test publish stuff

Update .gitlab-ci.yml
disable test
2024-03-04 09:55:52 +02:00 · 2024-03-01 14:13:31 +01:00 · 2024-03-01 14:56:14 +02:00 · 2024-03-01 14:51:59 +02:00 · 2024-03-01 12:11:53 +02:00 · 2024-03-01 12:05:11 +02:00
17 changed files with 1763 additions and 45 deletions
@@ -21,3 +21,16 @@ deploy:
    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
    - if: $CI_COMMIT_BRANCH =~ /^release/
    - if: $CI_COMMIT_TAG
+
+pages:
+  stage: build
+  tags:
+    - dind
+  script:
+    - echo "Generating Javadoc..."
+    - gradle generateJavaDoc -PjavadocDestinationDir="javadoc"
+    - mkdir public
+    - mv redaction-service-v1/redaction-service-server-v1/javadoc/* public/
+  artifacts:
+    paths:
+      - public
@@ -12,7 +12,7 @@ plugins {
 description = "redaction-service-server-v1"


-val layoutParserVersion = "0.93.0"
+val layoutParserVersion = "0.94.0"
 val jacksonVersion = "2.15.2"
 val droolsVersion = "9.44.0.Final"
 val pdfBoxVersion = "3.0.0"
@@ -84,9 +84,6 @@ tasks.test {
    maxHeapSize = "1024m"
 }

-
-
-
 tasks.named<BootBuildImage>("bootBuildImage") {

    environment.put("BPE_DELIM_JAVA_TOOL_OPTIONS", " ")
@@ -113,3 +110,40 @@ tasks.named<BootBuildImage>("bootBuildImage") {
        tags.set(listOf(dockerTag))
    }
 }
+
+fun parseDroolsImports(droolsFilePath: String): List<String> {
+    val imports = mutableListOf<String>()
+    val importPattern = Regex("^import\\s+(com\\.iqser\\.red\\.service\\.redaction\\.v1\\.[\\w.]+);")
+    val desiredPrefix = "com.iqser.red.service.redaction.v1"
+
+    File(droolsFilePath).forEachLine { line ->
+        importPattern.find(line)?.let { matchResult ->
+            val importPath = matchResult.groupValues[1].trim()
+            if (importPath.startsWith(desiredPrefix)) {
+                val formattedPath = importPath.replace('.', '/')
+                imports.add("$formattedPath.java")
+            }
+        }
+    }
+
+    return imports
+}
+
+val droolsImports = parseDroolsImports("redaction-service-v1/redaction-service-server-v1/src/main/resources/drools/all_rules_documine.drl")
+
+tasks.register("generateJavaDoc", Javadoc::class) {
+    dependsOn("compileJava")
+    dependsOn("delombok")
+    classpath = project.sourceSets["main"].runtimeClasspath
+    source = fileTree("${buildDir}/generated/sources/delombok/java/main") {
+        include(droolsImports)
+    }
+    destinationDir = file(project.findProperty("javadocDestinationDir")?.toString() ?: "")
+
+    options.memberLevel = JavadocMemberLevel.PUBLIC
+    (options as StandardJavadocDocletOptions).apply {
+        header = "Redaction Service ${project.version}"
+        footer = "Redaction Service ${project.version}"
+        title = "API Documentation for Redaction Service ${project.version}"
+    }
+}
@@ -135,10 +135,14 @@ public class Image implements GenericSemanticNode, IEntity {

        Map<Page, Rectangle2D> bboxImage = image.getBBox();
        Map<Page, Rectangle2D> bbox = this.getBBox();
-        Rectangle2D intersection = bboxImage.get(this.page).createIntersection(bbox.get(this.page));
-        double calculatedIntersection = intersection.getWidth() * intersection.getHeight();
-        double area = bbox.get(this.page).getWidth() * bbox.get(this.page).getHeight();
-        return (calculatedIntersection / area) > containmentThreshold;
+        //image needs to be on the same page
+        if(bboxImage.get(this.page) != null) {
+            Rectangle2D intersection = bboxImage.get(this.page).createIntersection(bbox.get(this.page));
+            double calculatedIntersection = intersection.getWidth() * intersection.getHeight();
+            double area = bbox.get(this.page).getWidth() * bbox.get(this.page).getHeight();
+            return (calculatedIntersection / area) > containmentThreshold;
+        }
+        return false;
    }


