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Getting Started with DCM4CHEE XDS 2.0.0

Requirements

Download and extract binary distribution package

DCM4CHEE XDS 2.x binary distributions for different databases can be obtained from Sourceforge. Extract (unzip) your chosen download to the directory of your choice.

Initialize Database

MySQL

  1. Enable remote access by commenting out skip-networking in configuration file my.conf.

  2. Create database and grant access to user

     > mysql -u root -p<root-password>
 mysql> CREATE DATABASE <database-name>;
 mysql> GRANT ALL ON <database-name>.* TO '<user-name>' IDENTIFIED BY '<user-password>';
 mysql> quit

  3. Create tables and indexes

     > mysql -u <user-name> -p<user-password> < $DCM4CHEE_XDS2/sql/create-table-mysql.ddl
 > mysql -u <user-name> -p<user-password> < $DCM4CHEE_XDS2/sql/create-index.ddl

PostgreSQL

  1. Create user with permission to create databases

     > createuser -U postgres -P -d <user-name>
 Enter password for new role: <user-password> 
 Enter it again: <user-password>

  2. Create database

     > createdb -U <user-name> <database-name>

  3. Create tables and indexes

     > psql -U <user-name> < $DCM4CHEE_XDS2/sql/create-table-psql.ddl
 > psql -U <user-name> < $DCM4CHEE_XDS2/sql/create-index.ddl

Firebird

  1. Define database name in configuration file aliases.conf:

     <database-name> = <database-file-path>

  2. Create user

     > gsec -user sysdba -password masterkey \
   -add <user-name> -pw <user-password>

  3. Create database, tables and indexes

     > isql 
 Use CONNECT or CREATE DATABASE to specify a database
 SQL> CREATE DATABASE 'localhost:<database-name>'
 CON> user '<user-name>' password '<user-password>';
 SQL> IN $DCM4CHEE_XDS2/sql/create-table-firebird.ddl;
 SQL> IN $DCM4CHEE_XDS2/sql/create-index.ddl;
 SQL> EXIT;

DB2

  1. Create database and grant authority to create tables to user (must match existing OS user)

     > sudo su db2inst1
 > db2
 db2 => CREATE DATABASE <database-name> PAGESIZE 16 K
 db2 => connect to <database-name>
 db2 => GRANT CREATETAB ON DATABASE TO USER <user-name>
 db2 => terminate

  2. Create tables and indexes

     > su <user-name>
 Password: <user-password>
 > db2 connect to <database-name>
 > db2 -t < $DCM4CHEE_XDS2/sql/create-table-db2.ddl
 > db2 -t < $DCM4CHEE_XDS2/sql/create-index.ddl
 > db2 terminate

Oracle 11g

TODO

Setup LDAP Server

OpenDJ

  1. Copy LDAP schema files for OpenDJ from DCM4CHEE XDS 2.x distribution to OpenDJ schema configuration directory:

    > cp $DCM4CHEE_XDS2/ldap/opendj/* $OPENDJ_HOME/config/schema/ [UNIX]
> copy %DCM4CHEE_XDS2%\ldap\opendj\* %OPENDJ_HOME%\config\schema\ [Windows]

  2. Run OpenDJ GUI based setup utility

    > $OPENDJ_HOME/setup

    Log the values choosen for

    • LDAP Listener port (1389)
    • Root User DN (cn=Directory Manager)
    • Root User Password (secret)
    • Directory Base DN (dc=example,dc=com)

    needed for the LDAP connection configuration of DCM4CHEE XDS 2.x.

  3. After initial setup, you may start and stop OpenDJ by

     > $OPENDJ_HOME/bin/start-ds
 > $OPENDJ_HOME/bin/stopt-ds

OpenLDAP

OpenLDAP binary distributions are available for most Linux distributions and for Windows.

OpenLDAP can be alternatively configured by

See also Converting old style slapd.conf file to cn=config format

OpenLDAP with slapd.conf configuration file

  1. Copy LDAP schema files for OpenLDAP from DCM4CHEE XDS 2.x distribution to OpenLDAP schema configuration directory:

    > cp $DCM4CHEE_XDS2/ldap/schema/* /etc/openldap/schema/ [UNIX]
> copy %DCM4CHEE_XDS2%\ldap\schema\* \Program Files\OpenLDAP\schema\ [Windows]

  2. Add references to schema files in slapd.conf, e.g.:

    include         /etc/openldap/schema/core.schema
include         /etc/openldap/schema/dicom.schema
include         /etc/openldap/schema/dcm4che.schema
include         /etc/openldap/schema/dcm4che-hl7.schema
include         /etc/openldap/schema/dcm4chee-xds2.schema

  3. You may also change the default values for

    suffix          "dc=my-domain,dc=com"
rootdn          "cn=Manager,dc=my-domain,dc=com"
rootpw          secret

    in slapd.conf.

