From 3047c804be01500d595eaf5b90d86209b15d075b Mon Sep 17 00:00:00 2001 From: Kilian Schuettler Date: Thu, 4 May 2023 00:53:54 +0200 Subject: [PATCH] RED-6009 - Document Tree Structure * removed ner entity validation due to poor performance --- .../redaction/adapter/NerEntitiesAdapter.java | 22 +- .../service/analyze/AnalyzeService.java | 4 +- .../adapter/NerEntitiesAdapterTest.java | 50 +- ...R_02_Volume_2_2018-09-06.NER_ENTITIES.json | 29806 ++++++++++++++++ 4 files changed, 29864 insertions(+), 18 deletions(-) create mode 100644 redaction-service-v1/redaction-service-server-v1/src/test/resources/ner_entities/S-Metolachlor_RAR_02_Volume_2_2018-09-06.NER_ENTITIES.json diff --git a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/redaction/adapter/NerEntitiesAdapter.java b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/redaction/adapter/NerEntitiesAdapter.java index 18b30f4d..bb5fb318 100644 --- a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/redaction/adapter/NerEntitiesAdapter.java +++ b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/redaction/adapter/NerEntitiesAdapter.java @@ -18,7 +18,9 @@ import com.iqser.red.service.redaction.v1.server.layoutparsing.document.graph.te import lombok.AccessLevel; import lombok.experimental.FieldDefaults; +import lombok.extern.slf4j.Slf4j; +@Slf4j @Service @FieldDefaults(level = AccessLevel.PRIVATE, makeFinal = true) public class NerEntitiesAdapter { @@ -33,20 +35,18 @@ public class NerEntitiesAdapter { /** - * Adds the appropriate Offsets to the entities from the NER Service and validates, that the values match. + * Adds the appropriate Offsets to the entities from the NER Service. * * @param nerEntitiesModel the Entities just as the NER Service returns them * @param documentGraph the document structure, from which the NER Service found the entities * @return a stream of validated entities */ - public List getValidatedEntities(NerEntitiesModel nerEntitiesModel, DocumentGraph documentGraph) { + public NerEntities toNerEntities(NerEntitiesModel nerEntitiesModel, DocumentGraph documentGraph) { - return addOffsetsAndFlatten(getStringStartOffsetsForMainSections(documentGraph), nerEntitiesModel) // - .filter(nerEntityModel -> nerEntityOffsetMatchesDocumentGraphOffsets(nerEntityModel, documentGraph.buildTextBlock())) - .map(nerEntityModel -> new NerEntities.NerEntity(nerEntityModel.getValue(), - new Boundary(nerEntityModel.getStartOffset(), nerEntityModel.getEndOffset()), - nerEntityModel.getType())) - .toList(); + return new NerEntities(addOffsetsAndFlatten(getStringStartOffsetsForMainSections(documentGraph), nerEntitiesModel).map(nerEntityModel -> new NerEntities.NerEntity( + nerEntityModel.getValue(), + new Boundary(nerEntityModel.getStartOffset(), nerEntityModel.getEndOffset()), + nerEntityModel.getType())).toList()); } @@ -150,12 +150,6 @@ public class NerEntitiesAdapter { } - private boolean nerEntityOffsetMatchesDocumentGraphOffsets(EntityRecognitionEntity nerEntity, TextBlock textBlock) { - - return nerEntity.getValue().contentEquals(textBlock.subSequence(nerEntity.getStartOffset(), nerEntity.getEndOffset())); - } - - private static Stream addOffsetsAndFlatten(List stringOffsetsForMainSections, NerEntitiesModel nerEntitiesModel) { nerEntitiesModel.getData().forEach((key, value) -> value.forEach(entityRecognitionEntity -> { diff --git