Compare commits

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Author SHA1 Message Date
Timo Bejan de841452ba checkstyle fix 2022-08-19 17:31:50 +03:00
Timo Bejan 96e8485afe RED-4835 - entity position not calculated correctly for duplicates where 1 is marked as false positive 2022-08-19 17:29:43 +03:00
Dominique Eiflaender ec49945682 Pull request #446: RED-4843: Disable jsondsl per default
Merge in RED/redaction-service from RED-4843 to master

* commit 'b64222938c64eeb006d62807a705918ffd2c585b':
  RED-4843: Disable jsondsl per default
2022-07-29 12:47:38 +02:00
deiflaender b64222938c RED-4843: Disable jsondsl per default 2022-07-29 12:43:35 +02:00
Timo Bejan e4823e20d4 Pull request #444: RED-4799 - remove FP entities from redactionlog
Merge in RED/redaction-service from RED-4799-3 to master

* commit '53428ec65296b9fac2c206e7bd89916c933fb5c8':
  RED-4799 - remove FP entities from redactionlog
2022-07-29 10:53:51 +02:00
Timo Bejan 53428ec652 RED-4799 - remove FP entities from redactionlog 2022-07-29 11:50:38 +03:00
Dominique Eiflaender ca270fb7de Pull request #443: RED-4843: Upgraded storage commons
Merge in RED/redaction-service from RED-4843 to master

* commit '06fe0dbd97cdf2011be17df07f8c409a221530a4':
  RED-4843: Upgraded storage commons
2022-07-29 10:41:24 +02:00
deiflaender 06fe0dbd97 RED-4843: Upgraded storage commons 2022-07-29 10:27:18 +02:00
Timo Bejan 1d8e86e4f6 Pull request #439: RED-4799
Merge in RED/redaction-service from RED-4799-fix to master

* commit '2b7972315f655bd296a03cae8cc5e4846d47bbce':
  RED-4799
2022-07-27 11:58:11 +02:00
Timo Bejan 2b7972315f RED-4799 2022-07-27 12:54:51 +03:00
Philipp Schramm 0af853dbfc Pull request #436: RED-4510: Added generated RedactionLog Json files and optimizations for RulesTest.java for Bamboo
Merge in RED/redaction-service from RED-4510-Rework to master

* commit '0544a42117a742de70325cd1a84e57d6829aaa25':
  RED-4510: Added generated RedactionLog Json files and optimizations for RulesTest.java for Bamboo
2022-07-26 17:08:59 +02:00
Philipp Schramm 0544a42117 RED-4510: Added generated RedactionLog Json files and optimizations for RulesTest.java for Bamboo 2022-07-26 17:06:04 +02:00
Timo Bejan 8bdfd6747d Pull request #435: RED-4686
Merge in RED/redaction-service from tbejan/pomxml-1658825710723 to master

* commit '80c0c25c069995790d6bd043657f50dc8de0a451':
  RED-4686
2022-07-26 11:01:22 +02:00
Timo Bejan 80c0c25c06 RED-4686 2022-07-26 10:55:17 +02:00
Timo Bejan 17baf9c0eb Pull request #433: RED-4686 - updated cyclic deps
Merge in RED/redaction-service from RED-4686 to master

* commit '090a6196000dfcd7a447c54224fba8eda4605380':
  RED-4686 - updated cyclic deps
2022-07-26 09:25:58 +02:00
Timo Bejan 090a619600 RED-4686 - updated cyclic deps 2022-07-26 10:22:50 +03:00
156 changed files with 63303 additions and 166 deletions
-1
View File
@@ -26,4 +26,3 @@
**/.DS_Store
**/classpath-data.json
**/dependencies-and-licenses-overview.txt
/redaction-service-v1/redaction-service-server-v1/src/test/resources/RedactionLog/
+1 -1
View File
@@ -32,7 +32,7 @@
<dependency>
<groupId>com.iqser.red</groupId>
<artifactId>platform-commons-dependency</artifactId>
<version>1.17.0</version>
<version>1.20.0</version>
<scope>import</scope>
<type>pom</type>
</dependency>
@@ -12,7 +12,7 @@
<artifactId>redaction-service-api-v1</artifactId>
<properties>
<persistence-service.version>1.240.0</persistence-service.version>
<persistence-service.version>1.254.0</persistence-service.version>
</properties>
<dependencies>
@@ -1,19 +1,14 @@
package com.iqser.red.service.redaction.v1.server.redaction.model;
import com.iqser.red.service.redaction.v1.model.Engine;
import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
import lombok.*;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import com.iqser.red.service.redaction.v1.model.Engine;
import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
import lombok.AllArgsConstructor;
import lombok.Builder;
import lombok.Data;
import lombok.EqualsAndHashCode;
import lombok.NoArgsConstructor;
@Data
@Builder
@NoArgsConstructor
@@ -24,6 +19,7 @@ public class Entity implements ReasonHolder {
private String word;
private String type;
private boolean redaction;
private boolean falsePositive;
private String redactionReason;
private String legalBasis;
private List<EntityPositionSequence> positionSequences = new ArrayList<>();
@@ -1,23 +1,5 @@
package com.iqser.red.service.redaction.v1.server.redaction.model;
import java.lang.annotation.ElementType;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
import java.lang.annotation.Target;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import com.iqser.red.service.persistence.service.v1.api.model.annotations.ManualRedactions;
import com.iqser.red.service.redaction.v1.model.ArgumentType;
import com.iqser.red.service.redaction.v1.model.Engine;
@@ -28,10 +10,19 @@ import com.iqser.red.service.redaction.v1.server.redaction.utils.EntitySearchUti
import com.iqser.red.service.redaction.v1.server.redaction.utils.FindEntityDetails;
import com.iqser.red.service.redaction.v1.server.redaction.utils.Patterns;
import com.iqser.red.service.redaction.v1.server.redaction.utils.SearchImplementation;
import lombok.Builder;
import lombok.Data;
import lombok.extern.slf4j.Slf4j;
import org.apache.commons.lang3.StringUtils;
import java.lang.annotation.ElementType;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
