Merge pull request #171 from samply/release-7.6.2

Release 7.6.2
samply · Apr 11, 2022 · 64e7b7a · 64e7b7a
2 parents d851780 + b34ac87
commit 64e7b7a
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,16 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/).
 
+## [7.6.2 - 2022-04-11]
+### Added
+- Use log4j implementation of slf4j-api (exclude all slf4j-simple dependencies)
+- Solving the problem with the nNGM POST request
+- Adaptations to the new MS-nNGM profiles
+- Removal of the composition profiles
+- Test HttpConnector Http Clients (Jersey 3 und Apache)
+- Allow false value configuration for bypass proxy for private networks property
+
+
 ## [7.6.1 - 2022-02-28]
 ### Fixed
 - Add Jersey 1 libraries for JSF 2

diff --git a/pom.xml b/pom.xml
@@ -11,7 +11,7 @@
   </parent>
 
   <artifactId>share-client</artifactId>
-  <version>7.6.1</version>
+  <version>7.6.2</version>
   <packaging>war</packaging>
 
   <name>Connector</name>
@@ -58,12 +58,12 @@
   <properties>
 
     <!-- Samply dependencies -->
-    <common-config.version>5.1.0</common-config.version>
+    <common-config.version>5.2.0</common-config.version>
     <share-common.version>4.4.0</share-common.version>
     <share-dto.version>5.2.0</share-dto.version>
     <jsf-renderer.version>2.0.0</jsf-renderer.version>
     <common-mailing.version>3.0.0</common-mailing.version>
-    <common-http.version>7.4.2</common-http.version>
+    <common-http.version>7.4.4</common-http.version>
     <common-ldmclient.centraxx.version>6.2.0</common-ldmclient.centraxx.version>
     <common-ldmclient.samplystore.biobank.version>3.0.0
     </common-ldmclient.samplystore.biobank.version>
@@ -97,30 +97,30 @@
     <datatables.version>1.11.3</datatables.version>
     <twbs-pagination.version>1.4.1</twbs-pagination.version>
     <jqplot.version>1.0.9.d96a669-1</jqplot.version>
-    <hapi.version>5.6.2</hapi.version>
+    <hapi.version>5.7.2</hapi.version>
     <directory-sync.version>0.1.0</directory-sync.version>
     <togglz.version>2.8.0</togglz.version>
     <swagger-ui.version>4.1.3</swagger-ui.version>
     <microprofile-openapi-api.version>3.0</microprofile-openapi-api.version>
-    <postgresql.version>42.3.2</postgresql.version>
+    <postgresql.version>42.3.3</postgresql.version>
     <commons-validator.version>1.7</commons-validator.version>
     <jsf.version>2.2.20</jsf.version>
     <javax.servlet-api.version>4.0.1</javax.servlet-api.version>
     <tink.version>1.6.1</tink.version>
     <jaxb2-maven-plugin.version>2.5.0</jaxb2-maven-plugin.version>
-    <json-path.version>2.6.0</json-path.version>
+    <json-path.version>2.7.0</json-path.version>
     <primefaces.version>11.0.0</primefaces.version>
     <junit-jupiter.version>5.8.2</junit-jupiter.version>
     <mockito-core.version>4.2.0</mockito-core.version>
-    <jackson-dataformat-xml.version>2.13.1</jackson-dataformat-xml.version>
+    <jackson-dataformat-xml.version>2.13.2</jackson-dataformat-xml.version>
 
     <sonar.organization>samply</sonar.organization>
     <sonar.host.url>https://sonarcloud.io</sonar.host.url>
     <commons-io.version>2.11.0</commons-io.version>
-    <log4j.version>2.17.1</log4j.version>
+    <log4j.version>2.17.2</log4j.version>
     <slf4j.version>1.7.36</slf4j.version>
 
-    <protobuf-java.version>3.19.3</protobuf-java.version>
+    <protobuf-java.version>3.19.4</protobuf-java.version>
 
