Added some logs

RED-2224: Fixed missing values in engines
Pull request #250 : RED-2223: Fixed adding annotations to rotated words on non rotated pages
2021-10-19 14:38:03 +02:00 · 2021-10-19 10:55:51 +02:00 · 2021-10-15 15:35:28 +02:00 · 2021-10-15 15:27:15 +02:00 · 2021-10-15 10:45:10 +02:00 · 2021-10-15 10:36:01 +02:00
27 changed files with 147 additions and 115 deletions
@@ -5,7 +5,7 @@
    <parent>
        <groupId>com.iqser.red</groupId>
        <artifactId>platform-docker-dependency</artifactId>
-        <version>1.0.0</version>
+        <version>1.1.0</version>
    </parent>
    <modelVersion>4.0.0</modelVersion>

@@ -13,6 +13,6 @@ RUN apt-get update \
    wget cabextract xfonts-utils fonts-liberation \
 && rm -rf /var/lib/apt/lists/*

-RUN curl http://ftp.br.debian.org/debian/pool/contrib/m/msttcorefonts/ttf-mscorefonts-installer_3.8_all.deb -o /tmp/ttf-mscorefonts-installer_3.8_all.deb \
+RUN curl http://ftp.debian.org/debian/pool/contrib/m/msttcorefonts/ttf-mscorefonts-installer_3.8_all.deb -o /tmp/ttf-mscorefonts-installer_3.8_all.deb \
 && dpkg -i /tmp/ttf-mscorefonts-installer_3.8_all.deb \
 && rm /tmp/ttf-mscorefonts-installer_3.8_all.deb \
@@ -5,7 +5,7 @@
    <parent>
        <artifactId>platform-dependency</artifactId>
        <groupId>com.iqser.red</groupId>
-        <version>1.1.3</version>
+        <version>1.1.5</version>
    </parent>
    <modelVersion>4.0.0</modelVersion>

@@ -22,7 +22,7 @@
    </modules>

    <properties>
-        <pdfbox.version>2.0.21</pdfbox.version>
+        <pdfbox.version>2.0.24</pdfbox.version>
    </properties>


@@ -32,7 +32,7 @@
            <dependency>
                <groupId>com.iqser.red</groupId>
                <artifactId>platform-commons-dependency</artifactId>
-                <version>1.3.6</version>
+                <version>1.7.0</version>
                <scope>import</scope>
                <type>pom</type>
            </dependency>
@@ -20,7 +20,7 @@
        <dependency>
            <groupId>com.iqser.red.service</groupId>
            <artifactId>persistence-service-api-v1</artifactId>
-            <version>0.16.0</version>
+            <version>0.44.0</version>
        </dependency>
    </dependencies>
 </project>
@@ -22,7 +22,7 @@ import java.util.Set;
 public class RedactionLogEntry {

    private String id;
-    private String typeId;
+    private String type;
    private String value;
    private String reason;
    private int matchedRule;
@@ -24,12 +24,12 @@
        <dependency>
            <groupId>org.drools</groupId>
            <artifactId>drools-core</artifactId>
-            <version>7.37.0.Final</version>
+            <version>7.59.0.Final</version>
        </dependency>
        <dependency>
            <groupId>org.kie</groupId>
            <artifactId>kie-spring</artifactId>
-            <version>7.37.0.Final</version>
+            <version>7.59.0.Final</version>
        </dependency>
        <dependency>
            <groupId>org.locationtech.jts</groupId>
@@ -39,7 +39,6 @@
        <dependency>
            <groupId>com.google.guava</groupId>
            <artifactId>guava</artifactId>
-            <version>29.0-jre</version>
        </dependency>

        <dependency>
@@ -72,10 +71,6 @@
            <artifactId>metric-commons</artifactId>
        </dependency>
        <!-- other external -->
-        <dependency>
-            <groupId>org.apache.commons</groupId>
-            <artifactId>commons-lang3</artifactId>
-        </dependency>
        <dependency>
            <groupId>org.apache.pdfbox</groupId>
            <artifactId>pdfbox</artifactId>
@@ -93,7 +88,6 @@
        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot-starter-amqp</artifactId>
-            <version>2.3.1.RELEASE</version>
        </dependency>

        <!-- test dependencies -->
@@ -107,12 +101,6 @@
            <artifactId>test-commons</artifactId>
            <scope>test</scope>
        </dependency>
-        <dependency>
-            <groupId>org.springframework.amqp</groupId>
-            <artifactId>spring-rabbit-test</artifactId>
-            <version>2.3.1</version>
-            <scope>test</scope>
-        </dependency>
    </dependencies>

    <build>
@@ -1,5 +1,6 @@
 package com.iqser.red.service.redaction.v1.server.controller;

+import com.amazonaws.services.kms.model.NotFoundException;
 import com.iqser.red.service.persistence.service.v1.api.model.dossiertemplate.dossier.file.FileType;
 import com.iqser.red.service.redaction.v1.model.*;
 import com.iqser.red.service.redaction.v1.resources.RedactionResource;
@@ -152,6 +153,10 @@ public class RedactionController implements RedactionResource {

        var redactionLog = redactionStorageService.getRedactionLog(redactionRequest.getDossierId(), redactionRequest.getFileId());

+        if (redactionLog == null) {
+            throw new NotFoundException("RedactionLog not present");
+        }
+
        log.info("Loaded redaction log with computationalVersion: {}", redactionLog.getAnalysisVersion());
        if (redactionLog.getAnalysisVersion() == 0) {
            // old redaction logs are returned directly
@@ -21,6 +21,7 @@ public class RedTextPosition {
    private float YDirAdj;
    private float width;
    private float heightDir;
+    private float widthDirAdj;

    // not used in reanalysis
    @JsonIgnore
@@ -1,5 +1,7 @@
 package com.iqser.red.service.redaction.v1.server.parsing.model;

