Re: Apache cTAKES - ResourceInitializationException
Pankaj, Caused by: java.lang.NullPointerException* * at java.io.Reader.init(Reader.java:78)* * at java.io.InputStreamReader.init(InputStreamReader.java:72)* My guess is you are trying to read something which is null. Hope it helps. Regards, Harpreet On Wednesday, May 27, 2015, Pankaj Shinde pankaj.shi...@krixi.com wrote: Hi, I want to parse clinical documents using Apache cTAKES. I have a set of clinical documents as plain texts. For this, I am using BagOfCUIsGenerator.java and cTAKES jars. I configured this in IntelliJ IDEA as a java project. When I try to run, I am getting exception and error as follows. Output: *log4j:WARN No appenders could be found for logger (org.springframework.validation.DataBinder).* *log4j:WARN Please initialize the log4j system properly.* *log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.* *Loading configuration.* *Loading feature templates.* *Loading lexica.* *Loading model:* ** *Exception in thread main org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine failed. (Descriptor: file:/D:/Dev/Savy/java_projects/cTakes/desc/ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml)* * at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:251)* * at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:155)* * at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)* * at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)* * at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)* * at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)* * at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)* * at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)* * at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)* * at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)* * at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)* * at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)* * at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)* * at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)* * at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)* * at org.apache.uima.fit.factory.AnalysisEngineFactory.createEngineFromPath(AnalysisEngineFactory.java:773)* * at org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.init(BagOfAnnotationsGenerator.java:60)* * at org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.init(BagOfAnnotationsGenerator.java:54)* * at BagOfCUIsGenerator.init(BagOfCUIsGenerator.java:21)* * at BagOfCUIsGenerator.main(BagOfCUIsGenerator.java:61)* * 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 com.intellij.rt.execution.application.AppMain.main(AppMain.java:134)* *Caused by: java.lang.NullPointerException* * at java.io.Reader.init(Reader.java:78)* * at java.io.InputStreamReader.init(InputStreamReader.java:72)* * at java.util.Scanner.init(Scanner.java:608)* * at org.apache.ctakes.assertion.medfacts.cleartk.extractors.ContextWordWindowExtractor.init(ContextWordWindowExtractor.java:55)* * at org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine.initialize_history_extractor(HistoryCleartkAnalysisEngine.java:58)* * at org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine.initialize(HistoryCleartkAnalysisEngine.java:49)* * at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:249)* * ... 24 more* *Process finished with exit code 1* Please help. Thanks Pankaj Shinde
Re: Getting Started with CTAKES
Hello All, I was just wondering if there would be a gathering of ctakes community at Apache Con next week? Regards, Harpreet On Wed, Apr 8, 2015 at 10:49 AM, Pei Chen chen...@apache.org wrote: Hi Abhishek, Yes, Jay and I will have a session at ApacheCon on Drug Monitoring using Spark/Hadoop and twitter feeds... Will be happy to meetup. Let's coordinate offline if you happen to be around the area and to see if we can meet up. --Pei On Tue, Apr 7, 2015 at 8:03 PM, Abhishek Srivastava abhis...@gmail.com wrote: Thanks for the thread. I would love to meet up with CTAKES people. Please let me know how can we coordinate this. Please reach out to me my email Id is abhishes -at- gmail -dot- com Does CTAKES have a session at apache con? *From:* Pei Chen [mailto:chen...@apache.org] *Sent:* Monday, April 6, 2015 10:07 AM *To:* u...@ctakes.apache.org *Subject:* Re: Getting Started with CTAKES I believe Tim started a thread on how to programmatically extract the entitis/cui's currently via this thread: http://mail-archives.apache.org/mod_mbox/ctakes-dev/201503.mbox/%3ce084d8efe2b03a408b324458c5212e9434c10...@chexmbx3a.chboston.org%3e A couple of us are going to be in Austin,TX for Apache Con so if you happen to be there, we can plan to meet up. --Pei On Sun, Apr 5, 2015 at 2:51 AM, Abhishek Srivastava abhis...@gmail.com wrote: I have already searched the archive of this mailing list however if this question is duplicate then please don't flame me. I have some experience with NLTK in Python. I have gone through some of the basic literature on natural language processing. Using NLTK I can perform entity extraction pretty easily. My questions are 1. is there a tutorial available on CTAKES from a development perspective. I need to use the API to perform entity extraction. (i need exact APIs). 2. How can someone build a custom corpus with CTAKES. I know it works in medical context but my use case is even narrower (like text related to gynecology) Also, lastly, is there anyone on this mailing list in Dallas region I would love to meet you in person. Regards, Abhishek.
Re: Creating my own dictionaries
I am not sure but not setting the classpath to the project could be the problem. On Tue, Mar 3, 2015 at 5:07 PM, Maite Meseure Hugues meseure.ma...@gmail.com wrote: Hi everyone, I am currently facing a problem to run The CreateLuceneIndexFromDelimitedFile class that allows to get a Lucene index and reads from a pipe-delimited file. the error message is: Could not find or load main class org.apache.ctakes.dictionary.lookup.tools.CreateLuceneIndexFromDelimitedFile (same thing for scripts/java/edu/mayo/bmi/dictionarytools/CreateLuceneIndexForExampleDrugs.java scripts/java/edu/mayo/bmi/dictionarytools/CreateLuceneIndexForSnomedLikeSample.java ) Does someone know what is the problem? Thank you for your time. -- -- Maïté Meseure Hugues
Re: v_snomed_fword_lookup view
Hello Clayton,
I do not know about ytex, but I did switch from dictionary-lookup to
dictionary-lookup-fast.
I update my ctakes-dictionary-lookup-fast project using maven.
I think I used Team- Update and switched to the latest revision available
and then
I downloaded new 3.2 resources from the for umls. and then I added these
resources to my
ctakes-dictionary-lookup-fast resources folder and also the classpath in
ctakes-clinical-pipeline.
Then I changed the pom.xml file which belongs to the whole ctakes project
and
added
dependency
groupIdorg.apache.ctakes/groupId
artifactIdctakes-dictionary-lookup-res/artifactId
version${ctakes.version}/version
/dependency
dependency
groupIdorg.apache.ctakes/groupId
artifactIdctakes-dictionary-lookup-fast/artifactId
version${ctakes.version}/version
/dependency
these two dependencies to the file.
After this, I also added the dependency
dependency
groupIdorg.apache.ctakes/groupId
artifactIdctakes-dictionary-lookup-fast/artifactId
/dependency
to the pom.xml of ctakes-clinical-pipeline.
And then add the resources folder in ctakes-clinical-pipeline using build
path configuration under add class option.
After this it should work.
Regards,
Harpreet
On Mon, Aug 11, 2014 at 12:44 PM, Clayton Turner caturn...@g.cofc.edu
wrote:
I still get the same error with the ctakes3.2 branch. Any suggestions?
On Mon, Aug 11, 2014 at 12:06 PM, Clayton Turner caturn...@g.cofc.edu
wrote:
I'm going to do a clean install through the repo rather than the binaries
and see if that fixes my issue because I think I just read a past post
saying the lookup2 folders exist there.