@@ -146,7 +150,7 @@ public class Image implements GenericSemanticNode, IEntity {

        Map<Page, Rectangle2D> bboxImage = image.getBBox();
        Map<Page, Rectangle2D> bbox = this.getBBox();
-        Rectangle2D intersection = bboxImage.get(this.page).createIntersection(bbox.get(this.page));
+        Rectangle2D intersection = bbox.get(this.page).createIntersection(bboxImage.get(this.page));
        double calculatedIntersection = intersection.getWidth() * intersection.getHeight();
        double area = bbox.get(this.page).getWidth() * bbox.get(this.page).getHeight();
        return (area / calculatedIntersection) > containmentThreshold;
@@ -26,10 +26,9 @@ import lombok.extern.slf4j.Slf4j;
@Slf4j
@Service
@RequiredArgsConstructor
-@FieldDefaults(makeFinal=true, level= AccessLevel.PRIVATE)
+@FieldDefaults(makeFinal = true, level = AccessLevel.PRIVATE)
 public class EntityChangeLogService {

-
    @Timed("redactmanager_computeChanges")
    public boolean computeChanges(List<EntityLogEntry> previousEntityLogEntries, List<EntityLogEntry> newEntityLogEntries, ManualRedactions manualRedactions, int analysisNumber) {

@@ -42,7 +41,9 @@ public class EntityChangeLogService {
        boolean hasChanges = false;

        for (EntityLogEntry entityLogEntry : newEntityLogEntries) {
-            Optional<EntityLogEntry> optionalPreviousEntity = previousEntityLogEntries.stream().filter(entry -> entry.getId().equals(entityLogEntry.getId())).findAny();
+            Optional<EntityLogEntry> optionalPreviousEntity = previousEntityLogEntries.stream()
+                    .filter(entry -> entry.getId().equals(entityLogEntry.getId()))
+                    .findAny();
            if (optionalPreviousEntity.isEmpty()) {
                hasChanges = true;
                entityLogEntry.getChanges().add(new Change(analysisNumber, ChangeType.ADDED, now));
@@ -63,15 +64,22 @@ public class EntityChangeLogService {


    private void addRemovedEntriesAsRemoved(List<EntityLogEntry> previousEntityLogEntries,
-                                                   List<EntityLogEntry> newEntityLogEntries,
-                                                   ManualRedactions manualRedactions,
-                                                   int analysisNumber,
-                                                   OffsetDateTime now) {
+                                            List<EntityLogEntry> newEntityLogEntries,
+                                            ManualRedactions manualRedactions,
+                                            int analysisNumber,
+                                            OffsetDateTime now) {

-        Set<String> existingIds = newEntityLogEntries.stream().map(EntityLogEntry::getId).collect(Collectors.toSet());
+        Set<String> existingIds = newEntityLogEntries.stream()
+                .map(EntityLogEntry::getId)
+                .collect(Collectors.toSet());
        List<EntityLogEntry> removedEntries = previousEntityLogEntries.stream()
                .filter(entry -> !existingIds.contains(entry.getId()))
+                .collect(Collectors.toList());
+        List<EntityLogEntry> removedDossierRedaction = removedEntries.stream()
+                .filter(e -> e.getState() == EntryState.REMOVED && e.getType().equals("dossier_redaction"))
                .toList();
+        previousEntityLogEntries.removeAll(removedDossierRedaction);
+        removedEntries.removeAll(removedDossierRedaction);
        removedEntries.forEach(entry -> entry.getChanges().add(new Change(analysisNumber, ChangeType.REMOVED, now)));
        removedEntries.forEach(entry -> entry.setState(EntryState.REMOVED));
        removedEntries.forEach(entry -> addManualChangeForDictionaryRemovals(entry, manualRedactions));
@@ -85,13 +93,15 @@ public class EntityChangeLogService {
            return;
        }