+import static java.util.stream.Collectors.toSet;
+
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.iqser.red.service.redaction.v1.model.Point;
@@ -244,7 +246,15 @@ public class TextPositionSequence implements CharSequence {
            posXInit = textPositions.get(0).getPageWidth() - textPositions.get(0).getYDirAdj() - 2;
            posXEnd = textPositions.get(0).getPageWidth() - textPositions.get(textPositions.size() - 1)
                    .getYDirAdj() + height;
-        } else {
+        } else if(textPositions.get(0).getRotation() == 0 && textPositions.stream().map(t -> t.getY()).collect(toSet()).size() > 1) {
+            posYInit = textPositions.get(0).getPageHeight() - getX1();
+            posYEnd = textPositions.get(0).getPageHeight() - getX2() - textPositions.get(0)
+                    .getWidthDirAdj() - textPositions.get(textPositions.size() - 1).getWidthDirAdj() - 3;
+            posXInit = textPositions.get(0).getPageWidth() - textPositions.get(0).getYDirAdj() - 2;
+            posXEnd = textPositions.get(0).getPageWidth() - textPositions.get(textPositions.size() - 1)
+                    .getYDirAdj() + height;
+        }
+        else {
            posXEnd = textPositions.get(textPositions.size() - 1)
                    .getXDirAdj() + textPositions.get(textPositions.size() - 1).getWidth() + 1;
            posYInit = textPositions.get(0).getPageHeight() - textPositions.get(0).getYDirAdj() - 2;
@@ -35,12 +35,11 @@ public class RedactionMessageReceiver {
    public void receiveAnalyzeRequest(String in) throws JsonProcessingException {

        var analyzeRequest = objectMapper.readValue(in, AnalyzeRequest.class);
-        log.info("Processing analyze request: {}", analyzeRequest);
+        log.info("Processing analyze request for file: {}", analyzeRequest.getFileId());
        AnalyzeResult result;
        if (analyzeRequest.isReanalyseOnlyIfPossible()) {
            result = analyzeService.reanalyze(analyzeRequest);
-            log.info("Successfully reanalyzed dossier {} file {} took: {}", analyzeRequest.getDossierId(), analyzeRequest
-                    .getFileId(), result.getDuration());
+            log.info("Successfully reanalyzed dossier {} file {} took: {}", analyzeRequest.getDossierId(), analyzeRequest.getFileId(), result.getDuration());
        } else {
            // TODO Seperate stucture analysis by other queue
            analyzeService.analyzeDocumentStructure(new StructureAnalyzeRequest(analyzeRequest.getDossierId(), analyzeRequest.getFileId()));
@@ -65,13 +65,13 @@ public class Dictionary {
    public boolean containsValue(String type, String value) {

        return localAccessMap.containsKey(type) && localAccessMap.get(type)
-                .getEntries().stream().map(DictionaryEntry::getValue).collect(toSet())
+                .getValues(false)
                .contains(value) || localAccessMap.containsKey(type) && localAccessMap.get(type)
-                .getLocalEntries()
+                .getValues(true)
                .contains(value) || localAccessMap.containsKey(RECOMMENDATION_PREFIX + type) && localAccessMap.get(RECOMMENDATION_PREFIX + type)
-                .getEntries().stream().map(DictionaryEntry::getValue).collect(toSet())
+                .getValues(false)
                .contains(value) || localAccessMap.containsKey(RECOMMENDATION_PREFIX + type) && localAccessMap.get(RECOMMENDATION_PREFIX + type)
-                .getLocalEntries()
+                .getValues(true)
                .contains(value);
    }

@@ -109,7 +109,7 @@ public class AnalyzeService {
        dictionaryService.updateExternalDictionary(dictionary, analyzeRequest.getDossierTemplateId(), analyzeRequest.getDossierId());

        List<RedactionLogEntry> redactionLogEntries = redactionLogCreatorService.createRedactionLog(pageEntities, text.getNumberOfPages(), analyzeRequest
-                .getDossierTemplateId(), analyzeRequest.getDossierId());
+                .getDossierTemplateId());

        var legalBasis = legalBasisClient.getLegalBasisMapping(analyzeRequest.getDossierTemplateId());
        var redactionLog = new RedactionLog(redactionServiceSettings.getAnalysisVersion(), redactionLogEntries, legalBasis, dictionary
@@ -162,7 +162,7 @@ public class AnalyzeService {

        PageEntities pageEntities = entityRedactionService.findEntities(dictionary, reanalysisSections, kieContainer, analyzeRequest, nerEntities);
        var newRedactionLogEntries = redactionLogCreatorService.createRedactionLog(pageEntities, text.getNumberOfPages(), analyzeRequest
-                .getDossierTemplateId(), analyzeRequest.getDossierId());
+                .getDossierTemplateId());

        redactionLog.getRedactionLogEntry().removeIf(entry -> sectionsToReanalyse.contains(entry.getSectionNumber()));
        redactionLog.getRedactionLogEntry().addAll(newRedactionLogEntries);
@@ -254,7 +254,7 @@ public class AnalyzeService {
        Rectangle position = entry.getPositions().get(0);

        return Image.builder()
-                .type(entry.getTypeId().split(":")[0])
+                .type(entry.getType())
                .position(new RedRectangle2D(position.getTopLeft().getX(), position.getTopLeft()
                        .getY(), position.getWidth(), position.getHeight()))
                .sectionNumber(entry.getSectionNumber())
@@ -84,7 +84,7 @@ public class DictionaryService {
            DictionaryRepresentation dictionaryRepresentation = new DictionaryRepresentation();

            var typeResponse = dossierId == null ? dictionaryClient.getAllTypesForDossierTemplate(dossierTemplateId) : dictionaryClient.getAllTypesForDossier(dossierId);
-            if (typeResponse != null && CollectionUtils.isNotEmpty(typeResponse)) {
+            if (CollectionUtils.isNotEmpty(typeResponse)) {