On Mon, Aug 11, 2014 at 11:52 AM, Clayton Turner caturn...@g.cofc.edu
wrote:
When navigating to ctakes-dictionary-lookup-fast\desc\analysis_engine
there are 2 files, assumedly analysis engines.
SnomedLookupAnnotator.xml and SnomedOvLookupAnnotator.xml
If I pick either, I put in my UMLS information but receive an error when
trying to run the CPE:
Initialization of CAS Processor with name SnomedOvLookupAnnotator
failed.
CausedBy: org.apache.uima.resource.ResourceConfigurationException:
Initialization of CAS processor with name SnomedOvLookupAnnotator
failed.
CausedBy: org.apache.uima.resource.ResourceInitializationException:
Error
initializing org.apache.uima.resource.impl.DataResource_impl from
descriptor
file:..SnomedLookupAnnotator.xml
CausedBy: org.apache.uima.resource.ResourceInitializationException:
Could
not
access the resource data at
file:org\apache\ctakes\dictionary\lookup2\Snomed2011ab_ctakesTui\cTakesSnomed.xml
Now, I don't even have a lookup2 folder and, subsequently the Tui
folder and cTakesSnomed.xml file. This seems to be the problem, but I'm
not
sure where these files are supposed to be grabbed from.
On Mon, Aug 11, 2014 at 11:47 AM, Clayton Turner caturn...@g.cofc.edu
wrote:
Hi again:
How exactly do you switch to using the cTakes dictionary-lookup-fast.
Do
I need to go in and alter xml files or is it as simple as adding a
certain
item to the list of analysis engines?
On Fri, Aug 8, 2014 at 3:48 PM, Finan, Sean
sean.fi...@childrens.harvard.edu wrote:
Hi Clayton,
I don't know how the ytex dictionary lookup works, so I'm afraid that
I
can't help you with an answer. Maybe Vijay is the best person to do
this.
If you aren't tied to ytex you could try the new cTakes
dictionary-lookup-fast. I tested Patient came in with a malar rash
and
it found malar and malar rash.
Vijay,
At some point the lookup-fast module will be the default for the
cTakes
clinical pipeline. In order to synchronize the ytex lookup with
cTakes,
would you like to eventually work together on reusing the same code
for
ytex? I have no idea what ytex does, but I know the ins and outs of
the
cdl-fast module.
Sean
-Original Message-
From: clayclay...@gmail.com [mailto:clayclay...@gmail.com] On
Behalf
Of
Clayton Turner
Sent: Friday, August 08, 2014 2:08 PM
To: dev@ctakes.apache.org
Subject: v_snomed_fword_lookup view
Hi Everyone:
I have a question about how the v_snomed_fword_lookup view works
when
running the CPE.
So my understanding of the view is that it is a view comprised of
the
ytex.umls_aui_fword table, the umls.mrconso table and bits/pieces
from
other umls tables.
I feel like this is not completely correct or my idea of how the
join
to
create the view works is off. For example, let's say I want the CPE
to find
malar (e.g. malar rash) as a concept in the annotations. It
never
happens after running my CPE descriptor and I cannot find it in my
v_snomed_fword_lookup view.
select count(*) from umls_aui_fword where fword='malar'; yields 34
results
select count(*) from umls.mrconso where str='malar'; yields 3
results.
So clearly these two tables know
Re: v_snomed_fword_lookup view
Yes, absolutely and
no problem at all.
Regards,
Harpreet
On Mon, Aug 11, 2014 at 1:16 PM, Finan, Sean
sean.fi...@childrens.harvard.edu wrote:
Thanks Harpreet,
That is definitely necessary to build!
Those lines should already be in the pom, but commented out. I think that
some version/branching issues may have arisen at some point wrt this module
...
If somebody beats me to it then cheers, otherwise I will try to check out
tonight and get all the bits in place.
Sean
-Original Message-
From: Harpreet Khanduja [mailto:hsk5...@rit.edu]
Sent: Monday, August 11, 2014 1:12 PM
To: dev@ctakes.apache.org
Subject: Re: v_snomed_fword_lookup view
Hello Clayton,
I do not know about ytex, but I did switch from dictionary-lookup to
dictionary-
lookup-fast.
I update my ctakes-dictionary-lookup-fast project using maven.
I think I used Team- Update and switched to the latest revision
available and
then
I downloaded new 3.2 resources from the for umls. and then I added
these
resources to my
ctakes-dictionary-lookup-fast resources folder and also the classpath
in ctakes-
clinical-pipeline.
Then I changed the pom.xml file which belongs to the whole ctakes
project and
added dependency groupIdorg.apache.ctakes/groupId
artifactIdctakes-dictionary-lookup-res/artifactId
version${ctakes.version}/version
/dependency
dependency
groupIdorg.apache.ctakes/groupId
artifactIdctakes-dictionary-lookup-fast/artifactId
version${ctakes.version}/version
/dependency
these two dependencies to the file.
After this, I also added the dependency
dependency
groupIdorg.apache.ctakes/groupId
artifactIdctakes-dictionary-lookup-fast/artifactId
/dependency
to the pom.xml of ctakes-clinical-pipeline.
And then add the resources folder in ctakes-clinical-pipeline using
build path
configuration under add class option.
After this it should work.
Regards,
Harpreet
On Mon, Aug 11, 2014 at 12:44 PM, Clayton Turner caturn...@g.cofc.edu
wrote:
I still get the same error with the ctakes3.2 branch. Any suggestions?
On Mon, Aug 11, 2014 at 12:06 PM, Clayton Turner
caturn...@g.cofc.edu
wrote:
I'm going to do a clean install through the repo rather than the
binaries and see if that fixes my issue because I think I just read
a past post saying the lookup2 folders exist there.
On Mon, Aug 11, 2014 at 11:52 AM, Clayton Turner
caturn...@g.cofc.edu
wrote:
When navigating to
ctakes-dictionary-lookup-fast\desc\analysis_engine
there are 2 files, assumedly analysis engines.
SnomedLookupAnnotator.xml and SnomedOvLookupAnnotator.xml
If I pick either, I put in my UMLS information but receive an error
when trying to run the CPE:
Initialization of CAS Processor with name SnomedOvLookupAnnotator
failed.
CausedBy: org.apache.uima.resource.ResourceConfigurationException:
Initialization of CAS processor with name SnomedOvLookupAnnotator
failed.
CausedBy: org.apache.uima.resource.ResourceInitializationException:
Error
initializing org.apache.uima.resource.impl.DataResource_impl from
descriptor file:..SnomedLookupAnnotator.xml
CausedBy: org.apache.uima.resource.ResourceInitializationException:
Could
not
access the resource data at
file:org\apache\ctakes\dictionary\lookup2\Snomed2011ab_ctakesTui\cTake
sSnomed.xml
Now, I don't even have a lookup2 folder and, subsequently the Tui
folder and cTakesSnomed.xml file. This seems to be the problem, but
I'm
not
sure where these files are supposed to be grabbed from.