-        manualRedactions.getIdsToRemove().stream()
+        manualRedactions.getIdsToRemove()
+                .stream()
                .filter(IdRemoval::isRemoveFromDictionary)//
                .filter(removed -> removed.getAnnotationId().equals(entry.getId()))//
                .findFirst()//
                .ifPresent(idRemove -> entry.getManualChanges().add(ManualChangeFactory.toManualChange(idRemove, false)));
    }

+
    private ChangeType calculateChangeType(EntryState state, EntryState previousState) {

        if (state.equals(previousState)) {
@@ -125,7 +125,7 @@ public class EntityLogCreatorService {
                .stream()
                .filter(entry -> (newEntityIds.contains(entry.getId()) || entry.getContainingNodeId().isEmpty() || sectionsToReanalyseIds.contains(entry.getContainingNodeId()
                                                                                                                                                           .get(0))))
-                .toList();
+                .collect(Collectors.toList());
        previousEntityLog.getEntityLogEntry().removeAll(previousEntriesFromReAnalyzedSections);

        boolean hasChanges = entityChangeLogService.computeChanges(previousEntriesFromReAnalyzedSections,
@@ -692,13 +692,22 @@ rule "ETC.3.1: Redact logos (vertebrate study)"


 // Rule unit: ETC.5
-rule "ETC.5.0: Ignore dossier_redaction entries if confidentiality is not 'confidential'"
+rule "ETC.5.0: Skip dossier_redaction entries if confidentiality is 'confidential'"
+    when
+        FileAttribute(label == "Confidentiality", value == "confidential")
+        $dossierRedaction: TextEntity(type() == "dossier_redaction")
+    then
+        $dossierRedaction.skip("ETC.5.0", "Ignore dossier_redaction when confidential");
+        $dossierRedaction.getIntersectingNodes().forEach(node -> update(node));
+    end
+
+rule "ETC.5.1: Remove dossier_redaction entries if confidentiality is not 'confidential'"
    when
        not FileAttribute(label == "Confidentiality", value == "confidential")
        $dossierRedaction: TextEntity(type() == "dossier_redaction")
    then
-        $dossierRedaction.ignore("ETC.5.0", "Ignore dossier redactions, when not confidential");
-        $dossierRedaction.getIntersectingNodes().forEach(node -> update(node));
+        $dossierRedaction.remove("ETC.5.1", "Remove dossier_redaction when not confidential");
+        retract($dossierRedaction);
    end


@@ -848,7 +857,7 @@ rule "MAN.3.2: Apply image recategorization"
 rule "MAN.3.3: Apply recategorization entities by default"
    salience 128
    when
-        $entity: IEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
+        $entity: TextEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
    then
        $entity.apply("MAN.3.3", "Recategorized entities are applied by default.", $entity.legalBasis());
    end
@@ -1150,13 +1150,22 @@ rule "ETC.4.2: Redact dossier dictionary entries"


 // Rule unit: ETC.5
-rule "ETC.5.0: Ignore dossier_redaction entries if confidentiality is not 'confidential'"
+rule "ETC.5.0: Skip dossier_redaction entries if confidentiality is 'confidential'"
+    when
+        FileAttribute(label == "Confidentiality", value == "confidential")
+        $dossierRedaction: TextEntity(type() == "dossier_redaction")
+    then
+        $dossierRedaction.skip("ETC.5.0", "Ignore dossier_redaction when confidential");
+        $dossierRedaction.getIntersectingNodes().forEach(node -> update(node));
+    end
+
+rule "ETC.5.1: Remove dossier_redaction entries if confidentiality is not 'confidential'"
    when
        not FileAttribute(label == "Confidentiality", value == "confidential")
        $dossierRedaction: TextEntity(type() == "dossier_redaction")
    then
-        $dossierRedaction.ignore("ETC.5.0", "Ignore dossier redactions, when not confidential");
-        $dossierRedaction.getIntersectingNodes().forEach(node -> update(node));
+        $dossierRedaction.remove("ETC.5.1", "Remove dossier_redaction when not confidential");
+        retract($dossierRedaction);
    end


