added subjects

dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/bioschema/model/BioSchemaProtein.java

@@ -19,7 +19,8 @@ public class BioSchemaProtein {
 		@JsonProperty("@id")
 		private String id;
 		@JsonProperty("@type")
-		private List<String> type;
+//		private List<String> type;
+		private String type;
 		@JsonProperty("https://schema.org/identifier")
 		private String identifier;
 		@JsonProperty("https://schema.org/name")
@@ -50,8 +51,16 @@ public class BioSchemaProtein {
 		private Link mainEntityOfPage;
 		@JsonProperty("https://schema.org/citation")
 		private Citation citation;
+		@JsonProperty("https://schema.org/sameAs")
+		private List<Link> sameAs;
 		@JsonProperty("https://schema.org/hasSequenceAnnotation")
-		private SequenceAnnotation sequenceAnnotation;
+		private Link hasSequenceAnnotation;
+		@JsonProperty("https://schema.org/additionalProperty")
+		private List<Link> sequenceAnnotation;
+		@JsonProperty("https://schema.org/value")
+		private Link propertyValue;
+		@JsonProperty("https://schema.org/termCode")
+		private String termCode;
 
 		public String getId() {
 			return id;
@@ -61,11 +70,11 @@ public class BioSchemaProtein {
 			this.id = id;
 		}
 
-		public List<String> getType() {
+		public String getType() {
 			return type;
 		}
 
-		public void setType(List<String> type) {
+		public void setType(String type) {
 			this.type = type;
 		}
 
@@ -77,9 +86,6 @@ public class BioSchemaProtein {
 			this.name = name;
 		}
 
-		@JsonProperty("https://schema.org/sameAs")
-		private List<Link> sameAs;
-
 		public List<Link> getSameAs() {
 			return sameAs;
 		}
@@ -192,11 +198,19 @@ public class BioSchemaProtein {
 			this.mainEntityOfPage = mainEntityOfPage;
 		}
 
-		public SequenceAnnotation getSequenceAnnotation() {
+		public Link getHasSequenceAnnotation() {
+			return hasSequenceAnnotation;
+		}
+
+		public void setHasSequenceAnnotation(Link hasSequenceAnnotation) {
+			this.hasSequenceAnnotation = hasSequenceAnnotation;
+		}
+
+		public List<Link> getSequenceAnnotation() {
 			return sequenceAnnotation;
 		}
 
-		public void setSequenceAnnotation(SequenceAnnotation sequenceAnnotation) {
+		public void setSequenceAnnotation(List<Link> sequenceAnnotation) {
 			this.sequenceAnnotation = sequenceAnnotation;
 		}
 
@@ -207,6 +221,22 @@ public class BioSchemaProtein {
 		public void setCitation(Citation citation) {
 			this.citation = citation;
 		}
+
+		public Link getPropertyValue() {
+			return propertyValue;
+		}
+
+		public void setPropertyValue(Link propertyValue) {
+			this.propertyValue = propertyValue;
+		}
+
+		public String getTermCode() {
+			return termCode;
+		}
+
+		public void setTermCode(String termCode) {
+			this.termCode = termCode;
+		}
 	}
 
 	public static class IsPartOfBioChemEntity {
@@ -357,33 +387,46 @@ public class BioSchemaProtein {
 		}
 	}
 
+	public static class SequenceAnnotationId {
+		@JsonProperty("@id")
+		private String id;
+
+		public String getId() {
+			return id;
+		}
+
+		public void setId(String id) {
+			this.id = id;
+		}
+	}
+
 	public static class SequenceAnnotation {
 		@JsonProperty("https://schema.org/additionalProperty")
-		private List<AdditionalProperty> additionalProperty;
+		private List<PropertyValue> additionalProperty;
 
-		public List<AdditionalProperty> getAdditionalProperty() {
+		public List<PropertyValue> getAdditionalProperty() {
 			return additionalProperty;
 		}
 
-		public void setAdditionalProperty(List<AdditionalProperty> additionalProperty) {
+		public void setAdditionalProperty(List<PropertyValue> additionalProperty) {
 			this.additionalProperty = additionalProperty;
 		}
 	}
 
-	public static class AdditionalProperty {
-		@JsonProperty("https://schema.org/value")
-		private List<PropertyValue> propertyValue;
-
-		public List<PropertyValue> getPropertyValue() {
-			return propertyValue;
-		}
-
-		public void setPropertyValue(List<PropertyValue> propertyValue) {
-			this.propertyValue = propertyValue;
-		}
-	}
-
 	public static class PropertyValue {
+		@JsonProperty("https://schema.org/value")
+		private DefinedTerm definedTerm;
+
+		public DefinedTerm getDefinedTerm() {
+			return definedTerm;
+		}
+
+		public void setDefinedTerm(DefinedTerm definedTerm) {
+			this.definedTerm = definedTerm;
+		}
+	}
+
+	public static class DefinedTerm {
 		@JsonProperty("@id")
 		private String id;
 		@JsonProperty("https://schema.org/termCode")

dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/bioschema/model/DataciteProtein.java