import java.lang.annotation.Target;
import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
@Data
@Slf4j
@@ -87,6 +78,7 @@ public class Section {
List<String> values = entitiesOfType.stream().map(Entity::getWord).collect(Collectors.toList());
Set<Entity> found = EntitySearchUtils.findEntities(searchText, new SearchImplementation(values, dictionary.isCaseInsensitiveDictionary(asType)), dictionary.getType(asType), new FindEntityDetails(asType, headline, sectionNumber, false, false, Engine.NER, EntityType.RECOMMENDATION));
EntitySearchUtils.clearAndFindPositions(found, searchableText, dictionary, manualRedactions);
found = found.stream().filter(f -> !f.isFalsePositive()).collect(Collectors.toSet());
Set<Entity> finalResult = new HashSet<>();
@@ -886,13 +878,11 @@ public class Section {
}
});
return EntitySearchUtils.clearAndFindPositions(found, searchableText, dictionary, manualRedactions);
var cleared = EntitySearchUtils.clearAndFindPositions(found, searchableText, dictionary, manualRedactions);
return cleared.stream().filter(f -> !f.isFalsePositive()).collect(Collectors.toSet());
}
private void redact(String type, int ruleNumber, String reason, String legalBasis, boolean redaction) {
entities.forEach(entity -> {
@@ -1,18 +1,5 @@
package com.iqser.red.service.redaction.v1.server.redaction.service;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.lang3.StringUtils;
import org.kie.api.runtime.KieContainer;
import org.springframework.stereotype.Service;
import com.iqser.red.service.persistence.service.v1.api.model.annotations.AnnotationStatus;
import com.iqser.red.service.persistence.service.v1.api.model.annotations.ManualRedactions;
import com.iqser.red.service.persistence.service.v1.api.model.annotations.entitymapped.IdRemoval;
@@ -22,24 +9,21 @@ import com.iqser.red.service.redaction.v1.model.Engine;
import com.iqser.red.service.redaction.v1.server.classification.model.SectionText;
import com.iqser.red.service.redaction.v1.server.client.model.NerEntities;
import com.iqser.red.service.redaction.v1.server.redaction.model.Dictionary;
import com.iqser.red.service.redaction.v1.server.redaction.model.DictionaryModel;
import com.iqser.red.service.redaction.v1.server.redaction.model.Entities;
import com.iqser.red.service.redaction.v1.server.redaction.model.Entity;
import com.iqser.red.service.redaction.v1.server.redaction.model.EntityPositionSequence;
import com.iqser.red.service.redaction.v1.server.redaction.model.EntityType;
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.model.SearchableText;
import com.iqser.red.service.redaction.v1.server.redaction.model.Section;
import com.iqser.red.service.redaction.v1.server.redaction.model.SectionSearchableTextPair;
import com.iqser.red.service.redaction.v1.server.redaction.model.*;
import com.iqser.red.service.redaction.v1.server.redaction.utils.EntitySearchUtils;
import com.iqser.red.service.redaction.v1.server.redaction.utils.FindEntityDetails;
import com.iqser.red.service.redaction.v1.server.redaction.utils.IdBuilder;
import com.iqser.red.service.redaction.v1.server.settings.RedactionServiceSettings;
import io.micrometer.core.annotation.Timed;
import lombok.RequiredArgsConstructor;
import lombok.extern.slf4j.Slf4j;
import org.apache.commons.lang3.StringUtils;
import org.kie.api.runtime.KieContainer;
import org.springframework.stereotype.Service;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
@Slf4j
@Service
@@ -51,7 +35,6 @@ public class EntityRedactionService {
private final SurroundingWordsService surroundingWordsService;
public PageEntities findEntities(Dictionary dictionary, List<SectionText> sectionTexts, KieContainer kieContainer,
AnalyzeRequest analyzeRequest, NerEntities nerEntities) {
@@ -262,7 +245,8 @@ public class EntityRedactionService {
nerFound.addAll(getNerValues(sectionNumber, nerEntities, cellStarts, headline));
}
return new Entities(EntitySearchUtils.clearAndFindPositions(found, searchableText, dictionary, manualRedactions), nerFound);
var cleared = EntitySearchUtils.clearAndFindPositions(found, searchableText, dictionary, manualRedactions);
return new Entities(cleared.stream().filter(e -> !e.isFalsePositive()).collect(Collectors.toSet()), nerFound);
}
@@ -1,28 +1,15 @@
package com.iqser.red.service.redaction.v1.server.redaction.utils;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
import com.iqser.red.service.persistence.service.v1.api.model.annotations.AnnotationStatus;
import com.iqser.red.service.persistence.service.v1.api.model.annotations.ManualRedactions;
import com.iqser.red.service.redaction.v1.server.redaction.model.Dictionary;
import com.iqser.red.service.redaction.v1.server.redaction.model.DictionaryModel;
import com.iqser.red.service.redaction.v1.server.redaction.model.Entity;
import com.iqser.red.service.redaction.v1.server.redaction.model.EntityPositionSequence;
import com.iqser.red.service.redaction.v1.server.redaction.model.EntityType;
import com.iqser.red.service.redaction.v1.server.redaction.model.Image;
import com.iqser.red.service.redaction.v1.server.redaction.model.SearchableText;
import com.iqser.red.service.redaction.v1.server.redaction.model.*;
import lombok.experimental.UtilityClass;
import lombok.extern.slf4j.Slf4j;
import java.util.*;
import java.util.stream.Collectors;
@Slf4j
@UtilityClass
@SuppressWarnings("PMD")
@@ -39,12 +26,10 @@ public class EntitySearchUtils {