                List<DictionaryModel> dictionary = typeResponse
                        .stream()
@@ -209,10 +209,10 @@ public class EntityRedactionService {
        for (DictionaryModel model : dictionary.getDictionaryModels()) {
            if (model.isCaseInsensitive()) {
                EntitySearchUtils.addOrAddEngine(found, EntitySearchUtils.find(lowercaseInputString, model.getValues(local), model
-                        .getType(), headline, sectionNumber, !local, model.isDossierDictionary(), Engine.DICTIONARY));
+                        .getType(), headline, sectionNumber, !local, model.isDossierDictionary(), local ? Engine.RULE : Engine.DICTIONARY));
            } else {
                EntitySearchUtils.addOrAddEngine(found, EntitySearchUtils.find(searchableString, model.getValues(local), model
-                        .getType(), headline, sectionNumber, !local, model.isDossierDictionary(), Engine.DICTIONARY));
+                        .getType(), headline, sectionNumber, !local, model.isDossierDictionary(), local ? Engine.RULE : Engine.DICTIONARY));
            }
        }

@@ -1,19 +1,17 @@
 package com.iqser.red.service.redaction.v1.server.redaction.service;

-import java.util.stream.Collectors;
-
 import com.iqser.red.service.persistence.service.v1.api.model.dossiertemplate.dossier.file.FileType;
-import org.apache.commons.codec.binary.Base64;
-import org.springframework.stereotype.Service;
-
 import com.iqser.red.service.redaction.v1.server.client.EntityRecognitionClient;
 import com.iqser.red.service.redaction.v1.server.client.model.EntityRecognitionRequest;
 import com.iqser.red.service.redaction.v1.server.client.model.EntityRecognitionSection;
 import com.iqser.red.service.redaction.v1.server.settings.RedactionServiceSettings;
 import com.iqser.red.service.redaction.v1.server.storage.RedactionStorageService;
-
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
+import org.apache.commons.codec.binary.Base64;
+import org.springframework.stereotype.Service;
+
+import java.util.stream.Collectors;

@Slf4j
@Service
@@ -31,20 +29,24 @@ public class NerAnalyserService {

            long start = System.currentTimeMillis();

-            var nerRequest = EntityRecognitionRequest.builder()
-                    .data(text.getSectionTexts()
-                            .stream()
-                            .map(sectionText -> new EntityRecognitionSection(sectionText.getSectionNumber(), new String(Base64
-                                    .encodeBase64(sectionText
-                                    .getText().getBytes()))))
-                            .collect(Collectors.toList()))
-                    .build();
+            if (text != null) {
+                var nerRequest = EntityRecognitionRequest.builder()
+                        .data(text.getSectionTexts()
+                                .stream()
+                                .map(sectionText -> new EntityRecognitionSection(sectionText.getSectionNumber(), new String(Base64
+                                        .encodeBase64(sectionText
+                                                .getText().getBytes()))))
+                                .collect(Collectors.toList()))
+                        .build();

-            var nerResponse = entityRecognitionClient.findAuthors(nerRequest);
+                var nerResponse = entityRecognitionClient.findAuthors(nerRequest);

-            log.info("Computing NER entities took: {} ms for dossierId {} and fileId {}", System.currentTimeMillis() - start, dossierId, fileId);
+                log.info("Computing NER entities took: {} ms for dossierId {} and fileId {}", System.currentTimeMillis() - start, dossierId, fileId);

-            redactionStorageService.storeObject(dossierId, fileId, FileType.NER_ENTITIES, nerResponse);
+                redactionStorageService.storeObject(dossierId, fileId, FileType.NER_ENTITIES, nerResponse);
+            } else {
+                log.warn("Warning, text for file: {} in dossier: {} is null", fileId, dossierId);
+            }
        }
    }

@@ -1,15 +1,5 @@
 package com.iqser.red.service.redaction.v1.server.redaction.service;

-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.stream.Collectors;
-
-import org.apache.commons.collections4.CollectionUtils;
-import org.springframework.stereotype.Service;
-
 import com.iqser.red.service.redaction.v1.model.Point;
 import com.iqser.red.service.redaction.v1.model.Rectangle;
 import com.iqser.red.service.redaction.v1.model.RedactionLogEntry;
@@ -20,8 +10,12 @@ import com.iqser.red.service.redaction.v1.server.redaction.model.EntityPositionS
 import com.iqser.red.service.redaction.v1.server.redaction.model.Image;
 import com.iqser.red.service.redaction.v1.server.redaction.model.PageEntities;
 import com.iqser.red.service.redaction.v1.server.redaction.utils.IdBuilder;
-
 import lombok.RequiredArgsConstructor;
+import org.apache.commons.collections4.CollectionUtils;
+import org.springframework.stereotype.Service;
+
+import java.util.*;
+import java.util.stream.Collectors;

@Service
@RequiredArgsConstructor
@@ -30,14 +24,13 @@ public class RedactionLogCreatorService {
    private final DictionaryService dictionaryService;


-    public List<RedactionLogEntry> createRedactionLog(PageEntities pageEntities, int numberOfPages,
-                                                      String dossierTemplateId, String dossierId) {
+    public List<RedactionLogEntry> createRedactionLog(PageEntities pageEntities, int numberOfPages, String dossierTemplateId) {

        List<RedactionLogEntry> entries = new ArrayList<>();

        for (int page = 1; page <= numberOfPages; page++) {
            if (pageEntities.getEntitiesPerPage().get(page) != null) {
-                entries.addAll(addEntries(pageEntities.getEntitiesPerPage(), page, dossierTemplateId, dossierId));
+                entries.addAll(addEntries(pageEntities.getEntitiesPerPage(), page, dossierTemplateId));
            }

            if (pageEntities.getImagesPerPage().get(page) != null) {
@@ -62,7 +55,7 @@ public class RedactionLogCreatorService {
                    .id(id)
                    .color(getColor(image.getType(), dossierTemplateId, image.isRedaction()))
                    .isImage(true)
-                    .typeId(IdBuilder.getTypeId(image.getType(), dossierTemplateId, null))
+                    .type(image.getType())
                    .redacted(image.isRedaction())
                    .reason(image.getRedactionReason())
                    .legalBasis(image.getLegalBasis())
@@ -86,7 +79,7 @@ public class RedactionLogCreatorService {
    }


