Marmelator/redaction-service
1
0
Fork 0
Code Issues Pull Requests 14 Actions Packages Projects Releases 622 Wiki Activity

Merge branch 'DM-285' into 'master'

Browse Source 
DM-285: sort dates in ComponentCreationService

Closes DM-285

See merge request redactmanager/redaction-service!148
This commit is contained in:
Kresnadi Budisantoso 2023-09-29 17:37:32 +02:00
commit a282d035aa
12 changed files with 1006 additions and 435 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

15
redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/ComponentLogCreatorService.java
View File

@ -1,7 +1,9 @@
package com.iqser.red.service.redaction.v1.server.service;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.stream.Collectors;
import java.util.Map;
import org.springframework.stereotype.Service;
@ -12,6 +14,7 @@ import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog
import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.Position;
import com.iqser.red.service.redaction.v1.server.model.component.Component;
import com.iqser.red.service.redaction.v1.server.model.component.Entity;
import com.iqser.red.service.redaction.v1.server.service.document.ComponentComparator;
import com.iqser.red.service.redaction.v1.server.service.document.EntityComparators;
@Service
@ -19,8 +22,12 @@ public class ComponentLogCreatorService {
public ComponentLog buildComponentLog(int analysisNumber, List<Component> components, long componentRulesVersion) {
List<ComponentLogEntry> componentLogComponents = components.stream()
.collect(Collectors.groupingBy(Component::getName, Collectors.mapping(this::buildComponentLogEntry, Collectors.toList())))
Map<String, List<ComponentLogEntryValue>> map = new HashMap<>();
components.stream().sorted(ComponentComparator.first()).forEach(component -> {
ComponentLogEntryValue componentLogEntryValue = buildComponentLogEntry(component);
map.computeIfAbsent(component.getName(), k -> new ArrayList<>()).add(componentLogEntryValue);
});
List<ComponentLogEntry> componentLogComponents = map
.entrySet()
.stream().map(entry -> new ComponentLogEntry(entry.getKey(), entry.getValue()))
.toList();
@ -34,7 +41,7 @@ public class ComponentLogCreatorService {
.value(component.getValue()).originalValue(component.getValue())
.componentRuleId(component.getMatchedRule().toString())
.valueDescription(component.getValueDescription())
.componentLogEntityReferences(toComponentEntityReferences(component.getReferences().stream().sorted(EntityComparators.start()).toList()))
.componentLogEntityReferences(toComponentEntityReferences(component.getReferences().stream().sorted(EntityComparators.first()).toList()))
.build();
}

33
redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/document/ComponentComparator.java Normal file
View File

@ -0,0 +1,33 @@
package com.iqser.red.service.redaction.v1.server.service.document;
import java.util.Comparator;
import com.iqser.red.service.redaction.v1.server.model.component.Component;
public class ComponentComparator implements Comparator<Component> {
public static ComponentComparator first() {
return new ComponentComparator();
}
@Override
public int compare(Component component1, Component component2) {
var firstEntity1 = component1.getReferences().stream().min(EntityComparators.first());
var firstEntity2 = component2.getReferences().stream().min(EntityComparators.first());
if (firstEntity1.isEmpty() && firstEntity2.isEmpty()) {
return 0;
}
if (firstEntity1.isEmpty() && firstEntity2.isPresent()) {
return -1;
}
if (firstEntity1.isPresent() && firstEntity2.isEmpty()) {
return 1;
}
return new EntityComparators.FirstEntity().compare(firstEntity1.get(), firstEntity2.get());
}
}

106
redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/document/ComponentCreationService.java
View File

@ -37,19 +37,20 @@ public class ComponentCreationService {
Set<Entity> referencedEntities = new HashSet<>();
/**
* Finds the first value from the collection of entities and creates a component from it. If no value is found, the fallback value is used instead.
*
* @param ruleIdentifier the identifier for the rule
* @param name the name of the operation
* @param entities the collection of entities to search for the first value
* @param fallback the value to be returned if no value is found in the collection
*/
public void firstOrElse(String ruleIdentifier, String name, Collection<Entity> entities, String fallback) {
private static List<Entity> findEntitiesFromLongestSection(Collection<Entity> entities) {
String valueDescription = String.format("First found value or else '%s'", fallback);
String value = entities.stream().min(EntityComparators.start()).map(Entity::getValue).orElse(fallback);
create(ruleIdentifier, name, value, valueDescription, entities);
var entitiesBySection = entities.stream().collect(Collectors.groupingBy(entity -> entity.getContainingNode().getHighestParent()));
Optional<SemanticNode> longestSection = entitiesBySection.entrySet()
.stream()
.sorted(Comparator.comparingInt(ComponentCreationService::getTotalLengthOfEntities).reversed())
.map(Map.Entry::getKey)
.findFirst();
if (longestSection.isEmpty()) {
return Collections.emptyList();
}
return entitiesBySection.get(longestSection.get());
}
@ -67,20 +68,27 @@ public class ComponentCreationService {
/**
* Joins entity values, and creates a component from the result.
* Finds the first value from the collection of entities and creates a component from it. If no value is found, the fallback value is used instead.
*
* @param ruleIdentifier The identifier of the rule.
* @param name The name of the entity.
* @param entities The collection of entities to process.
* @param ruleIdentifier the identifier for the rule
* @param name the name of the operation
* @param entities the collection of entities to search for the first value
* @param fallback the value to be returned if no value is found in the collection
*/
public void joining(String ruleIdentifier, String name, Collection<Entity> entities, String delimiter) {
public void firstOrElse(String ruleIdentifier, String name, Collection<Entity> entities, String fallback) {
String valueDescription = String.format("Joining all values with '%s'", delimiter);
String value = entities.stream().sorted(EntityComparators.start()).map(Entity::getValue).collect(Collectors.joining(delimiter));
String valueDescription = String.format("First found value of type %s or else '%s'", joinTypes(entities), fallback);
String value = entities.stream().min(EntityComparators.first()).map(Entity::getValue).orElse(fallback);
create(ruleIdentifier, name, value, valueDescription, entities);
}
private static String joinTypes(Collection<Entity> entities) {
return entities.stream().map(Entity::getType).distinct().collect(Collectors.joining(", "));
}
/**
* Creates a new component with the given parameters and inserts it into the kieSession.
*
@ -166,17 +174,16 @@ public class ComponentCreationService {
/**
* Joins all unique values from a collection of entities into a single string using a specified delimiter and creates a component from the result.
* Joins entity values, and creates a component from the result.
*
* @param ruleIdentifier the identifier of the rule
* @param name the name of the joining operation
* @param entities the collection of entities
* @param delimiter the delimiter to use for joining the values
* @param ruleIdentifier The identifier of the rule.
* @param name The name of the entity.
* @param entities The collection of entities to process.
*/
public void joiningUnique(String ruleIdentifier, String name, Collection<Entity> entities, String delimiter) {
public void joining(String ruleIdentifier, String name, Collection<Entity> entities, String delimiter) {
String valueDescription = String.format("Joining all values with '%s'", delimiter);
String value = entities.stream().sorted(EntityComparators.start()).map(Entity::getValue).distinct().collect(Collectors.joining(delimiter));
String valueDescription = String.format("Joining all values of type %s with '%s'", joinTypes(entities), delimiter);
String value = entities.stream().sorted(EntityComparators.first()).map(Entity::getValue).collect(Collectors.joining(delimiter));
create(ruleIdentifier, name, value, valueDescription, entities);
}
@ -208,18 +215,19 @@ public class ComponentCreationService {
}
private static List<Entity> findEntitiesFromLongestSection(Collection<Entity> entities) {
/**
* Joins all unique values from a collection of entities into a single string using a specified delimiter and creates a component from the result.
*
* @param ruleIdentifier the identifier of the rule
* @param name the name of the joining operation
* @param entities the collection of entities
* @param delimiter the delimiter to use for joining the values
*/
public void joiningUnique(String ruleIdentifier, String name, Collection<Entity> entities, String delimiter) {
var entitiesBySection = entities.stream().collect(Collectors.groupingBy(entity -> entity.getContainingNode().getHighestParent()));
Optional<SemanticNode> longestSection = entitiesBySection.entrySet()
.stream().sorted(Comparator.comparingInt(ComponentCreationService::getTotalLengthOfEntities).reversed()).map(Map.Entry::getKey)
.findFirst();
if (longestSection.isEmpty()) {
return Collections.emptyList();
}
return entitiesBySection.get(longestSection.get());
String valueDescription = String.format("Joining all unique values of type %s with '%s'", joinTypes(entities), delimiter);
String value = entities.stream().sorted(EntityComparators.first()).map(Entity::getValue).distinct().collect(Collectors.joining(delimiter));
create(ruleIdentifier, name, value, valueDescription, entities);
}
@ -297,7 +305,7 @@ public class ComponentCreationService {
if (entities.isEmpty()) {
return;
}
for (Entity entity : entities) {
entities.stream().sorted(EntityComparators.first()).forEach(entity -> {
BreakIterator iterator = BreakIterator.getSentenceInstance(Locale.ENGLISH);
iterator.setText(entity.getValue());
int start = iterator.first();
@ -308,7 +316,7 @@ public class ComponentCreationService {
String.format("Values of type '%s' as sentences", entity.getType()),
entity);
}
}
});
}
@ -346,8 +354,7 @@ public class ComponentCreationService {
*/
public void createComponentsForUnMappedEntities(String ruleIdentifier, Collection<Entity> entities) {
entities.stream()
.filter(entity -> !referencedEntities.contains(entity))
entities.stream().filter(entity -> !referencedEntities.contains(entity)).sorted(EntityComparators.first())
.forEach(entity -> create(ruleIdentifier, entity.getType(), entity.getValue(), "Unmapped Entity", List.of(entity)));
}
@ -375,7 +382,7 @@ public class ComponentCreationService {
*/
public void convertDates(String ruleIdentifier, String name, Collection<Entity> entities, String resultFormat) {
String valueDescription = String.format("Convert values of type to %s joined with ', '", resultFormat);
String valueDescription = String.format("Convert values of type '%s' to %s joined with ', '", joinTypes(entities), resultFormat);
List<String> unparsedDates = new LinkedList<>();
List<Date> dates = new LinkedList<>();
@ -407,10 +414,9 @@ public class ComponentCreationService {
*/
public void joiningFromSameTableRow(String ruleIdentifier, String name, Collection<Entity> entities) {
String types = entities.stream().map(Entity::getType).distinct().collect(Collectors.joining());
String types = entities.stream().map(Entity::getType).sorted(Comparator.reverseOrder()).distinct().collect(Collectors.joining(", "));
String valueDescription = String.format("Combine values of %s that are in same table row", types);
Map<Optional<Table>, List<Entity>> entitiesPerTable = entities.stream().collect(Collectors.groupingBy(this::getFirstTable));
entitiesPerTable.forEach((optionalTable, groupedEntities) -> {
entities.stream().collect(Collectors.groupingBy(this::getFirstTable)).forEach((optionalTable, groupedEntities) -> {
if (optionalTable.isEmpty()) {
groupedEntities.forEach(entity -> create(ruleIdentifier, name, entity.getValue(), valueDescription, entity));
}
@ -422,9 +428,13 @@ public class ComponentCreationService {
groupedEntities.stream()
.filter(entity -> entity.getContainingNode() instanceof TableCell)
.collect(Collectors.groupingBy(entity -> ((TableCell) entity.getContainingNode()).getRow()))
.forEach((row, entitiesInSameRow) -> create(ruleIdentifier,
.entrySet()
.stream()
.sorted(Comparator.comparingInt(Map.Entry::getKey))
.map(Map.Entry::getValue)
.forEach(entitiesInSameRow -> create(ruleIdentifier,
name,
entities.stream().map(Entity::getValue).collect(Collectors.joining(", ")),
entitiesInSameRow.stream().sorted(Comparator.comparing(Entity::getType).reversed()).map(Entity::getValue).collect(Collectors.joining(", ")),
valueDescription,
entitiesInSameRow));
});

25
redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/document/EntityComparators.java
View File

@ -6,7 +6,12 @@ import com.iqser.red.service.redaction.v1.server.model.component.Entity;
public abstract class EntityComparators implements Comparator<Entity> {
private static class LongestEntity implements Comparator<Entity> {
public static Comparator<Entity> first() {
return new FirstEntity();
}
public static class LongestEntity implements Comparator<Entity> {
@Override
public int compare(Entity Entity, Entity otherEntity) {
@ -16,26 +21,20 @@ public abstract class EntityComparators implements Comparator<Entity> {
}
private static class FirstEntity implements Comparator<Entity> {
@Override
public int compare(Entity Entity, Entity otherEntity) {
return Integer.compare(Entity.getStartOffset(), otherEntity.getStartOffset());
}
}
public static Comparator<Entity> length() {
return new LongestEntity();
}
public static class FirstEntity implements Comparator<Entity> {
public static Comparator<Entity> start() {
@Override
public int compare(Entity Entity, Entity otherEntity) {
return Integer.compare(Entity.getStartOffset(), otherEntity.getStartOffset());
}
return new FirstEntity();
}
}

3
redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/drools/ComponentDroolsExecutionService.java
View File

@ -21,6 +21,7 @@ import com.iqser.red.service.redaction.v1.server.RedactionServiceSettings;
import com.iqser.red.service.redaction.v1.server.model.component.Component;
import com.iqser.red.service.redaction.v1.server.model.component.Entity;
import com.iqser.red.service.redaction.v1.server.model.document.nodes.Document;
import com.iqser.red.service.redaction.v1.server.service.document.ComponentComparator;
import com.iqser.red.service.redaction.v1.server.service.document.ComponentCreationService;
import com.iqser.red.service.redaction.v1.server.utils.exception.DroolsTimeoutException;
@ -70,7 +71,7 @@ public class ComponentDroolsExecutionService {
}
List<FileAttribute> resultingFileAttributes = getFileAttributes(kieSession);
List<Component> components = getComponents(kieSession);
List<Component> components = getComponents(kieSession).stream().sorted(ComponentComparator.first()).toList();
kieSession.dispose();
return components;
}

2
redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/DocumineFloraTest.java
View File

@ -48,7 +48,7 @@ public class DocumineFloraTest extends AbstractRedactionIntegrationTest {
// @Disabled
public void titleExtraction() throws IOException {
AnalyzeRequest request = uploadFileToStorage("files/Documine/Flora/_000008810-0.2.pdf");
AnalyzeRequest request = uploadFileToStorage("files/Documine/Flora/A8591B/15-Curacron_ToxicidadeAgudaOral.pdf");
// AnalyzeRequest request = prepareStorage("files/Documine/Flora/ProblemDocs/SOLICITA_VICTRATO-GOLD-II_Item 21_Mutacao_Genica (1).pdf",
// "files/Documine/Flora/ProblemDocs/SOLICITA_VICTRATO-GOLD-II_Item 21_Mutacao_Genica (1).TABLES.json");

1
redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/manualchanges/ManualChangesEnd2EndTest.java
View File

@ -78,6 +78,7 @@ import lombok.SneakyThrows;
public class ManualChangesEnd2EndTest extends AbstractRedactionIntegrationTest {
private static final String RULES = loadFromClassPath("drools/rules.drl");
private static final String DM_RULES = loadFromClassPath("drools/documine_flora.drl");
@Autowired
private EntityEnrichmentService entityEnrichmentService;

10
redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/manualchanges/ManualChangesIntegrationTest.java
View File

@ -5,6 +5,7 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.wildfly.common.Assert.assertFalse;
import java.awt.geom.Rectangle2D;
import java.io.FileOutputStream;
import java.time.OffsetDateTime;
import java.util.Collection;
import java.util.Comparator;
@ -27,22 +28,30 @@ import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import com.iqser.red.service.persistence.service.v1.api.shared.model.AnalyzeRequest;
import com.iqser.red.service.persistence.service.v1.api.shared.model.AnalyzeResult;
import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.AnnotationStatus;
import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.Rectangle;
import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.entitymapped.IdRemoval;
import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.entitymapped.ManualForceRedaction;
import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.entitymapped.ManualRecategorization;
import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.entitymapped.ManualResizeRedaction;
import com.iqser.red.service.redaction.v1.server.annotate.AnnotateRequest;
import com.iqser.red.service.redaction.v1.server.annotate.AnnotateResponse;
import com.iqser.red.service.redaction.v1.server.document.graph.BuildDocumentIntegrationTest;
import com.iqser.red.service.redaction.v1.server.model.document.entity.EntityType;
import com.iqser.red.service.redaction.v1.server.model.document.entity.TextEntity;
import com.iqser.red.service.redaction.v1.server.model.document.entity.PositionOnPage;
import com.iqser.red.service.redaction.v1.server.model.document.nodes.Document;
import com.iqser.red.service.redaction.v1.server.model.document.nodes.Paragraph;
import com.iqser.red.service.redaction.v1.server.redaction.utils.OsUtils;
import com.iqser.red.service.redaction.v1.server.service.document.EntityCreationService;
import com.iqser.red.service.redaction.v1.server.service.document.EntityEnrichmentService;
import com.iqser.red.service.redaction.v1.server.service.ManualChangesApplicationService;
import com.iqser.red.service.redaction.v1.server.utils.exception.NotFoundException;
import com.knecon.fforesight.service.layoutparser.internal.api.queue.LayoutParsingType;
import lombok.SneakyThrows;
@Import(ManualChangesIntegrationTest.TestConfiguration.class)
public class ManualChangesIntegrationTest extends BuildDocumentIntegrationTest {
@ -249,6 +258,7 @@ public class ManualChangesIntegrationTest extends BuildDocumentIntegrationTest {
assertFalse(entity.removed());
}
private void assertRectanglesAlmostEqual(Collection<Rectangle2D> rects1, Collection<Rectangle2D> rects2) {
if (rects1.stream().allMatch(rect1 -> rects2.stream().anyMatch(rect2 -> rectanglesAlmostEqual(rect1, rect2)))) {

23
redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/service/document/EntityComparatorsTest.java Normal file
View File

@ -0,0 +1,23 @@
package com.iqser.red.service.redaction.v1.server.service.document;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.util.stream.Stream;
import org.junit.jupiter.api.Test;
import com.iqser.red.service.redaction.v1.server.model.component.Entity;
class EntityComparatorsTest {
@Test
public void testFirstEntity() {
Entity entity1 = Entity.builder().startOffset(0).build();
Entity entity2 = Entity.builder().startOffset(2).build();
Entity entity3 = Entity.builder().startOffset(20).build();
assertEquals(entity1, Stream.of(entity2, entity3, entity1).min(EntityComparators.first()).orElseThrow());
}
}

1071
redaction-service-v1/redaction-service-server-v1/src/test/resources/drools/documine_flora.drl
View File

File diff suppressed because it is too large Load Diff

152
redaction-service-v1/redaction-service-server-v1/src/test/resources/drools/documine_flora_components.drl
View File

@ -47,7 +47,7 @@ declare GuidelineMapping
//------------------------------------ Default Components rules ------------------------------------
rule "StudyTitle.0.0: Study Title"
rule "StudyTitle.0.0: First Title found"
when
$titleCandidates: List() from collect (Entity(type == "title"))
then
@ -55,7 +55,7 @@ rule "StudyTitle.0.0: Study Title"
end
rule "PerformingLaboratory.1.0: Performing Laboratory"
rule "PerformingLaboratory.1.0: Performing Laboratory name and country found in same section"
when
$laboratoryName: Entity(type == "laboratory_name", $node: containingNode)
$laboratoryCountry: Entity(type == "laboratory_country", containingNode == $node)
@ -64,7 +64,7 @@ rule "PerformingLaboratory.1.0: Performing Laboratory"
componentCreationService.create("PerformingLaboratory.1.0", "Performing_Laboratory", $laboratoryName.getValue() + ", " + $laboratoryCountry.getValue(), "Laboratory name and country found!", List.of($laboratoryName, $laboratoryCountry));
end
rule "PerformingLaboratory.2.0: Performing Laboratory"
rule "PerformingLaboratory.2.0: Performing Laboratory name but no country found in same section"
when
$laboratoryName: Entity(type == "laboratory_name", $node: containingNode)
not Entity(type == "laboratory_country", containingNode == $node)
@ -72,7 +72,7 @@ rule "PerformingLaboratory.2.0: Performing Laboratory"
componentCreationService.create("PerformingLaboratory.2.0", "Performing_Laboratory", $laboratoryName.getValue(), "Only laboratory name found!", List.of($laboratoryName));
end
rule "PerformingLaboratory.0.2: Performing Laboratory"
rule "PerformingLaboratory.0.2: Performing Laboratory not found"
salience -1
when
not Component(name == "Performing_Laboratory")
@ -81,30 +81,30 @@ rule "PerformingLaboratory.0.2: Performing Laboratory"
end
rule "ReportNumber.0.0: Report number"
rule "ReportNumber.0.0: First Report number found"
when
$reportNumberCandidates: List() from collect (Entity(type == "report_number"))
then
componentCreationService.firstOrElse("ReportNumber.0.0", "Report_number", $reportNumberCandidates, "");
componentCreationService.firstOrElse("ReportNumber.0.0", "Report_Number", $reportNumberCandidates, "");
end
rule "GLPStudy.0.0: GLP Study"
rule "GLPStudy.0.0: GLP Study found"
when
$glpStudyList: List(!isEmpty) from collect(Entity(type == "glp_study"))
then
componentCreationService.create("GLPStudy.0.0", "GLP_study", "Yes", "Yes if present, No if not", $glpStudyList);
componentCreationService.create("GLPStudy.0.0", "GLP_Study", "Yes", "Yes if present, No if not", $glpStudyList);
end
rule "GLPStudy.1.0: GLP Study"
rule "GLPStudy.1.0: GLP Study not found"
when
not Entity(type == "glp_study")
then
componentCreationService.create("GLPStudy.1.0", "GLP_study", "No", "Yes if present, No if not");
componentCreationService.create("GLPStudy.1.0", "GLP_Study", "No", "Yes if present, No if not");
end
rule "TestGuideline.0.0: create mappings"
rule "TestGuideline.0.0: create OECD number and year guideline mappings"
salience 2
when
Entity(type == "oecd_guideline_number")
@ -141,7 +141,7 @@ rule "TestGuideline.0.0: create mappings"
insert(new GuidelineMapping("487", "2016", "Nº 487: Micronucleus Human Lymphocytes (2016)"));
end
rule "TestGuideline.0.1: match test guidelines with mappings"
rule "TestGuideline.0.1: match OECD number and year with guideline mappings"
salience 1
when
GuidelineMapping($year: year, $number: number, $guideline: guideline)
@ -157,7 +157,7 @@ rule "TestGuideline.0.1: match test guidelines with mappings"
);
end
rule "TestGuideline.1.0: no mapping found"
rule "TestGuideline.1.0: no guideline mapping found"
when
not Component(name == "Test_Guidelines_1")
$guideLine: Entity(type == "oecd_guideline")
@ -165,23 +165,15 @@ rule "TestGuideline.1.0: no mapping found"
componentCreationService.create("TestGuideline.2.0", "Test_Guidelines_1", $guideLine.getValue(), "No Mapping for OECD number and year found, using fallback instead!", List.of($guideLine));
end
rule "TestGuideline.2.0: Test Guideline 2"
rule "TestGuideline.2.0: All values of EPA guideline and EC guidelines"
when
$epaGuideLines: List() from collect (Entity(type == "epa_guideline"))
$ecGuideLines: List() from collect (Entity(type == "ec_guideline"))
$guidelines: List() from collect (Entity(type == "epa_guideline" || type == "ec_guideline"))
then
componentCreationService.joining("TestGuideline.2.0",
"Test_Guideline_2",
Stream.of(
$epaGuideLines.stream(),
$ecGuideLines.stream())
.flatMap(a -> a)
.toList()
);
componentCreationService.joining("TestGuideline.2.0", "Test_Guidelines_2", $guidelines);
end
rule "StartDate.0.0: Experimental Starting Date"
rule "StartDate.0.0: All experimental start dates converted to dd/MM/yyyy"
when
$startDates: List(!isEmpty()) from collect (Entity(type == "experimental_start_date"))
then
@ -189,7 +181,7 @@ rule "StartDate.0.0: Experimental Starting Date"
end
rule "CompletionDate.0.0: Experimental Completion Date"
rule "CompletionDate.0.0: All experimental end dates converted to dd/MM/yyyy"
when
$endDates: List(!isEmpty()) from collect (Entity(type == "experimental_end_date"))
then
@ -197,26 +189,26 @@ rule "CompletionDate.0.0: Experimental Completion Date"
end
rule "AnalysisCertificate.0.0: Certificate of analysis batch identification"
rule "AnalysisCertificate.0.0: Unique values of certificate of analysis batch identification"
when
$batchNumbers: List(!isEmpty()) from collect (Entity(type == "batch_number"))
then
componentCreationService.joiningUnique("AnalysisCertificate.0.0", "Batch_Number", $batchNumbers);
componentCreationService.joiningUnique("AnalysisCertificate.0.0", "Certificate_of_Analysis_Batch_Identification", $batchNumbers);
end
rule "StudyConclusion.0.0: Study conclusion in first found section"
when
$oecdNumber: String() from List.of("402", "403", "404", "405", "425", "429", "436", "471")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$studyConclusions: List() from collect(Entity(type == "study_conclusion"))
then
componentCreationService.joiningUniqueFromFirstSectionOnly("Study_Conclusion.0.0", "Study_Conclusion", $studyConclusions);
componentCreationService.joiningFromFirstSectionOnly("StudyConclusion.0.0", "Study_Conclusion", $studyConclusions, " ");
end
rule "GuidelineDeviation.0.0: Guideline deviation as sentences"
when
$oecdNumber: String() from List.of("402", "403", "404", "405", "425", "429", "436", "471")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$guidelineDeviations: List() from collect (Entity(type == "guideline_deviation"))
then
componentCreationService.asSentences("GuidelineDeviation.0.0", "Deviation_from_the_Guideline", $guidelineDeviations);
@ -225,7 +217,7 @@ rule "GuidelineDeviation.0.0: Guideline deviation as sentences"
rule "Species.0.0: First found species"
when
$oecdNumber: String() from List.of("402", "403", "404", "405", "425", "429", "436", "471")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$species: List() from collect (Entity(type == "species"))
then
componentCreationService.firstOrElse("Species.0.0", "Species", $species, "");
@ -234,7 +226,7 @@ rule "Species.0.0: First found species"
rule "Strain.0.0: First found strain"
when
$oecdNumber: String() from List.of("402", "403", "404", "405", "425", "429", "436", "471")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$strain: List() from collect (Entity(type == "strain"))
then
componentCreationService.firstOrElse("Strain.0.0", "Strain", $strain, "");
@ -243,34 +235,34 @@ rule "Strain.0.0: First found strain"
rule "Conclusion.0.0: Unique values of Conclusion LD50"
when
$oecdNumber: String() from List.of("402", "403", "425", "436")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$conclusions: List() from collect (Entity(type == "ld50_value"))
then
componentCreationService.joiningUnique("Conclusion.0.0", "Conclusion_LD50_mg_per_kg", $conclusions, "");
componentCreationService.joiningUnique("Conclusion.0.0", "Conclusion_LD50_mg_per_kg", $conclusions);
end
rule "Conclusion0.1.0: Greater than found"
when
$oecdNumber: String() from List.of("402", "403", "425", "436")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$conclusions: List(!isEmpty()) from collect (Entity(type == "ld50_greater"))
then
componentCreationService.create("Conclusion.1.0", "Conclusion_LD50_Greater_than", "Greater Than", "\"Greater than\" value found", $conclusions);
componentCreationService.create("Conclusion.1.0", "Conclusion_LD50_Greater_than", "Greater than", "Entity of type 'ld50_greater' found", $conclusions);
end
rule "Conclusion.1.1: Greater than not found"
when
$oecdNumber: String() from List.of("402", "403", "425", "436")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
not Entity(type == "ld50_greater")
then
componentCreationService.create("Conclusion.1.1", "Conclusion_LD50_Greater_than", "", "No \"Greater than\" value found");
componentCreationService.create("Conclusion.1.1", "Conclusion_LD50_Greater_than", "", "No entity of type 'ld50_greater' found");
end
rule "Conclusion.2.0: Minimum confidence as unique values"
when
$oecdNumber: String() from List.of("402", "403", "425", "436")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$conclusions: List() from collect (Entity(type == "confidence_minimal"))
then
componentCreationService.joiningUnique("Conclusion.2.0", "Conclusion_Minimum_Confidence", $conclusions);
@ -279,7 +271,7 @@ rule "Conclusion.2.0: Minimum confidence as unique values"
rule "Conclusion.3.0: Maximum confidence as unique values"
when
$oecdNumber: String() from List.of("402", "403", "425", "436")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$conclusions: List() from collect (Entity(type == "confidence_maximal"))
then
componentCreationService.joiningUnique("Conclusion.3.0", "Conclusion_Maximum_Confidence", $conclusions);
@ -287,15 +279,23 @@ rule "Conclusion.3.0: Maximum confidence as unique values"
rule "Necropsy.0.0: Necropsy findings from longest section"
when
FileAttribute(label == "oecd_number", value == "402")
FileAttribute(label == "OECD Number", value == "402")
$necropsies: List() from collect (Entity(type == "necropsy_findings"))
then
componentCreationService.joiningFromLongestSectionOnly("Necropsy.0.0", "Necropsy_Findings", $necropsies);
componentCreationService.joiningFromLongestSectionOnly("Necropsy.0.0", "Necropsy_Findings", $necropsies, " ");
end
rule "Necropsy.0.1: Necropsy findings from longest section"
when
FileAttribute(label == "OECD Number", value == "403" || value == "436")
$necropsies: List() from collect (Entity(type == "necropsy_findings"))
then
componentCreationService.asSentences("Necropsy.0.0", "Necropsy_Findings", $necropsies);
end
rule "Necropsy.1.0: Doses mg per kg of Bodyweight as one block"
when
FileAttribute(label == "oecd_number", value == "402")
FileAttribute(label == "OECD Number", value == "402")
$dosages: List() from collect (Entity(type == "doses_(mg_kg_bw)"))
then
componentCreationService.joining("Necropsy.1.0", "Doses_mg_per_kg_bw", $dosages, " ");
@ -304,7 +304,7 @@ rule "Necropsy.1.0: Doses mg per kg of Bodyweight as one block"
rule "Necropsy.2.0: Necropsy findings as one block"
when
$oecdNumber: String() from List.of("403", "436")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$necropsies: List() from collect (Entity(type == "necropsy_findings"))
then
componentCreationService.joining("Necropsy.2.0", "Necropsy_Findings", $necropsies, " ");
@ -313,7 +313,7 @@ rule "Necropsy.2.0: Necropsy findings as one block"
rule "Necropsy.3.0: Conducted with 4 hours of exposure as one block"
when
$oecdNumber: String() from List.of("403", "436")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$exposures: List() from collect (Entity(type == "4h_exposure"))
then
componentCreationService.joining("Necropsy.3.0", "Conducted_with_4_Hours_of_Exposure", $exposures, " ");
@ -322,7 +322,7 @@ rule "Necropsy.3.0: Conducted with 4 hours of exposure as one block"
rule "StudyDesign.0.0: Study design as one block"
when
$oecdNumber: String() from List.of("404", "405", "429", "406", "428", "438", "439", "474", "487")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$studyDesigns: List() from collect (Entity(type == "study_design"))
then
componentCreationService.joining("StudyDesign.0.0", "Study_Design", $studyDesigns, " ");
@ -331,7 +331,7 @@ rule "StudyDesign.0.0: Study design as one block"
rule "Results.0.0: Results and conclusions as joined values"
when
$oecdNumber: String() from List.of("406", "428", "438", "439", "474", "487")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$results: List() from collect (Entity(type == "results_and_conclusion"))
then
componentCreationService.joining("Results.0.0", "Results_and_Conclusions", $results, " ");
@ -339,7 +339,7 @@ rule "Results.0.0: Results and conclusions as joined values"
rule "WeightBehavior.0.0: Weight change behavior as sentences"
when
FileAttribute(label == "oecd_number", value == "402")
FileAttribute(label == "OECD Number", value == "402")
$weightChanges: List() from collect (Entity(type == "weight_behavior_changes"))
then
componentCreationService.asSentences("WeightBehavior.0.0", "Weight_Behavior_Changes", $weightChanges);
@ -347,7 +347,7 @@ rule "WeightBehavior.0.0: Weight change behavior as sentences"
rule "MortalityStatement.0.0: Mortality statements as one block"
when
FileAttribute(label == "oecd_number", value == "402")
FileAttribute(label == "OECD Number", value == "402")
$mortalityStatements: List() from collect (Entity(type == "mortality_statement"))
then
componentCreationService.joining("MortalityStatement.0.0", "Mortality_Statement", $mortalityStatements, " ");
@ -355,7 +355,7 @@ rule "MortalityStatement.0.0: Mortality statements as one block"
rule "ClinicalObservations.0.0: Clinical observations as sentences"
when
FileAttribute(label == "oecd_number", value == "403")
FileAttribute(label == "OECD Number", value == "403")
$observations: List() from collect (Entity(type == "clinical_observations"))
then
componentCreationService.asSentences("MortalityStatement.0.0", "Clinical_Observations", $observations);
@ -363,7 +363,7 @@ rule "ClinicalObservations.0.0: Clinical observations as sentences"
rule "BodyWeight.0.0: Bodyweight changes as sentences"
when
FileAttribute(label == "oecd_number", value == "403")
FileAttribute(label == "OECD Number", value == "403")
$weightChanges: List() from collect (Entity(type == "bodyweight_changes"))
then
componentCreationService.asSentences("BodyWeight.0.0", "Body_Weight_Changes", $weightChanges);
@ -372,7 +372,7 @@ rule "BodyWeight.0.0: Bodyweight changes as sentences"
rule "Detailing.0.0: Detailing of reported changes as one block"
when
$oecdNumber: String() from List.of("404", "405")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$detailings: List() from collect (Entity(type == "detailing"))
then
componentCreationService.joining("Detailing.0.0", "Detailing_of_Reported_Changes", $detailings, " ");
@ -381,8 +381,8 @@ rule "Detailing.0.0: Detailing of reported changes as one block"
rule "Sex.0.0: Male sex found"
when
$oecdNumber: String() from List.of("405", "429")
FileAttribute(label == "oecd_number", value == $oecdNumber)
$males: List(!isEmpty) from collect (Entity(type == "sex", (value == "male" || value == "males")))
FileAttribute(label == "OECD Number", value == $oecdNumber)
$males: List(!isEmpty) from collect (Entity(type == "sex", (value.toLowerCase() == "male" || value.toLowerCase() == "males")))
then
componentCreationService.create("Sex.0.0", "Sex", "male", "male sex found", $males);
end
@ -390,8 +390,8 @@ rule "Sex.0.0: Male sex found"
rule "Sex.1.0: Female sex found"
when
$oecdNumber: String() from List.of("405", "429")
FileAttribute(label == "oecd_number", value == $oecdNumber)
$females: List(!isEmpty) from collect (Entity(type == "sex", (value == "female" || value == "females")))
FileAttribute(label == "OECD Number", value == $oecdNumber)
$females: List(!isEmpty) from collect (Entity(type == "sex", (value.toLowerCase() == "female" || value.toLowerCase() == "females")))
then
componentCreationService.create("Sex.0.0", "Sex", "female", "female sex found", $females);
end
@ -399,7 +399,7 @@ rule "Sex.1.0: Female sex found"
rule "NumberOfAnimals.0.0: Number of animals found"
when
$oecdNumber: String() from List.of("405", "429")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$numberOfAnimals: Entity(type == "number_of_animals")
then
componentCreationService.create("NumberOfAnimals.0.0", "Number_of_Animals", $numberOfAnimals.getValue(), "Number of animals found directly", $numberOfAnimals);
