0.7.2

num-codex · Nov 19, 2021 · 4f10caf · 4f10caf
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diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@ Details about the actual mapping can be found [here](docs/mappings.md).
 
 ## Command
 ```sh
-docker run **VOLUMES** ghcr.io/num-codex/odm2fhir **ARGUMENTS**
+docker run **ENVIRONMENTS** **VOLUMES** ghcr.io/num-codex/odm2fhir **ARGUMENTS**
 ```
 
 ### Arguments
@@ -23,9 +23,11 @@ docker run **VOLUMES** ghcr.io/num-codex/odm2fhir **ARGUMENTS**
 
 * `--fhir.identifier.assigner=**IDENTIFIER_ASSIGNER**` Add an identifier assigner.
 
-* `--fhir.updateascreate.enabled=true` Enable update-as-create (see [here](https://www.hl7.org/fhir/http.html#upsert)).
+* `--fhir.encounters.enabled=true` Enable encounters (enabled by default).
 
-* `--fhir.validation.enabled=true` Enable FHIR resource validation (see [here](#validation)).
+* `--fhir.updateascreate.enabled=true` Enable update-as-create (see [here](https://www.hl7.org/fhir/http.html#upsert), disabled by default).
+
+* `--fhir.validation.enabled=true` Enable FHIR resource validation (see [here](#validation), disabled by default).
 
 * `--cron="**CRON_PATTERN**"` Enable timed execution (see [here](https://docs.spring.io/spring-framework/docs/current/javadoc-api/org/springframework/scheduling/support/CronSequenceGenerator.html)).
 
@@ -44,6 +46,12 @@ docker run **VOLUMES** ghcr.io/num-codex/odm2fhir **ARGUMENTS**
 --odm.redcap.api.token=**ODM_REDCAP_API_TOKEN**
 ```
 
+#### HTTP(S) Proxy
+Enable HTTP(S) proxy by adding the environment to `**ENVIRONMENTS**`:
+```sh
+-e JAVA_TOOL_OPTIONS="-Dhttp.proxyHost=**HTTP_PROXY_HOST** -Dhttp.proxyPort=**HTTP_PROXY_PORT** -Dhttp.nonProxyHosts=**HTTP_NON_PROXY_HOSTS** -Dhttps.proxyHost=**HTTPS_PROXY_HOST** -Dhttps.proxyPort=**HTTPS_PROXY_PORT** -Dhttps.nonProxyHosts=**HTTPS_NON_PROXY_HOSTS**"
+```
+
 #### PKCS12 Certificate
 ```sh
 --odm.redcap.api.key.file.path=**ODM_REDCAP_API_KEY_FILE_PATH**
@@ -71,6 +79,9 @@ By default, all subjects within an ODM are processed. To process only subjects w
 --odm.dis.rest.password=**ODM_DIS_REST_PASSWORD**
 ```
 
+#### HTTP(S) Proxy
+(see [here](#https-proxy))
+
 #### PKCS12 Certificate
 ```sh
 --odm.dis.rest.key.file.path=**ODM_DIS_REST_KEY_FILE_PATH**
@@ -91,6 +102,9 @@ By default, all subjects within an ODM are processed. To process only subjects w
 --fhir.server.url=**FHIR_SERVER_URL**
 ```
 
+#### HTTP(S) Proxy
+(see [here](#https-proxy))
+
 #### BasicAuth
 ```sh
 --fhir.server.basicauth.username=**FHIR_SERVER_BASICAUTH_USERNAME**
@@ -120,6 +134,9 @@ Enable the use of an external terminology server by adding the argument(s) below
 --fhir.terminologyserver.url=**FHIR_TERMINOLOGYSERVER_URL**
 ```
 
+#### HTTP(S) Proxy
+(see [here](#https-proxy))
+
 #### BasicAuth
 ```sh
 --fhir.terminologyserver.basicauth.username=**FHIR_TERMINOLOGYSERVER_BASICAUTH_USERNAME**

diff --git a/docs/index.md b/docs/index.md
@@ -6,7 +6,7 @@ Details about the actual mapping can be found [here](mappings.md).
 
 ## Command
 ```sh
-docker run **VOLUMES** ghcr.io/num-codex/odm2fhir **ARGUMENTS**
+docker run **ENVIRONMENTS** **VOLUMES** ghcr.io/num-codex/odm2fhir **ARGUMENTS**
 ```
 
 ### Arguments
@@ -23,9 +23,11 @@ docker run **VOLUMES** ghcr.io/num-codex/odm2fhir **ARGUMENTS**
 
 * `--fhir.identifier.assigner=**IDENTIFIER_ASSIGNER**` Add an identifier assigner.
 