if (details.getEntityType() == EntityType.RECOMMENDATION) {
Set<Entity> falseRecommendations = find(inputString, type.getFalseRecommendationsSearch(), details.withEntityType(EntityType.FALSE_RECOMMENDATION));
removeFalsePositives(found, falseRecommendations);
found.addAll(falseRecommendations);
markFalsePositives(found, falseRecommendations);
} else {
Set<Entity> falsePositives = find(inputString, type.getFalsePositiveSearch(), details.withEntityType(EntityType.FALSE_POSITIVE));
removeFalsePositives(found, falsePositives);
found.addAll(falsePositives);
markFalsePositives(found, falsePositives);
}
return found;
@@ -93,7 +78,7 @@ public class EntitySearchUtils {
}
}
if (manualRedactions != null && manualRedactions.getResizeRedactions() != null && !manualRedactions.getResizeRedactions().isEmpty()){
if (manualRedactions != null && manualRedactions.getResizeRedactions() != null && !manualRedactions.getResizeRedactions().isEmpty()) {
applyResizeRedactions(entities, manualRedactions);
}
@@ -131,7 +116,11 @@ public class EntitySearchUtils {
}
public void removeFalsePositives(Set<Entity> entities, Set<Entity> falsePositives) {
public void markFalsePositives(Set<Entity> entities, Set<Entity> falsePositives) {
if (entities.size() == 2) {
log.info("asd");
}
List<Entity> wordsToRemove = new ArrayList<>();
for (Entity word : falsePositives) {
@@ -142,8 +131,12 @@ public class EntitySearchUtils {
}
}
}
wordsToRemove.forEach(entities::remove);
entities.removeAll(falsePositives);
wordsToRemove.forEach(e -> e.setFalsePositive(true));
for (var entity : entities) {
if (falsePositives.contains(entity)) {
entity.setFalsePositive(true);
}
}
}
@@ -152,13 +145,22 @@ public class EntitySearchUtils {
List<Entity> wordsToRemove = new ArrayList<>();
for (Entity word : entities) {
for (Entity inner : entities) {
// // skip cross-type false positives
// if(word.getEntityType() == EntityType.FALSE_POSITIVE && inner.getEntityType() == EntityType.ENTITY && !inner.getType().equals(word.getType())){
// continue;
// }
// // skip cross-type false reccommendations
// if(word.getEntityType() == EntityType.FALSE_RECOMMENDATION && inner.getEntityType() == EntityType.RECOMMENDATION && !inner.getType().equals(word.getType())){
// continue;
// }
if (inner.getWord().length() < word.getWord()
.length() && inner.getStart() >= word.getStart() && inner.getEnd() <= word.getEnd() && word != inner && word.getSectionNumber() == inner.getSectionNumber()) {
if (word.getEntityType().equals(EntityType.RECOMMENDATION) && inner.getEntityType().equals(EntityType.ENTITY)) {
wordsToRemove.add(word);
} else if(!(inner.getEntityType() == EntityType.FALSE_RECOMMENDATION && word.getEntityType() == EntityType.ENTITY ||
} else if (!(inner.getEntityType() == EntityType.FALSE_RECOMMENDATION && word.getEntityType() == EntityType.ENTITY ||
inner.getEntityType() == EntityType.ENTITY && word.getEntityType() == EntityType.FALSE_RECOMMENDATION)) {
if(inner.isResized()){
if (inner.isResized()) {
wordsToRemove.add(word);
} else {
wordsToRemove.add(inner);
@@ -3,6 +3,7 @@ package com.iqser.red.service.redaction.v1.server;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
import com.iqser.red.commons.jackson.ObjectMapperFactory;
import com.iqser.red.storage.commons.exception.StorageObjectDoesNotExist;
import com.iqser.red.storage.commons.service.StorageService;
import lombok.SneakyThrows;
@@ -62,11 +63,8 @@ public class FileSystemBackedStorageService implements StorageService {
}
private ObjectMapper getMapper() {
var objectMapper = new ObjectMapper();
objectMapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
objectMapper.registerModule(new JavaTimeModule());
objectMapper.findAndRegisterModules();
return objectMapper;
return ObjectMapperFactory.create();
}
@Override
@@ -27,7 +27,6 @@ import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.junit.After;
import org.junit.Before;
@@ -114,10 +113,13 @@ public class RulesTest {
private static final String IMPORTED_REDACTION = "imported_redaction";
private static final String PII = "PII";
private static final String RESOURCES_PATH = "src/test/resources/";
private static final String REDACTION_LOG_PATH = RESOURCES_PATH + "RedactionLog/";
private static final String REDACTION_LOG_PATH = "RedactionLog/";
private static final String REDACTION_LOG_RESOURCES_PATH = RESOURCES_PATH + REDACTION_LOG_PATH;
private final static String TEST_DOSSIER_TEMPLATE_ID = "123";
private final static String TEST_DOSSIER_ID = "123";
private String TEST_FILE_ID = "123";
private int counter = 0;
private int fileSize = 0;
private final Map<String, List<String>> dictionary = new HashMap<>();
private final Map<String, List<String>> dossierDictionary = new HashMap<>();
private final Map<String, List<String>> falsePositive = new HashMap<>();
@@ -176,7 +178,9 @@ public class RulesTest {
.hexColor("#ffe187")
.isHint(hintTypeMap.get(DOSSIER_REDACTIONS))
.isCaseInsensitive(caseInSensitiveMap.get(DOSSIER_REDACTIONS))
.isRecommendation(recommendationTypeMap.get(DOSSIER_REDACTIONS)).rank(rankTypeMap.get(DOSSIER_REDACTIONS)).build()));
.isRecommendation(recommendationTypeMap.get(DOSSIER_REDACTIONS))
.rank(rankTypeMap.get(DOSSIER_REDACTIONS))
.build()));
mockDictionaryCalls(null);
mockDictionaryCalls(0L);
@@ -196,7 +200,7 @@ public class RulesTest {
/**
* Generates RedactionLog for given file and saves it here: REDACTION_LOG_PATH.
