Re: 4.0.0 javadocs

[James Masanz]

Thanks Murali,

-- James


On Apr 24, 2017 10:11 PM, "Murali Minnah"  wrote:

Hello James,


4.0.0 apidocs are at: http://ctakes.apache.org/apidocs/4.0.0/

 now.

Best,
Murali

On Mon, Apr 24, 2017 at 11:30 AM, James Masanz 
wrote:

> Murali,
>
> Thanks all for getting  the 4.0 build done/artifacts pushed.
>
> Can we get the javadocs pushed to
>
> http://ctakes.apache.org/apidocs/4.0.0/
>
> thanks!
>
> -- James
>

Re: 4.0.0 javadocs

[Murali Minnah]

Hello James,


4.0.0 apidocs are at: http://ctakes.apache.org/apidocs/4.0.0/

 now.

Best,
Murali

On Mon, Apr 24, 2017 at 11:30 AM, James Masanz 
wrote:

> Murali,
>
> Thanks all for getting  the 4.0 build done/artifacts pushed.
>
> Can we get the javadocs pushed to
>
> http://ctakes.apache.org/apidocs/4.0.0/
>
> thanks!
>
> -- James
>

Re: cTAKES 4.0.0 Release

[Sivaram Arabandi, MD]

Congratulations to the entire cTAKES team for making this release happen!

__
Sivaram Arabandi, MD, MS

ONTOPRO

W:  http://ontopro.com/
Ph: 832.726.2322

Think Semantics. Tame Silos.


On Mon, Apr 24, 2017 at 8:02 AM, Murali Minnah  wrote:

> The Apache cTAKES team is pleased to announce the availability of the
> 4.0.0 release.
>
> For the complete release notes, please visit
> https://s.apache.org/ctakes-4.0.0-release-notes
>
> Apache clinical Text Analysis and Knowledge Extraction System (cTAKES) is
> an open-source natural language processing system for information
> extraction from electronic medical record clinical free-text.
>
> The release can be downloaded from
> http://ctakes.apache.org/downloads.cgi
>
> For further information, please visit the project website at
> http://ctakes.apache.org/
>
> -- The Apache cTAKES Team
>

Re: Docker

[Finan, Sean]

Hi John,

The dockerized ctakes that we use is very specialized.  It builds from the 
latest trunk, grabs and unpacks a custom dictionary, copies files to and from a 
secure s3 area, uses a custom cas consumer, etc.  It sets up an s3 tool, preps 
input and output directories, etc.  So, I have never actually created a "pure 
ctakes" container.  Below I've just kind of imagined what it might be like ...

# I would recommend that you use a very simple parent like
FROM openjdk:8

# Create a ctakes home directory
ENV CTAKES_DIR /ctakes_4/
RUN mkdir -p $CTAKES_DIR

# Download the ctakes 4.0 binary to a local directory and add it to your 
container (the add command also untars)
ADD localDir/apache-ctakes-4.0.0-bin.tar.gz $CTAKES_DIR
# Also download and unzip the ctakes sno_rx_16ab dictionary or copy in your 
custom dictionary

# run the default clinical pipeline
WORKDIR $CTAKES_DIR/apache-ctakes-4.0.0/
# Use ENTRYPOINT to specify the command.
ENTRYPOINT ["sh","-c","bin/runClinicalPipeline.sh"]
# use CMD and specify default run settings: .
CMD 
["-i","inputDir","--xmiOut","outputDir","--user","umlsUsername","--pass","umlsPassword"]



If you want to build and run the latest from trunk it would be something like 
this:

#Build from the Java 8 maven image (includes JDK 8 and Maven)
FROM maven:3.3-jdk-8

# We need subversion to checkout ctakes trunk.
# Docker best practice to get update and get install in the same run call.
RUN apt-get update && apt-get install -y \
  subversion \
   && rm -rf /var/lib/apt/lists/*

# Container Directory for ctakes source.
ENV CTAKES_SRC_DIR /ctakes_src/trunk/

# Create directories.
RUN mkdir -p $CTAKES_SRC_DIR

# Install ctakes.
WORKDIR $CTAKES_SRC_DIR/..
# Check out ctakes trunk
RUN svn checkout https://svn.apache.org/repos/asf/ctakes/trunk/
WORKDIR $CTAKES_SRC_DIR
RUN mvn -DskipTests compile