a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/redaction/service/analyze/AnalyzeService.java b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/redaction/service/analyze/AnalyzeService.java index d34c11a6..1f270093 100644 --- a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/redaction/service/analyze/AnalyzeService.java +++ b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/redaction/service/analyze/AnalyzeService.java @@ -160,7 +160,7 @@ public class AnalyzeService { Set sectionsToReanalyseIds = getSectionsToReanalyseIds(analyzeRequest, redactionLog, documentGraph, dictionaryIncrement); List sectionsToReAnalyse = getSectionsToReAnalyse(documentGraph, sectionsToReanalyseIds); - log.info("Should reanalyze {} sections for request: {}", sectionsToReAnalyse.size(), analyzeRequest); + log.info("Should reanalyze {} sections", sectionsToReAnalyse.size()); if (sectionsToReAnalyse.isEmpty()) { return finalizeAnalysis(analyzeRequest, startTime, redactionLog, documentGraph.getNumberOfPages(), dictionaryIncrement.getDictionaryVersion(), true, new HashSet<>()); @@ -213,7 +213,7 @@ public class AnalyzeService { if (redactionServiceSettings.isNerServiceEnabled()) { NerEntitiesModel nerEntitiesModel = redactionStorageService.getNerEntities(analyzeRequest.getDossierId(), analyzeRequest.getFileId()); log.info("Get NerEntitiesModel"); - nerEntities = new NerEntities(nerEntitiesAdapter.getValidatedEntities(nerEntitiesModel, documentGraph)); + nerEntities = nerEntitiesAdapter.toNerEntities(nerEntitiesModel, documentGraph); } else { nerEntities = new NerEntities(Collections.emptyList()); } diff --git a/redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/redaction/adapter/NerEntitiesAdapterTest.java b/redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/redaction/adapter/NerEntitiesAdapterTest.java index 2023bed2..8c01796e 100644 --- a/redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/redaction/adapter/NerEntitiesAdapterTest.java +++ b/redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/redaction/adapter/NerEntitiesAdapterTest.java @@ -19,6 +19,7 @@ import org.springframework.core.io.ClassPathResource; import com.iqser.red.commons.jackson.ObjectMapperFactory; import com.iqser.red.service.redaction.v1.server.client.model.NerEntitiesModel; import com.iqser.red.service.redaction.v1.server.document.graph.BuildDocumentGraphIntegrationTest; +import com.iqser.red.service.redaction.v1.server.layoutparsing.document.graph.Boundary; import com.iqser.red.service.redaction.v1.server.layoutparsing.document.graph.entity.RedactionEntity; import com.iqser.red.service.redaction.v1.server.layoutparsing.document.graph.entity.RedactionPosition; import com.iqser.red.service.redaction.v1.server.layoutparsing.document.graph.nodes.DocumentGraph; @@ -27,7 +28,9 @@ import com.iqser.red.service.redaction.v1.server.redaction.model.EntityType; import com.iqser.red.service.redaction.v1.server.visualization.service.PdfDraw; import lombok.SneakyThrows; +import lombok.extern.slf4j.Slf4j; +@Slf4j class NerEntitiesAdapterTest extends BuildDocumentGraphIntegrationTest { @Autowired @@ -57,7 +60,8 @@ class NerEntitiesAdapterTest extends BuildDocumentGraphIntegrationTest { ClassPathResource resource = new ClassPathResource(filePath); PDDocument pdDocument = PDDocument.load(resource.getInputStream()); - Stream unchangedAddressParts = nerEntitiesAdapter.getValidatedEntities(parseNerEntities(nerEntitiesFilePath), documentGraph) + Stream unchangedAddressParts = nerEntitiesAdapter.toNerEntities(parseNerEntities(nerEntitiesFilePath), documentGraph) + .getNerEntityList() .stream() .filter(e -> !e.type().equals("CBI_author")); List redactionEntities = Stream.concat(entityRecognitionEntities.stream(), unchangedAddressParts) @@ -78,9 +82,51 @@ class NerEntitiesAdapterTest extends BuildDocumentGraphIntegrationTest { } + @Test + @SneakyThrows + public void testGetNerEntitiesLargeFile() { + + String filePath = "files/Metolachlor/S-Metolachlor_RAR_02_Volume_2_2018-09-06.pdf"; + String nerEntitiesFilePath = "ner_entities/S-Metolachlor_RAR_02_Volume_2_2018-09-06.NER_ENTITIES.json"; + DocumentGraph documentGraph = buildGraphNoImages(filePath); + log.info("Graph built"); + NerEntitiesModel nerEntitiesModel = parseNerEntities(nerEntitiesFilePath); + log.info("Parsed NerEntitiesModel"); + NerEntities nerEntities = nerEntitiesAdapter.toNerEntities(nerEntitiesModel, documentGraph); + log.info("Validated and mapped"); + List nerEntityBoundaries = nerEntitiesAdapter.combineNerEntitiesToCbiAddressDefaults(nerEntities).toList(); + log.info("Combined to CBI_address"); + List cbiAddressEntities = nerEntityBoundaries.stream() + .map(b -> entityCreationService.byBoundary(b, "CBI_address", EntityType.RECOMMENDATION, documentGraph)) + .toList(); + assertFalse(cbiAddressEntities.isEmpty()); + assertTrue(cbiAddressEntities.stream().allMatch(entity -> entity.getBoundary().start() < entity.getBoundary().end())); + + ClassPathResource resource = new ClassPathResource(filePath); + PDDocument pdDocument = PDDocument.load(resource.getInputStream()); + List validatedEntities = nerEntitiesAdapter.toNerEntities(parseNerEntities(nerEntitiesFilePath), documentGraph) + .getNerEntityList() + .stream() + .map(e -> entityCreationService.byBoundary(e.boundary(), e.type(), EntityType.ENTITY, documentGraph)) + .toList(); + Stream.concat(cbiAddressEntities.stream(), validatedEntities.stream()) + .collect(Collectors.groupingBy(e -> e.getPages().stream().findFirst().get().getNumber())) + .forEach((pageNumber, entities) -> drawNerEntitiesAsPartsAndCombined(pageNumber, + getPositionsFromEntityOfType("CBI_author", entities), + getPositionsFromEntityNotOfType(List.of("CBI_author", "CBI_address"), entities), + getPositionsFromEntityOfType("CBI_address", entities), + pdDocument)); + + File outputFile = new File("/tmp/nerEntities.pdf"); + pdDocument.save(outputFile); + pdDocument.close(); + + } + + private List validateAndCombine(NerEntitiesModel nerEntitiesModel, DocumentGraph documentGraph) { - NerEntities nerEntities = new NerEntities(nerEntitiesAdapter.getValidatedEntities(nerEntitiesModel, documentGraph)); + NerEntities nerEntities = nerEntitiesAdapter.toNerEntities(nerEntitiesModel, documentGraph); List cbiAuthors = nerEntities.streamEntitiesOfType("CBI_author").toList(); Stream cbiAddress = nerEntitiesAdapter.combineNerEntitiesToCbiAddressDefaults(nerEntities) diff --git a/redaction-service-v1/redaction-service-server-v1/src/test/resources/ner_entities/S-Metolachlor_RAR_02_Volume_2_2018-09-06.NER_ENTITIES.json b/redaction-service-v1/redaction-service-server-v1/src/test/resources/ner_entities/S-Metolachlor_RAR_02_Volume_2_2018-09-06.NER_ENTITIES.json new file mode 100644 