Patient Registry suite installation

Patient Registry (PATREG)

The Patient Registry project is dedicated to the management of patient demographics and identifiers test data. It will embed connectors such as FHIR PDQm, PIXm or PAM.

Sources & binaries

The sources are accessible here: https://gitlab.inria.fr/gazelle/applications/test-execution/simulator/patient-registry

Bugs and issue tracking are accessible here : https://gazelle.ihe.net/jira/projects/PATREG. The name of the latest release, can be obtained in the “Releases” section.

To get official artifact (binaries), search for patient-registry in IHE Nexus : https://gazelle.ihe.net/nexus and select the patient-registry.jar artifact for download.

Installation

Patient Manager dependency

Patient Registry depends currently on the database of Patient Manager. Only patients created/managed in Patient Manager will be accessible in the Patient Registry Search API.
Please follow Patient Manager installation process.

Patient Registry needs at least Patient Manager version 9.11.6.

Application server

Patient registry need to be deployed on Widlfly-18.
Please read first the documentation on how to install and configure this server for Gazelle applications : general considerations for WildFly 18

Database configuration

Patient registry is using Patient Manager’s database. It only needs a datasource connection declared in wildfly 18.
See Setup datasources for gazelle applications

Datasource name : patientRegistryDS

Database name : pam-simulator

Deployment

Copy the jar artifact app.patient-registry-service-X.X.X.jar in the deployment folder of the wildfly installation under the name patient-registry.jar. This is important for the path on which Patient Registry’s web services will be exposed.

cp app.patient-registry-service-X.X.X.jar /usr/local/wildfly18/standalone/deployments/patient-registry.jar

Start wildfly. The API can be accessed at (depending on your configured host and port)

For Patient processing Service :

• GITB Processing Service : GET http://localhost:8380/patient-registry/PatientProcessingService/patient-processing-service?wsdl

For CrossReference Processing Service :

• GITB Processing Service : GET http://localhost:8380/patient-registry/CrossReferenceService/xref-processing-service?wsdl

PDQm Connector

PDQm Connector is a connector for Patient Registry. It is dedicated to interface FHIR requests defined in PDQm standard to and the Patient Registry API for patient demographics and identifiers test data management.

Sources & binaries (PDQm)

The sources are accessible here: https://gitlab.inria.fr/gazelle/applications/test-execution/simulator/pdqmsimulator

Bugs and issue tracking are accessible in the same project as the Patient Registry : https://gazelle.ihe.net/jira/projects/PATREG. The name of the latest release, can be obtained in the “Releases” section.

To get official artifact (binaries), search for pdqm-connector-service in IHE Nexus : https://gazelle.ihe.net/nexus and select the pdqm-connector.war artifact for download.

Installation (PDQm)

Patient Manager dependency (PDQm)

Same as Patient Manager Dependency for PATREG

AND PDQm also needs Patient Registry to be installed with connector version >1.0.x, you will need Patient Registry version >1.0.x.

Operational Preferences (PDQm)

PDQm connector defines mandatory Operational Preferences that you will have to define in your Application server. To know how to do that, see General considerations for WildFly 18

Define a resource in your server with name java:/app/gazelle/pdqm-connector/operational-preferences.

This resource should refer to a deployment.properties file. This file shall contain the following properties :

Application server (PDQm)

PDQm need to be deployed on Wildfly-18. Please read first the documentation on how to install and configure this server for Gazelle applications : General considerations for WildFly 18

Configure WildFly 18 f(PDQm)

Install factories module

1. Stop wildfly and go to:

    sudo mkdir -p /usr/local/wildfly18/modules/system/layers/base/net/ihe/gazelle/factories/main
    cd /usr/local/wildfly18/modules/system/layers/base/net/ihe/gazelle/factories/main
   

2. Download module factories.jar:

    sudo wget https://gazelle.ihe.net/wildfly18/factories.jar
   

3. Create module.xml file:

    <?xml version="1.0" encoding="UTF-8"?>
    <module xmlns="urn:jboss:module:1.1" name="net.ihe.gazelle.factories">
        <resources>
            <resource-root path="factories.jar"/>
        </resources>
        <dependencies>
            <module name="javax.api"/>
            <module name="javax.transaction.api"/>
            <module name="javax.servlet.api" optional="true"/>
        </dependencies>
    </module>
   

4. Add jboss:jboss-admin rights:

    sudo chown -R jboss:jboss-admin .
    sudo chmod -R 775 .
   