OpenLDAP with dynamic runtime configuration

  1. Import LDAP schema files for OpenLDAP runtime configuration, binding as root user of the config backend, using OpenLDAP CL utility ldapadd, e.g.:

    > ldapadd -xW -Dcn=config -f $DCM4CHEE_XDS2/ldap/slapd/dicom.ldif
> ldapadd -xW -Dcn=config -f $DCM4CHEE_XDS2/ldap/slapd/dcm4che.ldif
> ldapadd -xW -Dcn=config -f $DCM4CHEE_XDS2/ldap/slapd/dcm4che-hl7.ldif
> ldapadd -xW -Dcn=config -f $DCM4CHEE_XDS2/ldap/slapd/dcm4chee-xds2.ldif

    If you don't know the root user and its password of the config backend, you may look into /etc/openldap/slap.d/cn=config/olcDatabase={0}config.ldif:

    olcRootDN: cn=config
olcRootPW:: VmVyeVNlY3JldA==

    and decode the base64 decoded password, e.g:

    > echo -n VmVyeVNlY3JldA== | base64 -d
VerySecret

    or specify a new password in plan text, e.g:

    olcRootPW: VerySecret

  2. Directory Base DN and Root User DN can be modified by changing the values of attributes

    olcSuffix: dc=my-domain,dc=com
olcRootDN: cn=Manager,dc=my-domain,dc=com

    of object olcDatabase={1}bdb,cn=config by specifing the new values in a LDIF file (e.g. modify-baseDN.ldif)

    dn: olcDatabase={1}bdb,cn=config
changetype: modify
replace: olcSuffix
olcSuffix: dc=example,dc=com
-
replace: olcRootDN
olcRootDN: cn=Manager,dc=example,dc=com
-

    and applying it using OpenLDAP CL utility ldapmodify, e.g.:

    > ldapmodify -xW -Dcn=config -f modify-baseDN.ldif

Apache DS 2.0

  1. Install Apache DS 2.0.0-M8 on your system and start Apache DS.

  2. Install Apache Directory Studio 1.5.3 and create a new LDAP Connection with:

    Network Parameter:
    Hostname: localhost
    Port:     10398
Authentication Parameter:
    Bind DN or user: uid=admin,ou=system
    Bind password:   secret

  3. Import LDAP schema files for Apache DS:

    $DCM4CHEE_XDS2/ldap/apacheds/dicom.ldif
$DCM4CHEE_XDS2/ldap/apacheds/dcm4che.ldif
$DCM4CHEE_XDS2/ldap/apacheds/dcm4che-hl7.ldif
$DCM4CHEE_XDS2/ldap/apacheds/dcm4chee-xds2.ldif

    using the LDIF import function of Apache Directory Studio LDAP Browser.

  4. You may modify the default Directory Base DN dc=example,dc=com by changing the value of attribute

    ads-partitionsuffix: dc=example,dc=com`

    of object

    ou=config
+ ads-directoryServiceId=default
  + ou=partitions
      ads-partitionId=example

    using Apache Directory Studio LDAP Browser.

Import sample configuration into LDAP Server

  1. If not alread done, install Apache Directory Studio 1.5.3 and create a new LDAP Connection corresponding to your LDAP Server configuration, e.g:

    Network Parameter:
    Hostname: localhost
    Port:     1398
Authentication Parameter:
    Bind DN or user: cn=Directory Manager
    Bind password:   secret
Browser Options:
    Base DN: dc=example,dc=com

  2. If you configured a different Directory Base DN thandc=example,dc=com, you have to replace all occurrences of dc=example,dc=com in LDIF files

    $DCM4CHEE_XDS2/ldap/init-baseDN.ldif
$DCM4CHEE_XDS2/ldap/init-config.ldif
$DCM4CHEE_XDS2/ldap/sample-config.ldif

    by your Directory Base DN, e.g.:

    > cd $DCM4CHEE_XDS2/ldap
> sed -i s/dc=example,dc=com/dc=my-domain,dc=com/ init-baseDN.ldif
> sed -i s/dc=example,dc=com/dc=my-domain,dc=com/ init-config.ldif
> sed -i s/dc=example,dc=com/dc=my-domain,dc=com/ sample-config.ldif

  3. If there is not already a base entry in the directory data base, import $DCM4CHEE_XDS2/ldap/init-baseDN.ldif using the LDIF import function of Apache Directory Studio LDAP Browser.

