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12
Commits
| Author | SHA1 | Date | |
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e4823e20d4 | ||
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53428ec652 | ||
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ca270fb7de | ||
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06fe0dbd97 | ||
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1d8e86e4f6 | ||
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2b7972315f | ||
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0af853dbfc | ||
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0544a42117 | ||
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8bdfd6747d | ||
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80c0c25c06 | ||
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17baf9c0eb | ||
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090a619600 |
@@ -32,7 +32,7 @@
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<dependency>
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<groupId>com.iqser.red</groupId>
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<artifactId>platform-commons-dependency</artifactId>
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<version>1.17.0</version>
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<version>1.19.0</version>
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<scope>import</scope>
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<type>pom</type>
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</dependency>
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@@ -12,7 +12,7 @@
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<artifactId>redaction-service-api-v1</artifactId>
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<properties>
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<persistence-service.version>1.240.0</persistence-service.version>
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<persistence-service.version>1.254.0</persistence-service.version>
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</properties>
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<dependencies>
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+11
-2
@@ -40,11 +40,11 @@ public class EntitySearchUtils {
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if (details.getEntityType() == EntityType.RECOMMENDATION) {
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Set<Entity> falseRecommendations = find(inputString, type.getFalseRecommendationsSearch(), details.withEntityType(EntityType.FALSE_RECOMMENDATION));
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removeFalsePositives(found, falseRecommendations);
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found.addAll(falseRecommendations);
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// found.addAll(falseRecommendations);
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} else {
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Set<Entity> falsePositives = find(inputString, type.getFalsePositiveSearch(), details.withEntityType(EntityType.FALSE_POSITIVE));
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removeFalsePositives(found, falsePositives);
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found.addAll(falsePositives);
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// found.addAll(falsePositives);
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}
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return found;
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@@ -152,6 +152,15 @@ public class EntitySearchUtils {
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List<Entity> wordsToRemove = new ArrayList<>();
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for (Entity word : entities) {
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for (Entity inner : entities) {
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// // skip cross-type false positives
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// if(word.getEntityType() == EntityType.FALSE_POSITIVE && inner.getEntityType() == EntityType.ENTITY && !inner.getType().equals(word.getType())){
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// continue;
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// }
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// // skip cross-type false reccommendations
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// if(word.getEntityType() == EntityType.FALSE_RECOMMENDATION && inner.getEntityType() == EntityType.RECOMMENDATION && !inner.getType().equals(word.getType())){
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// continue;
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// }
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if (inner.getWord().length() < word.getWord()
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.length() && inner.getStart() >= word.getStart() && inner.getEnd() <= word.getEnd() && word != inner && word.getSectionNumber() == inner.getSectionNumber()) {
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if (word.getEntityType().equals(EntityType.RECOMMENDATION) && inner.getEntityType().equals(EntityType.ENTITY)) {
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+3
-5
@@ -3,6 +3,7 @@ package com.iqser.red.service.redaction.v1.server;
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import com.fasterxml.jackson.databind.DeserializationFeature;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
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import com.iqser.red.commons.jackson.ObjectMapperFactory;
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import com.iqser.red.storage.commons.exception.StorageObjectDoesNotExist;