# Run ctakes -- in my container I run a script that does more than run 
ctakes.  Below is basically a copy and reformatted paste.
#  mvn exec:exec -Dexec.executable="java" -Dexec.args="-cp %classpath -Xmx4G 
org.apache.ctakes.custom.pipeline.CustomRunner $DEID_TXT_DIR/$patient_num/ 
$I2B2_BSV_DIR/$patient_num/"

# Use ENTRYPOINT to specify the command.
ENTRYPOINT ["mvn","exec:exec","-Dexec.executable=\"java\"" "-Dexec.args=\"-cp 
%classpath -Xmx4G org.apache.ctakes.core.pipeline.PiperFileRunner\""]

# use CMD and specify default run settings: project name.
CMD 
["-i","inputDir","--xmiOut","outputDir","--user","umlsUserName","--pass","umlsPassword"]






From: John Travis Green 
Sent: Sunday, April 23, 2017 8:59 PM
To: dev@ctakes.apache.org
Subject: RE: Docker

Sean: if you have it dockerized at harvard can you share the setup files? 
Regarding legalities, this is for in-house work, not redistribution. I work for 
the federal government and to deploy with our security restrictions its very 
convenient to have it deployed as a docker instance.  Im a very strong advocate 
in the dod regarding ctakes use. I dont know of anyone else in my position 
pushing it. Were looking at some major uses regarding accessability of legacy 
data (recall the dod is transitioning to cerner, but we have a lot of data that 
will still need accessibility, not the least of which are physician 
researchers). But ctakes is difficult to deploy on dod systems because of our 
security requirements. If we can containerize it then it will make it more 
likely we use it.  Thanks, John



Keep in mind one very important thing:



You need to be very careful about redistribution of a umls database.  Many 
years ago ctakes had to get special permission to post a copy on sourceforge.  
As you all know, use of that distribution requires a umls username and password 
check per-ctakes launch.  This was also a requirement placed upon ctakes by the 
nlm per the agreement.



Public distribution of Oracle Java in a docker container is technically 
illegal, but in the beginning a lot of people were not reading eula info and 
went smooth criminal.  Strange but true.  Now people know to use OpenJDK.  I 
have not contacted the nlm regarding docker and the umls.  Has anybody else out 
there?  If so please let us know.



For a private container inclusion of the dictionary is fine (we have one at 
harvard).   Otherwise there are ways to use / copy s3 files at runtime, you 
would just need to document a static location for the database, etc. etc.



Sean



-Original Message-

From: Jay Vyas [mailto:jayunit100.apa...@gmail.com]
Sent: Sunday, April 23, 2017 5:56 AM

To: dev@ctakes.apache.org

Subject: Re: Docker



Dockerizing ctakes as a build was useful at one time for sure.



If running as a microservice remember the size of the image is problematic ; 
you don't want it on lots of different nodes if using something like kubernetes.



Also remember to make sure you run with Xmx args so that cgroups done constrain 
the jvm memory guess, otherwise you'll get 

Re: cTAKES 4.0.0 Release

[Lin, Chen]

Dear cTAKES Team,

Forgive me if I am wrong. I tried the ³release can be download from² link
and it linked me to the download page of cTAKES, which is still at version
3.2.2?
I tried ³User Installation² and ³Source Code² links, both were pointing to
3.2.2. Please help double check. Many thanks!

Best,
Chen

On 4/24/17, 9:02 AM, "Murali Minnah"  wrote:

>The Apache cTAKES team is pleased to announce the availability of the
>4.0.0 release.
>
>For the complete release notes, please visit
>https://urldefense.proofpoint.com/v2/url?u=https-3A__s.apache.org_ctakes-2
>D4.0.0-2Drelease-2Dnotes=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCop
>pxeFU=PZ241CwYZ3AszaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI=A2FzP6RQBwVmIxqik2oo
>9RNeUCs8LnoehYI--9myIuI=3ItGRigq2zUxMDfEBk2-fKT2rwHtu7QkfuPv1MxgTo8=
>
>Apache clinical Text Analysis and Knowledge Extraction System (cTAKES) is
>an open-source natural language processing system for information
>extraction from electronic medical record clinical free-text.
>
>The release can be downloaded from
>https://urldefense.proofpoint.com/v2/url?u=http-3A__ctakes.apache.org_down
>loads.cgi=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=PZ241Cw
>YZ3AszaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI=A2FzP6RQBwVmIxqik2oo9RNeUCs8LnoehYI
>--9myIuI=vcGx77tDkGzacKFboc1ejDzOES5GgRDGpK0YZVXNATU=
>
>For further information, please visit the project website at
>https://urldefense.proofpoint.com/v2/url?u=http-3A__ctakes.apache.org_=D
>wIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=PZ241CwYZ3AszaTEBtM2
>wl3EcIjNNNeKX8q7N_mt-aI=A2FzP6RQBwVmIxqik2oo9RNeUCs8LnoehYI--9myIuI=tX
>P9NXamRiOw7mP1_eYxUBLvh0VG73QYruEJDKPmu3k=
>
>-- The Apache cTAKES Team

RE: cTAKES 4.0.0 Release [SUSPICIOUS]

[Savova, Guergana]

Excellent work, cTAKES team! We are already looking forward to v4.1... Release 
soon, release early.

The formal announcement will go out tomorrow -- we are very appreciative of 
Sally's expertise and efforts (and the ASF PR office) in promoting this major 
release!

--Guergana

Guergana Savova, PhD, FACMI
Associate Professor
PI Natural Language Processing Lab
Boston Children's Hospital and Harvard Medical School
300 Longwood Avenue
Mailstop: BCH3092
Enders 144.1
Boston, MA 02115
Tel: (617) 919-2972
Fax: (617) 730-0817
guergana.sav...@childrens.harvard.edu
Harvard Scholar: http://scholar.harvard.edu/guergana_k_savova/biocv
http://ctakes.apache.org  
http://thyme.healthnlp.org 
http://cancer.healthnlp.org 
http://share.healthnlp.org
http://center.healthnlp.org  


-Original Message-
From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] 
Sent: Monday, April 24, 2017 9:33 AM
To: u...@ctakes.apache.org; dev@ctakes.apache.org; annou...@apache.org
Subject: Re: cTAKES 4.0.0 Release [SUSPICIOUS]

Congrats cTAKES team! This is an important milestone!

Tim





On Mon, 2017-04-24 at 09:02 -0400, Murali Minnah wrote:

> The Apache cTAKES team is pleased to announce the availability of the

> 4.0.0 release.

> 

> For the complete release notes, please visit

> https://urldefense.proofpoint.com/v2/url?u=https-3A__s.apache.org_ctakes-2D4.0.0-2Drelease-2Dnotes=DwIGaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=SeLHlpmrGNnJ9mI2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGmRCJNAr-rCmP=WdT9MyR7SjUw37IAH5QXuFcUwS4ShD531Pxte5A7z4Q=vwMjzd0TaH9TGT7Ew-2x6q_LQFiiO4iky3Iy8zmf9EM=
>  

> 

> Apache clinical Text Analysis and Knowledge Extraction System

> (cTAKES) is

> an open-source natural language processing system for information

> extraction from electronic medical record clinical free-text.

> 

> The release can be downloaded from

> https://urldefense.proofpoint.com/v2/url?u=http-3A__ctakes.apache.org_downloads.cgi=DwIGaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=SeLHlpmrGNnJ9mI2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGmRCJNAr-rCmP=WdT9MyR7SjUw37IAH5QXuFcUwS4ShD531Pxte5A7z4Q=QvJDR_vTNejF4s7uwNgJusOJ1BLYmnJoi0y8B8Priyw=
>  

> 

> For further information, please visit the project website at

> https://urldefense.proofpoint.com/v2/url?u=http-3A__ctakes.apache.org_=DwIGaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=SeLHlpmrGNnJ9mI2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGmRCJNAr-rCmP=WdT9MyR7SjUw37IAH5QXuFcUwS4ShD531Pxte5A7z4Q=HBd5K583Nzh_0eWV0gx504QQEf07QFZuegCTGCQUUQI=
>  

> 

> -- The Apache cTAKES Team

Re: cTAKES 4.0.0 Release

[Miller, Timothy]