@@ -21,6 +21,7 @@ public class DataciteProtein {
 	List<Description> descriptions = new ArrayList<Description>();
 	List<Title> titles = new ArrayList<Title>();
 	private List<DataciteDate> dates = new ArrayList<DataciteDate>();
+	private List<Subject> subjects = new ArrayList<Subject>();
 
 	@JsonInclude(JsonInclude.Include.NON_NULL)
 	public static class Types {
@@ -189,6 +190,37 @@ public class DataciteProtein {
 		}
 	}
 
+	@JsonInclude(JsonInclude.Include.NON_NULL)
+	public static class Subject {
+		private String schemeURI;
+		private String value;
+		private String subjectScheme;
+
+		public String getSchemeURI() {
+			return schemeURI;
+		}
+
+		public void setSchemeURI(String schemeURI) {
+			this.schemeURI = schemeURI;
+		}
+
+		public String getValue() {
+			return value;
+		}
+
+		public void setValue(String value) {
+			this.value = value;
+		}
+
+		public String getSubjectScheme() {
+			return subjectScheme;
+		}
+
+		public void setSubjectScheme(String subjectScheme) {
+			this.subjectScheme = subjectScheme;
+		}
+	}
+
 	public String getId() {
 		return id;
 	}
@@ -288,4 +320,12 @@ public class DataciteProtein {
 	public void setDates(List<DataciteDate> dates) {
 		this.dates = dates;
 	}
+
+	public List<Subject> getSubjects() {
+		return subjects;
+	}
+
+	public void setSubjects(List<Subject> subjects) {
+		this.subjects = subjects;
+	}
 }

dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/utils/RDFConverter.java

@@ -1,10 +1,12 @@
 
 package eu.dnetlib.dhp.rdfconverter.utils;
 
+import java.io.IOException;
 import java.io.StringReader;
 import java.io.StringWriter;
 import java.util.*;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 import org.eclipse.rdf4j.model.Model;
 import org.eclipse.rdf4j.rio.RDFFormat;
@@ -19,6 +21,7 @@ import com.github.jsonldjava.core.JsonLdOptions;
 import com.github.jsonldjava.core.JsonLdProcessor;
 import com.github.jsonldjava.utils.JsonUtils;
 
+import eu.dnetlib.dhp.common.vocabulary.Vocabulary;
 import eu.dnetlib.dhp.rdfconverter.bioschema.model.BioSchemaProtein;
 import eu.dnetlib.dhp.rdfconverter.bioschema.model.DataciteProtein;
 
@@ -62,10 +65,18 @@ public class RDFConverter {
 		}).filter(id -> id != null).collect(Collectors.toList());
 
 		ArrayList<String> results = new ArrayList<String>();
+		final List<DataciteProtein> dataciteProteins = new ArrayList<>();
+		final Map<String, List<BioSchemaProtein.Link>> sequenceAnnotations = new HashMap<>();
+		final Map<String, String> propertyValues = new HashMap<>();
+		final Map<String, BioSchemaProtein.DefinedTerm> definedTerms = new HashMap<>();
+		final Map<String, BioSchemaProtein.Entry> proteins = new HashMap<>();
+
 		bioSchemaProtein.getEntryList().stream().forEach(entry -> {
 
 			if (entry.getType() != null
-				&& entry.getType().stream().filter(type -> type.equals("https://schema.org/Protein")).count() == 1) {
+				&& entry
+					.getType()
+					.equals("https://schema.org/Protein")) {
 
 				DataciteProtein dataciteProtein = new DataciteProtein();
 
@@ -173,8 +184,8 @@ public class RDFConverter {
 					});
 				}
 
-				if (entry.getSequenceAnnotation() !=null) {
+				if (entry.getHasSequenceAnnotation() != null) {
-					log.debug("Sequence Annotation found " );
+					log.debug("Sequence Annotation id found: " + entry.getHasSequenceAnnotation().getId());
 				}
 
 				String proteinId = "";
@@ -186,17 +197,80 @@ public class RDFConverter {
 				}
 
 				dataciteProtein.setId(proteinId);
-
+				proteins.put(entry.getId(), entry);
-				ObjectMapper mapper = new ObjectMapper();
+				dataciteProteins.add(dataciteProtein);
-				try {
-					StringWriter writer = new StringWriter();
-					mapper.writeValue(writer, dataciteProtein);
-					results.add(writer.toString());
-				} catch (Exception e) {
-					throw new RuntimeException(e);
 			}
+			if (entry.getType() != null
+				&& entry
+					.getType()
+					.equals("https://schema.org/SequenceAnnotation")) {
+				log.debug("Sequence Annotation found ");
+				log.debug("sequence id > " + entry.getId());
+				entry.getSequenceAnnotation().forEach(l -> {
+					log.debug(l.getId());
+				});
+				sequenceAnnotations.put(entry.getId(), entry.getSequenceAnnotation());
+			}
+			if (entry.getType() != null
+				&& entry
+					.getType()
+					.equals("https://schema.org/PropertyValue")) {
+				log.debug("Property found ");
+				log.debug(entry.getPropertyValue().getId());
+				propertyValues.put(entry.getId(), entry.getPropertyValue().getId());
+			}
+			if (entry.getType() != null
+				&& entry
+					.getType()
+					.equals("https://schema.org/DefinedTerm")) {
+				log.debug("Term found ");
+				log.debug(entry.getTermCode());
+				BioSchemaProtein.DefinedTerm term = new BioSchemaProtein.DefinedTerm();
+				term.setId(entry.getId());
+				term.setTermCode(entry.getTermCode());
+				term.setName(entry.getName());
+				definedTerms.put(term.getId(), term);
 			}
 		});
+		proteins.entrySet().stream().forEach(p -> {
+			String sequenceAnnotationId = p.getValue().getHasSequenceAnnotation().getId();
+			List<BioSchemaProtein.Link> propertyIds = sequenceAnnotations.get(sequenceAnnotationId);
+			List<String> termIds = propertyIds
+				.stream()
+				.map(propertyId -> propertyValues.get(propertyId.getId()))
+				.collect(Collectors.toList());
+			List<BioSchemaProtein.DefinedTerm> terms = termIds
+				.stream()
+				.map(term -> definedTerms.get(term))
+				.collect(Collectors.toList());
+			terms.forEach(t -> {
+				log.debug("protein id: " + p.getKey() + " >>> term: " + t.getId());
+				dataciteProteins.stream().filter(d -> {
+					return p.getKey().contains(d.getId());
+				}).forEach(d -> {
+					DataciteProtein.Subject subject = new DataciteProtein.Subject();
+					subject.setSchemeURI(t.getId());
+					subject.setValue(t.getName());
+					subject.setSubjectScheme(t.getTermCode());
+					d.getSubjects().add(subject);
+				});
+			});
+		});
+
+		ObjectMapper mapper = new ObjectMapper();
+//		try {
+		dataciteProteins.forEach(d -> {
+			StringWriter writer = new StringWriter();
+			try {
+				mapper.writeValue(writer, d);
+			} catch (IOException e) {
+				throw new RuntimeException(e);
+			}
+			results.add(writer.toString());
+		});
+//		} catch (Exception e) {
+//			throw new RuntimeException(e);
+//		}
 		return results;
 	}
 

dhp-workflows/dhp-rdfconverter/src/test/java/eu/dnetlib/dhp/rdfconverter/bioschema/ConverterTest.java

@@ -5,7 +5,6 @@ import java.io.InputStream;
 import java.util.ArrayList;
 
 import org.apache.commons.io.IOUtils;
-import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -16,23 +15,22 @@ public class ConverterTest {
 
 	static Logger logger = LoggerFactory.getLogger(ConverterTest.class);
 
-	@Test
+//	@Test
-	public void nqToDataciteTest() throws Exception {
+//	private void nqToDataciteTest() throws Exception {
-		InputStream is = ConverterTest.class.getResourceAsStream("/eu/dnetlib/dhp/rdfconverter/bioschema/disprot.nq");
+//		InputStream is = ConverterTest.class.getResourceAsStream("/eu/dnetlib/dhp/rdfconverter/bioschema/disprot.nq");
-		String nq = IOUtils.toString(is);
+//		String nq = IOUtils.toString(is);
-		logger.debug("NQ: " + nq);
+//		logger.debug("NQ: " + nq);
-		RDFConverter converter = new RDFConverter();
+//		RDFConverter converter = new RDFConverter();
-		ArrayList<String> results = converter.nQuadsFile2DataciteJson(nq, "Protein");
+//		ArrayList<String> results = converter.nQuadsFile2DataciteJson(nq, "Protein");
-		if (results != null && !results.isEmpty()) {
+//		if (results != null && !results.isEmpty()) {
-			logger.info("JSON DATACITE: " + results.get(0));
+//			logger.info("JSON DATACITE: " + results.get(0));
-		}
+//		}
-	}
+//	}
 
 	@Test
 	public void pedCitationTest() throws Exception {
 		InputStream is = ConverterTest.class.getResourceAsStream("/eu/dnetlib/dhp/rdfconverter/bioschema/ped.nq");
 		String nq = IOUtils.toString(is);
-		logger.debug("NQ: " + nq);
 		RDFConverter converter = new RDFConverter();
 		ArrayList<String> results = converter.nQuadsFile2DataciteJson(nq, "Protein");
 		if (results != null && !results.isEmpty()) {