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medco-deployment/i2b2-server/i2b2-server-writedatasources.sh
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i2b2-server-writedatasources.sh
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#!/bin/bash
set -e
# meant to be called by Dockerfile of i2b2-server
cat > edu.harvard.i2b2.pm/etc/jboss/pm-ds.xml <<EOL
<?xml version="1.0" encoding="UTF-8"?>
<datasources xmlns="http://www.jboss.org/ironjacamar/schema">
<datasource jta="false" jndi-name="java:/PMBootStrapDS"
pool-name="PMBootStrapDS" enabled="true" use-ccm="false">
<connection-url>jdbc:postgresql://i2b2-database:5432/$I2B2_DOMAIN_NAME</connection-url>
<driver-class>org.postgresql.Driver</driver-class>
<driver>postgresql-9.2-1002.jdbc4.jar</driver>
<security>
<user-name>i2b2pm</user-name>
<password>$DB_PASSWORD</password>
</security>
<validation>
<validate-on-match>false</validate-on-match>
<background-validation>false</background-validation>
</validation>
<statement>
<share-prepared-statements>false</share-prepared-statements>
</statement>
</datasource>
</datasources>
EOL
cat > edu.harvard.i2b2.ontology/etc/jboss/ont-ds.xml <<EOL
<?xml version="1.0" encoding="UTF-8"?>
<datasources xmlns="http://www.jboss.org/ironjacamar/schema">
<datasource jta="false" jndi-name="java:/OntologyDemoDS"
pool-name="OntologyDemoDS" enabled="true" use-ccm="false">
<connection-url>jdbc:postgresql://i2b2-database:5432/$I2B2_DOMAIN_NAME</connection-url>
<driver-class>org.postgresql.Driver</driver-class>
<driver>postgresql-9.2-1002.jdbc4.jar</driver>
<security>
<user-name>i2b2metadata</user-name>
<password>$DB_PASSWORD</password>
</security>
<validation>
<validate-on-match>false</validate-on-match>
<background-validation>false</background-validation>
</validation>
<statement>
<share-prepared-statements>false</share-prepared-statements>
</statement>
</datasource>
<datasource jta="false" jndi-name="java:/OntologyBootStrapDS"
pool-name="OntologyBootStrapDS" enabled="true" use-ccm="false">
<connection-url>jdbc:postgresql://i2b2-database:5432/$I2B2_DOMAIN_NAME</connection-url>
<driver-class>org.postgresql.Driver</driver-class>
<driver>postgresql-9.2-1002.jdbc4.jar</driver>
<security>
<user-name>i2b2hive</user-name>
<password>$DB_PASSWORD</password>
</security>
<validation>
<validate-on-match>false</validate-on-match>
<background-validation>false</background-validation>
</validation>
<statement>
<share-prepared-statements>false</share-prepared-statements>
</statement>
</datasource>
<!-- SHRINE ontology datasource -->
<datasource jta="false" jndi-name="java:/OntologyShrineDS"
pool-name="OntologyShrineDS" enabled="true" use-ccm="false">
<connection-url>jdbc:postgresql://i2b2-database:5432/$I2B2_DOMAIN_NAME</connection-url>
<driver-class>org.postgresql.Driver</driver-class>
<driver>postgresql-9.2-1002.jdbc4.jar</driver>
<security>
<user-name>shrine_ont</user-name>
<password>$DB_PASSWORD</password>
</security>
<validation>
<validate-on-match>false</validate-on-match>
<background-validation>false</background-validation>
</validation>
<statement>
<share-prepared-statements>false</share-prepared-statements>
</statement>
</datasource>
</datasources>
EOL
cat > edu.harvard.i2b2.crc/etc/jboss/crc-ds.xml <<EOL
<?xml version="1.0" encoding="UTF-8"?>
<datasources xmlns="http://www.jboss.org/ironjacamar/schema">
<datasource jta="false" jndi-name="java:/CRCBootStrapDS"
pool-name="CRCBootStrapDS" enabled="true" use-ccm="false">
<connection-url>jdbc:postgresql://i2b2-database:5432/$I2B2_DOMAIN_NAME</connection-url>
<driver-class>org.postgresql.Driver</driver-class>
<driver>postgresql-9.2-1002.jdbc4.jar</driver>
<security>
<user-name>i2b2hive</user-name>
<password>$DB_PASSWORD</password>
</security>
<validation>
<validate-on-match>false</validate-on-match>
<background-validation>false</background-validation>
</validation>
<statement>
<share-prepared-statements>false</share-prepared-statements>
</statement>
</datasource>
<datasource jta="false" jndi-name="java:/QueryToolDemoDS"
pool-name="QueryToolDemoDS" enabled="true" use-ccm="false">
<connection-url>jdbc:postgresql://i2b2-database:5432/$I2B2_DOMAIN_NAME</connection-url>
<driver-class>org.postgresql.Driver</driver-class>
<driver>postgresql-9.2-1002.jdbc4.jar</driver>
<security>
<user-name>i2b2demodata</user-name>
<password>$DB_PASSWORD</password>
</security>
<validation>
<validate-on-match>false</validate-on-match>