* If the RedactionLog already exists, the generating will be skipped
* If the RedactionLog already exists, it will be overwritten
* Test is ignored, because it's for manual tests.
*/
@Ignore
@@ -204,20 +208,22 @@ public class RulesTest {
public void generateRedactionLogForOneFile() {
String fileName = "files/Compounds/31 A14111B - EU AIR3 - MCP Section 1 - Identity of the plant protection product.pdf";
generateAndSaveRedactionLog(fileName);
fileSize = 1;
generateAndSaveRedactionLog(fileName, true);
}
/**
* Generates RedactionLog for all files and saves it here: REDACTION_LOG_PATH.
* If a RedactionLog already exists, the generating will be skipped
* If a RedactionLog already exists, the generating for this will be skipped
* Please commit generated files, if not the following tests will fail
*/
@IfProfileValue(name = "test-groups", value = "rules-test")
@Test
public void generateRedactionLogForAllFiles() {
Set<String> files = getFileNames(new HashSet<>(), FileSystems.getDefault().getPath(RESOURCES_PATH));
System.out.println("Will generate RedactionLog for " + files.size() + " files.");
fileSize = files.size();
files.forEach(this::generateAndSaveRedactionLog);
}
@@ -225,20 +231,19 @@ public class RulesTest {
/**
* Analyses file and compares its RedactionLog with saved one from here: REDACTION_LOG_PATH.
* If RedactionLog Json does not exist, test will fail.
* Test is ignored, because it's for manual tests.
*/
@Ignore
@Test
public void analyseFileAndCompareRedactionLog() {
String fileName = "files/Compounds/31 A14111B - EU AIR3 - MCP Section 1 - Identity of the plant protection product.pdf";
String fileName = "files/RulesTest/SYNGENTA_EFSA_sanitisation_GFL_v1_withHighlights.pdf";
fileSize = 1;
analyseFileAndCompareRedactionLog(fileName);
}
/**
* Analyses all files and compares its RedactionLog with saved one from here: REDACTION_LOG_PATH.
* If RedactionLogs Json does not exist, test will fail.
* If RedactionLog Json for one file does not exist, whole test will fail.
*/
@IfProfileValue(name = "test-groups", value = "rules-test")
@Test
@@ -246,20 +251,28 @@ public class RulesTest {
Set<String> files = getFileNames(new HashSet<>(), FileSystems.getDefault().getPath(RESOURCES_PATH));
System.out.println("Will analyse " + files.size() + " files and compare its RedactionLogs.");
fileSize = files.size();
files.forEach(this::analyseFileAndCompareRedactionLog);
}
@SneakyThrows
private void generateAndSaveRedactionLog(String fileName) {
if (doesRedactionLogExist(fileName)) {
System.out.println("Skip generating RedactionLog as Json for " + fileName + " because it already exists.");
generateAndSaveRedactionLog(fileName, false);
}
@SneakyThrows
private void generateAndSaveRedactionLog(String fileName, boolean force) {
counter++;
if (!force && doesRedactionLogExist(fileName)) {
System.out.println("(" + counter + "/" + fileSize + ") Skip generating RedactionLog as Json for " + fileName + " because it already exists.");
} else {
generateTestFileId(fileName);
System.out.println("Generate RedactionLog as Json for " + fileName + " with fileId " + TEST_FILE_ID);
System.out.println("(" + counter + "/" + fileSize + ") Generate RedactionLog as Json for " + fileName + " with fileId " + TEST_FILE_ID);
loadNerForTest();
@@ -278,8 +291,9 @@ public class RulesTest {
@SneakyThrows
public void analyseFileAndCompareRedactionLog(String fileName) {
counter++;
generateTestFileId(fileName);
System.out.println("Analyse " + fileName + " with fileId " + TEST_FILE_ID + " and compare it with its saved RedactionLog");
System.out.println("(" + counter + "/" + fileSize + ") Analyse " + fileName + " with fileId " + TEST_FILE_ID + " and compare it with its saved RedactionLog");
RedactionLog savedRedactionLog = loadSavedRedactionLog(fileName);
@@ -299,7 +313,7 @@ public class RulesTest {
assertThat(redactionLog.getRulesVersion()).isEqualTo(savedRedactionLog.getRulesVersion());
assertThat(redactionLog.getLegalBasisVersion()).isEqualTo(savedRedactionLog.getLegalBasisVersion());
assertThat(redactionLog.getRedactionLogEntry().size()).isEqualTo(savedRedactionLog.getRedactionLogEntry().size());
assertThat(redactionLog.getRedactionLogEntry().stream().filter(r -> !r.isFalsePositive()).collect(Collectors.toSet()).size()).isEqualTo(savedRedactionLog.getRedactionLogEntry().stream().filter(r -> !r.isFalsePositive()).collect(Collectors.toSet()).size());
assertThat(redactionLog.getLegalBasis().size()).isEqualTo(savedRedactionLog.getLegalBasis().size());
for (RedactionLogLegalBasis redactionLegalBasis : redactionLog.getLegalBasis()) {
@@ -387,7 +401,7 @@ public class RulesTest {
assertThat(savedManualChange).isPresent();
}
assertThat(savedRedactionLogEntry.get().getEngines()).containsExactly(redactionLogEntry.getEngines().toArray(new Engine[0]));
assertThat(savedRedactionLogEntry.get().getEngines()).containsExactlyInAnyOrder(redactionLogEntry.getEngines().toArray(new Engine[0]));
