Spike: LLM NER
This commit is contained in:
Kilian Schüttler
parent
5ebe82b7ce
commit
4dc0a1fbdc
@ -28,6 +28,8 @@ tasks.named<Test>("test") {
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reports {
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junitXml.outputLocation.set(layout.buildDirectory.dir("reports/junit"))
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}
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minHeapSize = "512m"
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maxHeapSize = "2048m"
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}
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tasks.test {
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@ -17,6 +17,7 @@ val jacksonVersion = "2.15.2"
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val droolsVersion = "9.44.0.Final"
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val pdfBoxVersion = "3.0.0"
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val persistenceServiceVersion = "2.532.0"
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val llmServiceVersion = "1.11.0"
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val springBootStarterVersion = "3.1.5"
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val springCloudVersion = "4.0.4"
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val testContainersVersion = "1.19.7"
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@ -39,7 +40,7 @@ dependencies {
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exclude(group = "com.knecon.fforesight", module = "tenant-commons")
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}
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implementation("com.knecon.fforesight:layoutparser-service-internal-api:${layoutParserVersion}")
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implementation("com.knecon.fforesight:llm-service-api:${llmServiceVersion}")
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implementation("com.iqser.red.commons:spring-commons:6.2.0")
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implementation("com.iqser.red.commons:metric-commons:2.3.0")
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@ -48,7 +49,7 @@ dependencies {
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implementation("com.knecon.fforesight:tenant-commons:0.28.0")
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implementation("com.knecon.fforesight:keycloak-commons:0.30.0")
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implementation("com.knecon.fforesight:tracing-commons:0.5.0")
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implementation("com.knecon.fforesight:lifecycle-commons:0.6.0")
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implementation("com.knecon.fforesight:lifecycle-commons:0.7.0")
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implementation("com.fasterxml.jackson.module:jackson-module-afterburner:${jacksonVersion}")
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implementation("com.fasterxml.jackson.datatype:jackson-datatype-jsr310:${jacksonVersion}")
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@ -24,6 +24,8 @@ public class RedactionServiceSettings {
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private boolean azureNerServiceEnabled;
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private boolean llmNerServiceEnabled;
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private boolean priorityMode;
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private long dictionaryCacheMaximumSize = 100;
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@ -10,7 +10,6 @@ import com.iqser.red.service.redaction.v1.server.model.document.TextRange;
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import lombok.AccessLevel;
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import lombok.AllArgsConstructor;
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import lombok.Getter;
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import lombok.RequiredArgsConstructor;
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import lombok.experimental.FieldDefaults;
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/**
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@ -65,16 +64,22 @@ public class NerEntities {
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}
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/**
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* Represents a single NER entity with its value, text range, and type.
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*/
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public record NerEntity(String value, TextRange textRange, String type, Double confidence) {
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public record NerEntity(String value, TextRange textRange, String type, Double confidence, Engine engine) {
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public NerEntity(String value, TextRange textRange, String type) {
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this(value, textRange, type, null);
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this(value, textRange, type, null, Engine.NER);
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}
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}
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public enum Engine {
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NER,
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CLOUD_NER,
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LLM_NER
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}
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}
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@ -33,6 +33,7 @@ import com.iqser.red.service.redaction.v1.server.model.PrecursorEntity;
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import com.iqser.red.service.redaction.v1.server.model.dictionary.Dictionary;
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import com.iqser.red.service.redaction.v1.server.model.dictionary.DictionaryIncrement;
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import com.iqser.red.service.redaction.v1.server.model.dictionary.DictionaryVersion;
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import com.iqser.red.service.redaction.v1.server.model.document.TextRange;
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import com.iqser.red.service.redaction.v1.server.model.document.nodes.Document;
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import com.iqser.red.service.redaction.v1.server.model.document.nodes.SemanticNode;
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import com.iqser.red.service.redaction.v1.server.service.document.AreaGroupAnnotationService;
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@ -332,19 +333,38 @@ public class AnalysisPreparationService {
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NerEntities nerEntities;
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if (redactionServiceSettings.isNerServiceEnabled()) {
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nerEntities = NerEntitiesAdapter.toNerEntities(redactionStorageService.getNerEntities(analyzeRequest.getDossierId(), analyzeRequest.getFileId()), document);
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nerEntities = NerEntitiesAdapter.toNerEntities(redactionStorageService.getNerEntities(analyzeRequest.getDossierId(), analyzeRequest.getFileId()),
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document,
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NerEntities.Engine.NER);
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} else {