<background-validation>false</background-validation>
</validation>
<statement>
<share-prepared-statements>false</share-prepared-statements>
</statement>
</datasource>
</datasources>
EOL
cat > edu.harvard.i2b2.workplace/etc/jboss/work-ds.xml <<EOL
<?xml version="1.0" encoding="UTF-8"?>
<datasources xmlns="http://www.jboss.org/ironjacamar/schema">
<datasource jta="false" jndi-name="java:/WorkplaceBootStrapDS"
pool-name="WorkplaceBootStrapDS" enabled="true" use-ccm="false">
<connection-url>jdbc:postgresql://i2b2-database:5432/$I2B2_DOMAIN_NAME</connection-url>
<driver-class>org.postgresql.Driver</driver-class>
<driver>postgresql-9.2-1002.jdbc4.jar</driver>
<security>
<user-name>i2b2hive</user-name>
<password>$DB_PASSWORD</password>
</security>
<validation>
<validate-on-match>false</validate-on-match>
<background-validation>false</background-validation>
</validation>
<statement>
<share-prepared-statements>false</share-prepared-statements>
</statement>
</datasource>
<datasource jta="false" jndi-name="java:/WorkplaceDemoDS"
pool-name="WorkplaceDemoDS" enabled="true" use-ccm="false">
<connection-url>jdbc:postgresql://i2b2-database:5432/$I2B2_DOMAIN_NAME</connection-url>
<driver-class>org.postgresql.Driver</driver-class>
<driver>postgresql-9.2-1002.jdbc4.jar</driver>
<security>
<user-name>i2b2workdata</user-name>
<password>$DB_PASSWORD</password>
</security>
<validation>
<validate-on-match>false</validate-on-match>
<background-validation>false</background-validation>
</validation>
<statement>
<share-prepared-statements>false</share-prepared-statements>
</statement>
</datasource>
</datasources>
EOL
cat > edu.harvard.i2b2.im/etc/jboss/im-ds.xml <<EOL
<?xml version="1.0" encoding="UTF-8"?>
<datasources xmlns="http://www.jboss.org/ironjacamar/schema">
<datasource jta="false" jndi-name="java:/IMBootStrapDS"
pool-name="IMBootStrapDS" enabled="true" use-ccm="false">
<connection-url>jdbc:postgresql://i2b2-database:5432/$I2B2_DOMAIN_NAME</connection-url>
<driver-class>org.postgresql.Driver</driver-class>
<driver>postgresql-9.2-1002.jdbc4.jar</driver>
<security>
<user-name>i2b2hive</user-name>
<password>$DB_PASSWORD</password>
</security>
<validation>
<validate-on-match>false</validate-on-match>
<background-validation>false</background-validation>
</validation>
<statement>
<share-prepared-statements>false</share-prepared-statements>
</statement>
</datasource>
<datasource jta="false" jndi-name="java:/IMDemoDS"
pool-name="IMDemoDS" enabled="true" use-ccm="false">
<connection-url>jdbc:postgresql://i2b2-database:5432/$I2B2_DOMAIN_NAME</connection-url>
<driver-class>org.postgresql.Driver</driver-class>
<driver>postgresql-9.2-1002.jdbc4.jar</driver>
<security>
<user-name>i2b2imdata</user-name>
<password>$DB_PASSWORD</password>
</security>
<validation>
<validate-on-match>false</validate-on-match>
<background-validation>false</background-validation>
</validation>
<statement>
<share-prepared-statements>false</share-prepared-statements>
</statement>
</datasource>
</datasources>
EOL
cat > edu.harvard.i2b2.crc/etc/spring/CRCLoaderApplicationContext.xml <<EOL
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE beans PUBLIC "-//SPRING//DTD BEAN//EN" "http://www.springframework.org/dtd/spring-beans.dtd">
<beans>
<bean id="jaxbPackage"
class="org.springframework.beans.factory.config.ListFactoryBean">
<property name="sourceList">
<list>
<value>edu.harvard.i2b2.crc.loader.datavo.loader.query</value>
<value>edu.harvard.i2b2.crc.datavo.pdo</value>
<value>edu.harvard.i2b2.crc.datavo.i2b2message</value>
<value>edu.harvard.i2b2.crc.datavo.pm</value>
<value>edu.harvard.i2b2.crc.loader.datavo.fr</value>
</list>
</property>
</bean>
<bean id="appType" class="edu.harvard.i2b2.crc.datavo.i2b2message.ApplicationType">
<property name="applicationName" value="CRC Cell" />
<property name="applicationVersion" value="1.7" />
</bean>
<bean id="message_header"
class="edu.harvard.i2b2.crc.datavo.i2b2message.MessageHeaderType">
<property name="sendingApplication" ref="appType" />
</bean>
<bean id="CRCBootstrapDS" class="org.apache.commons.dbcp.BasicDataSource"
destroy-method="close">
<property name="driverClassName" value="org.postgresql.Driver" />
<property name="url" value="jdbc:postgresql://i2b2-database:5432/$I2B2_DOMAIN_NAME" />
<property name="username" value="i2b2hive" />
<property name="password" value="$DB_PASSWORD" />
</bean>
</beans>
EOL
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