@ -408,7 +408,7 @@ rule "NumberOfAnimals.0.0: Number of animals found"
rule "NumberOfAnimals.1.0: Count unique occurences of animals"
when
$oecdNumber: String() from List.of("405", "429")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
not Entity(type == "number_of_animals")
$animals: List() from collect (Entity(type == "animal_number"))
then
@ -418,16 +418,16 @@ rule "NumberOfAnimals.1.0: Count unique occurences of animals"
rule "ClinicalSigns.0.0: Clinical signs as sentences"
when
$oecdNumber: String() from List.of("425")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$clinicalSigns: List() from collect (Entity(type == "clinical_signs"))
then
componentCreationService.asSentences("ClinicalSigns.0.0", "Clinical_Signs", $clinicalSigns);
end
rule "DoseMortality.0.0: Dose mortality as sentences"
rule "DoseMortality.0.0: Dose mortality joined with dose from same table row"
when
$oecdNumber: String() from List.of("425")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$doseMortalities: List() from collect (Entity(type == "dose_mortality" || type == "dose_mortality_dose"))
then
componentCreationService.joiningFromSameTableRow("DoseMortality.0.0", "Dose_Mortality", $doseMortalities);
@ -436,7 +436,7 @@ rule "DoseMortality.0.0: Dose mortality as sentences"
rule "Mortality.0.0: Mortality as one block"
when
$oecdNumber: String() from List.of("425")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$mortalities: List() from collect (Entity(type == "mortality"))
then
componentCreationService.joining("Mortality.0.0", "Mortality", $mortalities, " ");
@ -445,8 +445,8 @@ rule "Mortality.0.0: Mortality as one block"
rule "Dosages.0.0: First found value of Dosages"
when
$oecdNumber: String() from List.of("425")
FileAttribute(label == "oecd_number", value == $oecdNumber)
$mortalities: List() from collect (Entity(type == "mortality"))
FileAttribute(label == "OECD Number", value == $oecdNumber)
$mortalities: List() from collect (Entity(type == "dosages"))
then
componentCreationService.firstOrElse("Dosages.0.0", "Dosages", $mortalities, "");
end
@ -454,7 +454,7 @@ rule "Dosages.0.0: First found value of Dosages"
rule "PrelimResults.0.0: Preliminary test results as sentences"
when
$oecdNumber: String() from List.of("429")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$results: List() from collect (Entity(type == "preliminary_test_results"))
then
componentCreationService.asSentences("PrelimResults.0.0", "Preliminary_Test_Results", $results);
@ -463,7 +463,7 @@ rule "PrelimResults.0.0: Preliminary test results as sentences"
rule "TestResults.0.0: Test results as one block"
when
$oecdNumber: String() from List.of("429")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$results: List() from collect (Entity(type == "test_results"))
then
componentCreationService.joining("TestResults.0.0", "Test_Results", $results, " ");
@ -472,34 +472,34 @@ rule "TestResults.0.0: Test results as one block"
rule "PositiveControl.0.0: Was the definitive study conducted with positive control"
when
$oecdNumber: String() from List.of("429")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$results: List() from collect (Entity(type == "positive_control"))
then
componentCreationService.joining("PositiveControl.0.0", "Was_the_definitive_study_conducted_with_positive_control", $results, " ");
end
rule "MainResults.0.0: Was the definitive study conducted with positive control"
rule "MainResults.0.0: Results from main study as one block"
when
$oecdNumber: String() from List.of("429")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$results: List() from collect (Entity(type == "results_(main_study)"))
then
componentCreationService.joining("MainResults.0.0", "Results_Main_Study", $results, " ");
end
rule "UsedApproach.0.0: Was the definitive study conducted with positive control"
rule "UsedApproach.0.0: Used approach found and mapped to 'Group'"
when
$oecdNumber: String() from List.of("429")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
$results: List(!isEmpty()) from collect (Entity(type == "approach_used"))
then
componentCreationService.create("UsedApproach.0.0", "What_was_the_approach_used", "Group", "'Group' when approach used is present, else 'Individual'", $results);
end
rule "UsedApproach.1.0: Was the definitive study conducted with positive control"
rule "UsedApproach.1.0: Used approach not found and thus 'Individual'"
when
$oecdNumber: String() from List.of("429")
FileAttribute(label == "oecd_number", value == $oecdNumber)
FileAttribute(label == "OECD Number", value == $oecdNumber)
not Entity(type == "approach_used")
then
componentCreationService.create("UsedApproach.1.0", "What_was_the_approach_used", "Individual", "'Group' when approach used is present, else 'Individual'");
@ -513,11 +513,10 @@ rule "DefaultComponents.999.0: Create components for all unmapped entities."
then
componentCreationService.createComponentsForUnMappedEntities("DefaultComponents.999.0", $allEntities);
end
*/
//------------------------------------ Component merging rules ------------------------------------
/*
rule "X.0.0: merge duplicate component references"
when
$first: Component()
@ -526,3 +525,4 @@ rule "X.0.0: merge duplicate component references"
$first.getReferences().addAll($duplicate.getReferences());
retract($duplicate);
end
*/

BIN
redaction-service-v1/redaction-service-server-v1/src/test/resources/files/new/402Study.pdf Normal file
View File

Binary file not shown.