-    public List<RedactionLogEntry> addEntries(Map<Integer, List<Entity>> entities, int page, String dossierTemplateId, String dossierId) {
+    public List<RedactionLogEntry> addEntries(Map<Integer, List<Entity>> entities, int page, String dossierTemplateId) {

        List<RedactionLogEntry> redactionLogEntities = new ArrayList<>();

@@ -98,7 +91,7 @@ public class RedactionLogCreatorService {

            for (EntityPositionSequence entityPositionSequence : entity.getPositionSequences()) {

-                RedactionLogEntry redactionLogEntry = createRedactionLogEntry(entity, dossierTemplateId, dossierId);
+                RedactionLogEntry redactionLogEntry = createRedactionLogEntry(entity, dossierTemplateId);
                if (processedIds.contains(entityPositionSequence.getId())) {

                    // TODO refactor this outer loop jump as soon as we have the time.
@@ -157,7 +150,7 @@ public class RedactionLogCreatorService {
    }


-    private RedactionLogEntry createRedactionLogEntry(Entity entity, String dossierTemplateId, String dossierId) {
+    private RedactionLogEntry createRedactionLogEntry(Entity entity, String dossierTemplateId) {

        Set<String> referenceIds = new HashSet<>();
        entity.getReferences().forEach(ref -> ref.getPositionSequences().forEach(pos -> referenceIds.add(pos.getId())));
@@ -167,7 +160,7 @@ public class RedactionLogCreatorService {
                .reason(entity.getRedactionReason())
                .legalBasis(entity.getLegalBasis())
                .value(entity.getWord())
-                .typeId(IdBuilder.getTypeId(entity.getType(), dossierTemplateId, entity.isDossierDictionaryEntry() ? dossierId : null))
+                .type(entity.getType())
                .redacted(entity.isRedaction())
                .isHint(isHint(entity.getType(), dossierTemplateId))
                .isRecommendation(isRecommendation(entity.getType(), dossierTemplateId))
@@ -207,5 +200,4 @@ public class RedactionLogCreatorService {
    }


-
 }
@@ -34,7 +34,7 @@ public class RedactionLogMergeService {
    public RedactionLog mergeRedactionLogData(RedactionLog redactionLog, String dossierTemplateId,
                                              ManualRedactions manualRedactions, Set<Integer> excludedPages) {

-        log.info("Merging Redaction log with manual redactions {}", manualRedactions);
+        log.info("Merging Redaction log with manual redactions");
        if (manualRedactions != null) {

            var manualRedactionLogEntries = addManualAddEntries(manualRedactions.getEntriesToAdd(), manualRedactions.getComments(), dossierTemplateId);
@@ -110,12 +110,12 @@ public class RedactionLogMergeService {
                String manualOverrideReason = null;
                if (imageRecategorization.getStatus().equals(AnnotationStatus.APPROVED)) {
                    redactionLogEntry.setStatus(AnnotationStatus.APPROVED);
-                    redactionLogEntry.setTypeId(IdBuilder.getTypeId(imageRecategorization.getType(), dossierTemplateId, null));
+                    redactionLogEntry.setType(imageRecategorization.getType());
                    manualOverrideReason = mergeReasonIfNecessary(redactionLogEntry.getReason(), ", recategorized by manual override");
                } else if (imageRecategorization.getStatus().equals(AnnotationStatus.REQUESTED)) {
                    manualOverrideReason = mergeReasonIfNecessary(redactionLogEntry.getReason(), ", requested to recategorize");
                    redactionLogEntry.setStatus(AnnotationStatus.REQUESTED);
-                    redactionLogEntry.setColor(getColor(getTypeFromTypeId(redactionLogEntry.getTypeId()), dossierTemplateId, false, redactionLogEntry
+                    redactionLogEntry.setColor(getColor(redactionLogEntry.getType(), dossierTemplateId, false, redactionLogEntry
                            .isRedacted(), false));
                    redactionLogEntry.setRecategorizationType(imageRecategorization.getType());
                } else {
@@ -135,12 +135,12 @@ public class RedactionLogMergeService {
                    redactionLogEntry.setRedacted(false);
                    redactionLogEntry.setStatus(AnnotationStatus.APPROVED);
                    manualOverrideReason = mergeReasonIfNecessary(redactionLogEntry.getReason(), ", removed by manual override");
-                    redactionLogEntry.setColor(getColor(getTypeFromTypeId(redactionLogEntry.getTypeId()), dossierTemplateId, false, redactionLogEntry
+                    redactionLogEntry.setColor(getColor(redactionLogEntry.getType(), dossierTemplateId, false, redactionLogEntry
                            .isRedacted(), true));
                } else if (manualRemoval.getStatus().equals(AnnotationStatus.REQUESTED)) {
                    manualOverrideReason = mergeReasonIfNecessary(redactionLogEntry.getReason(), ", requested to remove");
                    redactionLogEntry.setStatus(AnnotationStatus.REQUESTED);
-                    redactionLogEntry.setColor(getColor(getTypeFromTypeId(redactionLogEntry.getTypeId()), dossierTemplateId, true, redactionLogEntry
+                    redactionLogEntry.setColor(getColor(redactionLogEntry.getType(), dossierTemplateId, true, redactionLogEntry
                            .isRedacted(), false));
                } else {
                    redactionLogEntry.setStatus(AnnotationStatus.DECLINED);
@@ -160,14 +160,14 @@ public class RedactionLogMergeService {
                if (manualForceRedact.getStatus().equals(AnnotationStatus.APPROVED)) {
                    redactionLogEntry.setRedacted(true);
                    redactionLogEntry.setStatus(AnnotationStatus.APPROVED);
-                    redactionLogEntry.setColor(getColor(getTypeFromTypeId(redactionLogEntry.getTypeId()), dossierTemplateId, false, redactionLogEntry
+                    redactionLogEntry.setColor(getColor(redactionLogEntry.getType(), dossierTemplateId, false, redactionLogEntry
                            .isRedacted(), false));
                    manualOverrideReason = mergeReasonIfNecessary(redactionLogEntry.getReason(), ", forced by manual override");
                    redactionLogEntry.setLegalBasis(manualForceRedact.getLegalBasis());
                } else if (manualForceRedact.getStatus().equals(AnnotationStatus.REQUESTED)) {
                    manualOverrideReason = mergeReasonIfNecessary(redactionLogEntry.getReason(), ", requested to force redact");
                    redactionLogEntry.setStatus(AnnotationStatus.REQUESTED);
-                    redactionLogEntry.setColor(getColor(getTypeFromTypeId(redactionLogEntry.getTypeId()), dossierTemplateId, true, redactionLogEntry
+                    redactionLogEntry.setColor(getColor(redactionLogEntry.getType(), dossierTemplateId, true, redactionLogEntry
                            .isRedacted(), false));
                    redactionLogEntry.setLegalBasis(manualForceRedact.getLegalBasis());
                } else {
@@ -191,7 +191,7 @@ public class RedactionLogMergeService {
                } else if (manualLegalBasisChange.getStatus().equals(AnnotationStatus.REQUESTED)) {
                    manualOverrideReason = mergeReasonIfNecessary(redactionLogEntry.getReason(), ", legal basis change requested");
                    redactionLogEntry.setStatus(AnnotationStatus.REQUESTED);
-                    redactionLogEntry.setColor(getColor(getTypeFromTypeId(redactionLogEntry.getTypeId()), dossierTemplateId, true, redactionLogEntry
+                    redactionLogEntry.setColor(getColor(redactionLogEntry.getType(), dossierTemplateId, true, redactionLogEntry
                            .isRedacted(), false));
                    redactionLogEntry.setLegalBasisChangeValue(manualLegalBasisChange.getLegalBasis());
                } else {
@@ -258,13 +258,13 @@ public class RedactionLogMergeService {

