Merge pull request #47 from IBM/issue-46

Update build for OpenJDK 11 #46
LinuxForHealth · Sep 12, 2019 · 6a4401f · 6a4401f
2 parents 1e0552e + d3c2011
commit 6a4401f
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Showing 11 changed files with 43 additions and 18 deletions.
diff --git a/build/pre-integration-test.sh b/build/pre-integration-test.sh
@@ -72,7 +72,7 @@ tries=0
 status=0
 while [ $status -ne 200 -a $tries -lt ${MAX_TRIES} ]; do
     tries=$((tries + 1))
-    cmd="curl -k -o ${WORKSPACE}/metadata.json -I -w "%{http_code}" -u fhiruser:fhiruser $metadata_url"
+    cmd="curl -k -o ${WORKSPACE}/metadata.json -I -w "%{http_code}" -u fhiruser:change-password $metadata_url"
     echo "Executing[$tries]: $cmd"
     status=$($cmd)
     echo "Status code: $status"

diff --git a/fhir-client/pom.xml b/fhir-client/pom.xml
@@ -55,5 +55,9 @@
             <artifactId>jsonassert</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>jakarta.xml.bind</groupId>
+            <artifactId>jakarta.xml.bind-api</artifactId>
+        </dependency>
     </dependencies>
 </project>
diff --git a/fhir-examples/pom.xml b/fhir-examples/pom.xml
@@ -3,26 +3,29 @@
     xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <artifactId>fhir-examples</artifactId>
+    <groupId>com.ibm.watson.health</groupId>
+    <version>4.0.0-SNAPSHOT</version>
 
-    <parent>
-        <groupId>com.ibm.watson.health</groupId>
-        <artifactId>fhir-parent</artifactId>
-        <version>4.0.0-SNAPSHOT</version>
-        <relativePath>../fhir-parent</relativePath>
-    </parent>
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <maven.compiler.source>1.8</maven.compiler.source>
+        <maven.compiler.target>1.8</maven.compiler.target>
+    </properties>
 
     <build>
         <plugins>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-checkstyle-plugin</artifactId>
+                <version>4.0.0-SNAPSHOT</version>
                 <configuration>
                     <skip>true</skip>
                 </configuration>
             </plugin>
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>xml-maven-plugin</artifactId>
+                <version>1.0.2</version>
                 <configuration>
                     <skip>true</skip>
                 </configuration>

diff --git a/fhir-install/src/main/resources/scripts/fhirSmokeTest.sh b/fhir-install/src/main/resources/scripts/fhirSmokeTest.sh
@@ -22,14 +22,14 @@ echo -n "Checking if server $SERVER_HOST is accessible on port $SERVER_PORT ...
 echo "OK!"
 
 TMP_DIR=$(mktemp -d)
-curl -k -u fhiruser:fhiruser https://$SERVER_HOST:$SERVER_PORT/fhir-server/api/v4/metadata > $TMP_DIR/meta.json 2> /dev/null
+curl -k -u fhiruser:change-password https://$SERVER_HOST:$SERVER_PORT/fhir-server/api/v4/metadata > $TMP_DIR/meta.json 2> /dev/null
 
 echo -n "Checking FHIR server signature... "
-[ $(cat $TMP_DIR/meta.json | grep '"description" : "IBM Watson Health FHIR Server version ' | wc -l) != "1" ] && echo "Error! Signature not found." && exit 4
+[ $(cat $TMP_DIR/meta.json | grep '"description":"IBM Watson Health FHIR Server version ' | wc -l) != "1" ] && echo "Error! Signature not found." && exit 4
 echo "OK!"
 
 echo -n "Checking FHIR API version... "
-[ $(cat $TMP_DIR/meta.json | grep '"fhirVersion" : "4.0.0 - R4"' | wc -l) != "1" ] && echo "Error! Wrong FHIR version or version absent." && exit 5
+[ $(cat $TMP_DIR/meta.json | grep '"fhirVersion":"4.0.0"' | wc -l) != "1" ] && echo "Error! Wrong FHIR version or version absent." && exit 5
 echo "OK!"
 
 echo

diff --git a/fhir-model/pom.xml b/fhir-model/pom.xml
@@ -50,6 +50,10 @@
             <version>${project.version}</version>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>jakarta.annotation</groupId>
+            <artifactId>jakarta.annotation-api</artifactId>
+        </dependency>
     </dependencies>
 