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nerEntities = new NerEntities(Collections.emptyList());
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}
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if (redactionServiceSettings.isAzureNerServiceEnabled()) {
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NerEntitiesModel azureNerEntitiesModel = redactionStorageService.getAzureNerEntities(analyzeRequest.getDossierId(), analyzeRequest.getFileId());
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NerEntities azureNerEntities = NerEntitiesAdapter.toNerEntities(azureNerEntitiesModel, document);
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NerEntities azureNerEntities = NerEntitiesAdapter.toNerEntities(azureNerEntitiesModel, document, NerEntities.Engine.CLOUD_NER);
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nerEntities.merge(azureNerEntities);
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}
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if (redactionServiceSettings.isLlmNerServiceEnabled()) {
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NerEntities llmNerEntities = getLlmNerEntities(analyzeRequest);
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nerEntities.merge(llmNerEntities);
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}
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return nerEntities;
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}
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private NerEntities getLlmNerEntities(AnalyzeRequest analyzeRequest) {
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return new NerEntities(redactionStorageService.getLlmNerEntities(analyzeRequest.getDossierId(), analyzeRequest.getFileId()).getEntities()
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.stream()
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.map(e -> new NerEntities.NerEntity(e.getValue(),
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new TextRange(e.getStartOffset(), e.getEndOffset()),
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e.getType(),
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null,
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NerEntities.Engine.LLM_NER))
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.toList());
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}
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private EntityLog getEntityLog(AnalyzeRequest analyzeRequest) {
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EntityLog entityLogWithoutEntries = redactionStorageService.getEntityLogWithoutEntries(analyzeRequest.getDossierId(), analyzeRequest.getFileId());
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@ -392,16 +412,20 @@ public class AnalysisPreparationService {
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if (redactionServiceSettings.isNerServiceEnabled()) {
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NerEntitiesModel nerEntitiesModel = redactionStorageService.getNerEntities(analyzeRequest.getDossierId(), analyzeRequest.getFileId());
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nerEntitiesModel = filterNerEntitiesModelBySectionIds(sectionsToReanalyseIds, nerEntitiesModel);
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nerEntities = NerEntitiesAdapter.toNerEntities(nerEntitiesModel, document);
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nerEntities = NerEntitiesAdapter.toNerEntities(nerEntitiesModel, document, NerEntities.Engine.NER);
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} else {
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nerEntities = new NerEntities(Collections.emptyList());
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}
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if (redactionServiceSettings.isAzureNerServiceEnabled()) {
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NerEntitiesModel azureNerEntitiesModel = redactionStorageService.getAzureNerEntities(analyzeRequest.getDossierId(), analyzeRequest.getFileId());
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azureNerEntitiesModel = filterNerEntitiesModelBySectionIds(sectionsToReanalyseIds, azureNerEntitiesModel);
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NerEntities azureNerEntities = NerEntitiesAdapter.toNerEntities(azureNerEntitiesModel, document);
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NerEntities azureNerEntities = NerEntitiesAdapter.toNerEntities(azureNerEntitiesModel, document, NerEntities.Engine.CLOUD_NER);
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nerEntities.merge(azureNerEntities);
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}
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if (redactionServiceSettings.isLlmNerServiceEnabled()) {
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NerEntities llmNerEntities = getLlmNerEntities(analyzeRequest);
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nerEntities.merge(llmNerEntities);
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}
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return nerEntities;
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}
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@ -44,15 +44,29 @@ public class NerEntitiesAdapter {
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*
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* @param nerEntitiesModel the Entities just as the NER Service returns them
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* @param document the document structure, from which the NER Service found the entities
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* @param engine the origin of the NerEntities
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* @return a stream of validated entities
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*/
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public NerEntities toNerEntities(NerEntitiesModel nerEntitiesModel, Document document, NerEntities.Engine engine) {
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return new NerEntities(addOffsetsAndFlatten(getStringStartOffsetsForMainSectionsHeadersFooters(document), nerEntitiesModel).map(nerEntityModel -> new NerEntities.NerEntity(
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nerEntityModel.getValue(),
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new TextRange(nerEntityModel.getStartOffset(), nerEntityModel.getEndOffset()),
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nerEntityModel.getType(),
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nerEntityModel.getConfidence(),
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engine))
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.toList());
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}
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public NerEntities toNerEntities(NerEntitiesModel nerEntitiesModel, Document document) {
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return new NerEntities(addOffsetsAndFlatten(getStringStartOffsetsForMainSectionsHeadersFooters(document), nerEntitiesModel).map(nerEntityModel -> new NerEntities.NerEntity(
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nerEntityModel.getValue(),
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new TextRange(nerEntityModel.getStartOffset(), nerEntityModel.getEndOffset()),
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nerEntityModel.getType(),
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nerEntityModel.getConfidence()))
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nerEntityModel.getConfidence(),
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NerEntities.Engine.NER))
