RED-7679: Removed unnecessary logs and updated tables demo rules
This commit is contained in:
Ali Oezyetimoglu
parent
d4626fad8e
commit
47f5a340c8
@ -100,8 +100,6 @@ public class ComponentCreationService {
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*/
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public void create(String ruleIdentifier, String name, String value, String valueDescription, Collection<Entity> references) {
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System.out.println("AAAA: " + ruleIdentifier + " ; " + name + " ; " + value + " ; " + valueDescription + " ; " + references);
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referencedEntities.addAll(references);
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kieSession.insert(Component.builder()
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@ -469,11 +467,6 @@ public class ComponentCreationService {
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}
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public void joiningFromSameTableSeperatedByRow(String ruleIdentifier, String name, Collection<Entity> entities) {
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}
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private Optional<Table> getFirstTable(Entity entity) {
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SemanticNode node = entity.getContainingNode();
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@ -53,7 +53,7 @@ import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations
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import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.entitymapped.ManualForceRedaction;
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import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.entitymapped.ManualRecategorization;
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import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.entitymapped.ManualLegalBasisChange;
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import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.AnnotationStatus
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import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.AnnotationStatus;
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global Document document
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global EntityCreationService entityCreationService
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@ -65,7 +65,23 @@ global Dictionary dictionary
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query "getFileAttributes"
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$fileAttribute: FileAttribute()
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end
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//---------------------------------------------------------------------------
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//------------------------------------ Local dictionary search rules ------------------------------------
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// Rule unit: LocalDictionarySearch.0
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rule "LDS.0.0: Run local dictionary search"
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agenda-group "LOCAL_DICTIONARY_ADDS"
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salience -999
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when
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$dictionaryModel: DictionaryModel(!localEntriesWithMatchedRules.isEmpty()) from dictionary.getDictionaryModels()
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then
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entityCreationService.bySearchImplementation($dictionaryModel.getLocalSearch(), $dictionaryModel.getType(), EntityType.RECOMMENDATION, document)
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.forEach(entity -> {
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Collection<MatchedRule> matchedRules = $dictionaryModel.getLocalEntriesWithMatchedRules().get(entity.getValue());
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entity.addMatchedRules(matchedRules);
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});
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end
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// --------------------------------------- Your rules below this line --------------------------------------------------
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rule "TAB.0.0: Study Type File Attribute"
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when
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@ -106,7 +122,7 @@ rule "TAB.1.0: Full Table extraction (Guideline Deviation)"
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$table: Table() from $section.getParent().streamAllSubNodesOfType(NodeType.TABLE).toList()
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$tableCell: TableCell(!header) from $table.streamTableCells().toList()
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then
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entityCreationService.bySemanticNode($tableCell, "guideline_deviation", EntityType.ENTITY)
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entityCreationService.bySemanticNode($tableCell, "full_table_row", EntityType.ENTITY)
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.ifPresent(entity -> entity.apply("TAB.1.0", "full table extracted"));
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end
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@ -192,7 +208,7 @@ rule "TAB.7.0: Indicator (Species)"
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$section: Section(getHeadline().containsString("Entity-Based"))
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$table: Table() from $section.streamAllSubNodesOfType(NodeType.TABLE).toList()
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TableCell(isHeader(), containsString("Title"), $col: col) from $table.streamTableCells().toList()
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TableCell(hasEntitiesOfType("vertebrate"), $row: row) from $table.streamTableCells().toList()
