Merge pull request molgenis#7732 from tommydeboer/feature/icd10-decor…

…ator Add ICD-10 Expander Decorator
sidohaakma · Aug 24, 2018 · f6add8e · f6add8e
2 parents 7625148 + 454d111
commit f6add8e
Show file tree

Hide file tree

Showing 12 changed files with 701 additions and 0 deletions.
diff --git a/molgenis-app/pom.xml b/molgenis-app/pom.xml
@@ -267,6 +267,11 @@
             <artifactId>molgenis-data-i18n</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.molgenis</groupId>
+            <artifactId>molgenis-data-icd10</artifactId>
+            <version>${project.version}</version>
+        </dependency>
         <dependency>
             <groupId>org.molgenis</groupId>
             <artifactId>molgenis-i18n</artifactId>

diff --git a/molgenis-data-icd10/pom.xml b/molgenis-data-icd10/pom.xml
@@ -0,0 +1,54 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <parent>
+        <groupId>org.molgenis</groupId>
+        <artifactId>molgenis</artifactId>
+        <version>7.1.0-SNAPSHOT</version>
+    </parent>
+    <artifactId>molgenis-data-icd10</artifactId>
+
+    <name>data-icd10</name>
+    <description>ICD-10 related functionality</description>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-jar-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>test-jar</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+
+    <dependencies>
+        <dependency>
+            <groupId>org.molgenis</groupId>
+            <artifactId>molgenis-data</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <!-- third party dependencies -->
+        <dependency>
+            <groupId>org.springframework</groupId>
+            <artifactId>spring-context-support</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.google.code.findbugs</groupId>
+            <artifactId>findbugs-annotations</artifactId>
+            <scope>provided</scope>
+        </dependency>
+        <!-- test dependencies -->
+        <dependency>
+            <groupId>org.molgenis</groupId>
+            <artifactId>molgenis-test</artifactId>
+            <version>${project.version}</version>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+</project>
diff --git a/molgenis-data-icd10/src/main/java/org/molgenis/data/icd10/CollectionsQueryTransformer.java b/molgenis-data-icd10/src/main/java/org/molgenis/data/icd10/CollectionsQueryTransformer.java
@@ -0,0 +1,18 @@
+package org.molgenis.data.icd10;
+
+import org.molgenis.data.Entity;
+import org.molgenis.data.Query;
+
+/**
+ * Transforms a query on an attribute that refers to a ICD-10 repository
+ */
+public interface CollectionsQueryTransformer
+{
+	/**
+	 * @param query             the query to transform
+	 * @param icd10EntityTypeId the EntityType that contains the ICD-10 identifiers
+	 * @param expandAttribute   the attribute on which to apply the query transformation
+	 * @return a query containing expanded ICD-10 codes
+	 */
+	Query<Entity> transformQuery(Query<Entity> query, String icd10EntityTypeId, String expandAttribute);
+}
diff --git a/...nis-data-icd10/src/main/java/org/molgenis/data/icd10/CollectionsQueryTransformerImpl.java b/...nis-data-icd10/src/main/java/org/molgenis/data/icd10/CollectionsQueryTransformerImpl.java
@@ -0,0 +1,86 @@
+package org.molgenis.data.icd10;
+
+import com.google.common.collect.TreeTraverser;
+import org.molgenis.data.DataService;
+import org.molgenis.data.Entity;
+import org.molgenis.data.Query;
+import org.molgenis.data.QueryRule;
+import org.springframework.stereotype.Component;
+
+import java.util.Collection;
+import java.util.List;
+
+import static java.util.Collections.singletonList;
+import static java.util.Objects.requireNonNull;
+import static java.util.stream.Collectors.toList;
+
+@Component
+public class CollectionsQueryTransformerImpl implements CollectionsQueryTransformer
+{
+	private static final TreeTraverser<QueryRule> RULE_TRAVERSER = TreeTraverser.using(QueryRule::getNestedRules);
+
+	private final Icd10ClassExpander icd10ClassExpander;
+	private final DataService dataService;
+
+	CollectionsQueryTransformerImpl(Icd10ClassExpander icd10ClassExpander, DataService dataService)
