cda2vmr container

Steps required to build cda2vmr docker image:

Download opencds-cdstovmr-docker
Install Mercurial
Clone and build cda-web-service project
Copy cda-ws-web.war and cda-ws-ear.ear into docker folder
Download terminology files and place them into docker folder
Define the URL of the opencds instance on ejb-jar.xml
Build and deploy container

Download opencds-cdstovmr-docker

git clone https://bitbucket.org/opencds/opencds-cdstovmr-docker

In order to build this image you will need cda-ws-ear.ear and cda-ws-web.war files. These files can be obtained by cloning and building the cda-web-service project. First you need to install Mercurial (https://mercurial.selenic.com/) which is the control management tool used in this project.

Install Mercurial

sudo apt-get install mercurial

Clone and build project

hg clone https://bitbucket.org/sharps-ds2/cda-web-service
cd cda-web-service; mvn clean install

Copy the required files into opencds-cdstovmr-docker folder

cp cda-web-service/cda-ws-ear/target/cda-ws-ear.ear opencds-cdstovmr-docker/
cp cda-web-service/cda-ws-webapp/target/cda-ws-web.war opencds-cdstovmr-docker/

Also you need the following terminology resources. Place these five files into opencds-cdstovmr-docker folder.

From http://www.nlm.nih.gov/research/umls/

ICD9CM_SNOMED_MAP_1TO1.txt
ICD9CM_SNOMED_MAP_1TOM.txt
SNOMEDCT_CORE_SUBSET_201311.txt
tls_Icd10HumanReadableMap_INT_20131220.tsv

From http://www.hcup-us.ahrq.gov/toolssoftware/icd_10/ccs_icd10_2006.zip

ccs_icd10_2006.csv

The opencds-cdatovmr-docker folder should look like this:

opencds-cdstovmr-docker/
├── ccs_icd10_2006.csv
├── cda-ws-ear.ear
├── cda-ws-web.war
├── change_admin_password_func.sh
├── change_admin_password.sh
├── Dockerfile
├── ejb-jar.xml
├── enable_secure_admin.sh
├── ICD9CM_SNOMED_MAP_1TO1.txt
├── ICD9CM_SNOMED_MAP_1TOM.txt
├── log4j.properties
├── naivebayespredicate.properties
├── opencds_concept_generator.sh
├── opencds-decision-support-service-config.xml
├── readme.txt
├── reducer-env.properties
├── run.sh
├── SNOMEDCT_CORE_SUBSET_201311.txt
└── tls_Icd10HumanReadableMap_INT_20131220.tsv

Before build the image, edit the ejb-jar.xml file and define the URL of the OpenCDS service.

Define the URL of your opencds service on ejb-jar.xml

        <session>
            <ejb-name>OpenCdsServiceMGR</ejb-name>
            <env-entry>
                <env-entry-name>OPENCDS_ENDPOINT</env-entry-name>
                <env-entry-type>java.lang.String</env-entry-type>
                <env-entry-value>http://192.168.1.101:8081/opencds-decision-support-service-1.2.0-SNAPSHOT/evaluate</env-entry-value>
            </env-entry>

Build and deploy container

sudo docker build -t="opencds/cdatovmr" .
sudo docker run -p 8080:8080 -p 2222:22 -p 4848:4848 -p 8181:8181 -p 9009:9009 --name cdatovmr -i -t opencds/cdatovmr

By default the image includes the following four applications:

Inference analyzer - http://locahost:8080/SimplePredicateReducerVisualizer-1.0-SNAPSHOT
opencds service - http://localhost:8080/opencds-decision-support-service-1.2.0-SNAPSHOT/evaluate?wsdl
Predicate reducer Web service - http://localhost:8080/CdaService/Evaluate?wsdl
Predicate reducer web application - http://localhost:8080/cda-ws-web/

It is important to note that you can remove any of these applications by editing the Dockerfile.