On Mon, Aug 11, 2014 at 11:47 AM, Clayton Turner
caturn...@g.cofc.edu
wrote:
Hi again:
How exactly do you switch to using the cTakes
dictionary-lookup-fast.
Do
I need to go in and alter xml files or is it as simple as adding a
certain
item to the list of analysis engines?
On Fri, Aug 8, 2014 at 3:48 PM, Finan, Sean
sean.fi...@childrens.harvard.edu wrote:
Hi Clayton,
I don't know how the ytex dictionary lookup works, so I'm afraid
that
I
can't help you with an answer. Maybe Vijay is the best person to
do
this.
If you aren't tied to ytex you could try the new cTakes
dictionary-lookup-fast. I tested Patient came in with a malar
rash
and
it found malar and malar rash.
Vijay,
At some point the lookup-fast module will be the default for the
cTakes
clinical pipeline. In order to synchronize the ytex lookup with
cTakes,
would you like to eventually work together on reusing the same
code
for
ytex? I have no idea what ytex does, but I know the ins and outs
of
the
cdl-fast module.
Sean
-Original Message-
From: clayclay...@gmail.com [mailto:clayclay
Re: LabMentions
Thank you so much for letting me know. I will try my best to come up with it. Regards, Harpreet On Mon, Aug 4, 2014 at 4:42 PM, Masanz, James J. masanz.ja...@mayo.edu wrote: As far as I know, there isn't an annotator yet for creating LabMention annotations. We would welcome a contribution. - James Masanz -Original Message- From: Harpreet Khanduja [mailto:hsk5...@rit.edu] Sent: Friday, August 01, 2014 11:27 AM To: dev@ctakes.apache.org Subject: LabMentions Hello, Is there a way to include the annotation LabMentions in the pipeline? Thank you for your help. Regards, Harpreet
code value for vocabulary in dic-lookup-fast
Hello, I am using ctakes-dictionary-lookup-fast to annotation purposes. But, there is no value for code attribute like it was there when I used ctakes-dictionary-lookup. Is there any way I can find out the code attribute value using ctakes-dictionary-lookup-fast? Thank you so much for the help, Harpreet
Re: Lucene for UMLS2014
Hello, Thanks for your help. It works but it does not give me the code value associated with a cui for SNOMED vocabulary. How can I get the code value for SNOMED or any other vocabulary. codingScheme : CTakes, cui : C0085580, tui : T047, code : Thank you, Harpreet On Tue, Jul 22, 2014 at 4:19 PM, Harpreet Khanduja hsk5...@g.rit.edu wrote: I will try to do the same. Thank you, Harpreet On Tue, Jul 22, 2014 at 4:11 PM, Masanz, James J. masanz.ja...@mayo.edu wrote: I'm not an svn guru, but you can use Team-Update to get the latest of all the things you have not customized, plus SVN will tell you of the conflicts, and you can merge your customizations into the latest. I've done it when I haven't had many customizations to preserve. To get the new dictionary lookup (sub)project, you might have to do something to get it imported, such as going into the SVN repository exploring view and use Check out as Maven Project menu option on that (sub)project. -Original Message- From: Harpreet Khanduja [mailto:hsk5...@rit.edu] Sent: Tuesday, July 22, 2014 2:32 PM To: dev@ctakes.apache.org Subject: Re: Lucene for UMLS2014 Hello, I checked out 3.1.1 from trunk SVN. Thank you On Tue, Jul 22, 2014 at 2:29 PM, Masanz, James J. masanz.ja...@mayo.edu wrote: Did you download the source and import into eclipse, or did you check out 3.1.1 from SVN. If you checked it out from SVN, did you check it out from trunk, or from the tag for 3.1.1. -- James -Original Message- From: Harpreet Khanduja [mailto:hsk5...@rit.edu] Sent: Tuesday, July 22, 2014 12:49 PM To: dev@ctakes.apache.org Subject: Re: Lucene for UMLS2014 Hello, I am using ctakes 3.1.1 in eclipse and I have added my customizations to the project, but now I want to update it to 3.2 so that I can use ctakes-dictionary-lookup-fast. Is there any way to update the whole ctakes project to 3.2 without my customizations getting removed? It would be a great help. Thank you, Harpreet On Tue, Jul 22, 2014 at 10:53 AM, Harpreet Khanduja hsk5...@g.rit.edu wrote: Thank you so much for your help. Harpreet. On Mon, Jul 21, 2014 at 6:28 PM, Finan, Sean sean.fi...@childrens.harvard.edu wrote: Hi Harpreet, If you are willing to use cTakes 3.2, try the dictionary-lookup-fast module as a replacement of the default dictionary-lookup. That module has a new dictionary resource (hsql, not lucene) and slightly different methods for lookup and matching. In time trials it has been faster than the default module (hence the name). Accuracy depends upon the parameter settings, but in the tests performed so far the results are comparable or better. The new dictionary is much leaner than the current default dictionary, small enough to port from the hsql cached version to a hsql in-memory version. Using the in-memory version makes dictionary lookup practically instantaneous (hundredths of a second). Limited documentation is available in the module's doc/ directory. I will be on vacation for a week, but please don't hesitate to write if you have any questions. Sean From: Harpreet Khanduja [hsk5...@rit.edu] Sent: Thursday, July 17, 2014 5:07 PM To: dev@ctakes.apache.org Subject: Lucene for UMLS2014 Hello, I would be grateful if someone could help. I created a lucene index for umls2014 but only for snomed vocabulary. I did this because I thought this would reduce the dictionary look up time. But it still almost the same. Is there any other way to improve the dictionary look up time? Thank you, Harpreet
Re: Lucene for UMLS2014
Thank you so much for your help. Harpreet. On Mon, Jul 21, 2014 at 6:28 PM, Finan, Sean sean.fi...@childrens.harvard.edu wrote: Hi Harpreet, If you are willing to use cTakes 3.2, try the dictionary-lookup-fast module as a replacement of the default dictionary-lookup. That module has a new dictionary resource (hsql, not lucene) and slightly different methods for lookup and matching. In time trials it has been faster than the default module (hence the name). Accuracy depends upon the parameter settings, but in the tests performed so far the results are comparable or better. The new dictionary is much leaner than the current default dictionary, small enough to port from the hsql cached version to a hsql in-memory version. Using the in-memory version makes dictionary lookup practically instantaneous (hundredths of a second). Limited documentation is available in the module's doc/ directory. I will be on vacation for a week, but please don't hesitate to write if you have any questions. Sean From: Harpreet Khanduja [hsk5...@rit.edu] Sent: Thursday, July 17, 2014 5:07 PM To: dev@ctakes.apache.org Subject: Lucene for UMLS2014 Hello, I would be grateful if someone could help. I created a lucene index for umls2014 but only for snomed vocabulary. I did this because I thought this would reduce the dictionary look up time. But it still almost the same. Is there any other way to improve the dictionary look up time? Thank you, Harpreet
Re: Lucene for UMLS2014
