RE: managing ctakes resources on classpath
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
> > 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"
> > >> 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
> > 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
> > >> 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.(File.java:392)
> > >> at
> > >>
> > >>
> > org.apache.ctakes.core.resource.FileResourceImpl.load(FileResourceImpl
> > .ja
> > >> va:44)
> > >> at
> > >>
> > >>
> org.ap
Re: cTAKES min requirements
No objections here. On Aug 25, 2014, at 12:16 PM, Pei Chen wrote: > Since we default the runtime java heap sizes to 3g in 3.2.0, should we > update our documentation to officially only support 64bit? I can only > see models/pipelines being loaded into mem grow in size. I know it > may seem trivial, but I still know a few unfortunate souls still on 32 > bit systems… any objections in saying that it will essentially be no > longer supported. > > > --Pei
cTAKES min requirements
Since we default the runtime java heap sizes to 3g in 3.2.0, should we update our documentation to officially only support 64bit? I can only see models/pipelines being loaded into mem grow in size. I know it may seem trivial, but I still know a few unfortunate souls still on 32 bit systems… any objections in saying that it will essentially be no longer supported. --Pei
org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
Hi VJ,
While on the subject of unit tests-
I didn't get a chance to dig deeper and was hoping you would know the
cause of this unit test failure: > mvn clean install
2014-08-25 13:33:50,830 WARN net.sf.ehcache.CacheManager - Creating
a new instance of CacheManager using the diskStorePath
"/var/folders/qc/d7xd4zzs0_xcybv88skt5_7mgn/T/" which is already
used by an existing CacheManager.
The source of the configuration was
net.sf.ehcache.config.generator.ConfigurationSource$InputStreamConfigurationSource@7433a719.
The diskStore path for this CacheManager will be set to
/var/folders/qc/d7xd4zzs0_xcybv88skt5_7mgn/T//ehcache_auto_created_1408988030830.
To avoid this warning consider using the CacheManager factory methods
to create a singleton CacheManager or specifying a separate ehcache
configuration (ehcache.xml) for each CacheManager instance.
2014-08-25 13:33:51,082 WARN
org.hibernate.engine.jdbc.spi.SqlExceptionHelper - SQL Error: 62,
SQLState: S0010
2014-08-25 13:33:51,082 ERROR
org.hibernate.engine.jdbc.spi.SqlExceptionHelper - Unknown JDBC
escape sequence: {{db.schema}.MRCONSO mrconso0_ where mrconso0_.aui>?
and length(mrconso0_.aui)>0 and length(mrconso0_.str)<200 and
mrconso0_.lat='ENG' order by mrconso0_.aui
2014-08-25 13:33:51,085 WARN
org.apache.ctakes.ytex.umls.dao.UMLSDaoTest - sql exception - mrconso
probably doesn't exist, check error
org.hibernate.exception.SQLGrammarException: could not prepare statement
at
org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQLStateConversionDelegate.java:123)
at
org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:49)
at
org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:125)
at
org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:188)
at
org.hibernate.engine.jdbc.internal.StatementPreparerImpl.prepareQueryStatement(StatementPreparerImpl.java:159)
at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1859)
at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1836)
at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1816)
at org.hibernate.loader.Loader.doQuery(Loader.java:900)
at
org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:342)
at org.hibernate.loader.Loader.doList(Loader.java:2526)
at org.hibernate.loader.Loader.doList(Loader.java:2512)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2342)
at org.hibernate.loader.Loader.list(Loader.java:2337)
at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:495)
at
org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:357)
at
org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:195)
at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1269)
at org.hibernate.internal.QueryImpl.list(QueryImpl.java:101)
at
org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl.getAllAuiStr(UMLSDaoImpl.java:106)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at
org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:319)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at
org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at
org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:90)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy11.getAllAuiStr(Unknown Source)
at
org.apache.ctakes.ytex.umls.dao.UMLSDaoTest.testGetAllAuiStr(UMLSDaoTest.java:53)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at
org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:45)
at
org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
at
org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:42)
at
org.junit.internal.runners.statements.Invoke
Re: org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
That is an expected error having to do with the fact that UMLS isn't
installed in the test database that get's fired up for unit tests. That is
actually a warning (and should be interpreted as an error only if you do
have UMLS set up)
On Mon, Aug 25, 2014 at 9:02 PM, Pei Chen wrote:
> Hi VJ,
> While on the subject of unit tests-
>
> I didn't get a chance to dig deeper and was hoping you would know the
> cause of this unit test failure: > mvn clean install
>
> 2014-08-25 13:33:50,830 WARN net.sf.ehcache.CacheManager - Creating
> a new instance of CacheManager using the diskStorePath
> "/var/folders/qc/d7xd4zzs0_xcybv88skt5_7mgn/T/" which is already
> used by an existing CacheManager.