assertThat(savedRedactionLogEntry.get().getReference()).containsAll(redactionLogEntry.getReference());
assertThat(savedRedactionLogEntry.get().getImportedRedactionIntersections()).containsAll(redactionLogEntry.getImportedRedactionIntersections());
@@ -399,7 +413,7 @@ public class RulesTest {
private boolean doesRedactionLogExist(String pdfFileName) {
File pdfFile = new File(pdfFileName);
String directory = REDACTION_LOG_PATH + pdfFile.getParentFile().getPath();
String directory = REDACTION_LOG_RESOURCES_PATH + pdfFile.getParentFile().getPath();
String fileName = StringUtils.replace(pdfFile.getName(), ".pdf", ".json");
File file = new File(directory, fileName);
return file.exists();
@@ -421,7 +435,7 @@ public class RulesTest {
File pdfFile = new File(pdfFileName);
String directory = REDACTION_LOG_PATH + pdfFile.getParentFile().getPath();
String directory = REDACTION_LOG_RESOURCES_PATH + pdfFile.getParentFile().getPath();
File dr = new File(directory);
boolean created = dr.mkdirs();
if (created) {
@@ -441,8 +455,20 @@ public class RulesTest {
private RedactionLog loadSavedRedactionLog(String pdfFileName) {
File pdfFile = new File(pdfFileName);
String directory = REDACTION_LOG_PATH + pdfFile.getParentFile().getPath();
String directory = cleanPath(pdfFile.getParentFile().getPath());
if (StringUtils.contains(directory, RESOURCES_PATH)) {
if (!StringUtils.endsWith(directory, "/")) {
directory = directory + "/";
}
directory = directory + REDACTION_LOG_PATH;
} else {
if (StringUtils.startsWith(directory, "/")) {
directory = StringUtils.substring(directory, 1);
}
directory = REDACTION_LOG_RESOURCES_PATH + directory;
}
String fileName = StringUtils.replace(pdfFile.getName(), ".pdf", ".json");
File file = new File(directory, fileName);
assertThat(file).exists();
@@ -450,6 +476,31 @@ public class RulesTest {
}
@SneakyThrows
private Set<String> getFileNames(Set<String> fileNames, Path dir) {
try (DirectoryStream<Path> stream = Files.newDirectoryStream(dir)) {
for (Path path : stream) {
if (path.toFile().isDirectory()) {
getFileNames(fileNames, path);
} else if (StringUtils.endsWith(path.toAbsolutePath().toString(), ".pdf")) {
String absolutePath = cleanPath(path.toAbsolutePath().toString());
int pos = StringUtils.indexOf(absolutePath, RESOURCES_PATH) + RESOURCES_PATH.length();
fileNames.add(StringUtils.substring(absolutePath, pos));
}
}
}
return fileNames;
}
private String cleanPath(String path) {
return StringUtils.replace(path, "\\", "/");
}
@SneakyThrows
private void loadNerForTest() {
@@ -588,24 +639,6 @@ public class RulesTest {
}
@SneakyThrows
private Set<String> getFileNames(Set<String> fileNames, Path dir) {
try (DirectoryStream<Path> stream = Files.newDirectoryStream(dir)) {
for (Path path : stream) {
if (path.toFile().isDirectory()) {
getFileNames(fileNames, path);
} else if (StringUtils.endsWith(path.toAbsolutePath().toString(), ".pdf")) {
String absolutePath = path.toAbsolutePath().toString();
int pos = StringUtils.indexOf(absolutePath, StringUtils.replace(RESOURCES_PATH, "/", "\\")) + 18;
fileNames.add(StringUtils.substring(absolutePath, pos));
}
}
}
return fileNames;
}
private Type getDictionaryResponse(String type, boolean isDossierDictionary) {
return Type.builder()
@@ -5,9 +5,11 @@ import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
import com.iqser.red.service.persistence.service.v1.api.model.dossiertemplate.dossier.file.FileType;
import com.iqser.red.service.redaction.v1.model.AnalyzeRequest;
import com.iqser.red.service.redaction.v1.model.MessageType;
import com.iqser.red.service.redaction.v1.server.annotate.AnnotationService;
import lombok.SneakyThrows;
import lombok.extern.slf4j.Slf4j;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.io.ClassPathResource;
import java.time.OffsetDateTime;
@@ -19,6 +21,9 @@ public class AnalyseFileRealDataIntegrationTest extends LiveDataIntegrationTest
public static final String FILE_NAME = "test-file";
@Autowired
private AnnotationService annotationService;
@Test
@SneakyThrows
public void testFile() {
@@ -81,7 +86,19 @@ public class AnalyseFileRealDataIntegrationTest extends LiveDataIntegrationTest
redactionMessageReceiver.receiveAnalyzeRequest(in, false);
// var log = redactionStorageService.getRedactionLog("dossierId","fileId");
// var redactionLog = redactionStorageService.getRedactionLog("dossierId","fileId");
// redactionLog.getRedactionLogEntry().forEach(entry ->{
// log.info("Entry {}", entry);
// });
//
// var annotated = annotationService.annotate(AnnotateRequest.builder().fileId("fileId").dossierId("dossierId").build());
// annotated.getDocument();
//
// File tempFile = File.createTempFile("annotated",".pdf");
// IOUtils.write(annotated.getDocument(), new FileOutputStream(tempFile));
// log.warn("File saved to: {}",tempFile.getAbsolutePath());
// Runtime.getRuntime().exec("open "+tempFile.getAbsolutePath());
}
}
@@ -1,17 +1,21 @@
package com.iqser.red.service.redaction.v1.server.realdata;
import static org.assertj.core.api.AssertionsForClassTypes.assertThat;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.anyBoolean;
import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.nullable;
import static org.mockito.Mockito.when;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.iqser.red.service.persistence.service.v1.api.model.common.JSONPrimitive;
import com.iqser.red.service.persistence.service.v1.api.model.dossiertemplate.configuration.Colors;
import com.iqser.red.service.persistence.service.v1.api.model.dossiertemplate.type.DictionaryEntry;
import com.iqser.red.service.persistence.service.v1.api.model.dossiertemplate.type.Type;
import com.iqser.red.service.redaction.v1.server.Application;
import com.iqser.red.service.redaction.v1.server.FileSystemBackedStorageService;
import com.iqser.red.service.redaction.v1.server.client.*;
import com.iqser.red.service.redaction.v1.server.queue.RedactionMessageReceiver;
import com.iqser.red.service.redaction.v1.server.redaction.service.DictionaryService;
import com.iqser.red.service.redaction.v1.server.settings.RedactionServiceSettings;
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.junit.Before;
import org.junit.Test;
@@ -30,27 +34,14 @@ import org.springframework.core.io.Resource;
import org.springframework.core.io.support.ResourcePatternResolver;
import org.springframework.test.context.junit4.SpringRunner;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.iqser.red.service.persistence.service.v1.api.model.common.JSONPrimitive;
import com.iqser.red.service.persistence.service.v1.api.model.dossiertemplate.configuration.Colors;
import com.iqser.red.service.persistence.service.v1.api.model.dossiertemplate.type.DictionaryEntry;
import com.iqser.red.service.persistence.service.v1.api.model.dossiertemplate.type.Type;
import com.iqser.red.service.redaction.v1.server.Application;
import com.iqser.red.service.redaction.v1.server.FileSystemBackedStorageService;
import com.iqser.red.service.redaction.v1.server.client.DictionaryClient;
import com.iqser.red.service.redaction.v1.server.client.EntityRecognitionClient;
import com.iqser.red.service.redaction.v1.server.client.FileStatusProcessingUpdateClient;
import com.iqser.red.service.redaction.v1.server.client.LegalBasisClient;
import com.iqser.red.service.redaction.v1.server.client.RulesClient;
import com.iqser.red.service.redaction.v1.server.queue.RedactionMessageReceiver;
import com.iqser.red.service.redaction.v1.server.redaction.service.DictionaryService;
import com.iqser.red.service.redaction.v1.server.settings.RedactionServiceSettings;
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 java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import lombok.SneakyThrows;
import static org.assertj.core.api.AssertionsForClassTypes.assertThat;
import static org.mockito.ArgumentMatchers.*;
import static org.mockito.Mockito.when;
@RunWith(SpringRunner.class)
@SpringBootTest(classes = Application.class, webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT)
@@ -143,6 +134,7 @@ public class LiveDataIntegrationTest {
if (found.isPresent()) {
var type = types.stream().filter(t -> t.getType().equalsIgnoreCase(typeName)).findFirst().get();
type.setEntries(getEntries(typeName, type.getTypeId()));
type.setFalsePositiveEntries(getFalsePositiveEntries(typeName, type.getTypeId()));
return type;
} else {
@@ -196,7 +188,22 @@ public class LiveDataIntegrationTest {
Resource[] dictionaryResources = resourcePatternResolver.getResources("classpath:" + BASE_DIR + EFSA_SANITISATION_GFL_V1 + "dictionaries/**");
for (var resource : dictionaryResources) {
if (Objects.requireNonNull(resource.getFilename()).contains(typeName)) {
if (Objects.requireNonNull(resource.getFilename()).contains(typeName) && !resource.getFilename().contains("false_positive")) {
List<String> lines = IOUtils.readLines(resource.getInputStream());
return lines.stream().map(l -> new DictionaryEntry(0, l, 0L, false, typeId)).collect(Collectors.toList());
}
}
return new ArrayList<>();
}
@SneakyThrows
private List<DictionaryEntry> getFalsePositiveEntries(String typeName, String typeId) {
Resource[] dictionaryResources = resourcePatternResolver.getResources("classpath:" + BASE_DIR + EFSA_SANITISATION_GFL_V1 + "dictionaries/**");
for (var resource : dictionaryResources) {
if (Objects.requireNonNull(resource.getFilename()).contains(typeName) && resource.getFilename().contains("false_positive")) {
List<String> lines = IOUtils.readLines(resource.getInputStream());
return lines.stream().map(l -> new DictionaryEntry(0, l, 0L, false, typeId)).collect(Collectors.toList());
@@ -0,0 +1,533 @@
{
"analysisVersion": 1,
"analysisNumber": 0,
"redactionLogEntry": [
{
"id": "96c1362cb4ea87461d8f5f141df1912a",
"type": "PII",
"value": "patrick.gardinal@syngenta.com",
"reason": "Personal information found",
"matchedRule": 23,
"rectangle": false,
"legalBasis": "Article 39(e)(3) of Regulation (EC) No 178/2002",
"imported": false,