        return RedactionLogEntry.builder()
                .id(id)
-                .color(getColorForManualAdd(getTypeFromTypeId(manualRedactionEntry.getTypeId()), dossierTemplateId, manualRedactionEntry.getStatus()))
+                .color(getColorForManualAdd(manualRedactionEntry.getType(), dossierTemplateId, manualRedactionEntry.getStatus()))
                .reason(manualRedactionEntry.getReason())
                .isDictionaryEntry(manualRedactionEntry.isAddToDictionary())
                .isDossierDictionaryEntry(manualRedactionEntry.isAddToDossierDictionary())
                .legalBasis(manualRedactionEntry.getLegalBasis())
                .value(manualRedactionEntry.getValue())
-                .typeId(manualRedactionEntry.getTypeId())
+                .type(manualRedactionEntry.getType())
                .redacted(true)
                .isHint(false)
                .section(null)
@@ -324,12 +324,6 @@ public class RedactionLogMergeService {

    }

-    private String getTypeFromTypeId(String typeId){
-        return typeId.split(":")[0];
-    }
-
-
-

 }

@@ -146,11 +146,13 @@ public class EntitySearchUtils {
            }
            var existing = existingOptional.get();

-            if (dictionary.getDictionaryRank(existing.getType()) <= dictionary.getDictionaryRank(found.getType())) {
+            log.info("existing: {}", existing);
+            log.info("found: {} ", found);
+            if(existing.getType().equals(found.getType())){
+                existing.getEngines().addAll(found.getEngines());
+            } else if (dictionary.getDictionaryRank(existing.getType()) <= dictionary.getDictionaryRank(found.getType())){
                entities.remove(found);
                entities.add(found);
-            } else {
-                existing.getEngines().addAll(found.getEngines());
            }
        } else {
            entities.add(found);
@@ -11,8 +11,7 @@ public class Patterns {

    public static Map<String, Pattern> patternCache = new HashMap<>();

-    public static Pattern AUTHOR_TABLE_SPITTER = Pattern.compile("((((di)|(van)) )|[A-Z]’)?[A-ZÄÖÜ][\\wäöüéèê]{2,}( ?[A-ZÄÖÜ]{1,2}\\.)+|((((di)|(van)) )|[A-Z]’)?[A-ZÄÖÜ][\\wäöüéèê]{2,}( ?[A-ZÄÖÜ]{1,2} )+");
-
+    public static Pattern AUTHOR_TABLE_SPITTER = Pattern.compile("(((((di)|(van)) )|[A-Z]’)?[A-ZÄÖÜ][\\wäöüéèê]{2,500}( ?[A-ZÄÖÜ]{1,2}\\.){1,3})|(((((di)|(van)) )|[A-Z]’)?[A-ZÄÖÜ][\\wäöüéèê]{2,500}( ?[A-ZÄÖÜ]{1,2} ){1,3})");

    public Pattern getCompiledPattern(String pattern, boolean caseInsensitive) {

@@ -12,7 +12,7 @@ public class TextNormalizationUtilities {
     * @return Text without line-break hyphenation.
     */
    public static String removeHyphenLineBreaks(String text) {
-        return text.replaceAll("([^\\s\\d\\-]{2,})[\\-\\u00AD]\\R", "$1");
+        return text.replaceAll("([^\\s\\d\\-]{2,500})[\\-\\u00AD]\\R", "$1");
    }