     <maven-resources-plugin.version>3.2.0</maven-resources-plugin.version>
 
@@ -154,13 +154,33 @@
           <groupId>com.fasterxml.jackson.core</groupId>
           <artifactId>jackson-annotations</artifactId>
         </exclusion>
+        <exclusion>
+          <groupId>org.slf4j</groupId>
+          <artifactId>slf4j-api</artifactId>
+        </exclusion>
+        <exclusion>
+          <groupId>org.slf4j</groupId>
+          <artifactId>slf4j-simple</artifactId>
+        </exclusion>
       </exclusions>
     </dependency>
     <dependency>
       <groupId>com.fasterxml.jackson.dataformat</groupId>
       <artifactId>jackson-dataformat-xml</artifactId>
       <version>${jackson-dataformat-xml.version}</version>
+      <exclusions>
+        <exclusion>
+          <groupId>com.fasterxml.jackson.core</groupId>
+          <artifactId>jackson-databind</artifactId>
+        </exclusion>
+      </exclusions>
     </dependency>
+    <dependency>
+      <groupId>com.fasterxml.jackson.core</groupId>
+      <artifactId>jackson-databind</artifactId>
+      <version>2.13.2.2</version>
+    </dependency>
+
     <dependency>
       <groupId>de.samply</groupId>
       <artifactId>common-http</artifactId>
@@ -175,6 +195,10 @@
           <groupId>junit</groupId>
           <artifactId>junit</artifactId>
         </exclusion>
+        <exclusion>
+          <groupId>org.slf4j</groupId>
+          <artifactId>slf4j-simple</artifactId>
+        </exclusion>
       </exclusions>
     </dependency>
     <dependency>
@@ -202,6 +226,10 @@
           <groupId>junit</groupId>
           <artifactId>junit</artifactId>
         </exclusion>
+        <exclusion>
+          <groupId>org.slf4j</groupId>
+          <artifactId>slf4j-simple</artifactId>
+        </exclusion>
       </exclusions>
     </dependency>
     <dependency>
@@ -213,6 +241,10 @@
           <groupId>junit</groupId>
           <artifactId>junit</artifactId>
         </exclusion>
+        <exclusion>
+          <groupId>org.slf4j</groupId>
+          <artifactId>slf4j-simple</artifactId>
+        </exclusion>
       </exclusions>
     </dependency>
     <dependency>
@@ -244,6 +276,12 @@
       <groupId>de.samply</groupId>
       <artifactId>directory-sync</artifactId>
       <version>${directory-sync.version}</version>
+      <exclusions>
+        <exclusion>
+          <groupId>org.slf4j</groupId>
+          <artifactId>slf4j-simple</artifactId>
+        </exclusion>
+      </exclusions>
     </dependency>
 
     <!-- JSF 2 -->
@@ -289,6 +327,11 @@
       <artifactId>log4j-slf4j-impl</artifactId>
       <version>${log4j.version}</version>
     </dependency>
+    <dependency>
+      <groupId>org.slf4j</groupId>
+      <artifactId>slf4j-api</artifactId>
+      <version>${slf4j.version}</version>
+    </dependency>
 
     <!-- Third party libraries -->
     <dependency>
@@ -468,6 +511,12 @@
       <groupId>ca.uhn.hapi.fhir</groupId>
       <artifactId>hapi-fhir-base</artifactId>
       <version>${hapi.version}</version>
+      <exclusions>
+        <exclusion>
+          <groupId>org.slf4j</groupId>
+          <artifactId>jcl-over-slf4j</artifactId>
+        </exclusion>
+      </exclusions>
     </dependency>
     <dependency>
       <groupId>de.samply</groupId>

diff --git a/src/main/java/de/samply/share/client/fhir/FhirUtil.java b/src/main/java/de/samply/share/client/fhir/FhirUtil.java
@@ -39,9 +39,8 @@ public Bundle parseBundleResource(String bundleString, MediaType mediaType)
         return (Bundle) ctx.newXmlParser().parseResource(bundleString);
       }
     } catch (ConfigurationException | DataFormatException e) {
-      logger.error(e.getMessage(),e);
-      throw new FhirParseException("Error while parsing a " + mediaType.getSubtype() + " bundle.",
-          e);
+      throw new FhirParseException("Error while parsing a "
+              + mediaType.getSubtype() + " bundle: " + e.getMessage(), e);
     }
   }
 
@@ -56,7 +55,6 @@ public String encodeResourceToJson(Resource resource) throws FhirEncodeException
     try {
       return ctx.newJsonParser().encodeResourceToString(resource);
     } catch (DataFormatException e) {
-      logger.error(e.getMessage(),e);
       throw new FhirEncodeException("Error while encoding a bundle to json.", e);
     }
   }

diff --git a/src/main/java/de/samply/share/client/util/connector/CtsConnector.java b/src/main/java/de/samply/share/client/util/connector/CtsConnector.java
@@ -38,20 +38,10 @@
 import org.apache.http.HttpEntity;
 import org.apache.http.HttpHeaders;
 import org.apache.http.HttpHost;
-import org.apache.http.NameValuePair;
-import org.apache.http.StatusLine;
-import org.apache.http.client.CookieStore;
-import org.apache.http.client.entity.UrlEncodedFormEntity;
 import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpPost;
-import org.apache.http.client.protocol.HttpClientContext;
-import org.apache.http.cookie.Cookie;
 import org.apache.http.entity.StringEntity;
-import org.apache.http.impl.client.BasicCookieStore;
 import org.apache.http.impl.client.CloseableHttpClient;
-import org.apache.http.message.BasicNameValuePair;
-import org.apache.http.protocol.BasicHttpContext;
-import org.apache.http.protocol.HttpContext;
 import org.apache.http.util.EntityUtils;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Bundle;
@@ -60,13 +50,14 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+
 /**
  * A connector that handles all communication with the EDC system.
  */
 public class CtsConnector {
 