@@ -1411,7 +1420,7 @@ rule "MAN.3.2: Apply image recategorization"
 rule "MAN.3.3: Apply recategorization entities by default"
    salience 128
    when
-        $entity: IEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
+        $entity: TextEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
    then
        $entity.apply("MAN.3.3", "Recategorized entities are applied by default.", $entity.legalBasis());
    end
@@ -1278,7 +1278,7 @@ rule "MAN.3.2: Apply image recategorization"
 rule "MAN.3.3: Apply recategorization entities by default"
    salience 128
    when
-        $entity: IEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
+        $entity: TextEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
    then
        $entity.apply("MAN.3.3", "Recategorized entities are applied by default.", $entity.legalBasis());
    end
@@ -190,7 +190,7 @@ rule "MAN.3.2: Apply image recategorization"
 rule "MAN.3.3: Apply recategorization entities by default"
    salience 128
    when
-        $entity: IEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
+        $entity: TextEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
    then
        $entity.apply("MAN.3.3", "Recategorized entities are applied by default.", $entity.legalBasis());
    end
@@ -802,13 +802,22 @@ rule "ETC.4.0: Redact dossier dictionary entries"


 // Rule unit: ETC.5
-rule "ETC.5.0: Ignore dossier_redaction entries if confidentiality is not 'confidential'"
+rule "ETC.5.0: Skip dossier_redaction entries if confidentiality is 'confidential'"
+    when
+        FileAttribute(label == "Confidentiality", value == "confidential")
+        $dossierRedaction: TextEntity(type() == "dossier_redaction")
+    then
+        $dossierRedaction.skip("ETC.5.0", "Ignore dossier_redaction when confidential");
+        $dossierRedaction.getIntersectingNodes().forEach(node -> update(node));
+    end
+
+rule "ETC.5.1: Remove dossier_redaction entries if confidentiality is not 'confidential'"
    when
        not FileAttribute(label == "Confidentiality", value == "confidential")
        $dossierRedaction: TextEntity(type() == "dossier_redaction")
    then
-        $dossierRedaction.ignore("ETC.5.0", "Ignore dossier redactions, when not confidential");
-        $dossierRedaction.getIntersectingNodes().forEach(node -> update(node));
+        $dossierRedaction.remove("ETC.5.1", "Remove dossier_redaction when not confidential");
+        retract($dossierRedaction);
    end


@@ -1001,7 +1010,7 @@ rule "MAN.3.2: Apply image recategorization"
 rule "MAN.3.3: Apply recategorization entities by default"
    salience 128
    when
-        $entity: IEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
+        $entity: TextEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
    then
        $entity.apply("MAN.3.3", "Recategorized entities are applied by default.", $entity.legalBasis());
    end
@@ -214,7 +214,7 @@ rule "MAN.3.1: Apply entity recategorization of same type"
 rule "MAN.3.3: Apply recategorization entities by default"
    salience 128
    when
-        $entity: IEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
+        $entity: TextEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
    then
        $entity.apply("MAN.3.3", "Recategorized entities are applied by default.", $entity.legalBasis());
    end
@@ -340,7 +340,7 @@ rule "MAN.3.2: Apply image recategorization"
 rule "MAN.3.3: Apply recategorization entities by default"
    salience 128
    when
-        $entity: IEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
+        $entity: TextEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
    then
        $entity.apply("MAN.3.3", "Recategorized entities are applied by default.", $entity.legalBasis());
    end
@@ -240,7 +240,7 @@ rule "MAN.3.2: Apply image recategorization"
 rule "MAN.3.3: Apply recategorization entities by default"
    salience 128
    when
-        $entity: IEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
+        $entity: TextEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
    then
        $entity.apply("MAN.3.3", "Recategorized entities are applied by default.", $entity.legalBasis());
    end
@@ -449,14 +449,22 @@ rule "ETC.3.1: Redact logos (non vertebrate study)"