 }
@@ -4,10 +4,16 @@ import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.attribute.FileAttribute;
+import java.nio.file.attribute.PosixFilePermission;
+import java.nio.file.attribute.PosixFilePermissions;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Set;

 import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.SystemUtils;
 import org.apache.pdfbox.io.MemoryUsageSetting;
 import org.apache.pdfbox.pdmodel.PDDocument;
 import org.apache.pdfbox.pdmodel.PDPage;
@@ -59,7 +65,19 @@ public class PdfSegmentationService {
        PDDocument pdDocument = null;
        try {
            //create tempFile
-            File tempFile = File.createTempFile("document", ".pdf");
+            File tempFile;
+
+            if(SystemUtils.IS_OS_UNIX) {
+                FileAttribute<Set<PosixFilePermission>> attr = PosixFilePermissions.asFileAttribute(PosixFilePermissions.fromString("rwx------"));
+                tempFile = Files.createTempFile("document", ".pdf", attr).toFile();
+            }
+            else {
+                tempFile = Files.createTempFile("document", ".pdf").toFile();
+                tempFile.setReadable(true, true);
+                tempFile.setWritable(true, true);
+                tempFile.setExecutable(true, true);
+            }
+
            try (var fos = new FileOutputStream(tempFile)) {
                IOUtils.copy(documentInputStream, fos);

@@ -40,3 +40,4 @@ storage:
  bucket-name: 'redaction'
  region: 'us-east-1'
  endpoint: 'https://s3.amazonaws.com'
+  backend: 's3'
@@ -1,6 +1,7 @@
 package com.iqser.red.service.redaction.v1.server;

 import com.iqser.red.storage.commons.exception.StorageObjectDoesNotExist;
+import com.iqser.red.storage.commons.service.S3StorageService;
 import com.iqser.red.storage.commons.service.StorageService;
 import lombok.SneakyThrows;
 import org.apache.commons.io.IOUtils;
@@ -12,7 +13,7 @@ import java.io.FileOutputStream;
 import java.util.HashMap;
 import java.util.Map;

-public class FileSystemBackedStorageService extends StorageService {
+public class FileSystemBackedStorageService extends S3StorageService {

    private final Map<String, File> dataMap = new HashMap<>();

@@ -21,9 +21,11 @@ import com.iqser.red.service.redaction.v1.server.redaction.service.AnalyzeServic
 import com.iqser.red.service.redaction.v1.server.redaction.utils.ResourceLoader;
 import com.iqser.red.service.redaction.v1.server.redaction.utils.TextNormalizationUtilities;
 import com.iqser.red.service.redaction.v1.server.storage.RedactionStorageService;
+import com.iqser.red.storage.commons.StorageAutoConfiguration;
 import com.iqser.red.storage.commons.service.StorageService;
 import lombok.SneakyThrows;
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Ignore;
@@ -137,7 +139,7 @@ public class RedactionIntegrationTest {
    private final static String TEST_FILE_ID = "123";

    @Configuration
-    @EnableAutoConfiguration(exclude = {RabbitAutoConfiguration.class})
+    @EnableAutoConfiguration(exclude = {RabbitAutoConfiguration.class, StorageAutoConfiguration.class})
    public static class RedactionIntegrationTestConfiguration {

        @Bean
@@ -574,7 +576,7 @@ public class RedactionIntegrationTest {
                .fileId(TEST_FILE_ID)
                .build());

-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Annotated3.pdf")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Annotated3.pdf")) {
            fileOutputStream.write(annotateResponse.getDocument());
        }
        long rstart = System.currentTimeMillis();
@@ -682,17 +684,11 @@ public class RedactionIntegrationTest {
        var redactionLog = redactionStorageService.getRedactionLog(TEST_DOSSIER_ID, TEST_FILE_ID);
        var text = redactionStorageService.getText(TEST_DOSSIER_ID, TEST_FILE_ID);

-        redactionLog.getRedactionLogEntry().forEach(entry -> {
-            if (entry.isImage()) {
-                System.out.println("---->" + entry.getTypeId());
-            }
-        });
-
        long end = System.currentTimeMillis();

        System.out.println("first analysis duration: " + (end - start));

-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Test.json")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Test.json")) {
            fileOutputStream.write(objectMapper.writeValueAsBytes(redactionStorageService.getText(TEST_DOSSIER_ID, TEST_FILE_ID)));
        }

@@ -764,7 +760,7 @@ public class RedactionIntegrationTest {
                .fileId(TEST_FILE_ID)
                .build());

-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Annotated.pdf")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Annotated.pdf")) {
            fileOutputStream.write(annotateResponse.getDocument());
        }

@@ -800,7 +796,7 @@ public class RedactionIntegrationTest {
                .fileId(TEST_FILE_ID)
                .build());

-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Annotated.pdf")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Annotated.pdf")) {
            fileOutputStream.write(annotateResponse.getDocument());
        }
        long end = System.currentTimeMillis();
@@ -848,7 +844,7 @@ public class RedactionIntegrationTest {
        manualRedactionEntry.setAnnotationId(manualAddId);
        manualRedactionEntry.setFileId("fileId");
        manualRedactionEntry.setStatus(AnnotationStatus.REQUESTED);
-        manualRedactionEntry.setTypeId("name:" + TEST_DOSSIER_TEMPLATE_ID);
+        manualRedactionEntry.setType("name");
        manualRedactionEntry.setValue("O'Loughlin C.K.");
        manualRedactionEntry.setReason("Manual Redaction");
        manualRedactionEntry.setPositions(List.of(Rectangle
@@ -896,7 +892,7 @@ public class RedactionIntegrationTest {
                .fileId(TEST_FILE_ID)
                .build());

-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Annotated.pdf")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Annotated.pdf")) {
            fileOutputStream.write(annotateResponse.getDocument());
        }
        long end = System.currentTimeMillis();
@@ -922,7 +918,7 @@ public class RedactionIntegrationTest {

        RedactionResult result = redactionController.classify(redactionRequest);

-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Classified.pdf")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Classified.pdf")) {
            fileOutputStream.write(result.getDocument());
        }
    }
@@ -944,7 +940,7 @@ public class RedactionIntegrationTest {