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import com.iqser.red.storage.commons.service.StorageService;
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import lombok.SneakyThrows;
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@@ -62,11 +63,8 @@ public class FileSystemBackedStorageService implements StorageService {
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}
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private ObjectMapper getMapper() {
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var objectMapper = new ObjectMapper();
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objectMapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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objectMapper.registerModule(new JavaTimeModule());
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objectMapper.findAndRegisterModules();
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return objectMapper;
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return ObjectMapperFactory.create();
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}
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@Override
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+33
-27
@@ -113,12 +113,13 @@ public class RulesTest {
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private static final String IMPORTED_REDACTION = "imported_redaction";
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private static final String PII = "PII";
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private static final String RESOURCES_PATH = "src/test/resources/";
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private static final String REDACTION_LOG_PATH = "RedactionLog/";
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private static final String REDACTION_LOG_RESOURCES_PATH = RESOURCES_PATH + REDACTION_LOG_PATH;
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private final static String TEST_DOSSIER_TEMPLATE_ID = "123";
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private final static String TEST_DOSSIER_ID = "123";
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private String TEST_FILE_ID = "123";
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private int counter = 0;
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private int fileSize = 0;
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private final Map<String, List<String>> dictionary = new HashMap<>();
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private final Map<String, List<String>> dossierDictionary = new HashMap<>();
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private final Map<String, List<String>> falsePositive = new HashMap<>();
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@@ -207,6 +208,7 @@ public class RulesTest {
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public void generateRedactionLogForOneFile() {
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String fileName = "files/Compounds/31 A14111B - EU AIR3 - MCP Section 1 - Identity of the plant protection product.pdf";
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fileSize = 1;
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generateAndSaveRedactionLog(fileName, true);
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}
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@@ -221,6 +223,7 @@ public class RulesTest {
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Set<String> files = getFileNames(new HashSet<>(), FileSystems.getDefault().getPath(RESOURCES_PATH));
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System.out.println("Will generate RedactionLog for " + files.size() + " files.");
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fileSize = files.size();
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files.forEach(this::generateAndSaveRedactionLog);
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}
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@@ -232,9 +235,8 @@ public class RulesTest {
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@Test
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public void analyseFileAndCompareRedactionLog() {
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String fileName = "files/RulesTest/SYNGENTA_EFSA_sanitisation_GFL_v1_withHighlights.pdf"; //TODO PSC
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// String fileName = "scanned/VV-377031.pdf";
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// fileName = "files/new/A20622A izRMS (CZ) fRR Part B9.pdf";
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String fileName = "files/RulesTest/SYNGENTA_EFSA_sanitisation_GFL_v1_withHighlights.pdf";
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fileSize = 1;
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analyseFileAndCompareRedactionLog(fileName);
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}
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@@ -243,12 +245,13 @@ public class RulesTest {
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* Analyses all files and compares its RedactionLog with saved one from here: REDACTION_LOG_PATH.
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* If RedactionLog Json for one file does not exist, whole test will fail.
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*/
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@IfProfileValue(name = "test-groups", value = "rules-test") //TODO PSC
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@IfProfileValue(name = "test-groups", value = "rules-test")
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@Test
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public void analyseAllFilesAndCompareRedactionLogs() {
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Set<String> files = getFileNames(new HashSet<>(), FileSystems.getDefault().getPath(RESOURCES_PATH));