>
> The source of the configuration was
>
> net.sf.ehcache.config.generator.ConfigurationSource$InputStreamConfigurationSource@7433a719.
>
> The diskStore path for this CacheManager will be set to
>
> /var/folders/qc/d7xd4zzs0_xcybv88skt5_7mgn/T//ehcache_auto_created_1408988030830.
>
> To avoid this warning consider using the CacheManager factory methods
> to create a singleton CacheManager or specifying a separate ehcache
> configuration (ehcache.xml) for each CacheManager instance.
>
> 2014-08-25 13:33:51,082 WARN
> org.hibernate.engine.jdbc.spi.SqlExceptionHelper - SQL Error: 62,
> SQLState: S0010
>
> 2014-08-25 13:33:51,082 ERROR
> org.hibernate.engine.jdbc.spi.SqlExceptionHelper - Unknown JDBC
> escape sequence: {{db.schema}.MRCONSO mrconso0_ where mrconso0_.aui>?
> and length(mrconso0_.aui)>0 and length(mrconso0_.str)<200 and
> mrconso0_.lat='ENG' order by mrconso0_.aui
>
> 2014-08-25 13:33:51,085 WARN
> org.apache.ctakes.ytex.umls.dao.UMLSDaoTest - sql exception - mrconso
> probably doesn't exist, check error
>
> org.hibernate.exception.SQLGrammarException: could not prepare statement
>
> at
> org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQLStateConversionDelegate.java:123)
>
> at
> org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:49)
>
> at
> org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:125)
>
> at
> org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPreparationTemplate.prepareStatement(StatementPreparerImpl.java:188)
>
> at
> org.hibernate.engine.jdbc.internal.StatementPreparerImpl.prepareQueryStatement(StatementPreparerImpl.java:159)
>
> at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1859)
>
> at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1836)
>
> at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1816)
>
> at org.hibernate.loader.Loader.doQuery(Loader.java:900)
>
> at
> org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:342)
>
> at org.hibernate.loader.Loader.doList(Loader.java:2526)
>
> at org.hibernate.loader.Loader.doList(Loader.java:2512)
>
> at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2342)
>
> at org.hibernate.loader.Loader.list(Loader.java:2337)
>
> at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:495)
>
> at
> org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:357)
>
> at
> org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:195)
>
> at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1269)
>
> at org.hibernate.internal.QueryImpl.list(QueryImpl.java:101)
>
> at
> org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl.getAllAuiStr(UMLSDaoImpl.java:106)
>
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
>
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>
> at java.lang.reflect.Method.invoke(Method.java:606)
>
> at
> org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:319)
>
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
>
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
>
> at
> org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110)
>
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>
> at
> org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:90)
>
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
>
> at
> org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
>
> at com.sun.proxy.$Proxy11.getAllAuiStr(Unknown Source)
>
> at
> org.apache.ctakes.ytex.umls.dao.UMLSDaoTest.testGetAllAuiStr(UMLSDaoTest.java:53)
>
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeM
RE: org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
It logs it as a warn, but fails the test.
Should there it assertNotNull only if UMLS setup else, pass the test?
That way, for those folks are doing a default 'maven clean install, they won't
have to skipTests?
// UMLSDaoTest .testGetAllAuiStr() - Check to see if UMLS is setup before
checking?
Assert.assertNotNull(auis);
CTAKES-308
> -Original Message-
> From: vijay garla [mailto:vnga...@gmail.com]
> Sent: Monday, August 25, 2014 4:30 PM
> To: dev@ctakes.apache.org
> Subject: Re: org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
>
> That is an expected error having to do with the fact that UMLS isn't installed
> in the test database that get's fired up for unit tests. That is actually a
> warning (and should be interpreted as an error only if you do have UMLS set
> up)
>
>
> On Mon, Aug 25, 2014 at 9:02 PM, Pei Chen wrote:
>
> > Hi VJ,
> > While on the subject of unit tests-
> >
> > I didn't get a chance to dig deeper and was hoping you would know the
> > cause of this unit test failure: > mvn clean install
> >
> > 2014-08-25 13:33:50,830 WARN net.sf.ehcache.CacheManager - Creating
> > a new instance of CacheManager using the diskStorePath
> > "/var/folders/qc/d7xd4zzs0_xcybv88skt5_7mgn/T/" which is already
> > used by an existing CacheManager.
> >
> > The source of the configuration was
> >
> >
> net.sf.ehcache.config.generator.ConfigurationSource$InputStreamConfigura
> tionSource@7433a719.
> >
> > The diskStore path for this CacheManager will be set to
> >
> >
> /var/folders/qc/d7xd4zzs0_xcybv88skt5_7mgn/T//ehcache_auto_creat
> ed_1408988030830.