Hello, I am using ctakes 3.1.1 in eclipse and I have added my customizations to the project, but now I want to update it to 3.2 so that I can use ctakes-dictionary-lookup-fast. Is there any way to update the whole ctakes project to 3.2 without my customizations getting removed? It would be a great help. Thank you, Harpreet On Tue, Jul 22, 2014 at 10:53 AM, Harpreet Khanduja hsk5...@g.rit.edu wrote: Thank you so much for your help. Harpreet. On Mon, Jul 21, 2014 at 6:28 PM, Finan, Sean sean.fi...@childrens.harvard.edu wrote: Hi Harpreet, If you are willing to use cTakes 3.2, try the dictionary-lookup-fast module as a replacement of the default dictionary-lookup. That module has a new dictionary resource (hsql, not lucene) and slightly different methods for lookup and matching. In time trials it has been faster than the default module (hence the name). Accuracy depends upon the parameter settings, but in the tests performed so far the results are comparable or better. The new dictionary is much leaner than the current default dictionary, small enough to port from the hsql cached version to a hsql in-memory version. Using the in-memory version makes dictionary lookup practically instantaneous (hundredths of a second). Limited documentation is available in the module's doc/ directory. I will be on vacation for a week, but please don't hesitate to write if you have any questions. Sean From: Harpreet Khanduja [hsk5...@rit.edu] Sent: Thursday, July 17, 2014 5:07 PM To: dev@ctakes.apache.org Subject: Lucene for UMLS2014 Hello, I would be grateful if someone could help. I created a lucene index for umls2014 but only for snomed vocabulary. I did this because I thought this would reduce the dictionary look up time. But it still almost the same. Is there any other way to improve the dictionary look up time? Thank you, Harpreet
Re: Lucene for UMLS2014
Hello, I checked out 3.1.1 from trunk SVN. Thank you On Tue, Jul 22, 2014 at 2:29 PM, Masanz, James J. masanz.ja...@mayo.edu wrote: Did you download the source and import into eclipse, or did you check out 3.1.1 from SVN. If you checked it out from SVN, did you check it out from trunk, or from the tag for 3.1.1. -- James -Original Message- From: Harpreet Khanduja [mailto:hsk5...@rit.edu] Sent: Tuesday, July 22, 2014 12:49 PM To: dev@ctakes.apache.org Subject: Re: Lucene for UMLS2014 Hello, I am using ctakes 3.1.1 in eclipse and I have added my customizations to the project, but now I want to update it to 3.2 so that I can use ctakes-dictionary-lookup-fast. Is there any way to update the whole ctakes project to 3.2 without my customizations getting removed? It would be a great help. Thank you, Harpreet On Tue, Jul 22, 2014 at 10:53 AM, Harpreet Khanduja hsk5...@g.rit.edu wrote: Thank you so much for your help. Harpreet. On Mon, Jul 21, 2014 at 6:28 PM, Finan, Sean sean.fi...@childrens.harvard.edu wrote: Hi Harpreet, If you are willing to use cTakes 3.2, try the dictionary-lookup-fast module as a replacement of the default dictionary-lookup. That module has a new dictionary resource (hsql, not lucene) and slightly different methods for lookup and matching. In time trials it has been faster than the default module (hence the name). Accuracy depends upon the parameter settings, but in the tests performed so far the results are comparable or better. The new dictionary is much leaner than the current default dictionary, small enough to port from the hsql cached version to a hsql in-memory version. Using the in-memory version makes dictionary lookup practically instantaneous (hundredths of a second). Limited documentation is available in the module's doc/ directory. I will be on vacation for a week, but please don't hesitate to write if you have any questions. Sean From: Harpreet Khanduja [hsk5...@rit.edu] Sent: Thursday, July 17, 2014 5:07 PM To: dev@ctakes.apache.org Subject: Lucene for UMLS2014 Hello, I would be grateful if someone could help. I created a lucene index for umls2014 but only for snomed vocabulary. I did this because I thought this would reduce the dictionary look up time. But it still almost the same. Is there any other way to improve the dictionary look up time? Thank you, Harpreet
Re: Lucene for UMLS2014
I will try to do the same. Thank you, Harpreet On Tue, Jul 22, 2014 at 4:11 PM, Masanz, James J. masanz.ja...@mayo.edu wrote: I'm not an svn guru, but you can use Team-Update to get the latest of all the things you have not customized, plus SVN will tell you of the conflicts, and you can merge your customizations into the latest. I've done it when I haven't had many customizations to preserve. To get the new dictionary lookup (sub)project, you might have to do something to get it imported, such as going into the SVN repository exploring view and use Check out as Maven Project menu option on that (sub)project. -Original Message- From: Harpreet Khanduja [mailto:hsk5...@rit.edu] Sent: Tuesday, July 22, 2014 2:32 PM To: dev@ctakes.apache.org Subject: Re: Lucene for UMLS2014 Hello, I checked out 3.1.1 from trunk SVN. Thank you On Tue, Jul 22, 2014 at 2:29 PM, Masanz, James J. masanz.ja...@mayo.edu wrote: Did you download the source and import into eclipse, or did you check out 3.1.1 from SVN. If you checked it out from SVN, did you check it out from trunk, or from the tag for 3.1.1. -- James -Original Message- From: Harpreet Khanduja [mailto:hsk5...@rit.edu] Sent: Tuesday, July 22, 2014 12:49 PM To: dev@ctakes.apache.org Subject: Re: Lucene for UMLS2014 Hello, I am using ctakes 3.1.1 in eclipse and I have added my customizations to the project, but now I want to update it to 3.2 so that I can use ctakes-dictionary-lookup-fast. Is there any way to update the whole ctakes project to 3.2 without my customizations getting removed? It would be a great help. Thank you, Harpreet On Tue, Jul 22, 2014 at 10:53 AM, Harpreet Khanduja hsk5...@g.rit.edu wrote: Thank you so much for your help. Harpreet. On Mon, Jul 21, 2014 at 6:28 PM, Finan, Sean sean.fi...@childrens.harvard.edu wrote: Hi Harpreet, If you are willing to use cTakes 3.2, try the dictionary-lookup-fast module as a replacement of the default dictionary-lookup. That module has a new dictionary resource (hsql, not lucene) and slightly different methods for lookup and matching. In time trials it has been faster than the default module (hence the name). Accuracy depends upon the parameter settings, but in the tests performed so far the results are comparable or better. The new dictionary is much leaner than the current default dictionary, small enough to port from the hsql cached version to a hsql in-memory version. Using the in-memory version makes dictionary lookup practically instantaneous (hundredths of a second). Limited documentation is available in the module's doc/ directory. I will be on vacation for a week, but please don't hesitate to write if you have any questions. Sean From: Harpreet Khanduja [hsk5...@rit.edu] Sent: Thursday, July 17, 2014 5:07 PM To: dev@ctakes.apache.org Subject: Lucene for UMLS2014 Hello, I would be grateful if someone could help. I created a lucene index for umls2014 but only for snomed vocabulary. I did this because I thought this would reduce the dictionary look up time. But it still almost the same. Is there any other way to improve the dictionary look up time? Thank you, Harpreet
Lucene for UMLS2014
Hello, I would be grateful if someone could help. I created a lucene index for umls2014 but only for snomed vocabulary. I did this because I thought this would reduce the dictionary look up time. But it still almost the same. Is there any other way to improve the dictionary look up time? Thank you, Harpreet
ctakes_mentionsAnnotations
Hello developers, I am using apache ctakes from eclipse. I ran UIMA_CVD--clinical_documents_pipeline.launch from ctakes-clinical-pipeline project and I loaded AggregatePlainTextUMLSProcessor.xml My question is the values for features like medicationallergy, medicationfrequency, bodySide, bodyLocation of annotations like MedicationMention and ProcedureMention are null. Is there a way I can create the values for these features? It would be a great help. Thank you so much, Harpreet