Congrats cTAKES team! This is an important milestone!
Tim


On Mon, 2017-04-24 at 09:02 -0400, Murali Minnah wrote:
> The Apache cTAKES team is pleased to announce the availability of the
> 4.0.0 release.
> 
> For the complete release notes, please visit
> https://s.apache.org/ctakes-4.0.0-release-notes
> 
> Apache clinical Text Analysis and Knowledge Extraction System
> (cTAKES) is
> an open-source natural language processing system for information
> extraction from electronic medical record clinical free-text.
> 
> The release can be downloaded from
> http://ctakes.apache.org/downloads.cgi
> 
> For further information, please visit the project website at
> http://ctakes.apache.org/
> 
> -- The Apache cTAKES Team

Re: Docker

[Miller, Timothy]

One of those that Oleg found is my github repo which is very early
stages:
https://github.com/tmills/ctakes-docker

it can create 2 docker images, one for a UIMA AS queue server and
another that downloads ctakes, installs the dictionary, and starts a
basic concept extraction server with a UIMA AS descriptor. There is a
sample environment variables file where you need to enter your UMLS
credentials. It is a big image but because it is a simple pipeline it
can run with a smaller memory footprint. This project just started so
the reader end is underdeveloped, I've just been pointing to it from a
CVD with a remote descriptor.

Tim

On Sun, 2017-04-23 at 18:59 -0600, John Travis Green wrote:
> Sean: if you have it dockerized at harvard can you share the setup
> files? Regarding legalities, this is for in-house work, not
> redistribution. I work for the federal government and to deploy with
> our security restrictions its very convenient to have it deployed as
> a docker instance.  Im a very strong advocate in the dod regarding
> ctakes use. I dont know of anyone else in my position pushing it.
> Were looking at some major uses regarding accessability of legacy
> data (recall the dod is transitioning to cerner, but we have a lot of
> data that will still need accessibility, not the least of which are
> physician researchers). But ctakes is difficult to deploy on dod
> systems because of our security requirements. If we can containerize
> it then it will make it more likely we use it.  Thanks, John  
> 
> 
> 
> Keep in mind one very important thing:
> 
> 
> 
> You need to be very careful about redistribution of a umls
> database.  Many years ago ctakes had to get special permission to
> post a copy on sourceforge.  As you all know, use of that
> distribution requires a umls username and password check per-ctakes
> launch.  This was also a requirement placed upon ctakes by the nlm
> per the agreement.
> 
> 
> 
> Public distribution of Oracle Java in a docker container is
> technically illegal, but in the beginning a lot of people were not
> reading eula info and went smooth criminal.  Strange but true.  Now
> people know to use OpenJDK.  I have not contacted the nlm regarding
> docker and the umls.  Has anybody else out there?  If so please let
> us know.
> 
> 
> 
> For a private container inclusion of the dictionary is fine (we have
> one at harvard).   Otherwise there are ways to use / copy s3 files at
> runtime, you would just need to document a static location for the
> database, etc. etc.
> 
> 
> 
> Sean
> 
> 
> 
> -Original Message-
> 
> From: Jay Vyas [mailto:jayunit100.apa...@gmail.com]  
> Sent: Sunday, April 23, 2017 5:56 AM
> 
> To: dev@ctakes.apache.org
> 
> Subject: Re: Docker
> 
> 
> 
> Dockerizing ctakes as a build was useful at one time for sure.
> 
> 
> 
> If running as a microservice remember the size of the image is
> problematic ; you don't want it on lots of different nodes if using
> something like kubernetes.
> 
> 
> 
> Also remember to make sure you run with Xmx args so that cgroups done
> constrain the jvm memory guess, otherwise you'll get OOME errors.
> 
> 
> 
> > 
> > On Apr 23, 2017, at 4:38 AM, Oleg Tikhonov  wrote:
> > 
> >  
> > I've tried to create service from
> > 
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__hub.docker.com
> > _r_llin_docker-5Fapache-5Fctakes_-
> > 7E_dockerfile_=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxe
> > FU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=jQYowxW0GDNXw8kr
> > nlh_KgNiyydac8pJOidOHZ9T8R0=P2oSxIaW_ShWXNZ3wdqY6W-
> > Rz20Hy_FHp3JPXTHOdcw= , without
> > 
> > success.
> > 
> >  
> > However Docker file looks as follows:
> > 
> >  
> > FROM java:7
> > 
> > ADD https://urldefense.proofpoint.com/v2/url?u=http-3A__mirror.soft
> > aculous.com_apache_ctakes_ctakes-2D3.2.2_apache-2Dctakes-
> > 2D=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67Gvl
> > GZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=jQYowxW0GDNXw8krnlh_KgNiyyda
> > c8pJOidOHZ9T8R0=puah9D0M36Stz_sbDttCx3KRoSnBicoYAKkikXPuMCQ=  
> > 3.2.2-bin.tar.gz
> > 
> > ADD https://urldefense.proofpoint.com/v2/url?u=https-3A__storage.go
> > ogleapis.com_google-2Dcode-2Darchive-
> > 2Ddownloads_v2_=DwIFAg=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppx
> > eFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=jQYowxW0GDNXw8k
> > rnlh_KgNiyydac8pJOidOHZ9T8R0=I7CUV0TTeXZY4oqG5P1oMbQ3m2glTGzLEN5T
> > KzWGQuk=  
> > code.google.com/ytex/ctakes-ytex-lib-3.1.2-SNAPSHOT.zip
> > 
> > RUN tar -xzf apache-ctakes-3.2.2-bin.tar.gz
> > 
> > RUN ln -s /apache-ctakes-3.2.2 /apache-ctakes
> > 
> > RUN mkdir temp
> > 
> > RUN unzip ctakes-ytex-lib-3.1.2-SNAPSHOT.zip -d temp/
> > 
> > RUN cp -a temp/lib/. /apache-ctakes/lib/
> > 
> > RUN rm apache-ctakes-3.2.2-bin.tar.gz
> > 
> > RUN rm ctakes-ytex-lib-3.1.2-SNAPSHOT.zip
> > 
> > RUN rm -r temp
> > 
> >  
> > Hope it helps.
> > 
> >  
> >  
> >  
> >  
> > > 
> > > On Sun, Apr 23, 2017 at 8:00 AM, Oleg Tikhonov 
> > > wrote:
> > 
> 