> >
> > To avoid this warning consider using the CacheManager factory methods
> > to create a singleton CacheManager or specifying a separate ehcache
> > configuration (ehcache.xml) for each CacheManager instance.
> >
> > 2014-08-25 13:33:51,082 WARN
> > org.hibernate.engine.jdbc.spi.SqlExceptionHelper - SQL Error: 62,
> > SQLState: S0010
> >
> > 2014-08-25 13:33:51,082 ERROR
> > org.hibernate.engine.jdbc.spi.SqlExceptionHelper - Unknown JDBC
> > escape sequence: {{db.schema}.MRCONSO mrconso0_ where
> mrconso0_.aui>?
> > and length(mrconso0_.aui)>0 and length(mrconso0_.str)<200 and
> > mrconso0_.lat='ENG' order by mrconso0_.aui
> >
> > 2014-08-25 13:33:51,085 WARN
> > org.apache.ctakes.ytex.umls.dao.UMLSDaoTest - sql exception - mrconso
> > probably doesn't exist, check error
> >
> > org.hibernate.exception.SQLGrammarException: could not prepare
> > statement
> >
> > at
> > org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQ
> > LStateConversionDelegate.java:123)
> >
> > at
> > org.hibernate.exception.internal.StandardSQLExceptionConverter.convert
> > (StandardSQLExceptionConverter.java:49)
> >
> > at
> > org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionH
> > elper.java:125)
> >
> > at
> >
> org.hibernate.engine.jdbc.internal.StatementPreparerImpl$StatementPrep
> > arationTemplate.prepareStatement(StatementPreparerImpl.java:188)
> >
> > at
> > org.hibernate.engine.jdbc.internal.StatementPreparerImpl.prepareQueryS
> > tatement(StatementPreparerImpl.java:159)
> >
> > at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1859)
> >
> > at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1836)
> >
> > at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1816)
> >
> > at org.hibernate.loader.Loader.doQuery(Loader.java:900)
> >
> > at
> > org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loa
> > der.java:342)
> >
> > at org.hibernate.loader.Loader.doList(Loader.java:2526)
> >
> > at org.hibernate.loader.Loader.doList(Loader.java:2512)
> >
> > at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2342)
> >
> > at org.hibernate.loader.Loader.list(Loader.java:2337)
> >
> > at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:495)
> >
> > at
> > org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslato
> > rImpl.java:357)
> >
> > at
> >
> org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.j
> > ava:195)
> >
> > at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1269)
> >
> > at org.hibernate.internal.QueryImpl.list(QueryImpl.java:101)
> >
> > at
> >
> org.apache.ctakes.ytex.umls.dao.UMLSDaoImpl.getAllAuiStr(UMLSDaoImpl.j
> > ava:106)
> >
> > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> >
> > at
> >
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.j
> > ava:57)
> >
> > at
> >
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
> s
> > orImpl.java:43)
> >
> > at java.lang.reflect.Method.invoke(Method.java:606)
> >
> > at
> > org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflectio
> > n(AopUtils.java:319)
> >
> > at
> >
> org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoi
> > npoint(ReflectiveMethodInvocation.java:183)
> >
> > at
> >
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(
> R
RE: Change from SNOMEDCT to SNOMEDCT_US affecting v_snomed_fword_lookup
This has been done in trunk for the next patch 3.2.1 release:
https://issues.apache.org/jira/browse/CTAKES-309
Thanks for pointing this out- Would be great if someone could confirm the ytex
scripts works as expected with their latest version of umls.
> -Original Message-
> From: vijay garla [mailto:vnga...@gmail.com]
> Sent: Thursday, August 21, 2014 11:07 PM
> To: dev@ctakes.apache.org
> Subject: Re: Change from SNOMEDCT to SNOMEDCT_US affecting
> v_snomed_fword_lookup
>
> That would definitely make sense
>
> On Thursday, August 21, 2014, Chen, Pei
> wrote:
>
> > VJ,
> > Would it make sense to add in('SNOMEDCT_US') to the default
> > ctakes-ytex/scripts/data/**/insert_view.sql?
> > That way it'll support umls2011 as well as the newer 2014 naming
> > conventions?
> > Ex: inner join MRCONSO mrc on c.aui = mrc.aui and mrc.SAB in (
> > 'SNOMEDCT',
> > 'SNOMEDCT_US','RXNORM')
> >
> > --Pei
> >
> > > -Original Message-
> > > From: clayclay...@gmail.com
> > > [mailto:clayclay...@gmail.com
> > ] On Behalf Of
> > > Clayton Turner
> > > Sent: Thursday, August 21, 2014 4:25 PM
> > > To: dev@ctakes.apache.org
> > > Subject: Re: Change from SNOMEDCT to SNOMEDCT_US affecting
> > > v_snomed_fword_lookup
> > >
> > > Ah, I just switched to the ytex branch and all is good now. The
> > > SNOMED_US issue has been plaguing me for weeks now so thanks a
> million for that.
