RE: Preparing for an Apache cTAKES 3.2 Release?
Yes. It's only temporary to give folks a chance try out and transition to the new lookup algorithm (hence, the +1 for the -fast suffix rename). But open to biting the bullet and defaulting it now if folks are compelled to do so. -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Monday, June 16, 2014 11:36 AM To: dev@ctakes.apache.org Subject: RE: Preparing for an Apache cTAKES 3.2 Release? I guess that I've got one question at this point: Is the name being given to the -new- dictionary lookup module temporary or permanent? I was under the assumption that it was temporary and that with the switch to it being default (and eventually only) the module would simply be named dictionary-lookup. -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Monday, June 16, 2014 11:24 AM To: 'dev@ctakes.apache.org' Subject: RE: Preparing for an Apache cTAKES 3.2 Release? I'd rather something else than dictionary-lookup-fast. If we come up with something even faster than this one, having an older one called fast could be confusing. -Original Message- From: Dligach, Dmitriy [mailto:dmitriy.dlig...@childrens.harvard.edu] Sent: Monday, June 16, 2014 9:55 AM To: cTAKES Developer list Subject: Re: Preparing for an Apache cTAKES 3.2 Release? +1 Dima On Jun 16, 2014, at 9:42, Miller, Timothy timothy.mil...@childrens.harvard.edu wrote: Sorry to weigh in so late on this -- just returned from vacation. If we want to have a one release delay before making dictionary2 default for testing/documentation/configuration purposes, and there isn't an obvious function-related name, and the main difference is speed, maybe we could call it dictionary-lookup-fast? Besides being accurate and more descriptive than 2, it might lure people into trying it and give us some feedback. Tim On 06/16/2014 10:34 AM, Chen, Pei wrote: I'm making some significant updates to trunk that may cause some instability for this release. It should be mostly transparent, but let me know if you encounter any issues with trunk. Also, regarding the dictionary-lookup2. If there are no strong objections, we can leave default to as-is (old behavior). Folks who wish to give the new one a try are welcome to do so and we can change the default behavior in a future release. [ducks for cover now] --Pei -Original Message- From: ksa...@gmail.com [mailto:ksa...@gmail.com] On Behalf Of Karthik Sarma Sent: Wednesday, June 11, 2014 9:58 AM To: dev@ctakes.apache.org Subject: Re: Preparing for an Apache cTAKES 3.2 Release? Agreed On Wednesday, June 11, 2014, vijay garla vnga...@gmail.com wrote: regardless of the name, I think it would be incredibly helpful to have thorough documentation on the dictionary lookup, how to configure it, and how to create new dictionaries. I would venture to say that this is the most important component in cTAKES, and probably the one that has generated the most questions on the newsgroup. On Wed, Jun 11, 2014 at 9:21 AM, Finan, Sean sean.fi...@childrens.harvard.edu wrote: . The newer NER should have in its name the Behavior... I agree, but the *2 module is a complete replacement for the current lookup. It does not (really) have any different behavior, just a different implementation and performance. We plan to swap out the old with the new in the next release and get rid of the *2 suffix. So, any name provided now is just temporary - unless people don't like the name dictionary-lookup at all. In my original sandbox it was named RareWordLookup, a nod to its implementation. However, this doesn't help any users. Sean -Original Message- From: andy mcmurry [mailto:mcmurry.a...@gmail.com] Sent: Wednesday, June 11, 2014 3:09 AM To: dev@ctakes.apache.org Subject: Re: Preparing for an Apache cTAKES 3.2 Release? 2 doesn't mean much. The newer NER should have in its name the Behavior... Perhaps something like MetaMap Usage http://metamap.nlm.nih.gov/Docs/MM09_Usage.shtml -- allow_overmatches or --allow_concept_gaps or .other? Since yTex already provides a pluggable *DictionaryLookup, *that seems like the best place to define the differing Behavior / Usage. https://cwiki.apache.org/confluence/display/CTAKES/User's+Guide https://code.google.com/p/ytex/wiki/DictionaryLookup_V05 AndyMC On Tue, Jun 10, 2014 at 9:55 AM, britt fitch britt.fi...@gmail.com wrote: I don't have an issue with the *-2 name. I also don't have any objections to renaming it. It might be nice to keep the old dictionary code around for a release-worth of time but after that I would vote purging it. If someone needs it after that it'll be accessible in the archived releases. On Jun 10, 2014, at 12:48 PM, Chen, Pei
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
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 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
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
