From 4269e2f0d15f7f310d254a661030acfede7aabe2 Mon Sep 17 00:00:00 2001
From: Enrico Ottonello <enrico.ottonello@isti.cnr.it>
Date: Thu, 9 Dec 2021 14:59:01 +0100
Subject: [PATCH] added citation retrieving and conversion; added ped test

---
 .../bioschema/model/BioSchemaProtein.java     |  29 +--
 .../dhp/rdfconverter/utils/RDFConverter.java  |  18 +-
 .../rdfconverter/bioschema/ConverterTest.java |  15 +-
 .../dnetlib/dhp/rdfconverter/bioschema/ped.nq | 229 ++++++++++++++++++
 .../src/test/resources/log4j.properties       |  11 +
 5 files changed, 276 insertions(+), 26 deletions(-)
 create mode 100644 dhp-workflows/dhp-rdfconverter/src/test/resources/eu/dnetlib/dhp/rdfconverter/bioschema/ped.nq
 create mode 100644 dhp-workflows/dhp-rdfconverter/src/test/resources/log4j.properties

diff --git a/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/bioschema/model/BioSchemaProtein.java b/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/bioschema/model/BioSchemaProtein.java
index ffac36459..962644c07 100644
--- a/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/bioschema/model/BioSchemaProtein.java
+++ b/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/bioschema/model/BioSchemaProtein.java
@@ -14,8 +14,6 @@ public class BioSchemaProtein {
 	private List<Entry> entryList;
 	@JsonProperty("http://purl.org/pav/retrievedOn")
 	private DateTimeType retrievedOn;
-	@JsonProperty("citation")
-	private Citation citation;
 
 	public static class Entry {
 		@JsonProperty("@id")
@@ -50,6 +48,8 @@ public class BioSchemaProtein {
 		private IsPartOfBioChemEntity isPartOfBioChemEntity;
 		@JsonProperty("mainEntityOfPage")
 		private Link mainEntityOfPage;
+		@JsonProperty("https://schema.org/citation")
+		private Citation citation;
 
 		public String getId() {
 			return id;
@@ -190,6 +190,13 @@ public class BioSchemaProtein {
 			this.mainEntityOfPage = mainEntityOfPage;
 		}
 
+		public Citation getCitation() {
+			return citation;
+		}
+
+		public void setCitation(Citation citation) {
+			this.citation = citation;
+		}
 	}
 
 	public static class IsPartOfBioChemEntity {
@@ -328,19 +335,9 @@ public class BioSchemaProtein {
 	}
 
 	public static class Citation {
-		@JsonProperty("@type")
-		private String type;
 		@JsonProperty("@id")
 		private String id;
 
-		public String getType() {
-			return type;
-		}
-
-		public void setType(String type) {
-			this.type = type;
-		}
-
 		public String getId() {
 			return id;
 		}
@@ -373,12 +370,4 @@ public class BioSchemaProtein {
 	public void setRetrievedOn(DateTimeType retrievedOn) {
 		this.retrievedOn = retrievedOn;
 	}
-
-	public Citation getCitation() {
-		return citation;
-	}
-
-	public void setCitation(Citation citation) {
-		this.citation = citation;
-	}
 }
diff --git a/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/utils/RDFConverter.java b/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/utils/RDFConverter.java
index db5a38f2c..d57a548bf 100644
--- a/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/utils/RDFConverter.java
+++ b/dhp-workflows/dhp-rdfconverter/src/main/java/eu/dnetlib/dhp/rdfconverter/utils/RDFConverter.java
@@ -4,6 +4,7 @@ package eu.dnetlib.dhp.rdfconverter.utils;
 import java.io.StringReader;
 import java.io.StringWriter;
 import java.util.*;
+import java.util.stream.Collectors;
 
 import org.eclipse.rdf4j.model.Model;
 import org.eclipse.rdf4j.rio.RDFFormat;
@@ -42,6 +43,7 @@ public class RDFConverter {
 		Object jsonObject = JsonUtils.fromString(jsonLDBuffer);
 		Object compact = JsonLdProcessor.compact(jsonObject, new HashMap<>(), new JsonLdOptions());
 		String compactContent = JsonUtils.toString(compact);
+		log.debug("jsonld: " + compactContent);
 