-* `--fhir.updateascreate.enabled=true` Enable update-as-create (see [here](https://www.hl7.org/fhir/http.html#upsert)).
+* `--fhir.encounters.enabled=true` Enable encounters (enabled by default).
 
-* `--fhir.validation.enabled=true` Enable FHIR resource validation (see [here](#validation)).
+* `--fhir.updateascreate.enabled=true` Enable update-as-create (see [here](https://www.hl7.org/fhir/http.html#upsert), disabled by default).
+
+* `--fhir.validation.enabled=true` Enable FHIR resource validation (see [here](#validation), disabled by default).
 
 * `--cron="**CRON_PATTERN**"` Enable timed execution (see [here](https://docs.spring.io/spring-framework/docs/current/javadoc-api/org/springframework/scheduling/support/CronSequenceGenerator.html)).
 
@@ -44,6 +46,12 @@ docker run **VOLUMES** ghcr.io/num-codex/odm2fhir **ARGUMENTS**
 --odm.redcap.api.token=**ODM_REDCAP_API_TOKEN**
 ```
 
+#### HTTP(S) Proxy
+Enable HTTP(S) proxy by adding the environment to `**ENVIRONMENTS**`:
+```sh
+-e JAVA_TOOL_OPTIONS="-Dhttp.proxyHost=**HTTP_PROXY_HOST** -Dhttp.proxyPort=**HTTP_PROXY_PORT** -Dhttp.nonProxyHosts=**HTTP_NON_PROXY_HOSTS** -Dhttps.proxyHost=**HTTPS_PROXY_HOST** -Dhttps.proxyPort=**HTTPS_PROXY_PORT** -Dhttps.nonProxyHosts=**HTTPS_NON_PROXY_HOSTS**"
+```
+
 #### PKCS12 Certificate
 ```sh
 --odm.redcap.api.key.file.path=**ODM_REDCAP_API_KEY_FILE_PATH**
@@ -71,6 +79,9 @@ By default, all subjects within an ODM are processed. To process only subjects w
 --odm.dis.rest.password=**ODM_DIS_REST_PASSWORD**
 ```
 
+#### HTTP(S) Proxy
+(see [here](#https-proxy))
+
 #### PKCS12 Certificate
 ```sh
 --odm.dis.rest.key.file.path=**ODM_DIS_REST_KEY_FILE_PATH**
@@ -91,6 +102,9 @@ By default, all subjects within an ODM are processed. To process only subjects w
 --fhir.server.url=**FHIR_SERVER_URL**
 ```
 
+#### HTTP(S) Proxy
+(see [here](#https-proxy))
+
 #### BasicAuth
 ```sh
 --fhir.server.basicauth.username=**FHIR_SERVER_BASICAUTH_USERNAME**
@@ -120,6 +134,9 @@ Enable the use of an external terminology server by adding the argument(s) below
 --fhir.terminologyserver.url=**FHIR_TERMINOLOGYSERVER_URL**
 ```
 
+#### HTTP(S) Proxy
+(see [here](#https-proxy))
+
 #### BasicAuth
 ```sh
 --fhir.terminologyserver.basicauth.username=**FHIR_TERMINOLOGYSERVER_BASICAUTH_USERNAME**

diff --git a/pom.xml b/pom.xml
@@ -8,15 +8,15 @@
 
   <groupId>de.difuture.uds</groupId>
   <artifactId>odm2fhir</artifactId>
-  <version>0.7.1</version>
+  <version>0.7.2</version>
 
   <name>ODM2FHIR</name>
   <description>Mapper for GECCO based study/patient data in CDISC ODM to HL7 FHIR</description>
 
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>2.5.6</version>
+    <version>2.6.0</version>
   </parent>
 
