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 <o...@apache.org> 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_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxe > > FU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=jQYowxW0GDNXw8kr > > nlh_KgNiyydac8pJOidOHZ9T8R0&s=P2oSxIaW_ShWXNZ3wdqY6W- > > Rz20Hy_FHp3JPXTHOdcw&e= , 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&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67Gvl > > GZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=jQYowxW0GDNXw8krnlh_KgNiyyda > > c8pJOidOHZ9T8R0&s=puah9D0M36Stz_sbDttCx3KRoSnBicoYAKkikXPuMCQ&e= > > 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_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppx > > eFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=jQYowxW0GDNXw8k > > rnlh_KgNiyydac8pJOidOHZ9T8R0&s=I7CUV0TTeXZY4oqG5P1oMbQ3m2glTGzLEN5T > > KzWGQuk&e= > > 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 <o...@apache.org> > > > wrote: > > > > > > > > > > > Here is an output > > > > > > > > > > > *tmills/ctakes-as* cTAKES and UIMA-AS > > > binaries with > > > > > > > > a few scr... 0 > > > > > > > > *jayunit100/ctakes-example-image-mvn* > > > > > > > > 0 > > > > > > > > *llin/docker_apache_ctakes * Docker image for apache > > > > > > > > ctakes 0 [OK] > > > > > > > > > > > 0 - means stars/rating > > > > > > > > OK - means, automated. > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Sun, Apr 23, 2017 at 7:50 AM, Oleg Tikhonov <o...@apache.org > > > > > wrote: > > > > > > > > > > > > > > > > > Hi, > > > > > > > > > > > > > did you tried: > > > > > > > > > > > > > docker search ctakes ? > > > > > > > > > > > > > > > > > If any body did that, and put in the repository, you could have > > > > see it. > > > > > > > > > > > > > > > > > Oleg > > > > > > > > > > > > > > > > > On Sun, Apr 23, 2017 at 1:58 AM, John Travis Green < > > > > > > > > > > > > > john.travis.gr...@gmail.com> wrote: > > > > > > > > > > > > > > > > > > > > > > > Has anyone dockerized ctakes? If so do you mind sending the > > > > > Dockerfile, > > > > > > > > > > > > > > > > > > > thanks! John Green > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
