diff --git a/redaction-service-v1/redaction-service-server-v1/build.gradle.kts b/redaction-service-v1/redaction-service-server-v1/build.gradle.kts index d158ea0e..9a39bdf1 100644 --- a/redaction-service-v1/redaction-service-server-v1/build.gradle.kts +++ b/redaction-service-v1/redaction-service-server-v1/build.gradle.kts @@ -12,7 +12,7 @@ plugins { description = "redaction-service-server-v1" -val layoutParserVersion = "0.139.0" +val layoutParserVersion = "0.141.0" val jacksonVersion = "2.15.2" val droolsVersion = "9.44.0.Final" val pdfBoxVersion = "3.0.0" diff --git a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/client/model/EntityRecognitionSection.java b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/client/model/EntityRecognitionSection.java index bcc794a3..16705a0d 100644 --- a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/client/model/EntityRecognitionSection.java +++ b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/client/model/EntityRecognitionSection.java @@ -11,7 +11,7 @@ import lombok.NoArgsConstructor; @NoArgsConstructor public class EntityRecognitionSection { - private int sectionNumber; + private String sectionNumber; private String text; } diff --git a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/client/model/NerEntitiesModel.java b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/client/model/NerEntitiesModel.java index 8b7b9018..e087991f 100644 --- a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/client/model/NerEntitiesModel.java +++ b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/client/model/NerEntitiesModel.java @@ -13,6 +13,6 @@ import lombok.NoArgsConstructor; @AllArgsConstructor public class NerEntitiesModel { - private Map> data = new HashMap<>(); + private Map> data = new HashMap<>(); } diff --git a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/document/NerEntitiesAdapter.java b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/document/NerEntitiesAdapter.java index aab747b2..bca1c3ba 100644 --- a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/document/NerEntitiesAdapter.java +++ b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/document/NerEntitiesAdapter.java @@ -1,10 +1,13 @@ package com.iqser.red.service.redaction.v1.server.service.document; +import java.util.Arrays; import java.util.Collection; import java.util.Comparator; import java.util.LinkedList; import java.util.List; +import java.util.Map; import java.util.Set; +import java.util.stream.Collectors; import java.util.stream.Stream; import com.iqser.red.service.redaction.v1.server.client.model.EntityRecognitionEntity; @@ -14,7 +17,6 @@ import com.iqser.red.service.redaction.v1.server.model.document.TextRange; import com.iqser.red.service.redaction.v1.server.model.document.nodes.Document; import com.iqser.red.service.redaction.v1.server.model.document.nodes.NodeType; import com.iqser.red.service.redaction.v1.server.model.document.nodes.SemanticNode; -import com.iqser.red.service.redaction.v1.server.model.document.textblock.TextBlock; import lombok.AccessLevel; import lombok.experimental.FieldDefaults; @@ -44,11 +46,10 @@ public class NerEntitiesAdapter { */ public NerEntities toNerEntities(NerEntitiesModel nerEntitiesModel, Document document) { - return new NerEntities(addOffsetsAndFlatten(getStringStartOffsetsForMainSectionsHeadersFooters(document), - nerEntitiesModel).map(nerEntityModel -> new NerEntities.NerEntity(nerEntityModel.getValue(), - new TextRange(nerEntityModel.getStartOffset(), - nerEntityModel.getEndOffset()), - nerEntityModel.getType())) + return new