Merge pull request '[graph cleaning] improved instance type defaults' (#172) from graph_cleaning into beta

Reviewed-on: #172

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java

@@ -16,6 +16,8 @@ import com.github.sisyphsu.dateparser.DateParserUtils;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Sets;
 
+import eu.dnetlib.dhp.common.vocabulary.Vocabulary;
+import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
@@ -131,7 +133,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 		return true;
 	}
 
-	public static <T extends Oaf> T cleanup(T value) {
+	public static <T extends Oaf> T cleanup(T value, VocabularyGroup vocs) {
 		if (value instanceof Datasource) {
 			// nothing to clean here
 		} else if (value instanceof Project) {
@@ -250,6 +252,38 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 			if (Objects.nonNull(r.getInstance())) {
 
 				for (Instance i : r.getInstance()) {
+					if (!vocs.termExists(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getClassid())) {
+						if (r instanceof Publication) {
+							i
+								.setInstancetype(
+									OafMapperUtils
+										.qualifier(
+											"0038", "Other literature type", ModelConstants.DNET_PUBLICATION_RESOURCE,
+											ModelConstants.DNET_PUBLICATION_RESOURCE));
+						} else if (r instanceof Dataset) {
+							i
+								.setInstancetype(
+									OafMapperUtils
+										.qualifier(
+											"0039", "Other dataset type", ModelConstants.DNET_PUBLICATION_RESOURCE,
+											ModelConstants.DNET_PUBLICATION_RESOURCE));
+						} else if (r instanceof Software) {
+							i
+								.setInstancetype(
+									OafMapperUtils
+										.qualifier(
+											"0040", "Other software type", ModelConstants.DNET_PUBLICATION_RESOURCE,
+											ModelConstants.DNET_PUBLICATION_RESOURCE));
+						} else if (r instanceof OtherResearchProduct) {
+							i
+								.setInstancetype(
+									OafMapperUtils
+										.qualifier(
+											"0020", "Other ORP type", ModelConstants.DNET_PUBLICATION_RESOURCE,
+											ModelConstants.DNET_PUBLICATION_RESOURCE));
+						}
+					}
+
 					if (Objects.nonNull(i.getPid())) {
 						i.setPid(processPidCleaning(i.getPid()));
 					}

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

@@ -88,7 +88,7 @@ public class CleanGraphSparkJob {
 		readTableFromPath(spark, inputPath, clazz)
 			.map((MapFunction<T, T>) GraphCleaningFunctions::fixVocabularyNames, Encoders.bean(clazz))
 			.map((MapFunction<T, T>) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz))
-			.map((MapFunction<T, T>) GraphCleaningFunctions::cleanup, Encoders.bean(clazz))
+			.map((MapFunction<T, T>) value -> GraphCleaningFunctions.cleanup(value, vocs), Encoders.bean(clazz))
 			.filter((FilterFunction<T>) GraphCleaningFunctions::filter)
 			.write()
 			.mode(SaveMode.Overwrite)

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

@@ -151,8 +151,11 @@ public class GraphCleaningFunctionsTest {
 		assertEquals("0018", p_out.getInstance().get(0).getInstancetype().getClassid());
 		assertEquals("Annotation", p_out.getInstance().get(0).getInstancetype().getClassname());
 
-		assertEquals("0033", p_out.getInstance().get(1).getInstancetype().getClassid());
+		assertEquals("0027", p_out.getInstance().get(1).getInstancetype().getClassid());
-		assertEquals("Audiovisual", p_out.getInstance().get(1).getInstancetype().getClassname());
+		assertEquals("Model", p_out.getInstance().get(1).getInstancetype().getClassname());
+
+		assertEquals("xyz", p_out.getInstance().get(2).getInstancetype().getClassid());
+		assertEquals("xyz", p_out.getInstance().get(2).getInstancetype().getClassname());
 
 		assertEquals("CLOSED", p_out.getInstance().get(0).getAccessright().getClassid());
 		assertEquals("Closed Access", p_out.getInstance().get(0).getAccessright().getClassname());
@@ -167,7 +170,7 @@ public class GraphCleaningFunctionsTest {
 
 		List<Instance> poi = p_out.getInstance();
 		assertNotNull(poi);
-		assertEquals(2, poi.size());
+		assertEquals(3, poi.size());
 
 		final Instance poii = poi.get(0);
 		assertNotNull(poii);
@@ -195,7 +198,7 @@ public class GraphCleaningFunctionsTest {
 
 		assertEquals(5, p_out.getTitle().size());
 
-		Publication p_cleaned = GraphCleaningFunctions.cleanup(p_out);
+		Publication p_cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
 
 		assertEquals(3, p_cleaned.getTitle().size());
 
@@ -214,9 +217,12 @@ public class GraphCleaningFunctionsTest {
 
 		assertEquals("1970-10-07", p_cleaned.getDateofacceptance().getValue());
 
+		assertEquals("0038", p_cleaned.getInstance().get(2).getInstancetype().getClassid());
+		assertEquals("Other literature type", p_cleaned.getInstance().get(2).getInstancetype().getClassname());
+
 		final List<Instance> pci = p_cleaned.getInstance();
 		assertNotNull(pci);
-		assertEquals(2, pci.size());
+		assertEquals(3, pci.size());
 
 		final Instance pcii = pci.get(0);
 		assertNotNull(pcii);
@@ -284,7 +290,7 @@ public class GraphCleaningFunctionsTest {
 			.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/doiboostpub.json"));
 		Publication p_in = MAPPER.readValue(json, Publication.class);
 		Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping);
-		Publication cleaned = GraphCleaningFunctions.cleanup(p_out);
+		Publication cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
 
 		Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned));
 	}
@@ -295,7 +301,7 @@ public class GraphCleaningFunctionsTest {
 			.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/doiboostpub2.json"));
 		Publication p_in = MAPPER.readValue(json, Publication.class);
 		Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping);
-		Publication cleaned = GraphCleaningFunctions.cleanup(p_out);
+		Publication cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
 
 		Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned));
 

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java

@@ -708,7 +708,7 @@ class MappersTest {
 		assertEquals(1, p.getTitle().size());
 		assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
 
-		final Publication p_cleaned = cleanup(fixVocabularyNames(p));
+		final Publication p_cleaned = cleanup(fixVocabularyNames(p), vocs);
 
 		assertNotNull(p_cleaned.getTitle());
 		assertFalse(p_cleaned.getTitle().isEmpty());

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

@@ -481,14 +481,100 @@
         "value": "VIRTA"
       },
       "instancetype": {
-        "classid": "Audiovisual",
+        "classid": "Model",
-        "classname": "Audiovisual",
+        "classname": "Model",
         "schemeid": "dnet:publication_resource",
         "schemename": "dnet:publication_resource"
       },
       "url": [
         "http://dx.doi.org/10.1002/s21010127267xy"
       ]
+    },
+    {
+      "pid": [
+        {
+          "dataInfo": null,
+          "qualifier": {
+            "classid": "doi",
+            "classname": "doi",
+            "schemeid": "dnet:pid_types",
+            "schemename": "dnet:pid_types"
+          },
+          "value": "10.1002/s21010127267xy"
+        },
+        {
+          "dataInfo": null,
+          "qualifier": {
+            "classid": "doi",
+            "classname": "doi",
+            "schemeid": "dnet:pid_types",
+            "schemename": "dnet:pid_types"
+          },
+          "value": "10.1008/abcd"
+        }
+      ],
+      "alternateIdentifier": [
+        {
+          "dataInfo": null,
+          "qualifier": {
+            "classid": "doi",
+            "classname": "doi",
+            "schemeid": "dnet:pid_types",
+            "schemename": "dnet:pid_types"
+          },
+          "value": "10.1007/s109090161569x"
+        },
+        {
+          "dataInfo": null,
+          "qualifier": {
+            "classid": "doi",
+            "classname": "doi",
+            "schemeid": "dnet:pid_types",
+            "schemename": "dnet:pid_types"
+          },
+          "value": "10.1009/qwerty"
+        }
+      ],
+      "accessright": {
+        "classid": "CLOSED",
+        "classname": "CLOSED",
+        "schemeid": "dnet:access_modes",
+        "schemename": "dnet:access_modes"
+      },
+      "collectedfrom": {
+        "key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
+        "value": "VIRTA"
+      },
+      "dateofacceptance": {
+        "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"
+        },
+        "value": "2016-01-01"
+      },
+      "distributionlocation": "",
+      "hostedby": {
+        "key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
+        "value": "VIRTA"
+      },
+      "instancetype": {
+        "classid": "xyz",
+        "classname": "xyz",
+        "schemeid": "dnet:publication_resource",
+        "schemename": "dnet:publication_resource"
+      },
+      "url": [
+        "http://dx.doi.org/10.1002/t32121238378t"
+      ]
     }
   ],
   "journal": {