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.toList());
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}
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@ -31,6 +31,7 @@ import com.iqser.red.service.redaction.v1.server.model.document.DocumentData;
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import com.iqser.red.service.redaction.v1.server.utils.exception.NotFoundException;
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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 com.knecon.fforesight.llm.service.LlmNerEntities;
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import com.knecon.fforesight.service.layoutparser.internal.api.data.redaction.DocumentPage;
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import com.knecon.fforesight.service.layoutparser.internal.api.data.redaction.DocumentPositionData;
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import com.knecon.fforesight.service.layoutparser.internal.api.data.redaction.DocumentStructure;
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@ -306,6 +307,12 @@ public class RedactionStorageService {
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}
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public LlmNerEntities getLlmNerEntities(String dossierId, String fileId) {
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return storageService.readJSONObject(TenantContext.getTenantId(), StorageIdUtils.getStorageId(dossierId, fileId, FileType.LLM_NER_ENTITIES), LlmNerEntities.class);
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}
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@Timed("redactmanager_getAzureNerEntities")
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public NerEntitiesModel getAzureNerEntities(String dossierId, String fileId) {
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@ -25,6 +25,7 @@ import org.bson.BsonArray;
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import org.bson.BsonDocument;
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import org.bson.BsonString;
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import org.junit.jupiter.api.AfterEach;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.BeforeEach;
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import org.mockito.stubbing.Answer;
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import org.springframework.amqp.rabbit.core.RabbitAdmin;
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@ -218,6 +219,13 @@ public abstract class AbstractRedactionIntegrationTest {
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protected TenantAuthenticationManagerResolver tenantAuthenticationManagerResolver;
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@BeforeAll
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public static void init() {
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PDFNet.initialize("demo:1650351709282:7bd235e003000000004ec28a6743e1163a085e2115de2536ab6e2cfe5a");
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}
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@BeforeEach
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public void setup() {
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@ -237,8 +245,6 @@ public abstract class AbstractRedactionIntegrationTest {
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when(tenantProvider.getTenant(any())).thenReturn(builder().tenantId("redaction").mongoDBConnection(mongoDBConnection).build());
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tenantMongoLiquibaseExecutor.initializeTenant("redaction");
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PDFNet.initialize("demo:1650351709282:7bd235e003000000004ec28a6743e1163a085e2115de2536ab6e2cfe5a");
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}
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@ -283,8 +289,10 @@ public abstract class AbstractRedactionIntegrationTest {
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true));
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when(dictionaryClient.getDictionaryForType(DOSSIER_AUTHOR_TYPE_ID, version)).then((Answer<Type>) invocation -> getDictionaryResponse(DICTIONARY_AUTHOR, true));
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when(dictionaryClient.getAllTypesForDossierTemplate(TEST_DOSSIER_TEMPLATE_ID, version, true)).then((Answer<List<Type>>)invocation -> (getTemplateDictionaryTypeResponse()));
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when(dictionaryClient.getAllTypesForDossier(TEST_DOSSIER_ID, version, true)).then((Answer<List<Type>>)invocation -> ((getDossierDictionaryTypeResponse())));
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when(dictionaryClient.getAllTypesForDossierTemplate(TEST_DOSSIER_TEMPLATE_ID,
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version,
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true)).then((Answer<List<Type>>) invocation -> (getTemplateDictionaryTypeResponse()));
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when(dictionaryClient.getAllTypesForDossier(TEST_DOSSIER_ID, version, true)).then((Answer<List<Type>>) invocation -> ((getDossierDictionaryTypeResponse())));
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}
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@ -559,7 +567,6 @@ public abstract class AbstractRedactionIntegrationTest {
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}
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protected List<Type> getDossierDictionaryTypeResponse() {
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return dossierDictionary.keySet()
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@ -5,6 +5,8 @@ import static com.iqser.red.service.redaction.v1.server.testcontainers.MongoDBTe
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import static com.iqser.red.service.redaction.v1.server.testcontainers.MongoDBTestContainer.MONGO_USERNAME;
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import static com.knecon.fforesight.tenantcommons.model.TenantResponse.builder;
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import static org.mockito.ArgumentMatchers.any;
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import static org.mockito.ArgumentMatchers.anyBoolean;
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import static org.mockito.ArgumentMatchers.anyString;
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import static org.mockito.Mockito.when;
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import java.io.File;
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@ -12,6 +14,7 @@ import java.io.FileInputStream;
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import java.nio.file.FileVisitOption;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.HashMap;
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@ -36,6 +39,7 @@ import org.springframework.boot.test.context.SpringBootTest;
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import org.springframework.boot.test.mock.mockito.MockBean;
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import org.springframework.context.annotation.Import;
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import org.springframework.core.io.ClassPathResource;
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import org.springframework.data.redis.listener.RedisMessageListenerContainer;
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import org.springframework.test.context.junit.jupiter.SpringExtension;
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import com.fasterxml.jackson.databind.ObjectMapper;