NerEntities(addOffsetsAndFlatten(getStringStartOffsetsForMainSectionsHeadersFooters(document), nerEntitiesModel).map(nerEntityModel -> new NerEntities.NerEntity( + nerEntityModel.getValue(), + new TextRange(nerEntityModel.getStartOffset(), nerEntityModel.getEndOffset()), + nerEntityModel.getType())) .toList()); } @@ -161,11 +162,12 @@ public class NerEntitiesAdapter { } - private static Stream addOffsetsAndFlatten(List stringOffsetsForMainSectionsHeadersFooters, NerEntitiesModel nerEntitiesModel) { + private static Stream addOffsetsAndFlatten(Map, Integer> stringOffsetsForMainSectionsHeadersFooters, NerEntitiesModel nerEntitiesModel) { nerEntitiesModel.getData() .forEach((sectionNumber, listOfNerEntities) -> listOfNerEntities.forEach(entityRecognitionEntity -> { - int newStartOffset = entityRecognitionEntity.getStartOffset() + stringOffsetsForMainSectionsHeadersFooters.get(sectionNumber); + int newStartOffset = entityRecognitionEntity.getStartOffset() + stringOffsetsForMainSectionsHeadersFooters.getOrDefault(sectionNumberToTreeId(sectionNumber), + 0); entityRecognitionEntity.setStartOffset(newStartOffset); entityRecognitionEntity.setEndOffset(newStartOffset + entityRecognitionEntity.getValue().length()); })); @@ -175,14 +177,19 @@ public class NerEntitiesAdapter { } - private static List getStringStartOffsetsForMainSectionsHeadersFooters(Document document) { + private static List sectionNumberToTreeId(String sectionNumber) { + + return Arrays.stream(sectionNumber.split("\\.")) + .map(Integer::parseInt) + .collect(Collectors.toList()); + } + + + private static Map, Integer> getStringStartOffsetsForMainSectionsHeadersFooters(Document document) { return document.streamAllSubNodes() - .filter(child -> (child.getType().equals(NodeType.FOOTER) ||child.getType().equals(NodeType.HEADER) ||child.getType().equals(NodeType.SECTION))) - .map(SemanticNode::getTextBlock) - .map(TextBlock::getTextRange) - .map(TextRange::start) - .toList(); + .filter(child -> child.getType().equals(NodeType.FOOTER) || child.getType().equals(NodeType.HEADER) || child.getType().equals(NodeType.SECTION)) + .collect(Collectors.toMap(SemanticNode::getTreeId, child -> child.getTextBlock().getTextRange().start())); } } diff --git a/redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/document/graph/DocumentIEntityInsertionIntegrationTest.java b/redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/document/graph/DocumentIEntityInsertionIntegrationTest.java index 22a7fc0d..8bbb7845 100644 --- a/redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/document/graph/DocumentIEntityInsertionIntegrationTest.java +++ b/redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/document/graph/DocumentIEntityInsertionIntegrationTest.java @@ -308,7 +308,7 @@ public class DocumentIEntityInsertionIntegrationTest extends BuildDocumentIntegr assertEquals("2-[(2-(1-hydroxy-ethyl)-6methyl-phenyl-amino]propan-1-ol (", textEntity.getTextBefore()); assertEquals(" of metabolite of", textEntity.getTextAfter()); assertEquals(searchTerm, textEntity.getValue()); - assertEquals(7, textEntity.getIntersectingNodes().size()); + assertEquals(8, textEntity.getIntersectingNodes().size()); assertEquals("Table 2.7-1: List of substances and metabolites and related structural formula ", textEntity.getDeepestFullyContainingNode().getHeadline().getTextBlock().getSearchText()); assertTrue(textEntity.getPages() 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 index 90696b05..c050b72a 100644 --- 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 @@ -1,17 +1,11 @@ { - "dossierId": "f97e0c85-2af3-4e3a-990f-ba84e67cce92", - "fileId": "f402a639b70d5e82affa91748c3ff117", + "dossierId": "8fa9508a-f965-48db-8488-8e8319ad20e4", + "fileId": "0750ae0c23a696022b0a4163265c0356", "targetFileExtension": "SIMPLIFIED_TEXT.json.gz", "responseFileExtension": "NER_ENTITIES.json.gz", "X-TENANT-ID": "redaction", "data": { "0": [ - { - "value": "Germany", - "startOffset": 154, - "endOffset": 161, - "type": "COUNTRY" - }, { "value": "France", "startOffset": 190, @@ -19,1267 +13,26553 @@ "type": "COUNTRY" } ], - "1": [ + "1.1": [ { - "value": "When What", - "startOffset": 16, - "endOffset": 25, - "type": "STREET" + "value": "EFSA", + "startOffset": 55, + "endOffset": 59, + "type": "ORG" } ], - "2": [ + "2.9": [ { - "value": "Academic Press", - "startOffset": 1060, - "endOffset": 1074, + "value": "EFSA", + "startOffset": 708, + "endOffset": 712, + "type": "ORG" + } + ], + "2.11.1": [ + { + "value": "EU", + "startOffset": 109, + "endOffset": 111, "type": "ORG" }, { - "value": "Royal Society", - "startOffset": 1450, - "endOffset": 1463, - "type": "ORG" + "value": "Burkhard, N.", + "startOffset": 420, + "endOffset": 432, + "type": "CBI_author" }, { - "value": "Central Science Laboratory", - "startOffset": 1724, - "endOffset": 1750, - "type": "ORG" - }, - { - "value": "Safety Executive", - "startOffset": 2450, - "endOffset": 2466, - "type": "ORG" - }, - { - "value": "Oxford University Press", - "startOffset": 3597, - "endOffset": 3620, - "type": "ORG" - }, - { - "value": "Oxford", - "startOffset": 3622, - "endOffset": 3628, - "type": "STREET" - }, - { - "value": "Ciba- Geigy Ltd.", - "startOffset": 4138, - "endOffset": 4154, - "type": "ORG" - }, - { - "value": "Novartis", - "startOffset": 4186, - "endOffset": 4194, - "type": "ORG" - }, - { - "value": "Neumann", - "startOffset": 4304, - "endOffset": 4311, + "value": "Basel", + "startOffset": 540, + "endOffset": 545, "type": "CITY" }, { - "value": "CH", - "startOffset": 4313, - "endOffset": 4315, + "value": "EU", + "startOffset": 648, + "endOffset": 650, + "type": "ORG" + }, + { + "value": "Geoffroy, A.", + "startOffset": 703, + "endOffset": 715, + "type": "CBI_author" + }, + { + "value": "Basel", + "startOffset": 779, + "endOffset": 784, + "type": "CITY" + }, + { + "value": "Switzerland Rep.", + "startOffset": 786, + "endOffset": 802, "type": "COUNTRY" }, { - "value": "Ciba-Geigy", - "startOffset": 4437, - "endOffset": 4447, + "value": "Syngenta", + "startOffset": 832, + "endOffset": 840, "type": "ORG" }, { - "value": "EC", - "startOffset": 5030, - "endOffset": 5032, + "value": "EU", + "startOffset": 900, + "endOffset": 902, + "type": "ORG" + }, + { + "value": "Das, R.", + "startOffset": 955, + "endOffset": 962, + "type": "CBI_author" + }, + { + "value": "Muenchwilen", + "startOffset": 1035, + "endOffset": 1046, + "type": "CITY" + }, + { + "value": "Switzerland Rep.", + "startOffset": 1048, + "endOffset": 1064, "type": "COUNTRY" }, { - "value": "Green Algae (Selenas- trum capricornutum) under static condi- tions. Ciba-Geigy Ltd.", - "startOffset": 5051, - "endOffset": 5135, - "type": "ORG" - }, - { - "value": "Novartis", - "startOffset": 5167, - "endOffset": 5175, - "type": "ORG" - }, - { - "value": "Harlan Laboratories Ltd.", - "startOffset": 5414, - "endOffset": 5438, - "type": "ORG" - }, - { - "value": "Itingen", - "startOffset": 5440, - "endOffset": 5447, - "type": "ORG" - }, - { - "value": "Novartis Crop Protection AG", - "startOffset": 5850, - "endOffset": 5877, + "value": "EU", + "startOffset": 1155, + "endOffset": 1157, "type": "ORG" }, { "value": "Basel", - "startOffset": 5879, - "endOffset": 5884, + "startOffset": 1293, + "endOffset": 1298, "type": "CITY" }, { - "value": "Switzerland", - "startOffset": 5886, - "endOffset": 5897, + "value": "Switzerland Rep.", + "startOffset": 1300, + "endOffset": 1316, "type": "COUNTRY" }, { - "value": "Springborn Laboratories Inc.", - "startOffset": 5898, - "endOffset": 5926, + "value": "EU", + "startOffset": 1414, + "endOffset": 1416, "type": "ORG" }, { - "value": "Wareham", - "startOffset": 5928, - "endOffset": 5935, + "value": "Widmer, H.", + "startOffset": 1469, + "endOffset": 1479, + "type": "CBI_author" + }, + { + "value": "Basel", + "startOffset": 1528, + "endOffset": 1533, "type": "CITY" }, { - "value": "USA", - "startOffset": 5937, - "endOffset": 5940, + "value": "Switzerland Rep.", + "startOffset": 1535, + "endOffset": 1551, "type": "COUNTRY" }, { - "value": "Syngenta Harlan Laboratories Ltd.", - "startOffset": 6321, - "endOffset": 6354, + "value": "EU", + "startOffset": 1643, + "endOffset": 1645, "type": "ORG" }, { - "value": "Itingen", - "startOffset": 6356, - "endOffset": 6363, - "type": "ORG" - }, - { - "value": "Novartis Crop Protection AG", - "startOffset": 7136, - "endOffset": 7163, + "value": "EU", + "startOffset": 1763, + "endOffset": 1765, "type": "ORG" }, { "value": "Basel", - "startOffset": 7165, - "endOffset": 7170, + "startOffset": 2152, + "endOffset": 2157, + "type": "CITY" + }, + { + "value": "EU", + "startOffset": 2262, + "endOffset": 2264, + "type": "ORG" + }, + { + "value": "Das, R.", + "startOffset": 2313, + "endOffset": 2320, + "type": "CBI_author" + }, + { + "value": "Muenchwilen", + "startOffset": 2448, + "endOffset": 2459, + "type": "CITY" + }, + { + "value": "Switzerland Rep.", + "startOffset": 2461, + "endOffset": 2477, + "type": "COUNTRY" + }, + { + "value": "EU", + "startOffset": 2568, + "endOffset": 2570, + "type": "ORG" + }, + { + "value": "Das, R.", + "startOffset": 2619, + "endOffset": 2626, + "type": "CBI_author" + }, + { + "value": "Muenchwilen", + "startOffset": 2756, + "endOffset": 2767, + "type": "CITY" + }, + { + "value": "Switzerland Rep.", + "startOffset": 2769, + "endOffset": 2785, + "type": "COUNTRY" + }, + { + "value": "EU", + "startOffset": 2876, + "endOffset": 2878, + "type": "ORG" + }, + { + "value": "Muenchwilen", + "startOffset": 2987, + "endOffset": 2998, + "type": "CITY" + }, + { + "value": "Switzerland Rep.", + "startOffset": 3000, + "endOffset": 3016, + "type": "COUNTRY" + }, + { + "value": "EU", + "startOffset": 3107, + "endOffset": 3109, + "type": "ORG" + }, + { + "value": "Roth, M.", + "startOffset": 3160, + "endOffset": 3168, + "type": "CBI_author" + }, + { + "value": "M\u00fcnchwilen", + "startOffset": 3277, + "endOffset": 3287, + "type": "CITY" + }, + { + "value": "Switzerland Rep.", + "startOffset": 3289, + "endOffset": 3305, + "type": "COUNTRY" + }, + { + "value": "EU", + "startOffset": 3394, + "endOffset": 3396, + "type": "ORG" + }, + { + "value": "EU", + "startOffset": 3514, + "endOffset": 3516, + "type": "ORG" + }, + { + "value": "Burkhard, N.", + "startOffset": 3833, + "endOffset": 3845, + "type": "CBI_author" + }, + { + "value": "Basel", + "startOffset": 3938, + "endOffset": 3943, + "type": "COUNTRY" + }, + { + "value": "EU", + "startOffset": 4049, + "endOffset": 4051, + "type": "ORG" + }, + { + "value": "Muenchwilen", + "startOffset": 4169, + "endOffset": 4180, + "type": "CITY" + }, + { + "value": "Switzerland Rep.", + "startOffset": 4182, + "endOffset": 4198, + "type": "COUNTRY" + }, + { + "value": "EU", + "startOffset": 4289, + "endOffset": 4291, + "type": "ORG" + }, + { + "value": "Muenchwilen", + "startOffset": 4423, + "endOffset": 4434, + "type": "CITY" + }, + { + "value": "Switzerland Rep.", + "startOffset": 4436, + "endOffset": 4452, + "type": "COUNTRY" + }, + { + "value": "EU", + "startOffset": 4543, + "endOffset": 4545, + "type": "ORG" + }, + { + "value": "chwilen", + "startOffset": 4673, + "endOffset": 4680, "type": "CITY" }, { "value": "Switzerland", - "startOffset": 7172, - "endOffset": 7183, + "startOffset": 4682, + "endOffset": 4693, "type": "COUNTRY" }, { - "value": "Springborn Laboratories Inc.", - "startOffset": 7184, - "endOffset": 7212, + "value": "Syngenta", + "startOffset": 4716, + "endOffset": 4724, "type": "ORG" }, { - "value": "Wareham", - "startOffset": 7214, - "endOffset": 7221, + "value": "EU", + "startOffset": 4775, + "endOffset": 4777, + "type": "ORG" + }, + { + "value": "Muenchwilen", + "startOffset": 4917, + "endOffset": 4928, "type": "CITY" }, { - "value": "USA", - "startOffset": 7223, - "endOffset": 7226, + "value": "Switzerland Rep.", + "startOffset": 4930, + "endOffset": 4946, "type": "COUNTRY" }, { - "value": "Harlan Laboratories Ltd.", - "startOffset": 7692, - "endOffset": 7716, + "value": "EU", + "startOffset": 5037, + "endOffset": 5039, "type": "ORG" }, { - "value": "Itingen", - "startOffset": 7718, - "endOffset": 7725, + "value": "Keller, A.", + "startOffset": 5092, + "endOffset": 5102, + "type": "CBI_author" + }, + { + "value": "Basel", + "startOffset": 5189, + "endOffset": 5194, + "type": "CITY" + }, + { + "value": "Switzerland Rep.", + "startOffset": 5196, + "endOffset": 5212, + "type": "COUNTRY" + }, + { + "value": "EU", + "startOffset": 5293, + "endOffset": 5295, "type": "ORG" }, { - "value": "Novartis Crop Protection AG", - "startOffset": 8124, + "value": "EU", + "startOffset": 5413, + "endOffset": 5415, + "type": "ORG" + }, + { + "value": "Phaff, R.", + "startOffset": 5734, + "endOffset": 5743, + "type": "CBI_author" + }, + { + "value": "Basel", + "startOffset": 5848, + "endOffset": 5853, + "type": "CITY" + }, + { + "value": "Switzerland Rep.", + "startOffset": 5855, + "endOffset": 5871, + "type": "COUNTRY" + }, + { + "value": "EU", + "startOffset": 5952, + "endOffset": 5954, + "type": "ORG" + }, + { + "value": "Zetsch, C.", + "startOffset": 6007, + "endOffset": 6017, + "type": "CBI_author" + }, + { + "value": "Germany Rep.", + "startOffset": 6219, + "endOffset": 6231, + "type": "COUNTRY" + }, + { + "value": "EU", + "startOffset": 6312, + "endOffset": 6314, + "type": "ORG" + }, + { + "value": "Muenchwilen", + "startOffset": 6450, + "endOffset": 6461, + "type": "CITY" + }, + { + "value": "Switzerland Rep.", + "startOffset": 6463, + "endOffset": 6479, + "type": "COUNTRY" + }, + { + "value": "EU", + "startOffset": 6571, + "endOffset": 6573, + "type": "ORG" + }, + { + "value": "Crop Protection AG", + "startOffset": 6724, + "endOffset": 6742, + "type": "DEPARTMENT" + }, + { + "value": "Basel", + "startOffset": 6744, + "endOffset": 6749, + "type": "CITY" + }, + { + "value": "Switzerland Rep.", + "startOffset": 6751, + "endOffset": 6767, + "type": "COUNTRY" + }, + { + "value": "EU", + "startOffset": 6851, + "endOffset": 6853, + "type": "ORG" + }, + { + "value": "Basel", + "startOffset": 6987, + "endOffset": 6992, + "type": "CITY" + }, + { + "value": "Switzerland Rep.", + "startOffset": 6994, + "endOffset": 7010, + "type": "COUNTRY" + }, + { + "value": "EU", + "startOffset": 7108, + "endOffset": 7110, + "type": "ORG" + }, + { + "value": "Basel", + "startOffset": 7235, + "endOffset": 7240, + "type": "CITY" + }, + { + "value": "Switzerland Rep.", + "startOffset": 7242, + "endOffset": 7258, + "type": "COUNTRY" + }, + { + "value": "EU", + "startOffset": 7356, + "endOffset": 7358, + "type": "ORG" + }, + { + "value": "EU", + "startOffset": 7476, + "endOffset": 7478, + "type": "ORG" + }, + { 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