     <build>

diff --git a/...tion/src/main/java/com/ibm/watson/health/fhir/notification/util/FHIRNotificationUtil.java b/...tion/src/main/java/com/ibm/watson/health/fhir/notification/util/FHIRNotificationUtil.java
@@ -12,7 +12,6 @@
 import javax.json.JsonObject;
 import javax.json.JsonObjectBuilder;
 import javax.json.JsonReader;
-import javax.xml.bind.JAXBException;
 
 import com.ibm.watson.health.fhir.exception.FHIRException;
 import com.ibm.watson.health.fhir.model.util.FHIRUtil;
@@ -37,10 +36,9 @@ public static FHIRNotificationEvent toNotificationEvent(String jsonString) {
      * @param includeResource a flag that controls whether or not the resource object within
      * the event structure should be included in the serialized message.
      * @return the serialized message as a String
-     * @throws JAXBException
      * @throws FHIRException 
      */
-    public static String toJsonString(FHIRNotificationEvent event, boolean includeResource) throws JAXBException, FHIRException {
+    public static String toJsonString(FHIRNotificationEvent event, boolean includeResource) throws FHIRException {
         JsonObjectBuilder builder = Json.createObjectBuilder();
         builder.add("lastUpdated", event.getLastUpdated());
         builder.add("location", event.getLocation());

diff --git a/...on/src/main/java/com/ibm/watson/health/fhir/operation/registry/FHIROperationRegistry.java b/...on/src/main/java/com/ibm/watson/health/fhir/operation/registry/FHIROperationRegistry.java
@@ -17,8 +17,6 @@
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
-import javax.xml.bind.JAXBException;
-
 import com.ibm.watson.health.fhir.exception.FHIROperationException;
 import com.ibm.watson.health.fhir.model.resource.OperationOutcome.Issue;
 import com.ibm.watson.health.fhir.model.type.IssueSeverity;
@@ -49,7 +47,7 @@ private FHIROperationRegistry() {
                     continue;
                 }
                 operationMap.put(operation.getName(), operation);
-            } catch (ServiceConfigurationError | FHIRValidationException | JAXBException e) {
+            } catch (ServiceConfigurationError | FHIRValidationException e) {
                 log.log(Level.SEVERE, "Unable to validate operation $" + operationName + ". This operation will be skipped.", e);
             }
         }
@@ -60,7 +58,7 @@ private FHIROperationRegistry() {
         }
     }
 
-    private boolean isValid(FHIROperation operation) throws FHIRValidationException, JAXBException, FHIRValidationException {
+    private boolean isValid(FHIROperation operation) throws FHIRValidationException, FHIRValidationException {
         List<Issue> issues = FHIRValidator.validator(operation.getDefinition()).validate();
         if (!issues.isEmpty()) {
             for (Issue issue : issues) {

diff --git a/fhir-parent/pom.xml b/fhir-parent/pom.xml
@@ -259,6 +259,16 @@
                 <artifactId>jackson-annotations</artifactId>
                 <version>2.9.9</version>
             </dependency>
+            <dependency>
+                <groupId>jakarta.annotation</groupId>
+                <artifactId>jakarta.annotation-api</artifactId>
+                <version>1.3.5</version>
+            </dependency>
+            <dependency>
+                <groupId>jakarta.xml.bind</groupId>
+                <artifactId>jakarta.xml.bind-api</artifactId>
+                <version>2.3.2</version>
+            </dependency>
         </dependencies>
     </dependencyManagement>
 

diff --git a/fhir-persistence-jdbc/pom.xml b/fhir-persistence-jdbc/pom.xml
@@ -101,6 +101,10 @@
             <artifactId>jsonassert</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>jakarta.xml.bind</groupId>
+            <artifactId>jakarta.xml.bind-api</artifactId>
+        </dependency>
     </dependencies>
 
 </project>
diff --git a/fhir-swagger-generator/pom.xml b/fhir-swagger-generator/pom.xml
@@ -26,6 +26,10 @@
             <artifactId>fhir-search</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>jakarta.xml.bind</groupId>
+            <artifactId>jakarta.xml.bind-api</artifactId>
+        </dependency>
     </dependencies>
 
     <build>

diff --git a/fhir-tools/pom.xml b/fhir-tools/pom.xml
@@ -11,7 +11,7 @@
     <packaging>maven-plugin</packaging>
 
     <properties>
-        <surefire.plugin.version>2.20.1</surefire.plugin.version>
+        <surefire.plugin.version>3.0.0-M3</surefire.plugin.version>
         <!-- needed for generating jacoco aggregate report in fhir-coverage-reports -->
         <maven.surefire.report.plugin>${surefire.plugin.version}</maven.surefire.report.plugin>
         <jacoco.plugin.version>0.8.2</jacoco.plugin.version>