"redacted": true,
"section": "CP 1.2 Producer of the Plant Protection Product and the Active\nSubstances",
"color": [
0.4,
0.8,
1.0
],
"positions": [
{
"topLeft": {
"x": 286.92,
"y": 368.44
},
"width": 141.39014,
"height": 11.52,
"page": 5
}
],
"sectionNumber": 10,
"textBefore": "60 51 E-mail: ",
"textAfter": null,
"comments": [],
"startOffset": 295,
"endOffset": 324,
"imageHasTransparency": false,
"excluded": false,
"sourceId": null,
"changes": [
{
"analysisNumber": 0,
"type": "ADDED",
"dateTime": "2022-07-25T11:12:04.3835183+02:00"
}
],
"manualChanges": [],
"engines": [
"RULE"
],
"reference": [],
"importedRedactionIntersections": [],
"dossierDictionaryEntry": false,
"localManualRedaction": false,
"dictionaryEntry": false,
"image": false,
"falsePositive": false,
"manuallyRemoved": false,
"hint": false,
"recommendation": false
},
{
"id": "74b528293158d5266ace1eaf9ee2ad80",
"type": "PII",
"value": "+41 (0) 61 323 60 51",
"reason": "Personal information found",
"matchedRule": 23,
"rectangle": false,
"legalBasis": "Article 39(e)(3) of Regulation (EC) No 178/2002",
"imported": false,
"redacted": true,
"section": "Producer of the active substance: Cyprodinil",
"color": [
0.4,
0.8,
1.0
],
"positions": [
{
"topLeft": {
"x": 286.92,
"y": 169.96002
},
"width": 94.37213,
"height": 11.52,
"page": 5
}
],
"sectionNumber": 12,
"textBefore": "Gardinal Telephone number: ",
"textAfter": " E-mail: patrick.gardinal@syngenta.com",
"comments": [],
"startOffset": 188,
"endOffset": 208,
"imageHasTransparency": false,
"excluded": false,
"sourceId": null,
"changes": [
{
"analysisNumber": 0,
"type": "ADDED",
"dateTime": "2022-07-25T11:12:04.3835183+02:00"
}
],
"manualChanges": [],
"engines": [
"RULE"
],
"reference": [],
"importedRedactionIntersections": [],
"dossierDictionaryEntry": false,
"localManualRedaction": false,
"dictionaryEntry": false,
"image": false,
"falsePositive": false,
"manuallyRemoved": false,
"hint": false,
"recommendation": false
},
{
"id": "d282cd8f02e2628c14342ed52d69c517",
"type": "PII",
"value": "+41 (61) 323 6152",
"reason": "Personal information found",
"matchedRule": 23,
"rectangle": false,
"legalBasis": "Article 39(e)(3) of Regulation (EC) No 178/2002",
"imported": false,
"redacted": true,
"section": "CP 1.1 Applicant",
"color": [
0.4,
0.8,
1.0
],
"positions": [
{
"topLeft": {
"x": 286.92,
"y": 610.12
},
"width": 83.43994,
"height": 11.52,
"page": 5
}
],
"sectionNumber": 9,
"textBefore": "Micheletti Telephone number: ",
"textAfter": " E-mail: sebastien.micheletti@syngenta.com",
"comments": [],
"startOffset": 164,
"endOffset": 181,
"imageHasTransparency": false,
"excluded": false,
"sourceId": null,
"changes": [
{
"analysisNumber": 0,
"type": "ADDED",
"dateTime": "2022-07-25T11:12:04.3835183+02:00"
}
],
"manualChanges": [],
"engines": [
"RULE"
],
"reference": [],
"importedRedactionIntersections": [],
"dossierDictionaryEntry": false,
"localManualRedaction": false,
"dictionaryEntry": false,
"image": false,
"falsePositive": false,
"manuallyRemoved": false,
"hint": false,
"recommendation": false
},
{
"id": "245cfd060d4fb078bb211fabfce6d470",
"type": "PII",
"value": "patrick.gardinal@syngenta.com",
"reason": "Personal information found",
"matchedRule": 23,
"rectangle": false,
"legalBasis": "Article 39(e)(3) of Regulation (EC) No 178/2002",
"imported": false,
"redacted": true,
"section": "Producer of the active substance: Cyprodinil",
"color": [
0.4,
0.8,
1.0
],
"positions": [
{
"topLeft": {
"x": 286.92,
"y": 144.64001
},
"width": 141.39014,
"height": 11.52,
"page": 5
}
],
"sectionNumber": 12,
"textBefore": "60 51 E-mail: ",
"textAfter": null,
"comments": [],
"startOffset": 217,
"endOffset": 246,
"imageHasTransparency": false,
"excluded": false,
"sourceId": null,
"changes": [
{
"analysisNumber": 0,
"type": "ADDED",
"dateTime": "2022-07-25T11:12:04.3835183+02:00"
}
],
"manualChanges": [],
"engines": [
"RULE"
],
"reference": [],
"importedRedactionIntersections": [],
"dossierDictionaryEntry": false,
"localManualRedaction": false,
"dictionaryEntry": false,
"image": false,
"falsePositive": false,
"manuallyRemoved": false,
"hint": false,
"recommendation": false
},
{
"id": "67dc43606b8e1489a0594e5b779fa428",
"type": "PII",
"value": "Patrick Gardinal",
"reason": "Personal information found",
"matchedRule": 23,
"rectangle": false,
"legalBasis": "Article 39(e)(3) of Regulation (EC) No 178/2002",
"imported": false,
"redacted": true,
"section": "CP 1.2 Producer of the Plant Protection Product and the Active\nSubstances",
"color": [
0.4,
0.8,
1.0
],
"positions": [
{
"topLeft": {
"x": 286.92,
"y": 419.08
},
"width": 73.440186,
"height": 11.52,
"page": 5
}
],
"sectionNumber": 10,
"textBefore": "Basel; Switzerland Contact: ",
"textAfter": " Telephone number:",
"comments": [],
"startOffset": 231,
"endOffset": 247,
"imageHasTransparency": false,
"excluded": false,
"sourceId": null,
"changes": [
{
"analysisNumber": 0,
"type": "ADDED",
"dateTime": "2022-07-25T11:12:04.3835183+02:00"