   private static final Logger logger = LoggerFactory.getLogger(CtsConnector.class);
-  private static final String CONTENT_TYPE_CTS_FHIR_JSON = "application/fhir+json; fhirVersion=4.0";
+  private static final String CONTENT_TYPE_CTS_FHIR_JSON = "application/fhir+json";
   private static final String X_BK_PSEUDONYM_JSONPATHS = "X-BK-pseudonym-jsonpaths";
   private static final String X_BK_TARGET_URL = "X-BK-target-url";
 
@@ -128,10 +119,11 @@ public Response postPseudonmToCts(String bundleString, MediaType mediaType)
     HttpEntity entity = new StringEntity(pseudonymBundleAsString, Consts.UTF_8);
     HttpPost httpPost = new HttpPost(ctsBaseUrl);
     httpPost.setHeader(HttpHeaders.CONTENT_TYPE, CONTENT_TYPE_CTS_FHIR_JSON);
-    httpPost.setHeader("X-API-KEY", apiKey);
+    httpPost.setHeader(HttpHeaders.AUTHORIZATION, apiKey);
     httpPost.setEntity(entity);
     CloseableHttpResponse response = null;
     try {
+      response = httpClient.execute(httpPost);
       int statusCode = response.getStatusLine().getStatusCode();
       String message =
           "CTS server response: statusCode:" + statusCode + "; response: " + response.toString();
@@ -141,7 +133,7 @@ public Response postPseudonmToCts(String bundleString, MediaType mediaType)
       }
       return Response.status(statusCode).entity(message).build();
     } catch (IOException e) {
-      logger.error(e.getMessage(),e);
+      logger.error(e.getMessage(), e);
       throw new IOException(e);
     } finally {
       closeResponse(response);
@@ -167,7 +159,7 @@ public Response postLocalPatientToCentralCts(String patient)
     HttpEntity entity = new StringEntity(pseudonimisedPatient.toString(), Consts.UTF_8);
     HttpPost httpPost = new HttpPost(ctsBaseUrl);
     httpPost.setHeader(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON);
-    httpPost.setHeader("X-API-KEY", apiKey);
+    httpPost.setHeader(HttpHeaders.AUTHORIZATION, apiKey);
     httpPost.setEntity(entity);
     CloseableHttpResponse response = null;
     try {
@@ -181,7 +173,7 @@ public Response postLocalPatientToCentralCts(String patient)
       }
       return Response.status(statusCode).entity(message).build();
     } catch (IOException e) {
-      logger.error(e.getMessage(),e);
+      logger.error(e.getMessage(), e);
       throw new IOException(e);
     } finally {
       closeResponse(response);
@@ -220,7 +212,7 @@ public Response postLocalPatientToCentralCts(String patient,
     // Set up the API call
     HttpPost httpPost = new HttpPost(urlTarget);
     httpPost.setHeader(HttpHeaders.CONTENT_TYPE, MediaType.APPLICATION_JSON);
-    httpPost.setHeader("X-API-KEY", apiKey);
+    httpPost.setHeader(HttpHeaders.AUTHORIZATION, apiKey);
     for (Entry<String, Object> entry : headerMapToSend.entrySet()) {
       httpPost.setHeader(entry.getKey(), entry.getValue().toString());
     }
@@ -247,10 +239,10 @@ public Response postLocalPatientToCentralCts(String patient,
       logger.error("PostLocalPatientToCentralCts response: " + message);
       return Response.status(statusCode).entity(message).build();
     } catch (IOException e) {
-      logger.error(e.getMessage(),e);
+      logger.error(e.getMessage(), e);
       throw new IOException(e);
     } catch (StringIndexOutOfBoundsException | PathNotFoundException e) {
-      logger.error(e.getMessage(),e);
+      logger.error(e.getMessage(), e);
       throw new CtsConnectorException(e.getMessage());
     } finally {
       closeResponse(response);
@@ -350,7 +342,7 @@ private String replaceIdsWithEncryptedIds(String patientJson, List<String> ids,
    * @param bundle  the patient bundle
    * @param encrypt if the ids should encrypted or decrypted
    * @return the encrypted/decrypted bundle
-   * @throws GeneralSecurityException GeneralSecurityException
+   * @throws CtsConnectorException CtsConnectorException
    */
   private String cryptIds(Bundle bundle, boolean encrypt) throws CtsConnectorException {
     Crypt crypt = ApplicationBean.getCrypt();