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
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
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.
Re: cTAKES min requirements
No objections here. On Aug 25, 2014, at 12:16 PM, Pei Chen chen...@apache.org 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$1.runReflectiveCall(FrameworkMethod.java:45)
at
org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
at
org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:42)
at
Re: org.apache.ctakes.ytex.umls.dao.UMLSDaoTest
That is an expected error having to do with the fact that UMLS isn't
installed in the test database that get's fired up for unit tests. That is
actually a warning (and should be interpreted as an error only if you do
have UMLS set up)
On Mon, Aug 25, 2014 at 9:02 PM, Pei Chen chen...@apache.org wrote:
Hi VJ,
While on the subject of unit tests-
I didn't get a chance to dig deeper and was hoping you would know the
cause of this unit test failure: mvn clean install
2014-08-25 13:33:50,830 WARN net.sf.ehcache.CacheManager - Creating
a new instance of CacheManager using the diskStorePath
/var/folders/qc/d7xd4zzs0_xcybv88skt5_7mgn/T/ which is already
used by an existing CacheManager.
The source of the configuration was
net.sf.ehcache.config.generator.ConfigurationSource$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(NativeMethodAccessorImpl.java:57)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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 chen...@apache.org 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
eflectiveMethodInvocation.java:150)
at
org.springframework.transaction.interceptor.TransactionInterceptor.inv
oke(TransactionInterceptor.java:110)
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 pei.c...@childrens.harvard.edu
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 javascript:;
[mailto:clayclay...@gmail.com
javascript:;] On Behalf Of
Clayton Turner
Sent: Thursday, August 21, 2014 4:25 PM
To: dev@ctakes.apache.org javascript:;
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
caturn...@g.cofc.edu
javascript:;
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
tim.oconn...@gmail.com javascript:;
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
john.travis.gr...@gmail.com javascript:;
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
tim.oconn...@gmail.com javascript:;
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 fact that the UMLS database has at sometime in the
relatively
recent
past changed the SAB tag in the MRCONSO table for SNOMED
terms from SNOMEDCT to SNOMEDCT_US. I just had a newer
version of
UMLS
that uses SNOMEDCT_US. Thus when the install script tried to
create 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