index 00000000..1702a26b --- /dev/null +++ b/redaction-service-v1/redaction-service-server-v1/src/test/resources/ner_entities/S-Metolachlor_RAR_02_Volume_2_2018-09-06.NER_ENTITIES.json @@ -0,0 +1,29806 @@ +{ + "dossierId": "5e1978f3-5fc4-47ec-b486-f9223730416b", + "fileId": "0c67076f546628d43779332769e35909", + "targetFileExtension": "SIMPLIFIED_TEXT.json.gz", + "responseFileExtension": "NER_ENTITIES.json.gz", + "data": { + "0": [ + { + "value": "Germany", + "startOffset": 154, + "endOffset": 161, + "type": "COUNTRY" + }, + { + "value": "France", + "startOffset": 190, + "endOffset": 196, + "type": "COUNTRY" + }, + { + "value": "Germany", + "startOffset": 351, + "endOffset": 358, + "type": "COUNTRY" + }, + { + "value": "France", + "startOffset": 387, + "endOffset": 393, + "type": "COUNTRY" + }, + { + "value": "Germany", + "startOffset": 548, + "endOffset": 555, + "type": "COUNTRY" + }, + { + "value": "France", + "startOffset": 584, + "endOffset": 590, + "type": "COUNTRY" + }, + { + "value": "Germany", + "startOffset": 745, + "endOffset": 752, + "type": "COUNTRY" + }, + { + "value": "France", + "startOffset": 781, + "endOffset": 787, + "type": "COUNTRY" + }, + { + "value": "Germany", + "startOffset": 942, + "endOffset": 949, + "type": "COUNTRY" + }, + { + "value": "France", + "startOffset": 978, + "endOffset": 984, + "type": "COUNTRY" + }, + { + "value": "Germany", + "startOffset": 1139, + "endOffset": 1146, + "type": "COUNTRY" + }, + { + "value": "France", + "startOffset": 1175, + "endOffset": 1181, + "type": "COUNTRY" + } + ], + "1": [ + { + "value": "When What", + "startOffset": 16, + "endOffset": 25, + "type": "STREET" + } + ], + "2": [ + { + "value": "EC", + "startOffset": 1466, + "endOffset": 1468, + "type": "ORG" + }, + { + "value": "EC", + "startOffset": 2641, + "endOffset": 2643, + "type": "ORG" + } + ], + "5": [ + { + "value": "Burkhard, N.", + "startOffset": 470, + "endOffset": 482, + "type": "CBI_author" + }, + { + "value": "Geoffroy, A.", + "startOffset": 749, + "endOffset": 761, + "type": "CBI_author" + }, + { + "value": "Das, R.", + "startOffset": 1001, + "endOffset": 1008, + "type": "CBI_author" + }, + { + "value": "Sch\u00fcrch, H.", + "startOffset": 1256, + "endOffset": 1267, + "type": "CBI_author" + }, + { + "value": "Widmer, H.", + "startOffset": 1515, + "endOffset": 1525, + "type": "CBI_author" + }, + { + "value": "Burkhard, N.", + "startOffset": 2126, + "endOffset": 2138, + "type": "CBI_author" + }, + { + "value": "Das, R.", + "startOffset": 2355, + "endOffset": 2362, + "type": "CBI_author" + }, + { + "value": "Das, R.", + "startOffset": 2661, + "endOffset": 2668, + "type": "CBI_author" + }, + { + "value": "Lai, G.", + "startOffset": 2971, + "endOffset": 2978, + "type": "CBI_author" + }, + { + "value": "Roth, M.", + "startOffset": 3202, + "endOffset": 3210, + "type": "CBI_author" + }, + { + "value": "Burkhard, N.", + "startOffset": 3871, + "endOffset": 3883, + "type": "CBI_author" + }, + { + "value": "Stulz, J.", + "startOffset": 4136, + "endOffset": 4145, + "type": "CBI_author" + }, + { + "value": "Stulz, J.", + "startOffset": 4376, + "endOffset": 4385, + "type": "CBI_author" + }, + { + "value": "Stulz, J.", + "startOffset": 4630, + "endOffset": 4639, + "type": "CBI_author" + }, + { + "value": "Stulz, J.", + "startOffset": 4860, + "endOffset": 