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TableCell(hasEntitiesOfType("vertebrates"), $row: row) from $table.streamTableCells().toList()
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$cell: TableCell($col == col, $row == row) from $table.streamTableCells().toList()
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then
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entityCreationService.bySemanticNode($cell, "study_design", EntityType.ENTITY)
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@ -355,6 +371,22 @@ rule "X.0.0: Remove Entity contained by Entity of same type"
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end
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// Rule unit: X.1
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rule "X.1.0: Merge intersecting Entities of same type"
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salience 64
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when
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$first: TextEntity($type: type, $entityType: entityType, !resized(), active())
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$second: TextEntity(intersects($first), type == $type, entityType == $entityType, this != $first, !hasManualChanges(), active())
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then
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TextEntity mergedEntity = entityCreationService.mergeEntitiesOfSameType(List.of($first, $second), $type, $entityType, document);
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$first.remove("X.1.0", "merge intersecting Entities of same type");
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$second.remove("X.1.0", "merge intersecting Entities of same type");
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retract($first);
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retract($second);
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mergedEntity.getIntersectingNodes().forEach(node -> update(node));
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end
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// Rule unit: X.2
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rule "X.2.0: Remove Entity of type ENTITY when contained by FALSE_POSITIVE"
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salience 64
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@ -405,6 +437,31 @@ rule "X.5.0: Remove Entity of type RECOMMENDATION when contained by ENTITY"
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end
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// Rule unit: X.6
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rule "X.6.0: Remove Entity of lower rank, when contained by by entity of type ENTITY"
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salience 32
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when
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$higherRank: TextEntity($type: type, (entityType == EntityType.ENTITY || entityType == EntityType.HINT), active())
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$lowerRank: TextEntity(containedBy($higherRank), type != $type, dictionary.getDictionaryRank(type) < dictionary.getDictionaryRank($type), !hasManualChanges(), active())
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then
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$lowerRank.getIntersectingNodes().forEach(node -> update(node));
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$lowerRank.remove("X.6.0", "remove Entity of lower rank, when contained by entity of type ENTITY");
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retract($lowerRank);
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end
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rule "X.6.1: remove Entity of higher rank, when intersected by entity of type ENTITY and length of lower rank Entity is bigger than the higher rank Entity"
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salience 32
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when
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$higherRank: TextEntity($type: type, $value: value, (entityType == EntityType.ENTITY || entityType == EntityType.HINT), active())
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$lowerRank: TextEntity(intersects($higherRank), type != $type, dictionary.getDictionaryRank(type) < dictionary.getDictionaryRank($type), !hasManualChanges(), active(), $lowerRank.getValue().length() > $value.length())
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then
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$higherRank.getIntersectingNodes().forEach(node -> update(node));
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$higherRank.remove("X.6.1", "remove Entity of higher rank, when intersected by entity of type ENTITY and length of lower rank Entity is bigger than the higher rank Entity");
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retract($higherRank);
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end
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// Rule unit: X.7
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rule "X.7.0: remove all images"
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salience 512
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@ -428,19 +485,3 @@ rule "FA.1.0: Remove duplicate FileAttributes"
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retract($duplicate);
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end
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//------------------------------------ Local dictionary search rules ------------------------------------
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// Rule unit: LDS.0
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rule "LDS.0.0: Run local dictionary search"
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agenda-group "LOCAL_DICTIONARY_ADDS"
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salience -999
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when
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$dictionaryModel: DictionaryModel(!localEntriesWithMatchedRules.isEmpty()) from dictionary.getDictionaryModels()