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@ -47,7 +51,9 @@ import com.iqser.red.service.persistence.service.v1.api.shared.model.RuleFileTyp
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import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.ManualRedactions;
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import com.iqser.red.service.persistence.service.v1.api.shared.model.common.JSONPrimitive;
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import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemplate.dossier.file.FileType;
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import com.iqser.red.service.persistence.service.v1.api.shared.model.group.GroupAnnotationInternalResponse;
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import com.iqser.red.service.redaction.v1.server.client.DictionaryClient;
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import com.iqser.red.service.redaction.v1.server.client.GroupRedactionClient;
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import com.iqser.red.service.redaction.v1.server.client.LegalBasisClient;
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import com.iqser.red.service.redaction.v1.server.client.RulesClient;
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import com.iqser.red.service.redaction.v1.server.model.dictionary.Dictionary;
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@ -56,6 +62,7 @@ import com.iqser.red.service.redaction.v1.server.model.dictionary.DictionaryMode
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import com.iqser.red.service.redaction.v1.server.model.dictionary.DictionaryVersion;
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import com.iqser.red.service.redaction.v1.server.service.AnalyzeService;
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import com.iqser.red.service.redaction.v1.server.service.DictionaryService;
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import com.iqser.red.service.redaction.v1.server.service.websocket.RedisSyncedWebSocketService;
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import com.iqser.red.service.redaction.v1.server.storage.RedactionStorageService;
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import com.iqser.red.service.redaction.v1.server.testcontainers.MongoDBTestContainer;
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import com.iqser.red.service.redaction.v1.server.utils.exception.NotFoundException;
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@ -83,52 +90,48 @@ import lombok.extern.slf4j.Slf4j;
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* This way you can recreate what is happening on the stack almost exactly.
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*/ public class AnalysisEnd2EndTest {
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Path dossierTemplateToUse = Path.of(
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"/Users/maverickstuder/Documents/syngenta/redactmanager/prod-cp-eu-reg/EFSA_sanitisation_pre_GFL_v1"); // Add your dossier-template here
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Path dossierTemplateToUse = Path.of("/home/kschuettler/iqser/business-logic/documine/cpglobal/Flora SCM (Do Not Edit)"); // Add your dossier-template here
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ObjectMapper mapper = ObjectMapperFactory.create();
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final String TENANT_ID = "tenant";
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TestDossierTemplate testDossierTemplate;
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@Autowired
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StorageService storageService;
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@Autowired
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protected AnalyzeService analyzeService;
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@MockBean
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DictionaryService dictionaryService;
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@MockBean
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RabbitTemplate rabbitTemplate;
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TestDossierTemplate testDossierTemplate;
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@MockBean
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protected LegalBasisClient legalBasisClient;
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@MockBean
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protected RulesClient rulesClient;
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@MockBean
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protected DictionaryClient dictionaryClient;
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@MockBean
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private MongoConnectionProvider mongoConnectionProvider;
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@MockBean
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private TenantProvider tenantProvider;
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@Autowired
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protected MongoTestConfig mongoTestConfig;
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@Autowired
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protected TenantMongoLiquibaseExecutor tenantMongoLiquibaseExecutor;
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@MockBean
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protected TenantAuthenticationManagerResolver tenantAuthenticationManagerResolver;
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@MockBean
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protected GroupRedactionClient groupRedactionClient;
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@MockBean
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private RedisSyncedWebSocketService redisSyncedWebSocketService;
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@MockBean
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private RedisMessageListenerContainer redisPubsubContainer;
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@MockBean
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DictionaryService dictionaryService;
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@MockBean
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RabbitTemplate rabbitTemplate;
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@MockBean
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protected LegalBasisClient legalBasisClient;
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@MockBean
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protected RulesClient rulesClient;
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@MockBean
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protected DictionaryClient dictionaryClient;
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@MockBean
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private MongoConnectionProvider mongoConnectionProvider;
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@MockBean
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private TenantProvider tenantProvider;
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@Test
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@SneakyThrows
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public void runAnalysisEnd2End() {
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String folder = "/Users/maverickstuder/Documents/RedactManager/redaction-service/redaction-service-v1/redaction-service-server-v1/src/test/resources/files/files_end2end/file0"; // Should contain all files from minio directly, still zipped. Can contain multiple files.