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System.out.println("Will analyse " + files.size() + " files and compare its RedactionLogs.");
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fileSize = files.size();
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files.forEach(this::analyseFileAndCompareRedactionLog);
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}
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@@ -262,13 +265,14 @@ public class RulesTest {
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@SneakyThrows
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private void generateAndSaveRedactionLog(String fileName, boolean force) {
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counter++;
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if (!force && doesRedactionLogExist(fileName)) {
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System.out.println("Skip generating RedactionLog as Json for " + fileName + " because it already exists.");
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System.out.println("(" + counter + "/" + fileSize + ") Skip generating RedactionLog as Json for " + fileName + " because it already exists.");
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} else {
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generateTestFileId(fileName);
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System.out.println("Generate RedactionLog as Json for " + fileName + " with fileId " + TEST_FILE_ID);
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System.out.println("(" + counter + "/" + fileSize + ") Generate RedactionLog as Json for " + fileName + " with fileId " + TEST_FILE_ID);
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loadNerForTest();
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@@ -287,8 +291,9 @@ public class RulesTest {
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@SneakyThrows
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public void analyseFileAndCompareRedactionLog(String fileName) {
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counter++;
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generateTestFileId(fileName);
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System.out.println("Analyse " + fileName + " with fileId " + TEST_FILE_ID + " and compare it with its saved RedactionLog");
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System.out.println("(" + counter + "/" + fileSize + ") Analyse " + fileName + " with fileId " + TEST_FILE_ID + " and compare it with its saved RedactionLog");
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RedactionLog savedRedactionLog = loadSavedRedactionLog(fileName);
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@@ -396,7 +401,7 @@ public class RulesTest {
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assertThat(savedManualChange).isPresent();
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}
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assertThat(savedRedactionLogEntry.get().getEngines()).containsExactly(redactionLogEntry.getEngines().toArray(new Engine[0]));
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assertThat(savedRedactionLogEntry.get().getEngines()).containsExactlyInAnyOrder(redactionLogEntry.getEngines().toArray(new Engine[0]));
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assertThat(savedRedactionLogEntry.get().getReference()).containsAll(redactionLogEntry.getReference());
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assertThat(savedRedactionLogEntry.get().getImportedRedactionIntersections()).containsAll(redactionLogEntry.getImportedRedactionIntersections());
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@@ -471,6 +476,25 @@ public class RulesTest {
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}
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@SneakyThrows
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private Set<String> getFileNames(Set<String> fileNames, Path dir) {
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try (DirectoryStream<Path> stream = Files.newDirectoryStream(dir)) {
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for (Path path : stream) {
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if (path.toFile().isDirectory()) {
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getFileNames(fileNames, path);
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} else if (StringUtils.endsWith(path.toAbsolutePath().toString(), ".pdf")) {
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String absolutePath = cleanPath(path.toAbsolutePath().toString());
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int pos = StringUtils.indexOf(absolutePath, RESOURCES_PATH) + RESOURCES_PATH.length();
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fileNames.add(StringUtils.substring(absolutePath, pos));
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}
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}
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}
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return fileNames;
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}
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private String cleanPath(String path) {
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return StringUtils.replace(path, "\\", "/");
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@@ -615,24 +639,6 @@ public class RulesTest {
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}
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@SneakyThrows
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private Set<String> getFileNames(Set<String> fileNames, Path dir) {