4869, + "type": "CBI_author" + }, + { + "value": "Keller, A.", + "startOffset": 5126, + "endOffset": 5136, + "type": "CBI_author" + }, + { + "value": "Phaff, R.", + "startOffset": 5764, + "endOffset": 5773, + "type": "CBI_author" + }, + { + "value": "Zetsch, C.", + "startOffset": 6037, + "endOffset": 6047, + "type": "CBI_author" + }, + { + "value": "Stulz, J.", + "startOffset": 6395, + "endOffset": 6404, + "type": "CBI_author" + }, + { + "value": "Stamm, E.", + "startOffset": 6654, + "endOffset": 6663, + "type": "CBI_author" + }, + { + "value": "Sch\u00fcrch, H.", + "startOffset": 6934, + "endOffset": 6945, + "type": "CBI_author" + }, + { + "value": "Sch\u00fcrch, H.", + "startOffset": 7190, + "endOffset": 7201, + "type": "CBI_author" + }, + { + "value": "Sch\u00fcrch, H.", + "startOffset": 7820, + "endOffset": 7831, + "type": "CBI_author" + }, + { + "value": "Ryser, M.", + "startOffset": 8056, + "endOffset": 8065, + "type": "CBI_author" + }, + { + "value": "O\u2019Connor B.", + "startOffset": 8284, + "endOffset": 8295, + "type": "CBI_author" + }, + { + "value": "Stulz, J.", + "startOffset": 8626, + "endOffset": 8635, + "type": "CBI_author" + }, + { + "value": "Jackson W.", + "startOffset": 8876, + "endOffset": 8886, + "type": "CBI_author" + }, + { + "value": "Das, R.", + "startOffset": 9590, + "endOffset": 9597, + "type": "CBI_author" + }, + { + "value": "Smetolachlor Novartis Crop Protection AG", + "startOffset": 544, + "endOffset": 584, + "type": "ORG" + }, + { + "value": "Basel", + "startOffset": 586, + "endOffset": 591, + "type": "CITY" + }, + { + "value": "Switzerland", + "startOffset": 593, + "endOffset": 604, + "type": "COUNTRY" + }, + { + "value": "Ciba-Geigy Ltd.", + "startOffset": 808, + "endOffset": 823, + "type": "ORG" + }, + { + "value": "Basel", + "startOffset": 825, + "endOffset": 830, + "type": "CITY" + }, + { + "value": "Switzerland", + "startOffset": 832, + "endOffset": 843, + "type": "COUNTRY" + }, + { + "value": "Ciba-Geigy Muenchwilen AG", + "startOffset": 1054, + "endOffset": 1079, + "type": "ORG" + }, + { + "value": "Muenchwilen", + "startOffset": 1081, + "endOffset": 1092, + "type": "CITY" + }, + { + "value": "Switzerland", + "startOffset": 1094, + "endOffset": 1105, + "type": "COUNTRY" + }, + { + "value": "Ciba-Geigy Ltd.", + "startOffset": 1322, + "endOffset": 1337, + "type": "ORG" + }, + { + "value": "Basel", + "startOffset": 1339, + "endOffset": 1344, + "type": "CITY" + }, + { + "value": "Switzerland", + "startOffset": 1346, + "endOffset": 1357, + "type": "COUNTRY" + }, + { + "value": "Ciba-Geigy Ltd.", + "startOffset": 1557, + "endOffset": 1572, + "type": "ORG" + }, + { + "value": "Basel", + "startOffset": 1574, + "endOffset": 1579, + "type": "CITY" + }, + { + "value": "Switzerland", + "startOffset": 1581, + "endOffset": 1592, + "type": "COUNTRY" + }, + { + "value": "Novartis Crop Protection AG", + "startOffset": 2165, + "endOffset": 2192, + "type": "ORG" + }, + { + "value": "Basel", + "startOffset": 2194, + "endOffset": 2199, + "type": "CITY" + }, + { + "value": "Switzerland", + "startOffset": 2201, + "endOffset": 2212, + "type": "COUNTRY" + }, + { + "value": "Muenchwilen", + "startOffset": 2490, + "endOffset": 2501, + "type": "CITY" + }, + { + "value": "Switzerland", + "startOffset": 2503, + "endOffset": 2514, + "type": "COUNTRY" + }, + { + "value": "Ciba-Geigy Muenchwilen AG", + "startOffset": 