   <properties>
@@ -25,7 +25,7 @@
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 
-    <hapi-fhir.version>5.5.3</hapi-fhir.version>
+    <hapi-fhir.version>5.6.0</hapi-fhir.version>
     <jackson.version>2.13.0</jackson.version>
     <lombok.version>1.18.22</lombok.version>
     <spring-boot.version>${project.parent.version}</spring-boot.version>
@@ -74,6 +74,11 @@
       <artifactId>jackson-dataformat-xml</artifactId>
       <version>${jackson.version}</version>
     </dependency>
+    <dependency>
+      <groupId>com.fasterxml.jackson.dataformat</groupId>
+      <artifactId>jackson-dataformat-csv</artifactId>
+      <version>${jackson.version}</version>
+    </dependency>
     <dependency>
       <groupId>com.fasterxml.woodstox</groupId>
       <artifactId>woodstox-core</artifactId>
@@ -111,6 +116,9 @@
           <image>
             <name>${GITHUB_CONTAINER_REGISTRY_URL}/${project.artifactId}:${project.version}</name>
             <publish>true</publish>
+            <tags>
+              <tag>${GITHUB_CONTAINER_REGISTRY_URL}/${project.artifactId}:latest</tag>
+            </tags>
             <env>
               <BPE_DELIM_JAVA_TOOL_OPTIONS xml:space="preserve"> </BPE_DELIM_JAVA_TOOL_OPTIONS>
               <BPE_PREPEND_JAVA_TOOL_OPTIONS>-XX:MaxDirectMemorySize=265m</BPE_PREPEND_JAVA_TOOL_OPTIONS>

diff --git a/src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/StudyEvent.java b/src/main/java/de/difuture/uds/odm2fhir/fhir/mapper/StudyEvent.java
@@ -91,7 +91,8 @@ public Stream<DomainResource> map(Subject subject, StudyEventData studyEventData
 
     var encounter = new Encounter();
 
-    if (containsAny(studyEventData.getStudyEventOID(), "GECCOVISIT", "fall")) {
+    if (ENVIRONMENT.getProperty("fhir.encounters.enabled", Boolean.class, true) &&
+        containsAny(studyEventData.getStudyEventOID(), "GECCOVISIT", "fall")) {
       var value = format("%s-%s.%s",
                          studyEventData.getSubjectData().getSubjectKey(),
                          studyEventData.getStudyEventOID(), studyEventData.getStudyEventRepeatKey());

diff --git a/src/main/java/de/difuture/uds/odm2fhir/util/HTTPHelper.java b/src/main/java/de/difuture/uds/odm2fhir/util/HTTPHelper.java
@@ -63,6 +63,9 @@ public void setHttpClient(Environment environment) throws Exception {
         }));
 
     HTTP_CLIENT = HttpClientBuilder.create()
+                                   .useSystemProperties()
+                                   .setMaxConnTotal(100)
+                                   .setMaxConnPerRoute(100)
                                    .setSSLContext(sslContextBuilder.build())
                                    .setSSLHostnameVerifier(new NoopHostnameVerifier())
                                    .build();
@@ -74,12 +77,11 @@ public static IClientInterceptor createAuthInterceptor(String basicauthUsername,
     IClientInterceptor clientInterceptor = new BasicAuthInterceptor(basicauthUsername, basicauthPassword);
 
     if (isNoneBlank(oauth2TokenURL, oauth2ClientId, oauth2ClientSecret)) {
-      var httpPost = RequestBuilder
-          .post(oauth2TokenURL)
-          .addParameter("grant_type", "client_credentials")
-          .addParameter("client_id", oauth2ClientId)
-          .addParameter("client_secret", oauth2ClientSecret)
-          .build();
+      var httpPost = RequestBuilder.post(oauth2TokenURL)
+                                   .addParameter("grant_type", "client_credentials")
+                                   .addParameter("client_id", oauth2ClientId)
+                                   .addParameter("client_secret", oauth2ClientSecret)
+                                   .build();
 
       var content = HTTP_CLIENT.execute(httpPost).getEntity().getContent();
 

diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
@@ -8,13 +8,20 @@ odm:
 #    url: http://redcap/api/
 #    token: 12345ABCDE67890ABCDE12345ABCDEF0
 #    patientspercall: 1
+#    key:
+#      file.path: /some/path/client_certificate.p12
+#      password: change-password
 #  dis.rest:
 #    url: http://dis/m4export/resteasy/export
 #    studyname: COVID_GECCO
 #    username: gecco
 #    password: gecco
+#    key:
+#      file.path: /some/path/client_certificate.p12
+#      password: change-password
 
 fhir:
+#  encounters.enabled: true
 #  updateascreate.enabled: true
 #  validation:
 #    enabled: true
@@ -31,6 +38,9 @@ fhir:
 #      client:
 #        id: fhir
 #        secret: 1234567890
+#    key:
+#      file.path: /some/path/client_certificate.p12
+#      password: change-password
 #  terminologyserver:
 #    url: https://fhir-server:9443/fhir-server/api/v4/
 #    basicauth:
@@ -41,6 +51,9 @@ fhir:
 #      client:
 #        id: fhir
 #        secret: 1234567890
+#    key:
+#      file.path: /some/path/client_certificate.p12
+#      password: change-password
 #  identifier:
 #    assigner: Mein Krankenhaus
 #    system: