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RED-8825: general layoutparsing improvements

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* fix tests
This commit is contained in:
Kilian Schuettler 2024-04-30 11:55:18 +02:00
parent f0a70a5242
commit ae46c5f1ca
5 changed files with 103 additions and 67 deletions
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3
layoutparser-service/layoutparser-service-processor/src/main/java/com/knecon/fforesight/service/layoutparser/processor/LayoutParsingPipeline.java
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@ -53,6 +53,7 @@ import com.knecon.fforesight.service.layoutparser.processor.services.classificat
import com.knecon.fforesight.service.layoutparser.processor.services.classification.DocuMineClassificationService;
import com.knecon.fforesight.service.layoutparser.processor.services.classification.RedactManagerClassificationService;
import com.knecon.fforesight.service.layoutparser.processor.services.factory.DocumentGraphFactory;
import com.knecon.fforesight.service.layoutparser.processor.services.graphics.Box;
import com.knecon.fforesight.service.layoutparser.processor.services.graphics.GraphicExtractorService;
import com.knecon.fforesight.service.layoutparser.processor.services.mapper.DocumentDataMapper;
import com.knecon.fforesight.service.layoutparser.processor.services.mapper.TaasDocumentDataMapper;
@ -268,7 +269,7 @@ public class LayoutParsingPipeline {
TextRulingsClassifier.classifyUnderlinedAndStrikethroughText(words, cleanRulings);
var graphics = graphicExtractorService.extractPathElementGraphics(originDocument, pdPage, pageNumber, cleanRulings, stripper.getTextPositionSequences(), false);
List<Box> graphics = graphicExtractorService.extractPathElementGraphics(originDocument, pdPage, pageNumber, cleanRulings, stripper.getTextPositionSequences(), false);
pdfImages.computeIfAbsent(pageNumber, x -> new ArrayList<>())
.addAll(graphics.stream()

9
layoutparser-service/layoutparser-service-processor/src/main/java/com/knecon/fforesight/service/layoutparser/processor/services/blockification/RedactManagerBlockificationService.java
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@ -164,10 +164,11 @@ public class RedactManagerBlockificationService {
previous = block;
}
visualizations.addTextBlockVisualizations(chunkBlockList.stream()
.map(tb -> (TextPageBlock) tb)
.toList(), textPositions.get(0).getPage());
if (!textPositions.isEmpty()) {
visualizations.addTextBlockVisualizations(chunkBlockList.stream()
.map(tb -> (TextPageBlock) tb)
.toList(), textPositions.get(0).getPage());
}
return new ClassificationPage(chunkBlockList);
}

2
layoutparser-service/layoutparser-service-server/src/test/java/com/knecon/fforesight/service/layoutparser/server/LayoutparserEnd2EndTest.java
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@ -34,7 +34,7 @@ public class LayoutparserEnd2EndTest extends AbstractTest {
@Test
public void testLayoutParserEndToEnd() {
String filePath = "/home/kschuettler/Dokumente/TestFiles/RotateTextWithRulingsTestFile.pdf";
String filePath = "files/syngenta/CustomerFiles/54 Fludioxonil - EU AIR3 - Document E1 - Listing of Community and Member States MRLs.pdf";
runForFile(filePath);
}

154
layoutparser-service/layoutparser-service-server/src/test/java/com/knecon/fforesight/service/layoutparser/server/segmentation/PdfSegmentationServiceTest.java
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@ -52,28 +52,16 @@ public class PdfSegmentationServiceTest extends AbstractTest {
@Autowired
private ObjectMapper objectMapper;
@Autowired
private RedactManagerClassificationService redactManagerClassificationService;
@Autowired
private SectionsBuilderService sectionsBuilderService;
@SneakyThrows
public ClassificationDocument buildClassificationDocument(File originDocument, TableServiceResponse tableServiceResponse) {
ClassificationDocument classificationDocument = layoutParsingPipeline.parseLayout(LayoutParsingType.REDACT_MANAGER,
originDocument,
new ImageServiceResponse(),
tableServiceResponse,
new VisualLayoutParsingResponse(),
Map.of("file","document"));
redactManagerClassificationService.classifyDocument(classificationDocument);
sectionsBuilderService.buildSections(classificationDocument);
return classificationDocument;
return layoutParsingPipeline.parseLayout(LayoutParsingType.REDACT_MANAGER,
originDocument,
new ImageServiceResponse(),
tableServiceResponse,
new VisualLayoutParsingResponse(),
Map.of("file", "document"));
}
@ -127,13 +115,13 @@ public class PdfSegmentationServiceTest extends AbstractTest {
ClassificationDocument classificationDocument = buildClassificationDocument(pdfFileResource.getFile());
assertThat(classificationDocument.getHeaders()
.get(0).getTextBlocks().size()).isEqualTo(3);
.get(0).getTextBlocks().size()).isEqualTo(1);
assertThat(classificationDocument.getHeaders()
.get(0).getTextBlocks()
.get(0).getSequences().size()).isEqualTo(8);
.get(0).getSequences().size()).isEqualTo(12);
assertThat(classificationDocument.getHeaders()
.get(0).getTextBlocks()
.get(0).toString()).isEqualTo(textToSearch);
.get(0).toString()).contains(textToSearch);
Document document = DocumentGraphFactory.buildDocumentGraph(LayoutParsingType.REDACT_MANAGER, classificationDocument);
@ -157,7 +145,11 @@ public class PdfSegmentationServiceTest extends AbstractTest {
.flatMap(paragraph -> paragraph.getTables()
.stream())
.collect(Collectors.toList())).isNotEmpty();
var tables = document.getSections().stream().flatMap(paragraph -> paragraph.getTables().stream()).toList();
var tables = document.getSections()
.stream()
.flatMap(paragraph -> paragraph.getTables()
.stream())
.toList();
// Quality of the table parsing is not good, because the file is rotated at scanning.
// We only asset that the table border is not the page border.
@ -179,12 +171,12 @@ public class PdfSegmentationServiceTest extends AbstractTest {
imageServiceResponse.getData()
.forEach(imageMetadata -> images.computeIfAbsent(imageMetadata.getPosition().getPageNumber(), x -> new ArrayList<>())
.add(new ClassifiedImage(new Rectangle2D.Double(imageMetadata.getPosition().getX1(),
imageMetadata.getPosition().getY1(),
imageMetadata.getGeometry().getWidth(),
imageMetadata.getGeometry().getHeight()),
ImageType.valueOf(imageMetadata.getClassification().getLabel().toUpperCase(Locale.ROOT)),
imageMetadata.isAlpha(),
imageMetadata.getPosition().getPageNumber())));
imageMetadata.getPosition().getY1(),
imageMetadata.getGeometry().getWidth(),
imageMetadata.getGeometry().getHeight()),
ImageType.valueOf(imageMetadata.getClassification().getLabel().toUpperCase(Locale.ROOT)),
imageMetadata.isAlpha(),
imageMetadata.getPosition().getPageNumber())));
System.out.println("object");
}
@ -196,11 +188,22 @@ public class PdfSegmentationServiceTest extends AbstractTest {
ClassPathResource pdfFileResource = new ClassPathResource("files/syngenta/CustomerFiles/SinglePages/Spanning Cells - Page131_S-Metolachlor_RAR_01_Volume_1_2018-09-06.pdf");
ClassificationDocument document = buildClassificationDocument(pdfFileResource.getFile());
assertThat(document.getSections().stream().flatMap(paragraph -> paragraph.getTables().stream()).collect(Collectors.toList())).isNotEmpty();
TablePageBlock table = document.getSections().stream().flatMap(paragraph -> paragraph.getTables().stream()).toList().get(0);
assertThat(document.getSections()
.stream()
.flatMap(paragraph -> paragraph.getTables()
.stream())
.collect(Collectors.toList())).isNotEmpty();
TablePageBlock table = document.getSections()
.stream()
.flatMap(paragraph -> paragraph.getTables()
.stream())
.toList()
.get(0);
assertThat(table.getColCount()).isEqualTo(6);
assertThat(table.getRowCount()).isEqualTo(13);
assertThat(table.getRows().stream().mapToInt(List::size).sum()).isEqualTo(6 * 13);
assertThat(table.getRows()
.stream()
.mapToInt(List::size).sum()).isEqualTo(6 * 13);
}
@ -373,29 +376,30 @@ public class PdfSegmentationServiceTest extends AbstractTest {
validateTable(document, 0, 8, 8, 0, 0);
List<List<String>> values = Arrays.asList(Arrays.asList("Annex point Reference within DAR/RAR",
"Author, date",
"Study title",
"Analytical method Author, date, No.",
"Technique, LOQ of the method, validated working range",
"Method meets analytical validation criteria",
"Remarks (in case validation criteria are not met)",
"Acceptability of the method"),
Arrays.asList("Part (a) Methods in soil, water, sediment, air and any additional matrices used in support of environmental fate studies",
"Part (a) Methods in soil, water, sediment, air and any additional matrices used in support of environmental fate studies",
"Part (a) Methods in soil, water, sediment, air and any additional matrices used in support of environmental fate studies",
"Part (a) Methods in soil, water, sediment, air and any additional matrices used in support of environmental fate studies",
"Part (a) Methods in soil, water, sediment, air and any additional matrices used in support of environmental fate studies",
"Part (a) Methods in soil, water, sediment, air and any additional matrices used in support of environmental fate studies",
"Part (a) Methods in soil, water, sediment, air and any additional matrices used in support of environmental fate studies",
"Part (a) Methods in soil, water, sediment, air and any additional matrices used in support of environmental fate studies"),
Arrays.asList("CA 7.1.2.1.1 DAR (2009)",
"Evans P.G. 2001 TMJ4569B, VV-323245",
"Azoxystrobin Laboratory Degradation Study in Three Soil Types, Sampled from Holland and the United Kingdom",
"Method: RAM 269 Johnson R.I., Tummon O.J., Earl M. 1995 RJ1864B, VV-377731 Johnson R.I., Tummon O.J., Earl M. 1998 RAM 269/02, VV-124072 Johnson R.I., Tummon O.J., Earl M. 2000 RAM 269/03, VV-123986 Validation: Robinson N.J. 2001 TMJ4617B, VV-895845",
"LC-MS/MS LOQ: 0.01 mg/kg (R401553 (SYN50165 7), R402173 (SYN501114 )) or 0.02 mg/kg (azoxystrobin, R230310, R234886) Working range: 0.02-1.0 or 0.01-0.5 mg/kg (depending on analyte) Other supporting quantificati on methods: HPLC-UV GC-MSD",
"Y",
"N/A",
"Y"));
"Author, date",
"Study title",
"Analytical method Author, date, No.",
"Technique, LOQ of the method, validated working range",
"Method meets analytical validation criteria",
"Remarks (in case validation criteria are not met)",
"Acceptability of the method"),
Arrays.asList(
"Part (a) Methods in soil, water, sediment, air and any additional matrices used in support of environmental fate studies",
"Part (a) Methods in soil, water, sediment, air and any additional matrices used in support of environmental fate studies",
"Part (a) Methods in soil, water, sediment, air and any additional matrices used in support of environmental fate studies",
"Part (a) Methods in soil, water, sediment, air and any additional matrices used in support of environmental fate studies",
"Part (a) Methods in soil, water, sediment, air and any additional matrices used in support of environmental fate studies",
"Part (a) Methods in soil, water, sediment, air and any additional matrices used in support of environmental fate studies",
"Part (a) Methods in soil, water, sediment, air and any additional matrices used in support of environmental fate studies",
"Part (a) Methods in soil, water, sediment, air and any additional matrices used in support of environmental fate studies"),
Arrays.asList("CA 7.1.2.1.1 DAR (2009)",
"Evans P.G. 2001 TMJ4569B, VV-323245",
"Azoxystrobin Laboratory Degradation Study in Three Soil Types, Sampled from Holland and the United Kingdom",
"Method: RAM 269 Johnson R.I., Tummon O.J., Earl M. 1995 RJ1864B, VV-377731 Johnson R.I., Tummon O.J., Earl M. 1998 RAM 269/02, VV-124072 Johnson R.I., Tummon O.J., Earl M. 2000 RAM 269/03, VV-123986 Validation: Robinson N.J. 2001 TMJ4617B, VV-895845",
"LC-MS/MS LOQ: 0.01 mg/kg (R401553 (SYN50165 7), R402173 (SYN501114 )) or 0.02 mg/kg (azoxystrobin, R230310, R234886) Working range: 0.02-1.0 or 0.01-0.5 mg/kg (depending on analyte) Other supporting quantificati on methods: HPLC-UV GC-MSD",
"Y",
"N/A",
"Y"));
validateTable(document, 0, values);
@ -785,6 +789,7 @@ public class PdfSegmentationServiceTest extends AbstractTest {
}
@Test
public void testMergedEntities_Page26() throws IOException {
@ -802,7 +807,11 @@ public class PdfSegmentationServiceTest extends AbstractTest {
@SneakyThrows
private void toHtml(ClassificationDocument document, String filename) {
var tables = document.getSections().stream().flatMap(paragraph -> paragraph.getTables().stream()).toList();
var tables = document.getSections()
.stream()
.flatMap(paragraph -> paragraph.getTables()
.stream())
.toList();
StringBuilder sb = new StringBuilder();
int currentPage = 1;
@ -823,9 +832,19 @@ public class PdfSegmentationServiceTest extends AbstractTest {
private void validateTable(ClassificationDocument document, int tableIndex, int colCount, int rowCount, int emptyCellsCountCorrect, int emptyCellsCountIncorrect) {
TablePageBlock table = document.getSections().stream().flatMap(paragraph -> paragraph.getTables().stream()).toList().get(tableIndex);
TablePageBlock table = document.getSections()
.stream()
.flatMap(paragraph -> paragraph.getTables()
.stream())
.toList()
.get(tableIndex);
List<List<Cell>> rows = table.getRows();
int emptyCellsFoundFound = rows.stream().flatMap(List::stream).toList().stream().filter(f -> f.toString().isEmpty()).toList().size();
int emptyCellsFoundFound = rows.stream()
.flatMap(List::stream)
.toList()
.stream()
.filter(f -> f.toString().isEmpty())
.toList().size();
for (List<Cell> row : table.getRows()) {
row.forEach(r -> System.out.println(r.toString()));
@ -840,11 +859,20 @@ public class PdfSegmentationServiceTest extends AbstractTest {
private void validateTable(ClassificationDocument document, int tableIndex, List<List<String>> values) {
TablePageBlock table = document.getSections().stream().flatMap(paragraph -> paragraph.getTables().stream()).toList().get(tableIndex);
TablePageBlock table = document.getSections()
.stream()
.flatMap(paragraph -> paragraph.getTables()
.stream())
.toList()
.get(tableIndex);
List<List<Cell>> rows = table.getRows();
List<Cell> rowsFlattened = rows.stream().flatMap(List::stream).toList();
List<String> valuesFlattened = values.stream().flatMap(List::stream).toList();
List<Cell> rowsFlattened = rows.stream()
.flatMap(List::stream)
.toList();
List<String> valuesFlattened = values.stream()
.flatMap(List::stream)
.toList();
for (int i = 0; i < valuesFlattened.size(); i++) {
Cell cell = rowsFlattened.get(i);
@ -857,7 +885,11 @@ public class PdfSegmentationServiceTest extends AbstractTest {
private void validateTableSize(ClassificationDocument document, int tableSize) {
assertThat(document.getSections().stream().flatMap(paragraph -> paragraph.getTables().stream()).toList().size()).isEqualTo(tableSize);
assertThat(document.getSections()
.stream()
.flatMap(paragraph -> paragraph.getTables()
.stream())
.toList().size()).isEqualTo(tableSize);
}

2
layoutparser-service/layoutparser-service-server/src/test/java/com/knecon/fforesight/service/layoutparser/server/services/RulingCleaningServiceTest.java
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@ -81,6 +81,7 @@ public class RulingCleaningServiceTest extends BuildDocumentTest {
@Test
@Disabled
@SneakyThrows
public void testTableExtraction() {
@ -97,6 +98,7 @@ public class RulingCleaningServiceTest extends BuildDocumentTest {
}
@SneakyThrows
private void writeJsons(Path filename) {