cTAKES 4.0.0 Release

[Murali Minnah]

The Apache cTAKES team is pleased to announce the availability of the
4.0.0 release.

For the complete release notes, please visit
https://s.apache.org/ctakes-4.0.0-release-notes

Apache clinical Text Analysis and Knowledge Extraction System (cTAKES) is
an open-source natural language processing system for information
extraction from electronic medical record clinical free-text.

The release can be downloaded from
http://ctakes.apache.org/downloads.cgi

For further information, please visit the project website at
http://ctakes.apache.org/

-- The Apache cTAKES Team

Re: [VOTE] Release Apache cTAKES 4.0.0 (rc3)

[Murali Minnah]

[+1] to rc3.

Murali

On Fri, Apr 21, 2017 at 2:32 PM, James Masanz 
wrote:

> Hey Pei,
>
> Flipping the artifacts to dist on Monday would work. I would expect Sunday
> to be just as good - giving Saturday if anyone wants to test some on the
> weekend. But if Sunday isn't convenient, Monday works.
> Sean already made some updates (without publishing yet) of web links. I'll
> coordinate with him and I'll make sure they get published on Monday.  I'll
> also remove the words DRAFT from the user guide on the wiki and get some
> other documentation things finalized (such as filling in the full steps for
> an Eclipse install on the dev guide).
>
> Thanks,
> James
>
> On Fri, Apr 21, 2017 at 2:07 PM, Pei Chen  wrote:
>
> > Hi James,
> > That sounds good.  Looks like we should have enough +1 votes for rc3.
> > We can flip the artifacts to dist on Mon in case anyone wants to test
> > over the weekend?  Do you want to update the links on the web site on
> > Mon?
> >
> > On Thu, Apr 20, 2017 at 2:53 PM, James Masanz 
> > wrote:
> > > +1 for rc3 to be released as 4.0.0
> > >
> > > Pei, Sean, and Murali, knowing that Tuesdays are good days for release
> > > announcements, do you see any problem with announcing the release on
> > > Tuesday the 25th if we end up with enough votes by end of Friday or
> even
> > by
> > > the end of Saturday?  If there is, I'd be willing to help.
> > >
> > >
> > > On Thu, Apr 20, 2017 at 12:50 PM, Lin, Chen
>  > edu>
> > > wrote:
> > >
> > >> I have checked to run the temporal module of rc3 for event-event,
> > >> event-time, and DocTimeRel annotators. All evaluation scripts returned
> > >> proper outputs. Speaking of the temporal part:
> > >> +1
> > >>
> > >> Best,
> > >> Chen
> > >>
> > >>
> > >>
> > >> On 4/17/17, 11:47 PM, "Pei Chen"  wrote:
> > >>
> > >> >This is a call for a vote on releasing the following candidate (rc3)
> as
> > >> >Apache cTAKES 4.0.0.
> > >> >
> > >> >For more detailed information on the changes/release notes, please
> > visit:
> > >> >https://urldefense.proofpoint.com/v2/url?u=https-
> > >> 3A__issues.apache.org_jir
> > >> >a_secure_ReleaseNote.jspa-3FprojectId-3D12313621-
> > >> 26version-3D12340211=Dw
> > >> >IBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=
> > >> PZ241CwYZ3AszaTEBtM2w
> > >> >l3EcIjNNNeKX8q7N_mt-aI=VlkBaDDb0U8YoTQH0iGcuIpekrOEFC
> > >> c7o3NuMIG3zfQ=b0u
> > >> >PVZJQhSNcFOGGEYe31-jWNnHtpYOCwUP-7lp7FQ8=
> > >> >
> > >> >The release was made using the cTAKES release process documented
> here:
> > >> >https://urldefense.proofpoint.com/v2/url?u=https-
> > >> 3A__ctakes.apache.org_cta
> > >> >kes-2Drelease-2Dguide.html=DwIBaQ=qS4goWBT7poplM69zy_
> > >> 3xhKwEW14JZMSdioC
> > >> >oppxeFU=PZ241CwYZ3AszaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI=
> > >> VlkBaDDb0U8YoTQH0i
> > >> >GcuIpekrOEFCc7o3NuMIG3zfQ=qGG0kg6pqcCgN_zowUwigICdZm_
> > >> 41dYSVe3TGPqm-ts=
> > >> >
> > >> >
> > >> >The candidate is available at:
> > >> >https://urldefense.proofpoint.com/v2/url?u=https-
> > >> 3A__dist.apache.org_repos
> > >> >_dist_dev_ctakes_ctakes-2D4.0.0-2Drc3_apache-2Dctakes-2D4.
> > >> 0.0-2Dsrc.tar.gz
> > >> >=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=
> > >> PZ241CwYZ3AszaTE
> > >> >BtM2wl3EcIjNNNeKX8q7N_mt-aI=VlkBaDDb0U8YoTQH0iGcuIpekrOEFC
> > >> c7o3NuMIG3zfQ&
> > >> >s=YDysq7gIYqVaSYxzHSPMZFWXlriEztSp6wIkQQ079AI=
> > >> >/.zip
> > >> >
> > >> >The tag to be voted on:
> > >> >https://urldefense.proofpoint.com/v2/url?u=http-
> > >> 3A__svn.apache.org_repos_a
> > >> >sf_ctakes_tags_ctakes-2D4.0.0-2Drc3=DwIBaQ=
> > >> qS4goWBT7poplM69zy_3xhKwEW1
> > >> >4JZMSdioCoppxeFU=PZ241CwYZ3AszaTEBtM2wl3EcIjNNN
> > >> eKX8q7N_mt-aI=VlkBaDDb0
> > >> >U8YoTQH0iGcuIpekrOEFCc7o3NuMIG3zfQ=EPO9nj9p37_WnLh5q_
> > >> qzGZmE8n5zwhF_E72dY
> > >> >Z_ZPFU=
> > >> >The MD5 checksum of the tarball can be found at:
> > >> >https://urldefense.proofpoint.com/v2/url?u=https-
> > >> 3A__dist.apache.org_repos
> > >> >_dist_dev_ctakes_ctakes-2D4.0.0-2Drc3_apache-2Dctakes-2D4.
> > >> 0.0-2Dsrc.tar.gz
> > >> >.md5=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=
> > >> PZ241CwYZ3As
> > >> >zaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI=VlkBaDDb0U8YoTQH0iGcuIpekrOEFC
> > >> c7o3NuMIG3
> > >> >zfQ=BIXp-dYLC4yAC7LMclGzCm7Ru2wTiFw4NuSBSXHI4s8=
> > >> >/.zip.md5
> > >> >
> > >> >The signature of the tarball can be found at:
> > >> >https://urldefense.proofpoint.com/v2/url?u=https-
> > >> 3A__dist.apache.org_repos
> > >> >_dist_dev_ctakes_ctakes-2D4.0.0-2Drc3_apache-2Dctakes-2D4.
> > >> 0.0-2Dsrc.tar.gz
> > >> >.asc=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=
> > >> PZ241CwYZ3As
> > >> >zaTEBtM2wl3EcIjNNNeKX8q7N_mt-aI=VlkBaDDb0U8YoTQH0iGcuIpekrOEFC
> > >> c7o3NuMIG3
> > >> >zfQ=0F6kw80_ut6W6eb1XpZyhDjACfxPHzeyl7i4C6HJLRE=
> > >> >/.zip.asc
> > >> >
> > >> >Apache cTAKES' KEYS file, containing the PGP keys used to sign the
> > >> >release:
> > >> 