5. Stop Wildfly and edit standalone.xml in /usr/local/wildfly18/standalone/configuration ; add the factories binding in the naming subsystem :

Replace this property ${DEPLOYMENT_PROPERTIES} with your own path to the deployment property, which is stored in the pdqm-connector project : pdqm-connector/pdqm-connector-service/src/main/resources/deployment.properties

    <subsystem xmlns="urn:jboss:domain:naming:2.0">
       <bindings>
          <object-factory name="java:/app/gazelle/pdqm-connector/operational-preferences" module="net.ihe.gazelle.factories" class="net.ihe.gazelle.factories.PropertiesFactory">
             <environment>
                <property name="path" value="${DEPLOYMENT_PROPERTIES}"/>
             </environment>
          </object-factory>
       </bindings>
       <remote-naming/>
    </subsystem>

Database configuration (PDQm)

Same as Database for PATREG EXCEPT FOR :

Datasource name : pdqmConnectorDS
Database name : pam-simulator

Deployment (PDQm)

Copy the war artifact pdqm-connector-X.X.X.war in the deployment folder of the wildfly installation under the name pdqm-connector.war
This is important for the path on which connector’s web services will be exposed.

cp pdqm-connector-X.X.X.war /usr/local/wildfly18/standalone/deployments/pdqm-connector.war

Start wildfly. The API can be accessed at (depending on your configured host and port)

• Retrieve : GET https://www.example.com/pdqm-connector/Patient/{id}
• Search : POST https://www.example.com/pdqm-connector/Patient

PIXm Connector

PIXm Connector is a connector for Patient Registry. It is dedicated to interface FHIR requests defined in PIXm standard to and the Patient Registry API for patient demographics and identifiers test data management.

Sources & binaries (PIXm)

The sources are accessible here: https://gitlab.inria.fr/gazelle/applications/test-execution/simulator/pixm-connector.

Bugs and issue tracking are accessible in the same project as the Patient Registry : https://gazelle.ihe.net/jira/projects/PATREG. The name of the latest release, can be obtained in the “Releases” section.

To get official artifact (binaries), search for pixm-connector-service in IHE Nexus : https://gazelle.ihe.net/nexus and select the pixm-connector.war artifact for download.

Installation (PIXm)

Patient Manager dependency (PIXm)

Same as Patient Manager dependency for PATREG

PIXm also needs Patient Registry to be installed:

Matchbox and Http-Validator dependencies (PIXm)

Since 3.0.0 PIXm needs two deployed applications for validation:

• HTTP-validator with the install documentation here.
• Matchbox with the install documentation here

Operational Preferences

PIXm connector defines mandatory Operational Preferences that you will have to define in your Application server. To know how to do that, see General considerations for WildFly 18

/!\ Since 3.0.0 PIXm connector needs to be installed in Wildfly version that supports JDK 17. But the tutorial remains the same as Wildfly 18.

Define a resource in your server with name java:/app/gazelle/pixm-connector/operational-preferences.

<subsystem xmlns="urn:jboss:domain:naming:2.0">
<bindings>
<object-factory name="java:/app/gazelle/pixm-connector/operational-preferences" module="net.ihe.gazelle.factories" class="net.ihe.gazelle.factories.PropertiesFactory">
<environment>
<property name="path" value="${DEPLOYMENT_PROPERTIES}"/>
</environment>
</object-factory>
</bindings>
<remote-naming/>
</subsystem>

Replace this property ${DEPLOYMENT_PROPERTIES} with the path to the deployment.properties file (like /opt/pixm-connector/deployment.properties)

This file shall contain the following properties :

Since version 3.0.0 PIXm needs:

• endpoints for matchbox and http-validator
• profiles id (URL + headers validation with http-validator)
• profile canonical url (body validation with Matchbox FHIR)

Application server (PIXm)

Same as Application Server (PDQm) for both Wildfly 18 and Wildfly 30.

Deployment (PIXm)

Copy the war artifact pixm-connector-X.X.X.war (< 3.0.0) or pixm-connector-service-X.X.X.war (>= 3.0.0) in the deployment folder of the wildfly installation under the name pixm-connector.war.
This is important for the path on which connector’s web services will be exposed.

Before 3.0.0:

cp pixm-connector-X.X.X.war /usr/local/wildfly18/standalone/deployments/pixm-connector.war

Since 3.0.0:

cp pixm-connector-service-X.X.X.war /usr/local/wildfly30/standalone/deployments/pixm-connector.war

Start wildfly.

The API can be accessed at (depending on your configured host and port):

• ITI-104 : PUT/DELETE https://example.com/pixm-connector/fhir/Patient?identifier=patient.system%7Cpatient.id
• ITI-83 : GET https://example.com/pixm-connector/fhir/Patient/$ihe-pix?sourceIdentifier=patient.system%7Cpatient.id&targetSystem=targetSystem
• Capability statement : https://example.com/pixm-connector/fhir/metadata