Re: sectionSegmentAnnotator
Hello, Thank you so much for getting back, it works but I am trying to access the features (like segmentid, preferredText, begin and end ) of a segment object but I am not able to access these. I am using AnnotationFS curAnnot = (AnnotationFS) aIterator.get(); which is inside a method the method is recursive. and aIteraor is object of FSIterator. Thank you so much. Harpreet On Wed, Jul 2, 2014 at 11:10 AM, Chen, Pei pei.c...@childrens.harvard.edu wrote: One can try the CDASegmentAnnotator. Both are rules/regex based but it's much simpler and doesn't require the find struct 3rd party lib. Sent from my iPhone On Jul 1, 2014, at 10:19 PM, Harpreet Khanduja hsk5...@rit.edu wrote: Hello,p Thanks for getting back. I tried again and this is the error. Exception in thread main java.lang.NoSuchMethodError: org.jdom.Element.addContent(Lorg/jdom/Element;)Lorg/jdom/Element; at findstruct.StructModel$SM.process(StructModel.java:234) at findstruct.StructModel.process(StructModel.java:43) at findstruct.StructFinder.execute(StructFinder.java:53) at org.apache.ctakes.core.ae.SectionSegmentAnnotator.process(SectionSegmentAnnotator.java:90) at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.init(ASB_impl.java:409) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.init(ASB_impl.java:409) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267) at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267) at org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:80) at org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:91) Thank you so much, Harpreet On Tue, Jul 1, 2014 at 9:51 PM, Masanz, James J. masanz.ja...@mayo.edu wrote: Was the system you were trying to run cTAKES on connected to the internet at the time? In among all those messages is this line: Caused by: java.net.UnknownHostException: uts-ws.nlm.nih.gov Or perhaps it was just a temporary glitch in your connection? -- James -Original Message- From: Harpreet Khanduja [mailto:hsk5...@rit.edu] Sent: Tuesday, July 01, 2014 6:04 PM To: dev@ctakes.apache.org Subject: sectionSegmentAnnotator Hello, I would really appreciate if anyone could help me on this. I am trying to use SectionSegmentAnnotator in developer version of ctakes inside eclipse. I have included delegateAnalysisEngine key=SectionSegmentAnnotator import location=SectionSegmentAnnotator.xml/ /delegateAnalysisEngine and nodeSectionSegmentAnnotator/node in the file aggregateplaintextMLSprocessor.xml. I am getting the following error. Exception in thread main org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator failed. (Descriptor: file:/D:/workspaces/workspacectakes/ctakes/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254
sectionSegmentAnnotator
Hello, I would really appreciate if anyone could help me on this. I am trying to use SectionSegmentAnnotator in developer version of ctakes inside eclipse. I have included delegateAnalysisEngine key=SectionSegmentAnnotator import location=SectionSegmentAnnotator.xml/ /delegateAnalysisEngine and nodeSectionSegmentAnnotator/node in the file aggregateplaintextMLSprocessor.xml. I am getting the following error. Exception in thread main org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator failed. (Descriptor: file:/D:/workspaces/workspacectakes/ctakes/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425) at org.uimafit.factory.AnalysisEngineFactory.createAggregate(AnalysisEngineFactory.java:424) at org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:71) at org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:91) Caused by: org.apache.uima.resource.ResourceInitializationException at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:85) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) ... 25 more Caused by: java.net.UnknownHostException: uts-ws.nlm.nih.gov at java.net.AbstractPlainSocketImpl.connect(Unknown Source) at java.net.PlainSocketImpl.connect(Unknown Source) at java.net.SocksSocketImpl.connect(Unknown Source) at java.net.Socket.connect(Unknown Source) at sun.security.ssl.SSLSocketImpl.connect(Unknown Source) at sun.security.ssl.BaseSSLSocketImpl.connect(Unknown Source) at sun.net.NetworkClient.doConnect(Unknown Source) at sun.net.www.http.HttpClient.openServer(Unknown Source) at sun.net.www.http.HttpClient.openServer(Unknown Source) at sun.net.www.protocol.https.HttpsClient.init(Unknown Source) at sun.net.www.protocol.https.HttpsClient.New(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown Source) at sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown Source) at org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.isValidUMLSUser(UmlsDictionaryLookupAnnotator.java:99) at
Re: query
Hello Pei, Thank you so much for helping. Harpreet On Wed, Jun 18, 2014 at 11:08 AM, Pei Chen chen...@apache.org wrote: Harpreet, I just did a fresh checkout of trunk and could recreate the error. I think I see the issue- the orangebook hsqldb resource is empty on maven central. I'm hoping to fix that up today. --Pei On Tue, Jun 17, 2014 at 6:22 PM, Harpreet Khanduja hsk5...@rit.edu wrote: Hello Pei, I also ran from cmd line same exception and I checked pom.xml file on this location. https://svn.apache.org/repos/asf/ctakes/trunk The version mentioned in the file is 3.1.1. . Could you please tell me about the resources directory problem which I mentioned in the last email? Thank you so much for your time. Harpreet On Tue, Jun 17, 2014 at 5:45 PM, Chen, Pei pei.c...@childrens.harvard.edu wrote: If this is trunk, Can you do an 'svn update' to ensure you have the latest? If this is trunk you won't need to do a separate download- maven should download and unpack it automatically for you. Also try the command line alternative: 'mvn -PrunCVD compile' from the root dir. Let me know. Sent from my iPhone On Jun 17, 2014, at 5:37 PM, Harpreet Khanduja hsk5...@rit.edu wrote: Pei, Thank you for the quick reply. I am using CVD GUI within eclipse which is under ctakes-clinical-pipeline project.. resources launch UIMA_CVD---clinical_documents_pipeline.launch. I am using ctakes 3.1.1 and resouces also 3.1 I used this link for svn : https://svn.apache.org/repos/asf/ctakes/trunk when I downloaded ctakes using Eclipse. isn't this svn for ctakes 3.1.1? Thank you, Harpreet On Tue, Jun 17, 2014 at 5:29 PM, Pei Chen chen...@apache.org wrote: Harpreet, Are you using the CVD GUI? or within Eclipse IDE? Also which version cTAKES are you using? trunk? --Pei On Tue, Jun 17, 2014 at 5:13 PM, Harpreet Khanduja hsk5...@rit.edu wrote: Hello Pei, I would really appreciate if you could help me again. After talking to you and reading other email archives. I have done almost everything I could, but I am not able to use AggregatePlainTextUMLSProcessor.xml using UIMA_CVDclinical-pipeline.launch. Just to be sure. The resources folder that from http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.1.0.zip/download url is used to replace the resources folder which is already inside ctakes/ctakes-dictionary-lookup/ -- directoryor ctakes/ctakes-dictionary-lookup-res/source/main/ -- directory. And then which directory is used as a classpath to ctakes-clinical-pipeline project. I still get the same exception that I was getting earlier. I looked into the exception deeply and I found that the exception is thrown while creating a connection object ( iv_conn ) in JdbcConnectionResourceImpl.java ( line 109 or 110 ) which is inside ctakes- core/ src/main/java org.apache.ctakes.core.resource package. Thank you very much. Harpreet On Wed, Jun 11, 2014 at 4:33 PM, Chen, Pei pei.c...