}
],
"manualChanges": [],
"engines": [
"RULE"
],
"reference": [],
"importedRedactionIntersections": [],
"dossierDictionaryEntry": false,
"localManualRedaction": false,
"dictionaryEntry": false,
"image": false,
"falsePositive": false,
"manuallyRemoved": false,
"hint": false,
"recommendation": false
},
{
"id": "de79428457282a0781a827b322b5732a",
"type": "PII",
"value": "sebastien.micheletti@syngenta.com",
"reason": "Personal information found",
"matchedRule": 23,
"rectangle": false,
"legalBasis": "Article 39(e)(3) of Regulation (EC) No 178/2002",
"imported": false,
"redacted": true,
"section": "CP 1.1 Applicant",
"color": [
0.4,
0.8,
1.0
],
"positions": [
{
"topLeft": {
"x": 286.92,
"y": 584.8
},
"width": 161.04922,
"height": 10.98,
"page": 5
}
],
"sectionNumber": 9,
"textBefore": "323 6152 E-mail: ",
"textAfter": null,
"comments": [],
"startOffset": 190,
"endOffset": 223,
"imageHasTransparency": false,
"excluded": false,
"sourceId": null,
"changes": [
{
"analysisNumber": 0,
"type": "ADDED",
"dateTime": "2022-07-25T11:12:04.3835183+02:00"
}
],
"manualChanges": [],
"engines": [
"RULE"
],
"reference": [],
"importedRedactionIntersections": [],
"dossierDictionaryEntry": false,
"localManualRedaction": false,
"dictionaryEntry": false,
"image": false,
"falsePositive": false,
"manuallyRemoved": false,
"hint": false,
"recommendation": false
},
{
"id": "41340ab190d66ca6dce0ba965ce95f59",
"type": "PII",
"value": "Patrick Gardinal",
"reason": "Personal information found",
"matchedRule": 23,
"rectangle": false,
"legalBasis": "Article 39(e)(3) of Regulation (EC) No 178/2002",
"imported": false,
"redacted": true,
"section": "Producer of the active substance: Cyprodinil",
"color": [
0.4,
0.8,
1.0
],
"positions": [
{
"topLeft": {
"x": 286.92,
"y": 195.28003
},
"width": 73.440186,
"height": 11.52,
"page": 5
}
],
"sectionNumber": 12,
"textBefore": "Basel; Switzerland Contact: ",
"textAfter": " Telephone number:",
"comments": [],
"startOffset": 153,
"endOffset": 169,
"imageHasTransparency": false,
"excluded": false,
"sourceId": null,
"changes": [
{
"analysisNumber": 0,
"type": "ADDED",
"dateTime": "2022-07-25T11:12:04.3835183+02:00"
}
],
"manualChanges": [],
"engines": [
"RULE"
],
"reference": [],
"importedRedactionIntersections": [],
"dossierDictionaryEntry": false,
"localManualRedaction": false,
"dictionaryEntry": false,
"image": false,
"falsePositive": false,
"manuallyRemoved": false,
"hint": false,
"recommendation": false
},
{
"id": "02dd2efb100839e705cdcf6f3141d9d5",
"type": "PII",
"value": "Sebastien Micheletti",
"reason": "Personal information found",
"matchedRule": 23,
"rectangle": false,
"legalBasis": "Article 39(e)(3) of Regulation (EC) No 178/2002",
"imported": false,
"redacted": true,
"section": "CP 1.1 Applicant",
"color": [
0.4,
0.8,
1.0
],
"positions": [
{
"topLeft": {
"x": 286.92,
"y": 634.84
},
"width": 91.21478,
"height": 11.52,
"page": 5
}
],
"sectionNumber": 9,
"textBefore": "Basel; Switzerland Contact: ",
"textAfter": " Telephone number:",
"comments": [],
"startOffset": 125,
"endOffset": 145,
"imageHasTransparency": false,
"excluded": false,
"sourceId": null,
"changes": [
{
"analysisNumber": 0,
"type": "ADDED",
"dateTime": "2022-07-25T11:12:04.3835183+02:00"
}
],
"manualChanges": [],
"engines": [
"RULE"
],
"reference": [],
"importedRedactionIntersections": [],
"dossierDictionaryEntry": false,
"localManualRedaction": false,
"dictionaryEntry": false,
"image": false,
"falsePositive": false,
"manuallyRemoved": false,
"hint": false,
"recommendation": false
},
{
"id": "530c4f47f0afc48432bd849a90918f41",
"type": "PII",
"value": "+41 (0) 61 323 60 51",
"reason": "Personal information found",
"matchedRule": 23,
"rectangle": false,
"legalBasis": "Article 39(e)(3) of Regulation (EC) No 178/2002",
"imported": false,
"redacted": true,
"section": "CP 1.2 Producer of the Plant Protection Product and the Active\nSubstances",
"color": [
0.4,
0.8,
1.0
],
"positions": [
{
"topLeft": {
"x": 286.92,
"y": 393.76
},
"width": 94.37213,
"height": 11.52,
"page": 5
}
],
"sectionNumber": 10,
"textBefore": "Gardinal Telephone number: ",
"textAfter": " E-mail: patrick.gardinal@syngenta.com",
"comments": [],
"startOffset": 266,
"endOffset": 286,
"imageHasTransparency": false,
"excluded": false,
"sourceId": null,
"changes": [
{
"analysisNumber": 0,
"type": "ADDED",
"dateTime": "2022-07-25T11:12:04.3835183+02:00"
}
],
"manualChanges": [],
"engines": [
"RULE"
],
"reference": [],
"importedRedactionIntersections": [],
"dossierDictionaryEntry": false,
"localManualRedaction": false,
"dictionaryEntry": false,
"image": false,
"falsePositive": false,
"manuallyRemoved": false,
"hint": false,
"recommendation": false
}
],
"legalBasis": [],
"dictionaryVersion": 0,
"dossierDictionaryVersion": 0,
"rulesVersion": 0,
"legalBasisVersion": 0
}
@@ -0,0 +1 @@
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@@ -0,0 +1 @@
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