        RedactionResult result = redactionController.sections(redactionRequest);

-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Sections.pdf")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Sections.pdf")) {
            fileOutputStream.write(result.getDocument());
        }
    }
@@ -966,7 +962,7 @@ public class RedactionIntegrationTest {

        RedactionResult result = redactionController.htmlTables(redactionRequest);

-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Tables.html")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Tables.html")) {
            fileOutputStream.write(result.getDocument());
        }
    }
@@ -988,7 +984,7 @@ public class RedactionIntegrationTest {

        RedactionResult result = redactionController.htmlTables(redactionRequest);

-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Tables.html")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Tables.html")) {
            fileOutputStream.write(result.getDocument());
        }
    }
@@ -1058,7 +1054,7 @@ public class RedactionIntegrationTest {
                .fileId(TEST_FILE_ID)
                .build());

-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Annotated.pdf")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Annotated.pdf")) {
            fileOutputStream.write(annotateResponse.getDocument());
        }
        long end = System.currentTimeMillis();
@@ -1086,4 +1082,12 @@ public class RedactionIntegrationTest {
        }
    }

+    private static String getTemporaryDirectory() {
+        String tmpdir = System.getProperty("java.io.tmpdir");
+        if (StringUtils.isNotBlank(tmpdir)) {
+            return tmpdir;
+        }
+        return "/tmp";
+    }
+
 }
@@ -13,6 +13,7 @@ import com.iqser.red.service.redaction.v1.server.tableextraction.service.RulingC
 import com.iqser.red.service.redaction.v1.server.tableextraction.service.TableExtractionService;
 import org.junit.Ignore;
 import org.junit.Test;
+import org.junit.platform.commons.util.StringUtils;
 import org.junit.runner.RunWith;
 import org.kie.api.runtime.KieContainer;
 import org.springframework.amqp.rabbit.core.RabbitTemplate;
@@ -95,7 +96,7 @@ public class PdfSegmentationServiceTest {
            for (PdfImage image : page.getImages()) {
                try (ByteArrayOutputStream baos = new ByteArrayOutputStream()) {
                    ImageIO.write(image.getImage(), "png", baos);
-                    try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Image " + i + ".png")) {
+                    try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Image " + i + ".png")) {
                        fileOutputStream.write(baos.toByteArray());
                    }
                }
@@ -239,4 +240,12 @@ public class PdfSegmentationServiceTest {
                        .equals(firstTableHeaderCells))).isTrue();
    }