@childrens.harvard.edu wrote: Harpreet, Just curious- is maven able to connect to the internet (maven central repositories)? i.e. did you have to set your ~/.m2/settings.xml with proxy info if behind a firewall? If it was an intermittent issue, you can try clearing out the local ~/.m2/repository? --Pei -Original Message- From: Harpreet Khanduja [mailto:hsk5...@rit.edu] Sent: Wednesday, June 11, 2014 3:54 PM To: dev@ctakes.apache.org Subject: Re: query Pei, I had provided the classpath = ctakes-dictionay-look-up/resources to all the projects in ctakes. as it says in the documentation but there was nothing inside my target folder in ctakes-clinical-pipeline directory. So, then I ran maven compile and I got following error. [ERROR] Failed to execute goal on project ctakes-clinical-pipeline: Could not resolve dependencies for project org.apache.ctakes:ctakes-clinical-pipeline:jar:3.1.2-SNAPSHOT: Failed to collect dependencies for [org.apache.ctakes:ctakes-type-system:jar:3.1.2- SNAPSHOT (compile), org.apache.ctakes:ctakes-core:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-utils:jar:3.1.2-SNAPSHOT (compile), jdom:jdom:jar:1.0 (compile), junit:junit:jar:4.10 (test), org.apache.ctakes:ctakes-context-tokenizer:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-dictionary-lookup:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-preprocessor:jar:3.1.2-SNAPSHOT (compile
Re: query
Hello Pei, Are you able to use trunk now? Thank you, Harpreet On Wed, Jun 18, 2014 at 12:47 PM, Harpreet Khanduja hsk5...@g.rit.edu wrote: Hello Pei, Thank you so much for helping. Harpreet On Wed, Jun 18, 2014 at 11:08 AM, Pei Chen chen...@apache.org wrote: Harpreet, I just did a fresh checkout of trunk and could recreate the error. I think I see the issue- the orangebook hsqldb resource is empty on maven central. I'm hoping to fix that up today. --Pei On Tue, Jun 17, 2014 at 6:22 PM, Harpreet Khanduja hsk5...@rit.edu wrote: Hello Pei, I also ran from cmd line same exception and I checked pom.xml file on this location. https://svn.apache.org/repos/asf/ctakes/trunk The version mentioned in the file is 3.1.1. . Could you please tell me about the resources directory problem which I mentioned in the last email? Thank you so much for your time. Harpreet On Tue, Jun 17, 2014 at 5:45 PM, Chen, Pei pei.c...@childrens.harvard.edu wrote: If this is trunk, Can you do an 'svn update' to ensure you have the latest? If this is trunk you won't need to do a separate download- maven should download and unpack it automatically for you. Also try the command line alternative: 'mvn -PrunCVD compile' from the root dir. Let me know. Sent from my iPhone On Jun 17, 2014, at 5:37 PM, Harpreet Khanduja hsk5...@rit.edu wrote: Pei, Thank you for the quick reply. I am using CVD GUI within eclipse which is under ctakes-clinical-pipeline project.. resources launch UIMA_CVD---clinical_documents_pipeline.launch. I am using ctakes 3.1.1 and resouces also 3.1 I used this link for svn : https://svn.apache.org/repos/asf/ctakes/trunk when I downloaded ctakes using Eclipse. isn't this svn for ctakes 3.1.1? Thank you, Harpreet On Tue, Jun 17, 2014 at 5:29 PM, Pei Chen chen...@apache.org wrote: Harpreet, Are you using the CVD GUI? or within Eclipse IDE? Also which version cTAKES are you using? trunk? --Pei On Tue, Jun 17, 2014 at 5:13 PM, Harpreet Khanduja hsk5...@rit.edu wrote: Hello Pei, I would really appreciate if you could help me again. After talking to you and reading other email archives. I have done almost everything I could, but I am not able to use AggregatePlainTextUMLSProcessor.xml using UIMA_CVDclinical-pipeline.launch. Just to be sure. The resources folder that from http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.1.0.zip/download url is used to replace the resources folder which is already inside ctakes/ctakes-dictionary-lookup/ -- directoryor ctakes/ctakes-dictionary-lookup-res/source/main/ -- directory. And then which directory is used as a classpath to ctakes-clinical-pipeline project. I still get the same exception that I was getting earlier. I looked into the exception deeply and I found that the exception is thrown while creating a connection object ( iv_conn ) in JdbcConnectionResourceImpl.java ( line 109 or 110 ) which is inside ctakes- core/ src/main/java org.apache.ctakes.core.resource package. Thank you very much. Harpreet On Wed, Jun 11, 2014 at 4:33 PM, Chen, Pei pei.c...@childrens.harvard.edu wrote: Harpreet, Just curious- is maven able to connect to the internet (maven central repositories)? i.e. did you have to set your ~/.m2/settings.xml with proxy info if behind a firewall? If it was an intermittent issue, you can try clearing out the local ~/.m2/repository? --Pei -Original Message- From: Harpreet Khanduja [mailto:hsk5...@rit.edu] Sent: Wednesday, June 11, 2014 3:54 PM To: dev@ctakes.apache.org Subject: Re: query Pei, I had provided the classpath = ctakes-dictionay-look-up/resources to all the projects in ctakes. as it says in the documentation but there was nothing inside my target folder in ctakes-clinical-pipeline directory. So, then I ran maven compile and I got following error. [ERROR] Failed to execute goal on project ctakes-clinical-pipeline: Could not resolve dependencies for project org.apache.ctakes:ctakes-clinical-pipeline:jar:3.1.2-SNAPSHOT: Failed to collect dependencies for [org.apache.ctakes:ctakes-type-system:jar:3.1.2- SNAPSHOT (compile), org.apache.ctakes:ctakes-core:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-utils:jar:3.1.2-SNAPSHOT (compile), jdom:jdom:jar:1.0 (compile), junit:junit:jar:4.10 (test), org.apache.ctakes:ctakes-context-tokenizer:jar:3.1.2-SNAPSHOT (compile
Re: query
Pei, Thank you for the quick reply. I am using CVD GUI within eclipse which is under ctakes-clinical-pipeline project.. resources launch UIMA_CVD---clinical_documents_pipeline.launch. I am using ctakes 3.1.1 and resouces also 3.1 I used this link for svn : https://svn.apache.org/repos/asf/ctakes/trunk when I downloaded ctakes using Eclipse. isn't this svn for ctakes 3.1.1? Thank you, Harpreet On Tue, Jun 17, 2014 at 5:29 PM, Pei Chen chen...@apache.org wrote: Harpreet, Are you using the CVD GUI? or within Eclipse IDE? Also which version cTAKES are you using? trunk? --Pei On Tue, Jun 17, 2014 at 5:13 PM, Harpreet Khanduja hsk5...@rit.edu wrote: Hello Pei, I would really appreciate if you could help me again. After talking to you and reading other email archives. I have done almost everything I could, but I am not able to use AggregatePlainTextUMLSProcessor.xml using UIMA_CVDclinical-pipeline.launch. Just to be sure. The resources folder that from http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.1.0.zip/download url is used to replace the resources folder which is already inside ctakes/ctakes-dictionary-lookup/ -- directoryor ctakes/ctakes-dictionary-lookup-res/source/main/ -- directory. And then which directory is used as a classpath to ctakes-clinical-pipeline project. I still get the same exception that I was getting earlier. I looked into the exception deeply and I found that the exception is thrown while creating a connection object ( iv_conn ) in JdbcConnectionResourceImpl.java ( line 109 or 110 ) which is inside ctakes- core/ src/main/java org.apache.ctakes.core.resource package. Thank you very much. Harpreet On Wed, Jun 11, 2014 at 4:33 PM, Chen, Pei pei.c...