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try (DirectoryStream<Path> stream = Files.newDirectoryStream(dir)) {
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for (Path path : stream) {
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if (path.toFile().isDirectory()) {
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getFileNames(fileNames, path);
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} else if (StringUtils.endsWith(path.toAbsolutePath().toString(), ".pdf")) {
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String absolutePath = cleanPath(path.toAbsolutePath().toString());
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int pos = StringUtils.indexOf(absolutePath, RESOURCES_PATH) + RESOURCES_PATH.length();
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fileNames.add(StringUtils.substring(absolutePath, pos));
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}
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}
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}
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return fileNames;
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}
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private Type getDictionaryResponse(String type, boolean isDossierDictionary) {
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return Type.builder()
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{"analysisVersion":1,"analysisNumber":0,"redactionLogEntry":[{"id":"12ac3d26ce82a77e469c64d56081662d","type":"CBI_author","value":"Micheletti S","reason":"Author found","matchedRule":1,"rectangle":false,"legalBasis":"Article 39(e)(3) of Regulation (EC) No 178/2002","imported":false,"redacted":true,"section":"Table in: COPY OF THE APPLICATION FOR RENEWAL, MADE UNDER COMMISSION","color":[1.0,0.88235295,0.5294118],"positions":[{"topLeft":{"x":214.8,"y":639.64},"width":55.039078,"height":11.52,"page":4}],"sectionNumber":3,"textBefore":"Report: Document F/02, ","textAfter":". (2014). Cyprodinil","comments":[],"startOffset":23,"endOffset":35,"imageHasTransparency":false,"excluded":false,"sourceId":null,"changes":[{"analysisNumber":0,"type":"ADDED","dateTime":1658398559.316208600}],"manualChanges":[],"engines":["DICTIONARY"],"reference":[],"importedRedactionIntersections":[],"dossierDictionaryEntry":false,"recommendation":false,"hint":false,"dictionaryEntry":true,"falsePositive":false,"image":false,"localManualRedaction":false,"manuallyRemoved":false},{"id":"dd614353319e7c5a8cf8b3346dc12fac","type":"CBI_author","value":"Micheletti S","reason":"Author found","matchedRule":1,"rectangle":false,"legalBasis":"Article 39(e)(3) of Regulation (EC) No 178/2002","imported":false,"redacted":true,"section":"COPY OF THE APPLICATION FOR RENEWAL, MADE UNDER COMMISSION","color":[1.0,0.88235295,0.5294118],"positions":[{"topLeft":{"x":306.84,"y":667.12},"width":60.71997,"height":12.0,"page":4}],"sectionNumber":5,"textBefore":"F report (","textAfter":"., 2014).","comments":[],"startOffset":247,"endOffset":259,"imageHasTransparency":false,"excluded":false,"sourceId":null,"changes":[{"analysisNumber":0,"type":"ADDED","dateTime":1658398559.316208600}],"manualChanges":[],"engines":["DICTIONARY"],"reference":[],"importedRedactionIntersections":[],"dossierDictionaryEntry":false,"recommendation":false,"hint":false,"dictionaryEntry":true,"falsePositive":false,"image":false,"localManualRedaction":false,"manuallyRemoved":false}],"legalBasis":[],"dictionaryVersion":0,"dossierDictionaryVersion":0,"rulesVersion":0,"legalBasisVersion":0}
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{"analysisVersion":1,"analysisNumber":0,"redactionLogEntry":[{"id":"12ac3d26ce82a77e469c64d56081662d","type":"CBI_author","value":"Micheletti S","reason":"Author found","matchedRule":1,"rectangle":false,"legalBasis":"Article 39(e)(3) of Regulation (EC) No 178/2002","imported":false,"redacted":true,"section":"Table in: COPY OF THE APPLICATION FOR RENEWAL, MADE UNDER COMMISSION","color":[1.0,0.88235295,0.5294118],"positions":[{"topLeft":{"x":214.8,"y":639.64},"width":55.039078,"height":11.52,"page":4}],"sectionNumber":3,"textBefore":"Report: Document F/02, ","textAfter":". (2014). Cyprodinil","comments":[],"startOffset":23,"endOffset":35,"imageHasTransparency":false,"excluded":false,"sourceId":null,"changes":[{"analysisNumber":0,"type":"ADDED","dateTime":"2022-07-29T11:23:17.792388+03:00"}],"manualChanges":[],"engines":["DICTIONARY"],"reference":[],"importedRedactionIntersections":[],"hint":false,"image":false,"recommendation":false,"falsePositive":false,"dictionaryEntry":true,"dossierDictionaryEntry":false,"localManualRedaction":false,"manuallyRemoved":false},{"id":"dd614353319e7c5a8cf8b3346dc12fac","type":"CBI_author","value":"Micheletti S","reason":"Author found","matchedRule":1,"rectangle":false,"legalBasis":"Article 39(e)(3) of Regulation (EC) No 178/2002","imported":false,"redacted":true,"section":"COPY OF THE APPLICATION FOR RENEWAL, MADE UNDER COMMISSION","color":[1.0,0.88235295,0.5294118],"positions":[{"topLeft":{"x":306.84,"y":667.12},"width":60.71997,"height":12.0,"page":4}],"sectionNumber":5,"textBefore":"F report (","textAfter":"., 2014).","comments":[],"startOffset":247,"endOffset":259,"imageHasTransparency":false,"excluded":false,"sourceId":null,"changes":[{"analysisNumber":0,"type":"ADDED","dateTime":"2022-07-29T11:23:17.792391+03:00"}],"manualChanges":[],"engines":["DICTIONARY"],"reference":[],"importedRedactionIntersections":[],"hint":false,"image":false,"recommendation":false,"falsePositive":false,"dictionaryEntry":true,"dossierDictionaryEntry":false,"localManualRedaction":false,"manuallyRemoved":false}],"legalBasis":[],"dictionaryVersion":0,"dossierDictionaryVersion":0,"rulesVersion":0,"legalBasisVersion":0}
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