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then
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entityCreationService.bySearchImplementation($dictionaryModel.getLocalSearch(), $dictionaryModel.getType(), EntityType.RECOMMENDATION, document)
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.forEach(entity -> {
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Collection<MatchedRule> matchedRules = $dictionaryModel.getLocalEntriesWithMatchedRules().get(entity.getValue());
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entity.addMatchedRules(matchedRules);
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});
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end
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@ -51,17 +51,15 @@ rule "FullTable.1.1: All rows of matching table"
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when
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$tableRowValues: List() from collect (Entity(type == "full_table_row"))
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then
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componentCreationService.joiningFromSameTableRow("FullTable.1.1", "Full Table", $tableRowValues);
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componentCreationService.joiningFromSameTableRow("FullTable.1.1", "1.1 Full Table", $tableRowValues);
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end
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rule "IndivRowExtr.1.2: Individual rows of table"
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when
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$oecdNumber: String() from List.of("425")
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FileAttribute(label == "OECD Number", value == $oecdNumber)
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$clinicalSigns: List() from collect (Entity(type == "clinical_signs"))
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then
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componentCreationService.joining("IndivRowExtr.1.2", "Extracted experiment", $clinicalSigns, "\n");
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componentCreationService.joiningFromSameTableRow("IndivRowExtr.1.2", "1.2 Individual Rows", $clinicalSigns);
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end
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@ -69,27 +67,23 @@ rule "IndivColExtr.1.3: Individual column of table"
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when
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$tableColValues: List() from collect (Entity(type == "dosages"))
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then
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componentCreationService.joining("IndivColExtr.1.3", "Dosages", $tableColValues);
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componentCreationService.joiningFromSameTableRow("IndivColExtr.1.3", "1.3 Individual Column", $tableColValues);
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end
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/*
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rule "CombColExtr.2.1: Combined Columns Extraction"
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when
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$oecdNumber: String() from List.of("425")
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FileAttribute(label == "OECD Number", value == $oecdNumber)
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$doseMortalities: List() from collect (Entity(type == "dose_mortality" || type == "dose_mortality_dose"))
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then
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componentCreationService.joiningFromSameTableRow("DoseMortality.0.0", "Dose Mortality", $doseMortalities);
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componentCreationService.joiningFromSameTableRow("DoseMortality.0.0", "2.1 Combined Columns", $doseMortalities);
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end
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*/
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rule "ValueExtrRef.2.2: Cells containing dose for survived males"
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when
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$tableValues: List() from collect (Entity(type == "doses_mg_kg_bw"))
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then
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componentCreationService.joining("ValueExtrRef.2.2", "Doses", $tableValues);
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componentCreationService.joining("ValueExtrRef.2.2", "2.2 Individual Table Values", $tableValues);
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end
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@ -97,7 +91,7 @@ rule "AdvTableExtr.2.3: Cells containing dose for survived males"
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when
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$tableValues: List() from collect (Entity(type == "experiment_female_survived"))
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then
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componentCreationService.joining("AdvTableExtr.2.3", "Experiment Female Survived", $tableValues);
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componentCreationService.rowValueCount("AdvTableExtr.2.3", "2.3 Advanced Table Values", $tableValues);
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end
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@ -105,480 +99,5 @@ rule "EntityBasedExtr.2.4: Cells containing dose for survived males"
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when
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$tableValues: List() from collect (Entity(type == "study_design"))
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then
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componentCreationService.joiningFromSameTableRow("EntityBasedExtr.2.4", "Vertebrate in row", $tableValues);
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componentCreationService.joiningFromSameTableRow("EntityBasedExtr.2.4", "2.4 Entity-Based Values", $tableValues);
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end
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//------------------------------------ Default Components rules ------------------------------------
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rule "StudyTitle.0.0: First Title found"
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when
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$titleCandidates: List() from collect (Entity(type == "title"))
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then
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componentCreationService.firstOrElse("StudyTitle.0.0", "Study_Title", $titleCandidates, "");
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end
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rule "PerformingLaboratory.1.0: Performing Laboratory name and country found in same section"
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when
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$laboratoryName: Entity(type == "laboratory_name", $node: containingNode)
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$laboratoryCountry: Entity(type == "laboratory_country", containingNode == $node)
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not Entity(type == "laboratory_country", containingNode == $node, Math.abs($laboratoryName.startOffset - startOffset) < Math.abs($laboratoryName.startOffset - $laboratoryCountry.startOffset))
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then
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componentCreationService.create("PerformingLaboratory.1.0", "Performing_Laboratory", $laboratoryName.getValue() + ", " + $laboratoryCountry.getValue(), "Laboratory name and country found!", List.of($laboratoryName, $laboratoryCountry));
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end
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rule "PerformingLaboratory.2.0: Performing Laboratory name but no country found in same section"
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when
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$laboratoryName: Entity(type == "laboratory_name", $node: containingNode)
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not Entity(type == "laboratory_country", containingNode == $node)
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then
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componentCreationService.create("PerformingLaboratory.2.0", "Performing_Laboratory", $laboratoryName.getValue(), "Only laboratory name found!", List.of($laboratoryName));
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end
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rule "PerformingLaboratory.0.2: Performing Laboratory not found"
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salience -1
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when
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not Component(name == "Performing_Laboratory")
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then
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componentCreationService.create("PerformingLaboratory.0.2", "Performing_Laboratory", "", "fallback");
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end
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rule "ReportNumber.0.0: First Report number found"
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when
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$reportNumberCandidates: List() from collect (Entity(type == "report_number"))
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then
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componentCreationService.firstOrElse("ReportNumber.0.0", "Report_Number", $reportNumberCandidates, "");
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end
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rule "GLPStudy.0.0: GLP Study found"
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when
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$glpStudyList: List(!isEmpty) from collect(Entity(type == "glp_study"))
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then
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componentCreationService.create("GLPStudy.0.0", "GLP_Study", "Yes", "Yes if present, No if not", $glpStudyList);
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end
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rule "GLPStudy.1.0: GLP Study not found"
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when
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not Entity(type == "glp_study")
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then
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componentCreationService.create("GLPStudy.1.0", "GLP_Study", "No", "Yes if present, No if not");
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end
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rule "TestGuideline.0.0: create OECD number and year guideline mappings"
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salience 2
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when
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Entity(type == "oecd_guideline_number")
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Entity(type == "oecd_guideline_year")
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then
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insert(new GuidelineMapping("425", "2008", "Nº 425: Acute oral Toxicity - Up-and-Down Procedure (03/10/2008)"));
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insert(new GuidelineMapping("425", "2001", "Nº 425: Acute oral Toxicity - Up-and-Down Procedure (17/12/2001)"));
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insert(new GuidelineMapping("402", "2017", "Nº 402: Acute Dermal Toxicity (09/10/2017)"));
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insert(new GuidelineMapping("402", "1987", "Nº 402: Acute Dermal Toxicity (24/02/1987)"));
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insert(new GuidelineMapping("403", "2009", "Nº 403: Acute Inhalation Toxicity (08/09/2009)"));
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insert(new GuidelineMapping("403", "1981", "Nº 403: Acute Inhalation Toxicity (12/05/1981)"));
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insert(new GuidelineMapping("433", "2018", "Nº 433: Acute Inhalation Toxicity: Fixed Concentration Procedure (27/06/2018)"));
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insert(new GuidelineMapping("433", "2017", "Nº 433: Acute Inhalation Toxicity: Fixed Concentration Procedure (09/10/2017)"));
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insert(new GuidelineMapping("436", "2009", "Nº 436: Acute Inhalation Toxicity – Acute Toxic Class Method (08/09/2009)"));
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insert(new GuidelineMapping("404", "1981", "Nº 404: Acute Dermal Irritation/Corrosion (12/05/1981)"));
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insert(new GuidelineMapping("404", "1992", "Nº 404: Acute Dermal Irritation/Corrosion (17/07/1992)"));
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insert(new GuidelineMapping("404", "2002", "Nº 404: Acute Dermal Irritation/Corrosion (24/04/2002)"));
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insert(new GuidelineMapping("404", "2015", "Nº 404: Acute Dermal Irritation/Corrosion (28/07/2015)"));
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insert(new GuidelineMapping("405", "2017", "Nº 405: Acute Eye Irritation/Corrosion (09/10/2017)"));
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insert(new GuidelineMapping("405", "2012", "Nº 405: Acute Eye Irritation/Corrosion (02/10/2012)"));
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insert(new GuidelineMapping("405", "2002", "Nº 405: Acute Eye Irritation/Corrosion (24/04/2002)"));
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insert(new GuidelineMapping("405", "1987", "Nº 405: Acute Eye Irritation/Corrosion (24/02/1987)"));
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insert(new GuidelineMapping("429", "2002", "Nº 429: Skin Sensitisation: Local Lymph Node Assay (24/04/2002)"));
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insert(new GuidelineMapping("429", "2010", "Nº 429: Skin Sensitisation (23/07/2010)"));
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insert(new GuidelineMapping("442A", "2018", "Nº 442A: Skin Sensitization (23/07/2018)"));
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insert(new GuidelineMapping("442B", "2018", "Nº 442B: Skin Sensitization (27/06/2018)"));
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insert(new GuidelineMapping("471", "1997", "Nº 471: Bacterial Reverse Mutation Test (21/07/1997)"));
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insert(new GuidelineMapping("471", "2020", "Nº 471: Bacterial Reverse Mutation Test (26/06/2020)"));
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insert(new GuidelineMapping("406", "1992", "Nº 406: Skin Sensitisation (1992)"));
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insert(new GuidelineMapping("428", "2004", "Nº 428: Split-Thickness Skin test (2004)"));
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insert(new GuidelineMapping("438", "2018", "Nº 438: Eye Irritation (26/06/2018)"));
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insert(new GuidelineMapping("439", "2019", "Nº 439: Skin Irritation (2019)"));
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insert(new GuidelineMapping("474", "2016", "Nº 474: Micronucleus Bone Marrow Cells Rat (2016)"));
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insert(new GuidelineMapping("487", "2016", "Nº 487: Micronucleus Human Lymphocytes (2016)"));
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end
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rule "TestGuideline.0.1: match OECD number and year with guideline mappings"
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salience 1
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when
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not Component(name == "Test_Guidelines_1")
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GuidelineMapping($year: year, $number: number, $guideline: guideline)
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$guidelineNumber: Entity(type == "oecd_guideline_number", value == $number)
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$guidelineYear: Entity(type == "oecd_guideline_year", value == $year)
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then
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componentCreationService.create(
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"TestGuideline.0.0",
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"Test_Guidelines_1",
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$guideline,
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"OECD Number and guideline year mapped!",
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List.of($guidelineNumber, $guidelineYear)
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);
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end
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rule "TestGuideline.1.0: no guideline mapping found"
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when
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not Component(name == "Test_Guidelines_1")
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$guideLine: Entity(type == "oecd_guideline")
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then
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componentCreationService.create("TestGuideline.2.0", "Test_Guidelines_1", $guideLine.getValue(), "No Mapping for OECD number and year found, using fallback instead!", List.of($guideLine));
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end
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rule "TestGuideline.2.0: All values of EPA guideline and EC guidelines"
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when
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$guidelines: List() from collect (Entity(type == "epa_guideline" || type == "ec_guideline"))
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then
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componentCreationService.joining("TestGuideline.2.0", "Test_Guidelines_2", $guidelines);
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end
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rule "StartDate.0.0: All experimental start dates converted to dd/MM/yyyy"
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when
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$startDates: List() from collect (Entity(type == "experimental_start_date"))
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then
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componentCreationService.convertDates("StartDate.0.0", "Experimental_Starting_Date", $startDates);
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end
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rule "CompletionDate.0.0: All experimental end dates converted to dd/MM/yyyy"
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when
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$endDates: List() from collect (Entity(type == "experimental_end_date"))
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then
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componentCreationService.convertDates("CompletionDate.0.0", "Experimental_Completion_Date", $endDates);
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end
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rule "AnalysisCertificate.0.0: Unique values of certificate of analysis batch identification"
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when
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$batchNumbers: List() from collect (Entity(type == "batch_number"))
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then
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componentCreationService.joiningUnique("AnalysisCertificate.0.0", "Certificate_of_Analysis_Batch_Identification", $batchNumbers);
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end
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rule "StudyConclusion.0.0: Study conclusion in first found section"
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when
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$oecdNumber: String() from List.of("402", "403", "404", "405", "425", "429", "436", "471")
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FileAttribute(label == "OECD Number", value == $oecdNumber)
|
||||
$studyConclusions: List() from collect(Entity(type == "study_conclusion"))
|
||||
then
|
||||
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)
|
||||
$guidelineDeviations: List() from collect (Entity(type == "guideline_deviation"))
|
||||
then
|
||||
componentCreationService.joining("GuidelineDeviation.0.0", "Deviation_from_the_Guideline", $guidelineDeviations, "\n");
|
||||
end
|
||||
|
||||
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)
|
||||
$species: List() from collect (Entity(type == "species"))
|
||||
then
|
||||
componentCreationService.firstOrElse("Species.0.0", "Species", $species, "");
|
||||
end
|
||||
|
||||
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)
|
||||
$strain: List() from collect (Entity(type == "strain"))
|
||||
then
|
||||
componentCreationService.firstOrElse("Strain.0.0", "Strain", $strain, "");
|
||||
end
|
||||
|
||||
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)
|
||||
$conclusions: List() from collect (Entity(type == "ld50_value"))
|
||||
then
|
||||
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)
|
||||
$conclusions: List(!isEmpty()) from collect (Entity(type == "ld50_greater"))
|
||||
then
|
||||
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)
|
||||
not Entity(type == "ld50_greater")
|
||||
then
|
||||
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)
|
||||
$conclusions: List() from collect (Entity(type == "confidence_minimal"))
|
||||
then
|
||||
componentCreationService.joiningUnique("Conclusion.2.0", "Conclusion_Minimum_Confidence", $conclusions);
|
||||
end
|
||||
|
||||
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)
|
||||
$conclusions: List() from collect (Entity(type == "confidence_maximal"))
|
||||
then
|
||||
componentCreationService.joiningUnique("Conclusion.3.0", "Conclusion_Maximum_Confidence", $conclusions);
|
||||
end
|
||||
|
||||
rule "Necropsy.0.0: Necropsy findings from longest section"
|
||||
when
|
||||
FileAttribute(label == "OECD Number", value == "402")
|
||||
$necropsies: List() from collect (Entity(type == "necropsy_findings"))
|
||||
then
|
||||
componentCreationService.joiningFromLongestSectionOnly("Necropsy.0.0", "Necropsy_Findings", $necropsies, " ");
|
||||
end
|
||||
|
||||
rule "Necropsy.0.1: Necropsy findings joined with \n"
|
||||
when
|
||||
FileAttribute(label == "OECD Number", value == "403" || value == "436")
|
||||
$necropsies: List() from collect (Entity(type == "necropsy_findings"))
|
||||
then
|
||||
componentCreationService.joining("Necropsy.0.0", "Necropsy_Findings", $necropsies, "\n");
|
||||
end
|
||||
|
||||
rule "Necropsy.1.0: Doses mg per kg of Bodyweight as one block"
|
||||
when
|
||||
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, " ");
|
||||
end
|
||||
|
||||
rule "Necropsy.2.0: Conducted with 4 hours of exposure as one block"
|
||||
when
|
||||
$oecdNumber: String() from List.of("403", "436")
|
||||
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, " ");
|
||||
end
|
||||
|
||||
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)
|
||||
$studyDesigns: List() from collect (Entity(type == "study_design"))
|
||||
then
|
||||
componentCreationService.joining("StudyDesign.0.0", "Study_Design", $studyDesigns, " ");
|
||||
end
|
||||
|
||||
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)
|
||||
$results: List() from collect (Entity(type == "results_and_conclusion"))
|
||||
then
|
||||
componentCreationService.joining("Results.0.0", "Results_and_Conclusions", $results, " ");
|
||||
end
|
||||
|
||||
rule "WeightBehavior.0.0: Weight change behavior as sentences"
|
||||
when
|
||||
FileAttribute(label == "OECD Number", value == "402")
|
||||
$weightChanges: List() from collect (Entity(type == "weight_behavior_changes"))
|
||||
then
|
||||
componentCreationService.joining("WeightBehavior.0.0", "Weight_Behavior_Changes", $weightChanges, "\n");
|
||||
end
|
||||
|
||||
rule "MortalityStatement.0.0: Mortality statements as one block"
|
||||
when
|
||||
FileAttribute(label == "OECD Number", value == "402")
|
||||
$mortalityStatements: List() from collect (Entity(type == "mortality_statement"))
|
||||
then
|
||||
componentCreationService.joining("MortalityStatement.0.0", "Mortality_Statement", $mortalityStatements, " ");
|
||||
end
|
||||
|
||||
rule "ClinicalObservations.0.0: Clinical observations as sentences"
|
||||
when
|
||||
FileAttribute(label == "OECD Number", value == "403")
|
||||
$observations: List() from collect (Entity(type == "clinical_observations"))
|
||||
then
|
||||
componentCreationService.joining("MortalityStatement.0.0", "Clinical_Observations", $observations, "\n");
|
||||
end
|
||||
|
||||
rule "BodyWeight.0.0: Bodyweight changes as sentences"
|
||||
when
|
||||
FileAttribute(label == "OECD Number", value == "403")
|
||||
$weightChanges: List() from collect (Entity(type == "bodyweight_changes"))
|
||||
then
|
||||
componentCreationService.joining("BodyWeight.0.0", "Body_Weight_Changes", $weightChanges, "\n");
|
||||
end
|
||||
|
||||
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)
|
||||
$detailings: List() from collect (Entity(type == "detailing"))
|
||||
then
|
||||
componentCreationService.joining("Detailing.0.0", "Detailing_of_Reported_Changes", $detailings, " ");
|
||||
end
|
||||
|
||||
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.toLowerCase() == "male" || value.toLowerCase() == "males")))
|
||||
then
|
||||
componentCreationService.create("Sex.0.0", "Sex", "male", "male sex found", $males);
|
||||
end
|
||||
|
||||
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.toLowerCase() == "female" || value.toLowerCase() == "females")))
|
||||
then
|
||||
componentCreationService.create("Sex.0.0", "Sex", "female", "female sex found", $females);
|
||||
end
|
||||
|
||||
rule "NumberOfAnimals.0.0: Number of animals found"
|
||||
when
|
||||
$oecdNumber: String() from List.of("405", "429")
|
||||
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);
|
||||
end
|
||||
|
||||
rule "NumberOfAnimals.1.0: Count unique occurences of animals"
|
||||
when
|
||||
$oecdNumber: String() from List.of("405", "429")
|
||||
FileAttribute(label == "OECD Number", value == $oecdNumber)
|
||||
not Entity(type == "number_of_animals")
|
||||
$animals: List() from collect (Entity(type == "animal_number"))
|
||||
then
|
||||
componentCreationService.uniqueValueCount("NumberOfAnimals.1.0", "Number_of_Animals", $animals);
|
||||
end
|
||||
|
||||
rule "ClinicalSigns.0.0: Clinical signs as sentences"
|
||||
when
|
||||
$oecdNumber: String() from List.of("425")
|
||||
FileAttribute(label == "OECD Number", value == $oecdNumber)
|
||||
$clinicalSigns: List() from collect (Entity(type == "clinical_signs"))
|
||||
then
|
||||
componentCreationService.joining("ClinicalSigns.0.0", "Clinical_Signs", $clinicalSigns, "\n");
|
||||
end
|
||||
|
||||
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)
|
||||
$doseMortalities: List() from collect (Entity(type == "dose_mortality" || type == "dose_mortality_dose"))
|
||||
then
|
||||
componentCreationService.joiningFromSameTableRow("DoseMortality.0.0", "Dose_Mortality", $doseMortalities);
|
||||
end
|
||||
|
||||
rule "Mortality.0.0: Mortality as one block"
|
||||
when
|
||||
$oecdNumber: String() from List.of("425")
|
||||
FileAttribute(label == "OECD Number", value == $oecdNumber)
|
||||
$mortalities: List() from collect (Entity(type == "mortality"))
|
||||
then
|
||||
componentCreationService.joining("Mortality.0.0", "Mortality", $mortalities, " ");
|
||||
end
|
||||
|
||||
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 == "dosages"))
|
||||
then
|
||||
componentCreationService.firstOrElse("Dosages.0.0", "Dosages", $mortalities, "");
|
||||
end
|
||||
|
||||
rule "PrelimResults.0.0: Preliminary test results as sentences"
|
||||
when
|
||||
$oecdNumber: String() from List.of("429")
|
||||
FileAttribute(label == "OECD Number", value == $oecdNumber)
|
||||
$results: List() from collect (Entity(type == "preliminary_test_results"))
|
||||
then
|
||||
componentCreationService.joining("PrelimResults.0.0", "Preliminary_Test_Results", $results, "\n");
|
||||
end
|
||||
|
||||
rule "TestResults.0.0: Test results as one block"
|
||||
when
|
||||
$oecdNumber: String() from List.of("429")
|
||||
FileAttribute(label == "OECD Number", value == $oecdNumber)
|
||||
$results: List() from collect (Entity(type == "test_results"))
|
||||
then
|
||||
componentCreationService.joining("TestResults.0.0", "Test_Results", $results, " ");
|
||||
end
|
||||
|
||||
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)
|
||||
$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: Results from main study as one block"
|
||||
when
|
||||
$oecdNumber: String() from List.of("429")
|
||||
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: Used approach found and mapped to 'Group'"
|
||||
when
|
||||
$oecdNumber: String() from List.of("429")
|
||||
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: Used approach not found and thus 'Individual'"
|
||||
when
|
||||
$oecdNumber: String() from List.of("429")
|
||||
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'");
|
||||
end
|
||||
|
||||
/*
|
||||
rule "DefaultComponents.999.0: Create components for all unmapped entities."
|
||||
salience -999
|
||||
when
|
||||
$allEntities: List(!isEmpty()) from collect (Entity())
|
||||
then
|
||||
componentCreationService.createComponentsForUnMappedEntities("DefaultComponents.999.0", $allEntities);
|
||||
end
|
||||
*/
|
||||
|
||||
//------------------------------------ Component merging rules ------------------------------------
|
||||
/*
|
||||
rule "X.0.0: merge duplicate component references"
|
||||
when
|
||||
$first: Component()
|
||||
$duplicate: Component(this != $first, name == $first.name, value == $first.value)
|
||||
then
|
||||
$first.getReferences().addAll($duplicate.getReferences());
|
||||
retract($duplicate);
|
||||
end
|
||||
*/
|
||||
Loading…
x
Reference in New Issue
Block a user