@childrens.harvard.edu wrote: Harpreet, Just curious- is maven able to connect to the internet (maven central repositories)? i.e. did you have to set your ~/.m2/settings.xml with proxy info if behind a firewall? If it was an intermittent issue, you can try clearing out the local ~/.m2/repository? --Pei -Original Message- From: Harpreet Khanduja [mailto:hsk5...@rit.edu] Sent: Wednesday, June 11, 2014 3:54 PM To: dev@ctakes.apache.org Subject: Re: query Pei, I had provided the classpath = ctakes-dictionay-look-up/resources to all the projects in ctakes. as it says in the documentation but there was nothing inside my target folder in ctakes-clinical-pipeline directory. So, then I ran maven compile and I got following error. [ERROR] Failed to execute goal on project ctakes-clinical-pipeline: Could not resolve dependencies for project org.apache.ctakes:ctakes-clinical-pipeline:jar:3.1.2-SNAPSHOT: Failed to collect dependencies for [org.apache.ctakes:ctakes-type-system:jar:3.1.2- SNAPSHOT (compile), org.apache.ctakes:ctakes-core:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-utils:jar:3.1.2-SNAPSHOT (compile), jdom:jdom:jar:1.0 (compile), junit:junit:jar:4.10 (test), org.apache.ctakes:ctakes-context-tokenizer:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-dictionary-lookup:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-preprocessor:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-lvg:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-chunker:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-ne-contexts:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-pos-tagger:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-assertion:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-dependency-parser:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-dependency-parser-res:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-ytex:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-ytex-res:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-ytex-uima:jar:3.1.2-SNAPSHOT (compile)]: Failed to read artifact descriptor for org.apache.ctakes:ctakes-type-system:jar:3.1.2-SNAPSHOT: Failure to find org.apache.ctakes:ctakes:pom:3.1.2-SNAPSHOT in http://repository.apache.org/snapshots was cached in the local repository, resolution will not be reattempted until the update interval of apache.snapshots has elapsed or updates are forced - [Help 1] [ERROR] On Wed, Jun 11, 2014 at 2:17 PM, Chen, Pei pei.c...@childrens.harvard.edu wrote: Harpreet, I had a closer look at your log file and it looks like you were actually
Re: query
Hello Pei, I also ran from cmd line same exception and I checked pom.xml file on this location. https://svn.apache.org/repos/asf/ctakes/trunk The version mentioned in the file is 3.1.1. . Could you please tell me about the resources directory problem which I mentioned in the last email? Thank you so much for your time. Harpreet On Tue, Jun 17, 2014 at 5:45 PM, Chen, Pei pei.c...@childrens.harvard.edu wrote: If this is trunk, Can you do an 'svn update' to ensure you have the latest? If this is trunk you won't need to do a separate download- maven should download and unpack it automatically for you. Also try the command line alternative: 'mvn -PrunCVD compile' from the root dir. Let me know. Sent from my iPhone On Jun 17, 2014, at 5:37 PM, Harpreet Khanduja hsk5...@rit.edu wrote: Pei, Thank you for the quick reply. I am using CVD GUI within eclipse which is under ctakes-clinical-pipeline project.. resources launch UIMA_CVD---clinical_documents_pipeline.launch. I am using ctakes 3.1.1 and resouces also 3.1 I used this link for svn : https://svn.apache.org/repos/asf/ctakes/trunk when I downloaded ctakes using Eclipse. isn't this svn for ctakes 3.1.1? Thank you, Harpreet On Tue, Jun 17, 2014 at 5:29 PM, Pei Chen chen...@apache.org wrote: Harpreet, Are you using the CVD GUI? or within Eclipse IDE? Also which version cTAKES are you using? trunk? --Pei On Tue, Jun 17, 2014 at 5:13 PM, Harpreet Khanduja hsk5...@rit.edu wrote: Hello Pei, I would really appreciate if you could help me again. After talking to you and reading other email archives. I have done almost everything I could, but I am not able to use AggregatePlainTextUMLSProcessor.xml using UIMA_CVDclinical-pipeline.launch. Just to be sure. The resources folder that from http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.1.0.zip/download url is used to replace the resources folder which is already inside ctakes/ctakes-dictionary-lookup/ -- directoryor ctakes/ctakes-dictionary-lookup-res/source/main/ -- directory. And then which directory is used as a classpath to ctakes-clinical-pipeline project. I still get the same exception that I was getting earlier. I looked into the exception deeply and I found that the exception is thrown while creating a connection object ( iv_conn ) in JdbcConnectionResourceImpl.java ( line 109 or 110 ) which is inside ctakes- core/ src/main/java org.apache.ctakes.core.resource package. Thank you very much. Harpreet On Wed, Jun 11, 2014 at 4:33 PM, Chen, Pei pei.c...@childrens.harvard.edu wrote: Harpreet, Just curious- is maven able to connect to the internet (maven central repositories)? i.e. did you have to set your ~/.m2/settings.xml with proxy info if behind a firewall? If it was an intermittent issue, you can try clearing out the local ~/.m2/repository? --Pei -Original Message- From: Harpreet Khanduja [mailto:hsk5...@rit.edu] Sent: Wednesday, June 11, 2014 3:54 PM To: dev@ctakes.apache.org Subject: Re: query Pei, I had provided the classpath = ctakes-dictionay-look-up/resources to all the projects in ctakes. as it says in the documentation but there was nothing inside my target folder in ctakes-clinical-pipeline directory. So, then I ran maven compile and I got following error. [ERROR] Failed to execute goal on project ctakes-clinical-pipeline: Could not resolve dependencies for project org.apache.ctakes:ctakes-clinical-pipeline:jar:3.1.2-SNAPSHOT: Failed to collect dependencies for [org.apache.ctakes:ctakes-type-system:jar:3.1.2- SNAPSHOT (compile), org.apache.ctakes:ctakes-core:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-utils:jar:3.1.2-SNAPSHOT (compile), jdom:jdom:jar:1.0 (compile), junit:junit:jar:4.10 (test), org.apache.ctakes:ctakes-context-tokenizer:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-dictionary-lookup:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-preprocessor:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-lvg:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-chunker:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-ne-contexts:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-pos-tagger:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-assertion:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-dependency-parser:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-dependency-parser-res:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-ytex:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-ytex-res:jar:3.1.2-SNAPSHOT (compile), org.apache.ctakes:ctakes-ytex-uima:jar:3.1.2-SNAPSHOT (compile)]: Failed to read artifact descriptor
query
Hello,
I am trying to use ctakes as a developer. I am not able to use UMLS
resources when I run
the AEs which use UMLS Dictionary.