 // Rule unit: ETC.5
-rule "ETC.5.0: Ignore dossier_redaction entries if confidentiality is not 'confidential'"
+rule "ETC.5.0: Skip dossier_redaction entries if confidentiality is 'confidential'"
+    when
+        FileAttribute(label == "Confidentiality", value == "confidential")
+        $dossierRedaction: TextEntity(type() == "dossier_redaction")
+    then
+        $dossierRedaction.skip("ETC.5.0", "Ignore dossier_redaction when confidential");
+        $dossierRedaction.getIntersectingNodes().forEach(node -> update(node));
+    end
+
+rule "ETC.5.1: Remove dossier_redaction entries if confidentiality is not 'confidential'"
    when
        not FileAttribute(label == "Confidentiality", value == "confidential")
        $dossierRedaction: TextEntity(type() == "dossier_redaction")
    then
-        $dossierRedaction.ignore("ETC.5.0", "Ignore dossier redactions, when not confidential");
-        update($dossierRedaction);
-        $dossierRedaction.getIntersectingNodes().forEach(node -> update(node));
+        $dossierRedaction.remove("ETC.5.1", "Remove dossier_redaction when not confidential");
+        retract($dossierRedaction);
    end


@@ -1159,13 +1159,22 @@ rule "ETC.4.2: Redact dossier dictionary entries"


 // Rule unit: ETC.5
-rule "ETC.5.0: Ignore dossier_redaction entries if confidentiality is not 'confidential'"
+rule "ETC.5.0: Skip dossier_redaction entries if confidentiality is 'confidential'"
+    when
+        FileAttribute(label == "Confidentiality", value == "confidential")
+        $dossierRedaction: TextEntity(type() == "dossier_redaction")
+    then
+        $dossierRedaction.skip("ETC.5.0", "Ignore dossier_redaction when confidential");
+        $dossierRedaction.getIntersectingNodes().forEach(node -> update(node));
+    end
+
+rule "ETC.5.1: Remove dossier_redaction entries if confidentiality is not 'confidential'"
    when
        not FileAttribute(label == "Confidentiality", value == "confidential")
        $dossierRedaction: TextEntity(type() == "dossier_redaction")
    then
-        $dossierRedaction.ignore("ETC.5.0", "Ignore dossier redactions, when not confidential");
-        $dossierRedaction.getIntersectingNodes().forEach(node -> update(node));
+        $dossierRedaction.remove("ETC.5.1", "Remove dossier_redaction when not confidential");
+        retract($dossierRedaction);
    end