  4. If there are not already DICOM configuration root entries in the directory data base, import $DCM4CHEE_XDS2/ldap/init-config.ldif using the LDIF import function of Apache Directory Studio LDAP Browser.

  5. Import $DCM4CHEE_XDS2/ldap/sample-config.ldif using the LDIF import function of Apache Directory Studio LDAP Browser.

  6. By default configuration, the HL7 service of DCM4CHEE XDS2 registry does not accept remote connections. To enable remote connections, replace the value of attribute

    dicomHostname=localhost

    of the 2 dicomNetworkConnection objects

    dc=example,dc=com
+ cn=XDS Configuration
  + cn=Devices
    + dicomDeviceName=dcm4chee-xds2-registry
        cn=hl7
        cn=hl7-tls

    by the actual hostname of your system, using Apache Directory Studio LDAP Browser.

Setup JBoss AS 7

  1. Adjust DCM4CHEE XDS2 LDAP Connection configuration file $DCM4CHEE_ARC/configuration/dcm4chee-xds2/ldap.properties:

    java.naming.factory.initial=com.sun.jndi.ldap.LdapCtxFactory
java.naming.ldap.attributes.binary=dicomVendorData
java.naming.provider.url=ldap://localhost:1389/dc=example,dc=com
java.naming.security.principal=cn=Directory Manager
java.naming.security.credentials=secret

    to your LDAP Server configuration.

  2. Install DCM4CHE 3.0.1 libraries as JBoss AS 7 module:

    > cd  $JBOSS_HOME
> unzip $DCM4CHEE_XDS2/jboss-module/dcm4che-jboss-modules-3.0.1.zip

  3. Install QueryDSL 2.8.1 libraries as JBoss AS 7 module:

    > cd  $JBOSS_HOME
> unzip $DCM4CHEE_ARC/jboss-module/querydsl-jboss-modules-2.8.1.zip

  4. Install JDBC Driver. DCM4CHEE Archive 4.x binary distributions do not include a JDBC driver for the database for license issues. You may download it from:

    The JDBC driver can be installed either as a deployment or as a core module. See

    Installation as deployment is limited to JDBC 4-compliant driver consisting of one JAR.

    For installation as a core module, $DCM4CHEE_ARC/jboss-module/jdbc-jboss-modules-1.0.0-<database>.zip already provides a module definition file module.xml. You just need to extract the ZIP file into $JBOSS_HOME and copy the JDBC Driver file(s) into the sub-directory, e.g.:

    > cd $JBOSS_HOME
> unzip $DCM4CHEE_ARC/jboss-module/jdbc-jboss-modules-1.0.0-db2.zip
> cd $DB2_HOME/java
> cp db2jcc4.jar db2jcc_license_cu.jar $JBOSS_HOME/modules/com/ibm/db2/main/

    Verify, that the actual JDBC Driver file(s) name matches the path(s) in the provided module.xml, e.g.:

     <?xml version="1.0" encoding="UTF-8"?>
 <module xmlns="urn:jboss:module:1.1" name="com.ibm.db2">
     <resources>
         <resource-root path="db2jcc4.jar"/>
         <resource-root path="db2jcc_license_cu.jar"/>
     </resources>
 
     <dependencies>
         <module name="javax.api"/>
         <module name="javax.transaction.api"/>
     </dependencies>
 </module>

  5. Start JBoss AS 7 in standalone mode with the Java EE 6 Full Profile configuration. To preserve the original JBoss AS 7 configuration you may copy the original configuration file for JavaEE 6 Full Profile:

    > cd $JBOSS_HOME/standalone/configuration/
> cp standalone-full.xml dcm4chee-xds2.xml

    and start JBoss AS 7 specifying the new configuration file:

    > $JBOSS_HOME/bin/standalone.sh -c dcm4chee-xds2.xml [UNIX]
> %JBOSS_HOME%\bin\standalone.bat -c dcm4chee-xds2.xml [Windows]

    Verify, that JBoss AS 7 started successfully, e.g.:

    =========================================================================

  JBoss Bootstrap Environment

  JBOSS_HOME: /home/gunter/jboss7

  JAVA: /usr/lib/jvm/java-6-openjdk/bin/java

  JAVA_OPTS:  -server -XX:+UseCompressedOops -XX:+TieredCompilation ...

=========================================================================

13:01:48,788 INFO  [org.jboss.modules] JBoss Modules version 1.1.1.GA
13:01:48,926 INFO  [org.jboss.msc] JBoss MSC version 1.0.2.GA
13:01:48,969 INFO  [org.jboss.as] JBAS015899: JBoss AS 7.1.1.Final "Brontes" starting
:
13:01:51,239 INFO  [org.jboss.as] (Controller Boot Thread) JBAS015874: JBoss AS 7.1.1.Final "Brontes" started ...

    Running JBoss AS 7 in domain mode should work, but was not yet tested.

  6. Add JDBC Driver into the server configuration using JBoss AS 7 CLI in a new console window:

    > $JBOSS_HOME/bin/jboss-cli.sh -c [UNIX]
> %JBOSS_HOME%\bin\jboss-cli.bat -c [Windows]
[standalone@localhost:9999 /] /subsystem=datasources/jdbc-driver=<driver-name>:add(driver-module-name=<module-name>)

    You may choose any <driver-name> for the JDBC Driver, <module-name> must match the name defined in the module definition file module.xml of the JDBC driver, e.g.:

    [standalone@localhost:9999 /] /subsystem=datasources/jdbc-driver=db2:add(driver-module-name=com.ibm.db2)

  7. Create and enable a new Data Source bound to JNDI name java:/xdsDS using JBoss AS 7 CLI:

    [standalone@localhost:9999 /] data-source add --name=xdsDS \
>     --driver-name=<driver-name> \
>     --connection-url=<jdbc-url> \
>     --jndi-name=java:/xdsDS \
>     --user-name=<user-name> \
>     --password=<user-password>
[standalone@localhost:9999 /] data-source enable --name=xdsDS

    The format of <jdbc-url> is JDBC Driver specific, e.g.:

    • MySQL: jdbc:mysql://localhost:3306/<database-name>
    • PostgreSQL: jdbc:postgresql://localhost:5432/<database-name>
    • Firebird: jdbc:firebirdsql:localhost/3050:<database-name>
    • DB2: jdbc:db2://localhost:50000/<database-name>
    • Oracle: jdbc:oracle:thin:@localhost:1521:<database-name>
    • Microsoft SQL Server: jdbc:sqlserver://localhost:1433;databaseName=<database-name>

  8. At default, DCM4CHEE XDS 2.x will look for the LDAP connection configuration file at

     $JBOSS_HOME/standalone/configuration/dcm4chee-xds2/ldap.properties

    You may specify a different location by system property org.dcm4chee.xds.ldapPropertiesURL using JBoss AS 7 CLI:

     [standalone@localhost:9999 /] /system-property=org.dcm4chee.xds.ldapPropertiesURL:add(value=<url>)

    If DCM4CHEE XDS 2.x cannot find the LDAP connection configuration on the specified location, it will try to fetch the Archive configuration from Java Preferences.

  9. At default, DCM4CHEE XDS 2.x will assume dcm4chee-xds2-registry as its Device Name, used to find its configuration in the configuration backend (LDAP Server or Java Preferences). You may specify a different Device Name by system property org.dcm4chee.xds.deviceName using JBoss AS 7 CLI:

     [standalone@localhost:9999 /] /system-property=org.dcm4chee.xds.deviceName:add(value=<device-name>)

  10. Deploy DCM4CHEE XDS 2.x using JBoss AS 7 CLI, e.g.:

    [standalone@localhost:9999 /] deploy $DCM4CHEE_XDS2/deploy/dcm4chee-xds2-ear-2.0.0-mysql.ear

    Verify that DCM4CHEE XDS was deployed and started successfully, e.g.:

  11. You may undeploy DCM4CHEE XDS at any time using JBoss AS 7 CLI, e.g.:

    [standalone@localhost:9999 /] undeploy dcm4chee-xds2-ear-2.0.0-mysql.ear

Testing DCM4CHEE XDS 2.x