I have signed up on the UMLS website and I am using the correct email and
password.
I have specified username and password in
Dictionary Lookup: cTAKES_HOME/desc/ctakes-dictionary-
lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml*
But I keep getting the exception. I would really appreciate any help on
this.
OUTPUT THAT I GET on running AggregatePlaintextUMLSProcessor.xml :
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].
11 Jun 2014 13:07:01 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
11 Jun 2014 13:07:01 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
11 Jun 2014 13:07:01 INFO ContextDependentTokenizerAnnotator - Finite
state machines loaded.
11 Jun 2014 13:07:01 INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip
11 Jun 2014 13:07:03 INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
11 Jun 2014 13:07:03 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg
with config file =
D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-lookup\resources\org\apache\ctakes\lvg\data\config\lvg.properties
11 Jun 2014 13:07:03 INFO LvgCmdApiResourceImpl - config file absolute
path =
D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-lookup\resources\org\apache\ctakes\lvg\data\config\lvg.properties
11 Jun 2014 13:07:03 INFO LvgCmdApiResourceImpl - cwd =
D:\workspaces\workspace_cTakes\ctakes\ctakes-clinical-pipeline
11 Jun 2014 13:07:03 INFO LvgCmdApiResourceImpl - cd
D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-lookup\resources\org\apache\ctakes\lvg\
11 Jun 2014 13:07:03 INFO LvgCmdApiResourceImpl - cd
D:\workspaces\workspace_cTakes\ctakes\ctakes-clinical-pipeline
11 Jun 2014 13:07:04 INFO JdbcConnectionResourceImpl - Connection
established to:
jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/umls2011ab/umls
Exception in thread main
org.apache.uima.resource.ResourceInitializationException
at
org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:130)
at
org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)
at
org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
at
org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
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:123)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
Re: query
Pei,
I had provided the classpath = ctakes-dictionay-look-up/resources to all
the projects in ctakes.
as it says in the documentation but there was nothing inside my target
folder in ctakes-clinical-pipeline directory.
So, then I ran maven compile and I got following error.
[ERROR] Failed to execute goal on project ctakes-clinical-pipeline: Could
not resolve dependencies for project
org.apache.ctakes:ctakes-clinical-pipeline:jar:3.1.2-SNAPSHOT: Failed to
collect dependencies for
[org.apache.ctakes:ctakes-type-system:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-core:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-utils:jar:3.1.2-SNAPSHOT (compile),
jdom:jdom:jar:1.0 (compile), junit:junit:jar:4.10 (test),
org.apache.ctakes:ctakes-context-tokenizer:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-dictionary-lookup:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-preprocessor:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-lvg:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-chunker:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-ne-contexts:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-pos-tagger:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-assertion:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-dependency-parser:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-dependency-parser-res:jar:3.1.2-SNAPSHOT
(compile), org.apache.ctakes:ctakes-ytex:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-ytex-res:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-ytex-uima:jar:3.1.2-SNAPSHOT (compile)]: Failed to
read artifact descriptor for
org.apache.ctakes:ctakes-type-system:jar:3.1.2-SNAPSHOT: Failure to find
org.apache.ctakes:ctakes:pom:3.1.2-SNAPSHOT in
http://repository.apache.org/snapshots was cached in the local repository,
resolution will not be reattempted until the update interval of
apache.snapshots has elapsed or updates are forced - [Help 1]
[ERROR]
On Wed, Jun 11, 2014 at 2:17 PM, Chen, Pei pei.c...@childrens.harvard.edu
wrote:
Harpreet,
I had a closer look at your log file and it looks like you were actually
trying to run it from Eclipse IDE?
If so, just ensure that the resources do exist in the classpath.
If it's within eclipse ide, the plugin should download and unpack the umls
dictionaries automatically actually. (you can check the below to ensure it
exists
target/classes/org/apache/ctakes/dictionary/lookup/umls2011ab/)
You can also try running 'mvn clean compile' from the command line as well.
-Original Message-
From: Harpreet Khanduja [mailto:hsk5...@rit.edu]
Sent: Wednesday, June 11, 2014 2:09 PM
To: dev@ctakes.apache.org
Subject: Re: query
Hello,
Thanks for the reply, but I have already done that and I made sure
that
these resources are there all over again.
Harpreet
On Wed, Jun 11, 2014 at 1:49 PM, Pei Chen chen...@apache.org wrote:
Harpreet,
Ensure that you have downloaded the dictionaries (umls) per download
page:
http://ctakes.apache.org/downloads.cgi
Resources
Resources are required to run most of cTAKES. They are available for
download from SourceForge: ctakes-resources-3.1.0.zip
http://sourceforge.net/projects/ctakesresources/files/ctakes-resources
-3.1.0.zip/download
.
Please download, unzip and add/merge the contents to the existing
resources directory. Follow the User
https://cwiki.apache.org/confluence/x/oxAHAg
or Developer https://cwiki.apache.org/confluence/x/nxAHAg Install
Guide to direct you through the installation process.
On Wed, Jun 11, 2014 at 1:45 PM, Harpreet Khanduja hsk5...@rit.edu
wrote:
Hello,
I am trying to use ctakes as a developer. I am not able to use
UMLS resources when I run
the AEs which use UMLS Dictionary.
I have signed up on the UMLS website and I am using the correct
email
and
password.
I have specified username and password in
Dictionary Lookup: cTAKES_HOME/desc/ctakes-dictionary-
lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml*
But I keep getting the exception. I would really appreciate any
help on this.
OUTPUT THAT I GET on running AggregatePlaintextUMLSProcessor.xml :
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].
11 Jun 2014 13:07:01 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
11 Jun 2014 13:07:01 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger
