RED-6009: Document Tree Structure

* fixed build
* slight refactor of AnnotationService

bamboo-specs/src/main/resources/scripts/build-java.sh

@@ -54,7 +54,7 @@ mvn -f ${bamboo_build_working_directory}/$SERVICE_NAME-v1/pom.xml \
     -Dmaven.wagon.http.ssl.insecure=true \
     -Dmaven.wagon.http.ssl.allowall=true \
     -Dmaven.wagon.http.ssl.ignore.validity.dates=true \
-    -DaltDeploymentRepository=iqser_release::default::https://nexus.iqser.com/repository/red-platform-releases
+    -DaltDeploymentRepository=knecon_release::default::https://nexus.knecon.com/repository/red-platform-releases
 
 mvn --no-transfer-progress \
     -f ${bamboo_build_working_directory}/$SERVICE_NAME-image-v1/pom.xml \

bamboo-specs/src/main/resources/scripts/sonar-java.sh

@@ -22,7 +22,7 @@ then
         -f ${bamboo_build_working_directory}/$SERVICE_NAME-v1/pom.xml \
         sonar:sonar \
         -Dsonar.projectKey=RED_$SERVICE_NAME \
-        -Dsonar.host.url=https://sonarqube.iqser.com \
+        -Dsonar.host.url=https://sonarqube.knecon.com \
         -Dsonar.login=${bamboo_sonarqube_api_token_secret} \
         -Dsonar.branch.name=${bamboo_planRepository_1_branch} \
         -Dsonar.dependencyCheck.jsonReportPath=target/dependency-check-report.json \
@@ -34,7 +34,7 @@ else
         -f ${bamboo_build_working_directory}/$SERVICE_NAME-v1/pom.xml \
         sonar:sonar \
         -Dsonar.projectKey=RED_$SERVICE_NAME \
-        -Dsonar.host.url=https://sonarqube.iqser.com \
+        -Dsonar.host.url=https://sonarqube.knecon.com \
         -Dsonar.login=${bamboo_sonarqube_api_token_secret} \
         -Dsonar.pullrequest.key=${bamboo_repository_pr_key} \
         -Dsonar.pullrequest.branch=${bamboo_repository_pr_sourceBranch} \

redaction-service-image-v1/pom.xml

@@ -3,9 +3,9 @@
          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <parent>
-        <groupId>com.iqser.red</groupId>
+        <groupId>com.knecon.fforesight</groupId>
         <artifactId>platform-docker-dependency</artifactId>
-        <version>1.2.0</version>
+        <version>0.1.0</version>
         <relativePath/>
     </parent>
     <modelVersion>4.0.0</modelVersion>

redaction-service-v1/pom.xml

@@ -54,10 +54,12 @@
                 <plugin>
                     <groupId>org.sonarsource.scanner.maven</groupId>
                     <artifactId>sonar-maven-plugin</artifactId>
+                    <version>3.9.0.2155</version>
                 </plugin>
                 <plugin>
                     <groupId>org.owasp</groupId>
                     <artifactId>dependency-check-maven</artifactId>
+                    <version>6.3.1</version>
                     <configuration>
                         <format>ALL</format>
                     </configuration>
@@ -65,12 +67,6 @@
                 <plugin>
                     <groupId>org.jacoco</groupId>
                     <artifactId>jacoco-maven-plugin</artifactId>
-                    <version>0.8.8</version>
-                    <configuration>
-                        <excludes>
-                            <exclude>org/drools/**/*</exclude>
-                        </excludes>
-                    </configuration>
                     <executions>
                         <execution>
                             <id>prepare-agent</id>
@@ -88,5 +84,27 @@
                 </plugin>
             </plugins>
         </pluginManagement>
+        <plugins>
+            <plugin>
+                <groupId>org.jacoco</groupId>
+                <artifactId>jacoco-maven-plugin</artifactId>
+                <version>0.8.8</version>
+                <executions>
+                    <execution>
+                        <id>prepare-agent</id>
+                        <goals>
+                            <goal>prepare-agent</goal>
+                        </goals>
+                    </execution>
+                    <execution>
+                        <id>report</id>
+                        <goals>
+                            <goal>report-aggregate</goal>
+                        </goals>
+                        <phase>verify</phase>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
     </build>
 </project>

redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/RedactionIntegrationTest.java

@@ -689,13 +689,6 @@ public class RedactionIntegrationTest extends AbstractRedactionIntegrationTest {
         analyzeService.analyzeDocumentStructure(new StructureAnalyzeRequest(request.getDossierId(), request.getFileId()));
         AnalyzeResult result = analyzeService.analyze(request);
 
-        String annotatedFileName = Paths.get(filePath).getFileName().toString().replace(".pdf", "_annotated.pdf");
-        File tmpFile = Paths.get(OsUtils.getTemporaryDirectory(), annotatedFileName).toFile();
-        AnnotateResponse annotateResponse = annotationService.annotate(AnnotateRequest.builder().dossierId(TEST_DOSSIER_ID).fileId(TEST_FILE_ID).build());
-        try (FileOutputStream fileOutputStream = new FileOutputStream(tmpFile)) {
-            fileOutputStream.write(annotateResponse.getDocument());
-        }
-
         RedactionLog redactionLog = redactionStorageService.getRedactionLog(TEST_DOSSIER_ID, TEST_FILE_ID);
         assertTrue(redactionLog.getRedactionLogEntry().stream().anyMatch(entry -> entry.getValue().equals("Desiree et al")));
         assertTrue(redactionLog.getRedactionLogEntry().stream().anyMatch(entry -> entry.getValue().equals("Melanie et al.")));
@@ -724,9 +717,9 @@ public class RedactionIntegrationTest extends AbstractRedactionIntegrationTest {
         AnalyzeResult reanalyzeResult = analyzeService.reanalyze(request);
 
         redactionLog = redactionStorageService.getRedactionLog(TEST_DOSSIER_ID, TEST_FILE_ID);
-        annotatedFileName = Paths.get(filePath).getFileName().toString().replace(".pdf", "_annotated2.pdf");
+        String annotatedFileName = Paths.get(filePath).getFileName().toString().replace(".pdf", "_annotated2.pdf");
-        tmpFile = Paths.get(OsUtils.getTemporaryDirectory(), annotatedFileName).toFile();
+        File tmpFile = Paths.get(OsUtils.getTemporaryDirectory(), annotatedFileName).toFile();
-        annotateResponse = annotationService.annotate(AnnotateRequest.builder().dossierId(TEST_DOSSIER_ID).fileId(TEST_FILE_ID).build());
+        AnnotateResponse annotateResponse = annotationService.annotate(AnnotateRequest.builder().dossierId(TEST_DOSSIER_ID).fileId(TEST_FILE_ID).build());
         try (FileOutputStream fileOutputStream = new FileOutputStream(tmpFile)) {
             fileOutputStream.write(annotateResponse.getDocument());
         }

redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/annotate/AnnotationService.java

@@ -71,14 +71,14 @@ public class AnnotationService {
                 annotateRequest.getFileId(),
                 FileType.ORIGIN));
 
-        var mergedRedactionLog = redactionStorageService.getRedactionLog(annotateRequest.getDossierId(), annotateRequest.getFileId());
+        var redactionLog = redactionStorageService.getRedactionLog(annotateRequest.getDossierId(), annotateRequest.getFileId());
         var sectionsGrid = redactionStorageService.getSectionGrid(annotateRequest.getDossierId(), annotateRequest.getFileId());
 
         try (PDDocument pdDocument = PDDocument.load(storedObjectStream, MemoryUsageSetting.setupTempFileOnly())) {
             pdDocument.setAllSecurityToBeRemoved(true);
 
             dictionaryService.updateDictionary(annotateRequest.getDossierTemplateId(), annotateRequest.getDossierId());
-            annotate(pdDocument, mergedRedactionLog, sectionsGrid);
+            annotate(pdDocument, redactionLog, sectionsGrid);
 
             try (ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream()) {
                 pdDocument.save(byteArrayOutputStream);
@@ -117,6 +117,9 @@ public class AnnotationService {
         List<PDAnnotation> annotations = pdPage.getAnnotations();
 
         for (RedactionLogEntry entry : logEntries) {
+            if (entry.lastChangeIsRemoved()) {
+                continue;
+            }
             annotations.addAll(createAnnotation(entry, page, pdPage.getRotation(), pdPage.getCropBox()));
         }
     }