Re: cTAKES 4.0rc3 - custom dictionary needs rebuilding?

[David Kincaid]

I got it figured out. I was using the wrong URL path for the database.
Working great now!

- Dave

On Sun, Apr 23, 2017 at 12:31 PM, David Kincaid 
wrote:

> Thanks for the reply, James. I'm not very familiar with HSQLDB, so I may
> be doing it wrong, but I launched the GUI using "java
> -jar hsqldb-2.3.4.jar" and then tried to connect to the DB by changing the
> "Type" to "HSQL Database Engine Standalone" and then setting the URL to
> point to my custom dictionary directory. It throws a SQLException that says
> "wrong database file version". Is there some other step I'm missing?
>
> - Dave
>
> On Sat, Apr 22, 2017 at 10:31 PM, James Masanz 
> wrote:
>
>> Dave,
>>
>> It's an oversight that we didn't document that. Thanks for pointing that
>> out! I'll  update the documentation tomorrow and post again with proper
>> details of the command to use.
>>
>> The short answer is that hsqldb jar includes a GUI. You use the 2.3.4
>> version of that jar, which is included with the cTAKES 4.0 convenience
>> binary, to open your database. Then you close (shutdown) your DB and it
>> gets converted to 2.3.4 for you. But if the .properties file for your DB
>> indicates it's readonly, you need to have edited the properties file first
>> to remove that. That gives you the idea. I'll write it up properly
>> tomorrow.
>>
>> Thanks for testing,
>> -- James
>>
>>
>> *Sent from my phone.*
>>
>> On Apr 22, 2017 9:39 PM, "David Kincaid"  wrote:
>>
>> I finally had some time this weekend to give 4.0.0rc3 a run. The install
>> and configuration instructions worked perfectly on my Linux laptop and I
>> was able to use CVD to run the clinical pipeline successfully against some
>> of the clinical notes I have here.
>>
>> However, I ran into a problem when I tried running my own customized
>> pipeline that includes a custom dictionary that I create (to include the
>> SNOMED veterinary extension). I get an exception while it's loading that
>> the dictionary is not the correct version. So, I assume I just need to
>> recreate that custom database? Or is there a migration utility from the
>> old
>> database version to the new version?
>>
>> I don't remember seeing mention of this, but certainly could have missed
>> it. If it's not in the release notes or install/upgrade instructions it
>> probably should be there.
>>
>> Thanks to everyone for pulling this release together and getting it out
>> the
>> door!
>>
>> - Dave
>>
>
>

Re: cTAKES 4.0rc3 - custom dictionary needs rebuilding?

[David Kincaid]

Thanks for the reply, James. I'm not very familiar with HSQLDB, so I may be
doing it wrong, but I launched the GUI using "java -jar hsqldb-2.3.4.jar"
and then tried to connect to the DB by changing the "Type" to "HSQL
Database Engine Standalone" and then setting the URL to point to my custom
dictionary directory. It throws a SQLException that says "wrong database
file version". Is there some other step I'm missing?