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String folder = "/home/kschuettler/Downloads/New Folder (4)/17a25133-e098-4610-b553-d1bf11a56d96/560e6ab1ab4754b9a62fd2e6d4d71327"; // Should contain all files from minio directly, still zipped. Can contain multiple files.
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Path absoluteFolderPath;
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if (folder.startsWith("files")) { // if it starts with "files" it is most likely in the resources folder, else it should be an absolute path
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@ -175,7 +178,7 @@ import lombok.extern.slf4j.Slf4j;
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when(mongoConnectionProvider.getMongoDBConnection(any())).thenReturn(mongoDBConnection);
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when(tenantProvider.getTenant(any())).thenReturn(builder().tenantId(TENANT_ID).mongoDBConnection(mongoDBConnection).build());
|
||||
|
||||
tenantMongoLiquibaseExecutor.initializeTenant("redaction");
|
||||
tenantMongoLiquibaseExecutor.initializeTenant(TENANT_ID);
|
||||
|
||||
testDossierTemplate = new TestDossierTemplate(dossierTemplateToUse);
|
||||
when(dictionaryService.updateDictionary(any(), any())).thenReturn(new DictionaryVersion(0, 0));
|
||||
@ -185,6 +188,10 @@ import lombok.extern.slf4j.Slf4j;
|
||||
String type = invocation.getArgument(0);
|
||||
return testDossierTemplate.testDictionary.isHint(type);
|
||||
});
|
||||
when(groupRedactionClient.getGroupAnnotations(anyString(), anyString(), anyBoolean())).thenReturn(GroupAnnotationInternalResponse.builder()
|
||||
.textGroupAnnotations(new ArrayList<>())
|
||||
.areaGroupAnnotations(new ArrayList<>())
|
||||
.build());
|
||||
when(dictionaryService.getColor(any(String.class), any())).thenAnswer(invocation -> {
|
||||
String type = invocation.getArgument(0);
|
||||
return testDossierTemplate.testDictionary.getType(type).getColor();
|
||||
@ -284,9 +291,14 @@ import lombok.extern.slf4j.Slf4j;
|
||||
if (fileType.isEmpty()) {
|
||||
return Optional.empty();
|
||||
}
|
||||
try (var fis = new FileInputStream(path.toFile()); var in = new GZIPInputStream(fis);) {
|
||||
storageService.storeObject(TENANT_ID, RedactionStorageService.StorageIdUtils.getStorageId(request.getDossierId(), request.getFileId(), fileType.get()), in);
|
||||
|
||||
if (path.getFileName().endsWith(".gz")) {
|
||||
try (var fis = new FileInputStream(path.toFile()); var in = new GZIPInputStream(fis);) {
|
||||
storageService.storeObject(TENANT_ID, RedactionStorageService.StorageIdUtils.getStorageId(request.getDossierId(), request.getFileId(), fileType.get()), in);
|
||||
}
|
||||
} else {
|
||||
try (var in = new FileInputStream(path.toFile())) {
|
||||
storageService.storeObject(TENANT_ID, RedactionStorageService.StorageIdUtils.getStorageId(request.getDossierId(), request.getFileId(), fileType.get()), in);
|
||||
}
|
||||
}
|
||||
return fileType;
|
||||
}
|
||||
|
||||
@ -133,9 +133,9 @@ public class RedactionIntegrationTest extends RulesIntegrationTest {
|
||||
mockDictionaryCalls(null);
|
||||
|
||||
when(groupRedactionClient.getGroupAnnotations(anyString(), anyString(), anyBoolean())).thenReturn(GroupAnnotationInternalResponse.builder()
|
||||
.textGroupAnnotations(Collections.emptyList())
|
||||
.areaGroupAnnotations(Collections.emptyList())
|
||||
.build());
|
||||
.textGroupAnnotations(Collections.emptyList())
|
||||
.areaGroupAnnotations(Collections.emptyList())
|
||||
.build());
|
||||
|
||||
when(dictionaryClient.getColors(TEST_DOSSIER_TEMPLATE_ID)).thenReturn(colors);
|
||||
}
|
||||
|
||||
Loading…
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Reference in New Issue
Block a user