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 ec8ef756..e1fc1bb3 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 = "0.94.0" +val layoutParserVersion = "0.96.0" 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/model/document/nodes/Document.java b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/Document.java index 8b9b1177..e876c620 100644 --- a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/Document.java +++ b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/Document.java @@ -57,7 +57,7 @@ public class Document implements GenericSemanticNode { public TextBlock getTextBlock() { if (textBlock == null) { - textBlock = streamTerminalTextBlocksInOrder().collect(new TextBlockCollector()); + textBlock = GenericSemanticNode.super.getTextBlock(); } return textBlock; } @@ -72,8 +72,7 @@ public class Document implements GenericSemanticNode { public Stream streamTerminalTextBlocksInOrder() { - return streamAllNodes().filter(SemanticNode::isLeaf) - .map(SemanticNode::getLeafTextBlock); + return streamAllNodes().filter(SemanticNode::isLeaf).map(SemanticNode::getTextBlock); } diff --git a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/DuplicatedParagraph.java b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/DuplicatedParagraph.java new file mode 100644 index 00000000..247a3865 --- /dev/null +++ b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/DuplicatedParagraph.java @@ -0,0 +1,34 @@ +package com.iqser.red.service.redaction.v1.server.model.document.nodes; + +import java.util.stream.Stream; + +import com.iqser.red.service.redaction.v1.server.model.document.textblock.TextBlock; +import com.iqser.red.service.redaction.v1.server.model.document.textblock.TextBlockCollector; + +import lombok.Data; +import lombok.EqualsAndHashCode; +import lombok.experimental.SuperBuilder; + +@Data +@EqualsAndHashCode(callSuper = true) +@SuperBuilder +public class DuplicatedParagraph extends Paragraph { + + TextBlock unsortedLeafTextBlock; + + + @Override + public TextBlock getTextBlock() { + + return Stream.of(leafTextBlock, unsortedLeafTextBlock).collect(new TextBlockCollector()); + + } + + + @Override + public String toString() { + + return super.toString(); + } + +} diff --git a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/Paragraph.java b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/Paragraph.java index e9061be4..21bdc4ed 100644 --- a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/Paragraph.java +++ b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/Paragraph.java @@ -17,11 +17,12 @@ import lombok.Builder; import lombok.Data; import lombok.EqualsAndHashCode; import lombok.experimental.FieldDefaults; +import lombok.experimental.SuperBuilder; @Data -@Builder +@SuperBuilder @AllArgsConstructor -@FieldDefaults(level = AccessLevel.PRIVATE) +@FieldDefaults(level = AccessLevel.PROTECTED) @EqualsAndHashCode(onlyExplicitlyIncluded = true) public class Paragraph implements GenericSemanticNode { diff --git a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/Section.java b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/Section.java index 9c2bdac9..6199fc85 100644 --- a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/Section.java +++ b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/Section.java @@ -69,9 +69,7 @@ public class Section implements GenericSemanticNode { public TextBlock getTextBlock() { if (textBlock == null) { - textBlock = streamAllSubNodes().filter(SemanticNode::isLeaf) - .map(SemanticNode::getLeafTextBlock) - .collect(new TextBlockCollector()); + textBlock = GenericSemanticNode.super.getTextBlock(); } return textBlock; } diff --git a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/SemanticNode.java b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/SemanticNode.java index 798875ec..77f7ea76 100644 --- a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/SemanticNode.java +++ b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/SemanticNode.java @@ -19,6 +19,7 @@ import com.iqser.red.service.redaction.v1.server.model.document.TextRange; import com.iqser.red.service.redaction.v1.server.model.document.entity.TextEntity; import com.iqser.red.service.redaction.v1.server.model.document.textblock.AtomicTextBlock; import com.iqser.red.service.redaction.v1.server.model.document.textblock.TextBlock; +import com.iqser.red.service.redaction.v1.server.model.document.textblock.TextBlockCollector; import com.iqser.red.service.redaction.v1.server.service.document.NodeVisitor; import com.iqser.red.service.redaction.v1.server.utils.RectangleTransformations; import com.iqser.red.service.redaction.v1.server.utils.RedactionSearchUtility; @@ -41,7 +42,11 @@ public interface SemanticNode { * * @return TextBlock containing all AtomicTextBlocks that are located under this Node. */ - TextBlock getTextBlock(); + default TextBlock getTextBlock() { + + return streamAllSubNodes().filter(SemanticNode::isLeaf).map(SemanticNode::getTextBlock).collect(new TextBlockCollector()); + } + /** diff --git a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/Table.java b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/Table.java index f6259528..95abbe0d 100644 --- a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/Table.java +++ b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/nodes/Table.java @@ -408,9 +408,7 @@ public class Table implements SemanticNode { public TextBlock getTextBlock() { if (textBlock == null) { - textBlock = streamAllSubNodes().filter(SemanticNode::isLeaf) - .map(SemanticNode::getLeafTextBlock) - .collect(new TextBlockCollector()); + textBlock = SemanticNode.super.getTextBlock(); } return textBlock; } diff --git a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/document/DocumentGraphMapper.java b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/document/DocumentGraphMapper.java index 1a9a3531..cd783be3 100644 --- a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/document/DocumentGraphMapper.java +++ b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/document/DocumentGraphMapper.java @@ -9,6 +9,7 @@ import java.util.NoSuchElementException; import java.util.Set; import com.iqser.red.service.redaction.v1.server.model.document.DocumentTree; +import com.iqser.red.service.redaction.v1.server.model.document.nodes.DuplicatedParagraph; import com.iqser.red.service.redaction.v1.server.model.document.nodes.Footer; import com.iqser.red.service.redaction.v1.server.model.document.nodes.Header; import com.iqser.red.service.redaction.v1.server.model.document.nodes.Image; @@ -66,7 +67,7 @@ public class DocumentGraphMapper { SemanticNode node = switch (entryData.getType()) { case SECTION -> buildSection(context); - case PARAGRAPH -> buildParagraph(context); + case PARAGRAPH -> buildParagraph(context, entryData.getProperties()); case HEADLINE -> buildHeadline(context); case HEADER -> buildHeader(context); case FOOTER -> buildFooter(context); @@ -148,13 +149,22 @@ public class DocumentGraphMapper { } - private Paragraph buildParagraph(Context context) { + private Paragraph buildParagraph(Context context, Map properties) { + + if (PropertiesMapper.isDuplicateParagraph(properties)) { + + DuplicatedParagraph duplicatedParagraph = DuplicatedParagraph.builder().documentTree(context.documentTree).build(); + + Long[] unsortedTextblockIds = PropertiesMapper.getUnsortedTextblockIds(properties); + duplicatedParagraph.setUnsortedLeafTextBlock(toTextBlock(unsortedTextblockIds, context, duplicatedParagraph)); + return duplicatedParagraph; + } return Paragraph.builder().documentTree(context.documentTree).build(); } - private TextBlock toTextBlock(Long[] atomicTextBlockIds, Context context, SemanticNode parent) { + private TextBlock toTextBlock(Long[] atomicTextBlockIds, Context context, SemanticNode parent) { return Arrays.stream(atomicTextBlockIds) .map(atomicTextBlockId -> getAtomicTextBlock(context, parent, atomicTextBlockId)) diff --git a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/document/PropertiesMapper.java b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/document/PropertiesMapper.java index dec16250..cce935b9 100644 --- a/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/document/PropertiesMapper.java +++ b/redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/document/PropertiesMapper.java @@ -49,4 +49,23 @@ public class PropertiesMapper { return new Rectangle2D.Float(floats.get(0), floats.get(1), floats.get(2), floats.get(3)); } + + public static boolean isDuplicateParagraph(Map properties) { + + return properties.containsKey(DocumentStructure.DuplicateParagraphProperties.UNSORTED_TEXTBLOCK_ID); + } + + + public static Long[] getUnsortedTextblockIds(Map properties) { + + return toLongArray(properties.get(DocumentStructure.DuplicateParagraphProperties.UNSORTED_TEXTBLOCK_ID)); + } + + + public static Long[] toLongArray(String ids) { + + return Arrays.stream(ids.substring(1, ids.length() - 1).trim().split(",")).map(Long::valueOf).toArray(Long[]::new); + } + + } diff --git a/redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/RedactionIntegrationTest.java b/redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/RedactionIntegrationTest.java index e4b6e961..65562ee7 100644 --- a/redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/RedactionIntegrationTest.java +++ b/redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/RedactionIntegrationTest.java @@ -246,6 +246,7 @@ public class RedactionIntegrationTest extends AbstractRedactionIntegrationTest { @Test + @SneakyThrows public void redactionExpansionOverlap() { // F. Lastname, J. Doe, M. Mustermann @@ -297,7 +298,7 @@ public class RedactionIntegrationTest extends AbstractRedactionIntegrationTest { @Test public void titleExtraction() throws IOException { - AnalyzeRequest request = uploadFileToStorage("files/Metolachlor/S-Metolachlor_RAR_01_Volume_1_2018-09-06.pdf"); + AnalyzeRequest request = uploadFileToStorage("files/new/crafted document.pdf"); System.out.println("Start Full integration test"); analyzeDocumentStructure(LayoutParsingType.REDACT_MANAGER, request); System.out.println("Finished structure analysis"); 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 f952c80b..acfdebc6 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 @@ -272,7 +272,7 @@ public class DocumentIEntityInsertionIntegrationTest extends BuildDocumentIntegr public void assertTextBeforeAndTextAfterForHeadlineMetolachlor() { Document document = buildGraph("files/Metolachlor/S-Metolachlor_RAR_01_Volume_1_2018-09-06"); - String searchTerm = "absorption, distribution, metabolism"; + String searchTerm = "of subject matter"; int start = document.getTextBlock().indexOf(searchTerm); assert start != -1; start = document.getTextBlock().indexOf(searchTerm, start + 1); @@ -282,16 +282,16 @@ public class DocumentIEntityInsertionIntegrationTest extends BuildDocumentIntegr TextEntity textEntity = TextEntity.initialEntityNode(textRange, "123", EntityType.ENTITY, document); entityCreationService.addEntityToGraph(textEntity, document); - assertEquals("2.6.1 Summary of ", textEntity.getTextBefore()); - assertEquals(" and excretion in", textEntity.getTextAfter()); - assertEquals("2.6.1 Summary of absorption, distribution, metabolism and excretion in mammals ", + assertEquals("1 Statement ", textEntity.getTextBefore()); + assertEquals(" and purpose for", textEntity.getTextAfter()); + assertEquals("1 Statement of subject matter and purpose for which this report has been prepared and background information on the application ", textEntity.getDeepestFullyContainingNode().getHeadline().getTextBlock().getSearchText()); assertEquals(searchTerm, textEntity.getValue()); assertEquals(3, textEntity.getIntersectingNodes().size()); - assertEquals(4, textEntity.getDeepestFullyContainingNode().getNumberOnPage()); + assertEquals(1, textEntity.getDeepestFullyContainingNode().getNumberOnPage()); assertTrue(textEntity.getPages() .stream() - .allMatch(pageNode -> pageNode.getNumber() == 33)); + .allMatch(pageNode -> pageNode.getNumber() == 9)); assertInstanceOf(Headline.class, textEntity.getDeepestFullyContainingNode()); assertSameOffsetInAllIntersectingNodes(searchTerm, textEntity); 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 1702a26b..ac706f29 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 @@ -1,29806 +1 @@ -{ - "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, - 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