> > >
> > >
> > > On Thu, Aug 21, 2014 at 2:13 PM, Clayton Turner
> > > > >
> > > wrote:
> > >
> > > > Awesome. This is just what I needed for the longest time.
> > > >
> > > > I'm having a slight issue. When running either the ytex pipeline
> > > > or ytex version of the AggregatePlaintextUMLSProcessor I get an
> > > > error during initialization.
> > > >
> > > > My DictionaryLookupAnnotator.xml is raising a
> > > > org.apache.uima.resource.ResourceInitializationException causedby:
> > > > java.lang.ClassNotFoundException:
> > > > edu.mayo.bmi.uima.lookup.ae.FirstTokenPermLookupInitializerImpl
> > > >
> > > > I feel like I may have drifted away from what I need, though,
> > > > because before this the CPE was complaining about a lack of
> > > > LookupDesc_SNOMED.xml file. I found a ytex version of this on a
> > > > google code site somewhere and pasted it where the CPE was looking
> > > > for it. Now
> > > this error is coming up.
> > > >
> > > > Could my problem be solved with just a re-run of the ant script
> > > > (was just trying to avoid since it takes ages) or is it a different
> > > > issue?
> > > >
> > > >
> > > > On Tue, Aug 19, 2014 at 12:58 PM, Tim O'Connell
> > > > >
> > > > wrote:
> > > >
> > > >> Hi John,
> > > >>
> > > >> I'm not sure what was going on with the @db.schema@ error,
> > > >> although I was getting it as well before with my prior build of
> > > >> 3.1.2 - I assume that you've fixed something (thank you!) to make
> > > >> this go away. I rebuilt everything from scratch and it's working now.
> > > >>
> > > >> I think one other thing I had to change was that after I had
> > > >> finished the install/build, the cTakes version of
> > > >> LookupDesc_Db.xml doesn't work (in
> > > >> resources\org\apache\ctakes\dictionary\lookup) - I'm pretty sure
> > > >> I had to copy in an older version of the file from 3.1.1 to get
> > > >> the default cTakes AggregatePlaintextUMLSProcessor pipeline
> > > >> working, although please double-check that as my memory is a little
> foggy.
> > > >>
> > > >> But yes, here's what I have working since re-building:
> > > >> 1. ytex-pipeline.xml
> > > >> 2. ytex version of AggregatePlaintextUMLSProcessor.xml
> > > >> 3. cTakes version of AggregatePlaintextUMLSProcessor.xml (with
> > > >> swapping the LookupDesc_Db.xml file as above)
> > > >>
> > > >> I've even made modifications to the ytex version of
> > > >> LookupDesc_SNOMED.xml to get it tagging Disease Disorders, along
> > > >> with
> > > database modifications to
> > > >> have it store these entries as well, which is working great.
> > Literally,
> > > >> everything is working perfectly now.
> > > >>
> > > >> Still so much for me to learn! Let me know if you need any more
> > details.
> > > >>
> > > >> All the best,
> > > >> Tim
> > > >>
> > > >>
> > > >>
> > > >> On Tue, Aug 19, 2014 at 4:31 AM, John Green
> > > >> >
> > > >> wrote:
> > > >>
> > > >> > I have not had time to implement this - to clarify out of
> > > >> > curiosity,
> > > >> does
> > > >> > this clear up the @db.schema@ error Tim? And did you
> > > >> > successfully run ytex with the ctakes dictionary-lookup?
> > > >> >
> > > >> >
> > > >> > JG
> > > >> > —
> > > >> > Sent from Mailbox for iPhone
> > > >> >
> > > >> > On Sat, Aug 16, 2014 at 2:53 AM, Tim O'Connell
> > > >> > >
> > > >> > wrote:
> > > >> >
> > > >> > > Hi folks,
> > > >> > > I was having an issue with the current build (from svn) of
> > > >> > > ctakes/ytex
> > > >> > not
> > > >> > > identifying any annotations as some folks on this board. I
> > > >> > > traced it
> > > >> to
> > > >> > > the
Re: Microsoft - MSDN - Is the support continuing for ASF committers?
Just an fyi - link for MSDN subscription license(s) for committers http://mail-archives.apache.org/mod_mbox/www-community/201305.mbox/%3c518b85e7.7000...@lehmi.de%3E https://svn.apache.org/repos/private/committers/donated-licenses/msdn-subscription.html
Re: managing ctakes resources on classpath
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 . 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 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 > > > > 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" > > > >> 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.Patter