+	{
+		this.icd10ClassExpander = requireNonNull(icd10ClassExpander);
+		this.dataService = requireNonNull(dataService);
+	}
+
+	@Override
+	public Query<Entity> transformQuery(Query<Entity> query, String icd10EntityTypeId, String expandAttribute)
+	{
+		if (query != null && query.getRules() != null && !query.getRules().isEmpty())
+		{
+			query.getRules()
+				 .forEach(rule -> RULE_TRAVERSER.preOrderTraversal(rule)
+												.filter(nestedRule -> isTransformableRule(nestedRule, expandAttribute))
+												.forEach(nestedRule -> transformQueryRule(nestedRule,
+														icd10EntityTypeId)));
+		}
+
+		return query;
+	}
+
+	private void transformQueryRule(QueryRule rule, String icd10EntityTypeId)
+	{
+		List<Object> queryValues;
+
+		switch (rule.getOperator())
+		{
+			case EQUALS:
+				queryValues = singletonList(rule.getValue());
+				rule.setOperator(QueryRule.Operator.IN);
+				break;
+			case IN:
+				//noinspection unchecked
+				queryValues = (List<Object>) rule.getValue();
+				break;
+			default:
+				throw new IllegalStateException("Can't expand queries other than IN or EQUALS");
+		}
+
+		List<Entity> diseaseTypes = dataService.findAll(icd10EntityTypeId, queryValues.stream()).collect(toList());
+
+		rule.setValue(expandDiseaseTypes(diseaseTypes));
+	}
+
+	/**
+	 * Returns <code>true</code> if a rule is 'IN' or 'EQUALS' on the attribute that should be expanded
+	 */
+	private boolean isTransformableRule(QueryRule nestedRule, String expandAttribute)
+	{
+		return nestedRule != null && nestedRule.getField() != null && nestedRule.getField().equals(expandAttribute) && (
+				nestedRule.getOperator() == QueryRule.Operator.IN
+						|| nestedRule.getOperator() == QueryRule.Operator.EQUALS);
+	}
+
+	/**
+	 * Expand ICD-10 entities with all their children, grandchildren, etc.
+	 */
+	private Collection<Entity> expandDiseaseTypes(List<Entity> diseaseTypes)
+	{
+		return icd10ClassExpander.expandClasses(diseaseTypes);
+	}
+}
diff --git a/molgenis-data-icd10/src/main/java/org/molgenis/data/icd10/Icd10ClassExpander.java b/molgenis-data-icd10/src/main/java/org/molgenis/data/icd10/Icd10ClassExpander.java
@@ -0,0 +1,13 @@
+package org.molgenis.data.icd10;
+
+import org.molgenis.data.Entity;
+
+import java.util.Collection;
+
+/**
+ * Expands a list of 'eu_bbmri_eric_disease_types' entities to include all of their children.
+ */
+public interface Icd10ClassExpander
+{
+	Collection<Entity> expandClasses(Collection<Entity> diseaseClasses);
+}
diff --git a/molgenis-data-icd10/src/main/java/org/molgenis/data/icd10/Icd10ClassExpanderImpl.java b/molgenis-data-icd10/src/main/java/org/molgenis/data/icd10/Icd10ClassExpanderImpl.java
@@ -0,0 +1,89 @@
+package org.molgenis.data.icd10;
+
+import com.google.common.collect.TreeTraverser;
+import org.molgenis.data.Entity;
+import org.springframework.stereotype.Component;
+
+import javax.annotation.Nonnull;
+import java.util.Collection;
+import java.util.stream.Stream;
+import java.util.stream.StreamSupport;
+
+import static java.util.stream.Collectors.toList;
+
+@Component
+public class Icd10ClassExpanderImpl implements Icd10ClassExpander
+{
+	private static final String DISEASE_CLASS_CHILDREN_ATTRIBUTE_NAME = "children";
+
+	@Override
+	public Collection<Entity> expandClasses(Collection<Entity> diseaseClasses)
+	{
+		return diseaseClasses.stream()
+							 .flatMap(this::expandClass)
+							 .map(this::toDiseaseClass)
+							 .distinct()
+							 .map(this::toEntity)
+							 .collect(toList());
+	}
+
+	private Stream<Entity> expandClass(Entity diseaseClass)
+	{
+		Iterable<Entity> diseaseClasses = new DiseaseClassTreeTraverser().postOrderTraversal(diseaseClass);
+		return StreamSupport.stream(diseaseClasses.spliterator(), false);
+	}
+
+	private DiseaseClass toDiseaseClass(Entity entity)
+	{
+		return new DiseaseClass(entity);
+	}
+
+	private Entity toEntity(DiseaseClass diseaseClass)
+	{
+		return diseaseClass.getEntity();
+	}
+
+	/**
+	 * Disease class entity wrapper with equals and hashCode implementation.
+	 */
+	private static class DiseaseClass
+	{
+		private final Entity entity;
+
+		private DiseaseClass(Entity entity)
+		{
+			this.entity = entity;
+		}
+
+		private Entity getEntity()
+		{
+			return entity;
+		}
+
+		@Override
+		public boolean equals(Object o)
+		{
+			if (this == o) return true;
+			if (o == null || getClass() != o.getClass()) return false;
+
+			DiseaseClass that = (DiseaseClass) o;
+
+			return entity.getIdValue().equals(that.entity.getIdValue());
+		}
+
+		@Override
+		public int hashCode()
+		{
+			return entity.getIdValue().hashCode();
+		}
+	}
+
+	private static class DiseaseClassTreeTraverser extends TreeTraverser<Entity>
+	{
+		@Override
+		public Iterable<Entity> children(@Nonnull Entity diseaseClassEntity)
+		{
+			return diseaseClassEntity.getEntities(DISEASE_CLASS_CHILDREN_ATTRIBUTE_NAME);
+		}
+	}
+}
diff --git a/molgenis-data-icd10/src/main/java/org/molgenis/data/icd10/Icd10ExpanderDecorator.java b/molgenis-data-icd10/src/main/java/org/molgenis/data/icd10/Icd10ExpanderDecorator.java
@@ -0,0 +1,65 @@
+package org.molgenis.data.icd10;
+
+import org.molgenis.data.AbstractRepositoryDecorator;
+import org.molgenis.data.Entity;
+import org.molgenis.data.Query;
+import org.molgenis.data.Repository;
+import org.molgenis.data.aggregation.AggregateQuery;
+import org.molgenis.data.aggregation.AggregateResult;
+import org.molgenis.data.support.AggregateQueryImpl;
+
+import java.util.stream.Stream;
+
+import static java.util.Objects.requireNonNull;
+
+class Icd10ExpanderDecorator extends AbstractRepositoryDecorator<Entity>
+{
+	private final CollectionsQueryTransformer queryTransformer;
+	private final String icd10EntityTypeId;
+	private final String expandAttribute;
+
+	Icd10ExpanderDecorator(Repository<Entity> delegateRepository, CollectionsQueryTransformer queryTransformer,
+			String icd10EntityTypeId, String expandAttribute)
+	{
+		super(delegateRepository);
+		this.queryTransformer = requireNonNull(queryTransformer);
+		this.icd10EntityTypeId = requireNonNull(icd10EntityTypeId);
+		this.expandAttribute = requireNonNull(expandAttribute);
+	}
+
+	@Override
+	public long count(Query<Entity> query)
+	{
+		query = query != null ? transformQuery(query) : null;
+		return delegate().count(query);
+	}
+
+	@Override
+	public Entity findOne(Query<Entity> query)
+	{
+		query = query != null ? transformQuery(query) : null;
+		return delegate().findOne(query);
+	}
+
+	@Override
+	public Stream<Entity> findAll(Query<Entity> query)
+	{
+		query = query != null ? transformQuery(query) : null;
+		return delegate().findAll(query);
+	}
+
+	@Override
+	public AggregateResult aggregate(AggregateQuery aggregateQuery)
+	{
+		Query<Entity> q = aggregateQuery.getQuery();
+		Query<Entity> transformedQuery = q != null ? transformQuery(q) : null;
+		aggregateQuery = new AggregateQueryImpl(aggregateQuery.getAttributeX(), aggregateQuery.getAttributeY(),
+				aggregateQuery.getAttributeDistinct(), transformedQuery);
+		return delegate().aggregate(aggregateQuery);
+	}
+
+	private Query<Entity> transformQuery(Query<Entity> query)
+	{
+		return queryTransformer.transformQuery(query, icd10EntityTypeId, expandAttribute);
+	}
+}