2771, + "endOffset": 2796, + "type": "ORG" + }, + { + "value": "Muenchwilen", + "startOffset": 2798, + "endOffset": 2809, + "type": "CITY" + }, + { + "value": "Switzerland", + "startOffset": 2811, + "endOffset": 2822, + "type": "COUNTRY" + }, + { + "value": "Muenchwilen", + "startOffset": 3029, + "endOffset": 3040, + "type": "CITY" + }, + { + "value": "Switzerland", + "startOffset": 3042, + "endOffset": 3053, + "type": "COUNTRY" + }, + { + "value": "Novartis Crop Protection M\u00fcnchwilen AG", + "startOffset": 3279, + "endOffset": 3317, + "type": "ORG" + }, + { + "value": "M\u00fcnchwilen", + "startOffset": 3319, + "endOffset": 3329, + "type": "CITY" + }, + { + "value": "Switzerland", + "startOffset": 3331, + "endOffset": 3342, + "type": "COUNTRY" + }, + { + "value": "Novartis Crop Protection AG", + "startOffset": 3947, + "endOffset": 3974, + "type": "ORG" + }, + { + "value": "Basel", + "startOffset": 3976, + "endOffset": 3981, + "type": "CITY" + }, + { + "value": "Switzerland", + "startOffset": 3983, + "endOffset": 3994, + "type": "COUNTRY" + }, + { + "value": "Ciba-Geigy Muenchwilen AG", + "startOffset": 4178, + "endOffset": 4203, + "type": "ORG" + }, + { + "value": "Muenchwilen", + "startOffset": 4205, + "endOffset": 4216, + "type": "CITY" + }, + { + "value": "Switzerland", + "startOffset": 4218, + "endOffset": 4229, + "type": "COUNTRY" + }, + { + "value": "Ciba-Geigy Muenchwilen AG", + "startOffset": 4432, + "endOffset": 4457, + "type": "ORG" + }, + { + "value": "Muenchwilen", + "startOffset": 4459, + "endOffset": 4470, + "type": "CITY" + }, + { + "value": "Switzerland", + "startOffset": 4472, + "endOffset": 4483, + "type": "COUNTRY" + }, + { + "value": "Ciba-Geigy Muenchwilen AG", + "startOffset": 4676, + "endOffset": 4701, + "type": "ORG" + }, + { + "value": "Muenchwilen", + "startOffset": 4703, + "endOffset": 4714, + "type": "CITY" + }, + { + "value": "Switzerland", + "startOffset": 4716, + "endOffset": 4727, + "type": "COUNTRY" + }, + { + "value": "Ciba-Geigy Muenchwilen AG", + "startOffset": 4924, + "endOffset": 4949, + "type": "ORG" + }, + { + "value": "Muenchwilen", + "startOffset": 4951, + "endOffset": 4962, + "type": "CITY" + }, + { + "value": "Switzerland", + "startOffset": 4964, + "endOffset": 4975, + "type": "COUNTRY" + }, + { + "value": "Ciba-Geigy Ltd.", + "startOffset": 5206, + "endOffset": 5221, + "type": "ORG" + }, + { + "value": "Basel", + "startOffset": 5223, + "endOffset": 5228, + "type": "CITY" + }, + { + "value": "Switzerland", + "startOffset": 5230, + "endOffset": 5241, + "type": "COUNTRY" + }, + { + "value": "Novartis Crop Protection AG", + "startOffset": 5849, + "endOffset": 5876, + "type": "ORG" + }, + { + "value": "Basel", + "startOffset": 5878, + "endOffset": 5883, + "type": "CITY" + }, + { + "value": "Switzerland", + "startOffset": 5885, + "endOffset": 5896, + "type": "COUNTRY" + }, + { + "value": "Fraunhofer Institut", + "startOffset": 6179, + "endOffset": 6198, + "type": "ORG" + }, + { + "value": "Toxikologie und Aerosolforschung, Hannover", + "startOffset": 6203, + "endOffset": 6245, + "type": "CITY" + }, + { + "value": "Germany", + "startOffset": 6247, + "endOffset": 6254, + "type": "COUNTRY" + }, + { + "value": "Ciba-Geigy Muenchwilen AG", + "startOffset": 6451, + "endOffset": 6476, + "type": "ORG" + }, + { + "value": 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