@@ -1434,7 +1443,7 @@ rule "MAN.3.2: Apply image recategorization"
 rule "MAN.3.3: Apply recategorization entities by default"
    salience 128
    when
-        $entity: IEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
+        $entity: TextEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
    then
        $entity.apply("MAN.3.3", "Recategorized entities are applied by default.", $entity.legalBasis());
    end
@@ -1424,7 +1424,7 @@ rule "MAN.3.2: Apply image recategorization"
 rule "MAN.3.3: Apply recategorization entities by default"
    salience 128
    when
-        $entity: IEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
+        $entity: TextEntity(getManualOverwrite().getRecategorized().orElse(false), !dictionary.isHint(type()))
    then
        $entity.apply("MAN.3.3", "Recategorized entities are applied by default.", $entity.legalBasis());
    end
Author	SHA1	Message	Date
Andrei Isvoran	97291ffcae	test publish stuff	2024-03-04 09:55:52 +02:00
Kevin Tumma	9a9867e739	Update .gitlab-ci.yml	2024-03-01 14:13:31 +01:00
Andrei Isvoran	aa20a5c201	disable test	2024-03-01 14:56:14 +02:00
Andrei Isvoran	600394c366	change gitlab-ci	2024-03-01 14:51:59 +02:00
Andrei Isvoran	8fd9855b2c	add public to it	2024-03-01 12:11:53 +02:00
Andrei Isvoran	2a8f1ecdd2	add public to it	2024-03-01 12:05:11 +02:00
Andrei Isvoran	6202e95ad8	change to pages	2024-03-01 11:59:26 +02:00
Andrei Isvoran	b1fee50718	change to pages	2024-03-01 11:53:27 +02:00
Andrei Isvoran	3a59bff246	add publish keyword	2024-03-01 11:49:19 +02:00
Andrei Isvoran	57683d49b6	fix path	2024-03-01 11:48:06 +02:00
Andrei Isvoran	0fd01fa1c3	add dependsOn(delombok)	2024-03-01 11:44:37 +02:00
Andrei Isvoran	6d66e5dac3	add sleep	2024-03-01 11:24:59 +02:00
Andrei Isvoran	446c3e56a8	draft	2024-03-01 11:23:45 +02:00
Andrei Isvoran	daab1f1b0a	draft	2024-03-01 10:10:24 +02:00
Andrei Isvoran	af70705250	draft	2024-03-01 10:06:55 +02:00
Andrei Isvoran	f29f8626e9	draft	2024-03-01 09:59:31 +02:00
Andrei Isvoran	940e6e7b42	draft	2024-03-01 09:52:13 +02:00
Andrei Isvoran	c08ad75893	draft	2024-03-01 09:49:55 +02:00
Andrei Isvoran	b8d9b101c9	draft	2024-03-01 09:47:28 +02:00
Andrei Isvoran	a1ea354225	draft	2024-03-01 09:39:53 +02:00
Andrei Isvoran	e9f516580e	draft	2024-02-29 17:48:02 +02:00
Andrei Isvoran	b006b8c1ab	draft	2024-02-29 17:36:31 +02:00
Andrei Isvoran	78912adeb6	draft	2024-02-29 17:33:23 +02:00
Andrei Isvoran	9bbff158c0	draft	2024-02-29 17:28:33 +02:00
Andrei Isvoran	6e0b343de3	draft	2024-02-29 17:21:39 +02:00
Andrei Isvoran	5bc9b60623	draft	2024-02-29 17:16:09 +02:00
Andrei Isvoran	e8b32681ce	draft	2024-02-29 16:40:59 +02:00
Andrei Isvoran	d29b6bf816	draft	2024-02-29 16:39:09 +02:00
Corina Olariu	b6ad1b5e91	Merge branch 'RED-8590' into 'master' RED-8590 - Missing reason for added CBI Address, recategorized LOGO and signature Closes RED-8590 See merge request redactmanager/redaction-service!293	2024-02-29 13:17:56 +01:00
Corina Olariu	5f961b0f99	RED-8590 - Missing reason for added CBI Address, recategorized LOGO and signature	2024-02-29 13:17:56 +01:00
Andrei Isvoran	89dea4138a	Merge branch 'RED-8586' into 'master' RED-8586 - Fix confidentiality rules Closes RED-8586 See merge request redactmanager/redaction-service!294	2024-02-29 12:58:23 +01:00
Andrei Isvoran	4fb8b10429	RED-8586 - Fix confidentiality rules	2024-02-29 12:58:23 +01:00
Yannik Hampe	f09a4e4d42	Merge branch 'RED-8481-rules' into 'master' RED-8481: use visual layout parser for signature extraction Closes RED-8481 See merge request redactmanager/redaction-service!296	2024-02-29 09:19:41 +01:00
Yannik Hampe	ab5dc2f46b	RED-8481: use visual layout parser for signature extraction	2024-02-29 09:19:41 +01:00