WIP: graph cleaner implementation

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRule.java

@@ -1,86 +1,70 @@
 
 package eu.dnetlib.dhp.oa.graph.clean;
 
-import java.lang.reflect.Field;
+import com.google.common.collect.Maps;
-import java.util.Arrays;
+import eu.dnetlib.dhp.schema.oaf.Field;
-import java.util.LinkedList;
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
-import java.util.List;
+import org.apache.commons.lang3.StringUtils;
-import java.util.Objects;
-
 import org.apache.spark.api.java.function.MapFunction;
 
 import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
 import eu.dnetlib.dhp.schema.oaf.Oaf;
 import eu.dnetlib.dhp.schema.oaf.Qualifier;
 
+import java.util.Map;
+import java.util.Objects;
+import java.util.function.Function;
+
 public class CleaningRule<T extends Oaf> implements MapFunction<T, T> {
 
 	private VocabularyGroup vocabularies;
 
+	private Map<Class, Function<Object, Object>> mapping = Maps.newHashMap();
+
+
 	public CleaningRule(VocabularyGroup vocabularies) {
 		this.vocabularies = vocabularies;
+
+		mapping.put(Qualifier.class, o -> patchQualifier(o));
+		mapping.put(StructuredProperty.class, o -> patchSp(o));
+		mapping.put(Field.class, o -> patchStringField(o));
 	}
 
 	@Override
 	public T call(T value) throws Exception {
 
-		doClean(value);
+		OafNavigator.apply(value, mapping);
 
 		return value;
 	}
 
-	private void doClean(Object o) {
+	private Object patchQualifier(Object o) {
-		if (Objects.isNull(o)) {
+		Qualifier q = (Qualifier) o;
-			return;
+		if (vocabularies.vocabularyExists(q.getSchemeid())) {
-		}
+			return vocabularies.lookup(q.getSchemeid(), q.getClassid());
-
-		if (o instanceof Iterable) {
-			for (Object oi : (Iterable) o) {
-				doClean(oi);
-			}
-		} else {
-
-			Class clazz = o.getClass();
-
-			if (clazz.isPrimitive()
-				|| o instanceof Integer
-				|| o instanceof Double
-				|| o instanceof Float
-				|| o instanceof Long
-				|| o instanceof Boolean
-				|| o instanceof String) {
-				return;
-			} else {
-				try {
-					for (Field field : getAllFields(new LinkedList<>(), clazz)) {
-						field.setAccessible(true);
-						Object value = field.get(o);
-						if (value instanceof Qualifier) {
-							Qualifier q = (Qualifier) value;
-							if (vocabularies.vocabularyExists(q.getSchemeid())) {
-								field.set(o, vocabularies.lookup(q.getSchemeid(), q.getClassid()));
-							}
-
-						} else {
-							doClean(value);
-						}
-					}
-				} catch (IllegalAccessException | IllegalArgumentException e) {
-					throw new RuntimeException(e);
-				}
-			}
 		}
+		return o;
 	}
 
-	private static List<Field> getAllFields(List<Field> fields, Class<?> clazz) {
+	private Object patchSp(Object o) {
-		fields.addAll(Arrays.asList(clazz.getDeclaredFields()));
+		StructuredProperty sp = (StructuredProperty) o;
+		if (StringUtils.isBlank(sp.getValue())) {
+			return null;
+		}
+		return o;
+	}
 
-		final Class<?> superclass = clazz.getSuperclass();
+	private Object patchStringField(Object o) {
-		if (Objects.nonNull(superclass) && superclass.getPackage().equals(Oaf.class.getPackage())) {
+		Field f = (Field) o;
-			getAllFields(fields, superclass);
+		try {
+			if (StringUtils.isBlank((String) f.getValue())) {
+				return null;
+			}
+		} catch (ClassCastException e) {
+			// ignored on purpose
 		}
 
-		return fields;
+		return o;
 	}
 
 	public VocabularyGroup getVocabularies() {

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator.java

@@ -1,4 +1,151 @@
+
 package eu.dnetlib.dhp.oa.graph.clean;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.common.collect.Lists;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import scala.Tuple2;
+
+import java.beans.BeanInfo;
+import java.beans.IntrospectionException;
+import java.beans.Introspector;
+import java.beans.PropertyDescriptor;
+import java.lang.reflect.Field;
+import java.lang.reflect.InvocationTargetException;
+import java.util.*;
+import java.util.function.Function;
+
 public class OafNavigator {
+
+	public static <E extends Oaf> E apply(E oaf, Map<Class, Function<Object, Object>> mapping) {
+		reflect(oaf, mapping);
+		return oaf;
+	}
+
+	public static void reflect(Object o, Map<Class, Function<Object, Object>> mapping) {
+		visit(o, mapping);
+	}
+
+	public static void visit(final Object thingy, Map<Class, Function<Object, Object>> mapping) {
+
+		try {
+			final Class<?> clazz = thingy.getClass();
+
+			if (!isPrimitive(thingy) && clazz.getPackage().equals(Oaf.class.getPackage())) {
+
+				final BeanInfo beanInfo = Introspector.getBeanInfo(clazz);
+
+				for (final PropertyDescriptor descriptor : beanInfo.getPropertyDescriptors()) {
+					try {
+						final Object value = descriptor.getReadMethod().invoke(thingy);
+
+						if (value != null && !isPrimitive(value)) {
+
+							System.out.println("VISITING " + descriptor.getName() + " " + descriptor.getPropertyType());
+
+							if (Iterable.class.isAssignableFrom(descriptor.getPropertyType())) {
+								for(Object vi : (Iterable) value) {
+
+									visit(vi, mapping);
+								}
+							} else {
+
+								if (mapping.keySet().contains(value.getClass())) {
+									final Object newValue = mapping.get(value.getClass()).apply(value);
+									System.out.println("PATCHING " + descriptor.getName()+ " " + descriptor.getPropertyType());
+									System.out.println("OLD VALUE " + getObjectMapper().writeValueAsString(value));
+									System.out.println("NEW VALUE " + getObjectMapper().writeValueAsString(newValue));
+									descriptor.getWriteMethod().invoke(newValue);
+								}
+
+								visit(value, mapping);
+							}
+						}
+
+					} catch (final IllegalArgumentException e) {
+						// handle this please
+					} catch (final IllegalAccessException e) {
+						// and this also
+					} catch (final InvocationTargetException e) {
+						// and this, too
+					} catch (JsonProcessingException e) {
+						e.printStackTrace();
+					}
+				}
+			}
+		} catch (final IntrospectionException e) {
+			// do something sensible here
+		}
+	}
+
+	private static ObjectMapper getObjectMapper() {
+		final ObjectMapper mapper = new ObjectMapper();
+		return mapper;
+	}
+
+	private static void navigate(Object o, Map<Class, Function<Object, Object>> mapping) {
+		if (Objects.isNull(o) || isPrimitive(o)) {
+			return;
+		} else {
+			try {
+				for (Field field : getAllFields(o.getClass())) {
+					System.out.println(field.getName());
+					field.setAccessible(true);
+					Object value = field.get(o);
+
+					if (Objects.nonNull(value)) {
+						final Class<?> fieldType = field.getType();
+						if ((fieldType.isArray() && !fieldType.getComponentType().isPrimitive())) {
+							Object[] fs = (Object[]) value;
+							for (Object fi : fs) {
+								navigate(fi, mapping);
+							}
+						} if (Iterable.class.isAssignableFrom(fieldType)) {
+							Iterable fs = (Iterable) value;
+							for (Object fi : fs) {
+								navigate(fi, mapping);
+							}
+						} else {
+							if (mapping.keySet().contains(value.getClass())) {
+								System.out.println("PATCHING " + field.getName());
+								field.set(o, mapping.get(value.getClass()).apply(value));
+							}
+						}
+					}
+				}
+
+			} catch (IllegalAccessException | IllegalArgumentException e) {
+				throw new RuntimeException(e);
+			}
+		}
+	}
+
+	private static boolean isPrimitive(Object o) {
+		return o.getClass().isPrimitive()
+			|| o instanceof Class
+			|| o instanceof Integer
+			|| o instanceof Double
+			|| o instanceof Float
+			|| o instanceof Long
+			|| o instanceof Boolean
+			|| o instanceof String
+			|| o instanceof Byte;
+	}
+
+	private static List<Field> getAllFields(Class<?> clazz) {
+		return getAllFields(new LinkedList<>(), clazz);
+	}
+
+	private static List<Field> getAllFields(List<Field> fields, Class<?> clazz) {
+		fields.addAll(Arrays.asList(clazz.getDeclaredFields()));
+
+		final Class<?> superclass = clazz.getSuperclass();
+		if (Objects.nonNull(superclass) && superclass.getPackage().equals(Oaf.class.getPackage())) {
+			getAllFields(fields, superclass);
+		}
+
+		return fields;
+	}
+
 }

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java

@@ -105,7 +105,10 @@ public class VocabularyGroup implements Serializable {
 	}
 
 	public Qualifier getTermAsQualifier(final String vocId, final String id) {
-		return vocs.get(vocId.toLowerCase()).getTermAsQualifier(id);
+		if (vocabularyExists(vocId)) {
+			return vocs.get(vocId.toLowerCase()).getTermAsQualifier(id);
+		}
+		return OafMapperUtils.qualifier(id, id, "", "");
 	}
 
 	public Qualifier getSynonymAsQualifier(final String vocId, final String syn) {

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleTest.java

@@ -7,6 +7,7 @@ import static org.mockito.Mockito.lenient;
 import java.io.IOException;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Objects;
 import java.util.Set;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
@@ -15,6 +16,7 @@ import org.apache.commons.io.IOUtils;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
+import org.junit.platform.commons.util.StringUtils;
 import org.mockito.Mock;
 import org.mockito.junit.jupiter.MockitoExtension;
 
@@ -82,6 +84,11 @@ public class CleaningRuleTest {
 		// TODO add more assertions to verity the cleaned values
 		System.out.println(MAPPER.writeValueAsString(p_out));
 
+		assertTrue(
+			p_out
+				.getPid()
+				.stream()
+				.allMatch(sp -> StringUtils.isNotBlank(sp.getValue())));
 	}
 
 	private Stream<Qualifier> getAuthorPidTypes(Publication pub) {

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json

@@ -380,6 +380,28 @@
         "schemename": "dnet:pid_types"
       },
       "value": "10.1007/s109090161569x"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "sysimport:crosswalk:datasetarchive",
+          "classname": "sysimport:crosswalk:datasetarchive",
+          "schemeid": "dnet:provenanceActions",
+          "schemename": "dnet:provenanceActions"
+        },
+        "trust": "0.9"
+      },
+      "qualifier": {
+        "classid": "doi",
+        "classname": "doi",
+        "schemeid": "dnet:pid_types",
+        "schemename": "dnet:pid_types"
+      },
+      "value": ""
     }
   ],
   "relevantdate": [