+    private static String getTemporaryDirectory() {
+        String tmpdir = System.getProperty("java.io.tmpdir");
+        if (StringUtils.isNotBlank(tmpdir)) {
+            return tmpdir;
+        }
+        return "/tmp";
+    }
+
 }
@@ -18,3 +18,10 @@ platform.multi-tenancy:
 redaction-service:
  enable-image-classification: false
  enable-entity-recognition: false
+
+storage:
+  signer-type: 'AWSS3V4SignerType'
+  bucket-name: 'redaction'
+  region: 'us-east-1'
+  endpoint: 'https://s3.amazonaws.com'
+  backend: 's3'
Author	SHA1	Message	Date
Dominique Eifländer	2f66d223fd	Added some logs	2021-10-19 14:38:03 +02:00
Dominique Eifländer	fa8f598763	RED-2224: Fixed missing values in engines	2021-10-19 10:55:51 +02:00
Dominique Eiflaender	46c6385d11	Pull request #250 : RED-2223: Fixed adding annotations to rotated words on non rotated pages Merge in RED/redaction-service from RED-2223 to master * commit '6005c476962dcdfd1d4e4fabf10fa840377b78db': RED-2223: Fixed adding annotations to rotated words on non rotated pages	2021-10-15 15:35:28 +02:00
Dominique Eifländer	6005c47696	RED-2223: Fixed adding annotations to rotated words on non rotated pages	2021-10-15 15:27:15 +02:00
Dominique Eiflaender	ac556dfc9f	Pull request #249 : RED-2468: Fixed push recommendations to dictionary Merge in RED/redaction-service from RED-2468 to master * commit '15d836644b6a74273e81de361091d6ea1b71bea9': RED-2468: Fixed push recommendations to dictionary	2021-10-15 10:45:10 +02:00
Dominique Eifländer	15d836644b	RED-2468: Fixed push recommendations to dictionary	2021-10-15 10:36:01 +02:00
Ali Oezyetimoglu	d0cd3853cc	Pull request #248 : RED-2263: fixed Regex-Issue that can lead to stack overflow in redaction-service Merge in RED/redaction-service from RED-2263-rs1 to master * commit 'b96c39d5e58317e989faf8dc881ee6e596dbf363': RED-2263: fixed Regex-Issue that can lead to stack overflow in redaction-service	2021-10-14 13:21:58 +02:00
aoezyetimoglu	b96c39d5e5	RED-2263: fixed Regex-Issue that can lead to stack overflow in redaction-service	2021-10-14 13:04:49 +02:00
Timo Bejan	b83baf4bc4	Pull request #247 : RED-2334 Merge in RED/redaction-service from 3.0-efsa-readiness to master * commit '8bfe8acb85e33502f4978b12b5cc09f68a602f47': RED-2334	2021-10-13 09:24:16 +02:00
Timo Bejan	8bfe8acb85	RED-2334	2021-10-12 17:23:28 +03:00
Ali Oezyetimoglu	57f6bd77ed	Pull request #246 : RED-2246: updated platform-commons-dependency Merge in RED/redaction-service from RED-2246-rs1 to master * commit '15ed333478313f3f23d439ad6163553f9b68760e': RED-2246: updated platform-commons-dependency	2021-10-08 15:30:38 +02:00
aoezyetimoglu	15ed333478	RED-2246: updated platform-commons-dependency	2021-10-08 15:18:48 +02:00
Timo Bejan	b3393a5f16	Pull request #245 : RED-2378 Merge in RED/redaction-service from 3.0-efsa-readiness to master * commit 'a299a326eb5587cd76b19ba848f5a771e2741edc': RED-2378	2021-10-08 13:59:30 +02:00
Timo Bejan	a299a326eb	RED-2378	2021-10-08 14:13:50 +03:00
Philipp Schramm	1034066e38	Pull request #244 : Bugfix/workaround for windows Merge in RED/redaction-service from bugfix/workaround-for-windows to master * commit '535316c3a7740f61c682ae3d938f33671660c667': Bugfix with 'posix:permissions' for Windows systems Just a test without PosixFilePermission	2021-10-07 16:51:34 +02:00
Philipp Schramm	535316c3a7	Bugfix with 'posix:permissions' for Windows systems	2021-10-07 15:35:42 +02:00
Philipp Schramm	1e86073dff	Just a test without PosixFilePermission	2021-10-07 14:35:44 +02:00
Philipp Schramm	5dc0e1932e	Get temporary directory for tests dynamically to prevent issues with Windows systems	2021-10-07 14:12:39 +02:00
Philipp Schramm	8f75ff89a1	Use platform-docker-dependency version 1.1.0 which contains bugfix for Windows systems	2021-10-07 14:02:51 +02:00
Timo Bejan	1e61ea8736	Pull request #243 : Updated Persistence Service Version Merge in RED/redaction-service from 3.0-efsa-readiness to master * commit '0fa4c54490422cf06f0a9034e3e9a83c78a66f6e': Updated Persistence Service Version	2021-10-07 09:12:46 +02:00
Timo Bejan	0fa4c54490	Updated Persistence Service Version	2021-10-07 10:06:36 +03:00
Dominique Eiflaender	243b4e4808	Pull request #242 : RED-2172: Enbled to configure azure blob storage as storage backend Merge in RED/redaction-service from RED-2172 to master * commit 'e22e454fb5c16b326183179193bf24a8e7d724be': RED-2172: Enbled to configure azure blob storage as storage backend	2021-10-06 15:13:09 +02:00
Dominique Eifländer	e22e454fb5	RED-2172: Enbled to configure azure blob storage as storage backend	2021-10-06 15:02:44 +02:00
Ali Oezyetimoglu	4316f36484	Pull request #241 : RED-2261 rs7 Merge in RED/redaction-service from RED-2261-rs7 to master * commit '22ae1ad6a98a0db4383e545c931d41111d0463ed': RED-2261: update dependencies RED-2261: update dependencies	2021-10-04 16:47:17 +02:00
aoezyetimoglu	22ae1ad6a9	RED-2261: update dependencies	2021-10-01 15:31:39 +02:00
aoezyetimoglu	e7fc3f8079	RED-2261: update dependencies	2021-10-01 14:56:19 +02:00
Ali Oezyetimoglu	8f54adc8e6	Pull request #239 : RED-2261: update dependencies Merge in RED/redaction-service from RED-2261-rs5 to master * commit '94622a90f373248ed0c10d7c6d7fddbee65c3028': RED-2261: update dependencies	2021-10-01 13:18:53 +02:00
aoezyetimoglu	94622a90f3	RED-2261: update dependencies	2021-10-01 10:59:37 +02:00
Ali Oezyetimoglu	58383467bb	Pull request #238 : RED-2261: update dependencies Merge in RED/redaction-service from RED-2261-rs4 to master * commit '8f31abf8dc9817be3a9a110eefd33ee919ae5313': RED-2261: update dependencies	2021-09-30 17:00:57 +02:00
aoezyetimoglu	8f31abf8dc	RED-2261: update dependencies	2021-09-30 16:54:28 +02:00
Ali Oezyetimoglu	71e698da9d	Pull request #237 : RED-2261 rs3 Merge in RED/redaction-service from RED-2261-rs3 to master * commit 'f3b6a2e57e00fc3892370408f6ba0a70b20791a1': RED-2261: update dependencies RED-2261: update dependencies	2021-09-30 16:51:41 +02:00
aoezyetimoglu	f3b6a2e57e	RED-2261: update dependencies	2021-09-30 16:41:35 +02:00
aoezyetimoglu	a058bb996b	RED-2261: update dependencies	2021-09-30 16:00:35 +02:00
Ali Oezyetimoglu	8633b02f4e	Pull request #233 : RED-2272: Make sure publicly writable directories are used safely && regex upper bound Merge in RED/redaction-service from RED-2272-rs1 to master * commit 'c4e47a48f8973ca1bbd602727a205647deb809fe': RED-2272: Make sure publicly writable directories are used safely && regex upper bound RED-2272: Make sure publicly writable directories are used safely && regex upper bound	2021-09-30 12:45:46 +02:00
aoezyetimoglu	c4e47a48f8	RED-2272: Make sure publicly writable directories are used safely && regex upper bound	2021-09-30 12:37:01 +02:00
aoezyetimoglu	adba0f99a0	RED-2272: Make sure publicly writable directories are used safely && regex upper bound	2021-09-30 11:51:48 +02:00
Timo Bejan	10ae7fc20d	Pull request #232 : typeId to type internal refactor Merge in RED/redaction-service from persistence-service-integration to master * commit 'dcd6d9d2c9cb66ad55e08d82a6044ea1b01c54eb': fixed pmd typeId to type internal refactor	2021-09-29 15:57:45 +02:00
Timo Bejan	dcd6d9d2c9	fixed pmd	2021-09-29 16:52:06 +03:00
Timo Bejan	0856c542bc	typeId to type internal refactor	2021-09-29 16:34:04 +03:00
Dominique Eiflaender	dd8a07d2ad	Pull request #231 : Fixed update dictionary request Merge in RED/redaction-service from UpdateDictionaryFix to master * commit 'ded1b6eb66bd179589cb6191f748e39ea834a7a6': Fixed update dictionary request	2021-09-29 09:49:45 +02:00