] > > Sent: Monday, August 25, 2014 12:38 AM > > To: [email protected] > > 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 > > <[email protected] > > > 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:[email protected]] > > > >> Sent: Wednesday, August 20, 2014 1:39 PM > > > >> To: [email protected] > > > >> 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" > > > >> <[email protected]> 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 > > > >> <[email protected]> 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. > > > > > > > > > > >