- Dave

On Sat, Apr 22, 2017 at 10:31 PM, James Masanz 
wrote:

> Dave,
>
> It's an oversight that we didn't document that. Thanks for pointing that
> out! I'll  update the documentation tomorrow and post again with proper
> details of the command to use.
>
> The short answer is that hsqldb jar includes a GUI. You use the 2.3.4
> version of that jar, which is included with the cTAKES 4.0 convenience
> binary, to open your database. Then you close (shutdown) your DB and it
> gets converted to 2.3.4 for you. But if the .properties file for your DB
> indicates it's readonly, you need to have edited the properties file first
> to remove that. That gives you the idea. I'll write it up properly
> tomorrow.
>
> Thanks for testing,
> -- James
>
>
> *Sent from my phone.*
>
> On Apr 22, 2017 9:39 PM, "David Kincaid"  wrote:
>
> I finally had some time this weekend to give 4.0.0rc3 a run. The install
> and configuration instructions worked perfectly on my Linux laptop and I
> was able to use CVD to run the clinical pipeline successfully against some
> of the clinical notes I have here.
>
> However, I ran into a problem when I tried running my own customized
> pipeline that includes a custom dictionary that I create (to include the
> SNOMED veterinary extension). I get an exception while it's loading that
> the dictionary is not the correct version. So, I assume I just need to
> recreate that custom database? Or is there a migration utility from the old
> database version to the new version?
>
> I don't remember seeing mention of this, but certainly could have missed
> it. If it's not in the release notes or install/upgrade instructions it
> probably should be there.
>
> Thanks to everyone for pulling this release together and getting it out the
> door!
>
> - Dave
>

Re: cTAKES 4.0rc3 - custom dictionary needs rebuilding?

[David Kincaid]

Sorry about this. Actually no, it's not working. I just created a new blank
database apparently in a new directory. Still having the original problem
trying to open the DB in HSQL GUI. Any ideas?

- Dave

On Sun, Apr 23, 2017 at 2:23 PM, David Kincaid 
wrote:

> I got it figured out. I was using the wrong URL path for the database.
> Working great now!
>
> - Dave
>
> On Sun, Apr 23, 2017 at 12:31 PM, David Kincaid 
> wrote:
>
>> Thanks for the reply, James. I'm not very familiar with HSQLDB, so I may
>> be doing it wrong, but I launched the GUI using "java
>> -jar hsqldb-2.3.4.jar" and then tried to connect to the DB by changing the
>> "Type" to "HSQL Database Engine Standalone" and then setting the URL to
>> point to my custom dictionary directory. It throws a SQLException that says
>> "wrong database file version". Is there some other step I'm missing?
>>
>> - Dave
>>
>> On Sat, Apr 22, 2017 at 10:31 PM, James Masanz 
>> wrote:
>>
>>> Dave,
>>>
>>> It's an oversight that we didn't document that. Thanks for pointing that
>>> out! I'll  update the documentation tomorrow and post again with proper
>>> details of the command to use.
>>>
>>> The short answer is that hsqldb jar includes a GUI. You use the 2.3.4
>>> version of that jar, which is included with the cTAKES 4.0 convenience
>>> binary, to open your database. Then you close (shutdown) your DB and it
>>> gets converted to 2.3.4 for you. But if the .properties file for your DB
>>> indicates it's readonly, you need to have edited the properties file
>>> first
>>> to remove that. That gives you the idea. I'll write it up properly
>>> tomorrow.
>>>
>>> Thanks for testing,
>>> -- James
>>>
>>>
>>> *Sent from my phone.*
>>>
>>> On Apr 22, 2017 9:39 PM, "David Kincaid"  wrote:
>>>
>>> I finally had some time this weekend to give 4.0.0rc3 a run. The install
>>> and configuration instructions worked perfectly on my Linux laptop and I
>>> was able to use CVD to run the clinical pipeline successfully against
>>> some
>>> of the clinical notes I have here.
>>>
>>> However, I ran into a problem when I tried running my own customized
>>> pipeline that includes a custom dictionary that I create (to include the
>>> SNOMED veterinary extension). I get an exception while it's loading that
>>> the dictionary is not the correct version. So, I assume I just need to
>>> recreate that custom database? Or is there a migration utility from the
>>> old
>>> database version to the new version?
>>>
>>> I don't remember seeing mention of this, but certainly could have missed
>>> it. If it's not in the release notes or install/upgrade instructions it
>>> probably should be there.
>>>
>>> Thanks to everyone for pulling this release together and getting it out
>>> the
>>> door!
>>>
>>> - Dave
>>>
>>
>>
>