 		ObjectMapper objectMapper = new ObjectMapper();
 		objectMapper.enable(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY);
@@ -50,7 +52,14 @@ public class RDFConverter {
 		BioSchemaProtein bioSchemaProtein = objectMapper.readValue(compactContent, BioSchemaProtein.class);
 		log.debug("BioSchema id: " + bioSchemaProtein.getId());
 		BioSchemaProtein.DateTimeType retrievedOnType = bioSchemaProtein.getRetrievedOn();
-		BioSchemaProtein.Citation citation = bioSchemaProtein.getCitation();
+
+		List<String> citations = bioSchemaProtein.getEntryList().stream().map(entry -> {
+			if (entry.getCitation() != null) {
+				BioSchemaProtein.Citation citationInfo = entry.getCitation();
+				return citationInfo.getId();
+			}
+			return null;
+		}).filter(id -> id != null).collect(Collectors.toList());
 
 		ArrayList<String> results = new ArrayList<String>();
 		bioSchemaProtein.getEntryList().stream().forEach(entry -> {
@@ -59,9 +68,10 @@ public class RDFConverter {
 				&& entry.getType().stream().filter(type -> type.equals("https://schema.org/Protein")).count() == 1) {
 
 				DataciteProtein dataciteProtein = new DataciteProtein();
-				if (citation != null) {
-					addRelatedIdentifier(dataciteProtein, citation.getId(), "CitedBy");
-				}
+
+				citations.forEach(citation -> {
+					addRelatedIdentifier(dataciteProtein, citation, "CitedBy");
+				});
 
 				DataciteProtein.Types types = new DataciteProtein.Types();
 				types.setResourceType("Protein");
diff --git a/dhp-workflows/dhp-rdfconverter/src/test/java/eu/dnetlib/dhp/rdfconverter/bioschema/ConverterTest.java b/dhp-workflows/dhp-rdfconverter/src/test/java/eu/dnetlib/dhp/rdfconverter/bioschema/ConverterTest.java
index e4042fe8b..a6945ced8 100644
--- a/dhp-workflows/dhp-rdfconverter/src/test/java/eu/dnetlib/dhp/rdfconverter/bioschema/ConverterTest.java
+++ b/dhp-workflows/dhp-rdfconverter/src/test/java/eu/dnetlib/dhp/rdfconverter/bioschema/ConverterTest.java
@@ -17,11 +17,22 @@ public class ConverterTest {
 	static Logger logger = LoggerFactory.getLogger(ConverterTest.class);
 
 	@Test
-//	@Disabled
 	public void nqToDataciteTest() throws Exception {
 		InputStream is = ConverterTest.class.getResourceAsStream("/eu/dnetlib/dhp/rdfconverter/bioschema/disprot.nq");
 		String nq = IOUtils.toString(is);
-		logger.info("NQ: " + nq);
+		logger.debug("NQ: " + nq);
+		RDFConverter converter = new RDFConverter();
+		ArrayList<String> results = converter.nQuadsFile2DataciteJson(nq, "Protein");
+		if (results != null && !results.isEmpty()) {
+			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()) {
diff --git a/dhp-workflows/dhp-rdfconverter/src/test/resources/eu/dnetlib/dhp/rdfconverter/bioschema/ped.nq b/dhp-workflows/dhp-rdfconverter/src/test/resources/eu/dnetlib/dhp/rdfconverter/bioschema/ped.nq
new file mode 100644
index 000000000..babe3aeef
--- /dev/null
+++ b/dhp-workflows/dhp-rdfconverter/src/test/resources/eu/dnetlib/dhp/rdfconverter/bioschema/ped.nq
@@ -0,0 +1,229 @@
+<https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1> <http://purl.org/pav/retrievedFrom> <https://proteinensemble.org/PED00014> .
+<https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1> <http://purl.org/pav/retrievedOn> "2021-12-06T11:52:22"^^<http://www.w3.org/2001/XMLSchema#dateTime> .
+<https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1> <http://purl.org/pav/createdWith> <https://github.com/HW-SWeL/BMUSE/releases/tag/0.5.2> .
+<https://proteinensemble.org/PED00014> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <https://schema.org/CollectionPage> <https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1> .
+<https://proteinensemble.org/PED00014> <https://schema.org/citation> <https://identifiers.org/pubmed:20399186> <https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1> .
+<https://proteinensemble.org/PED00014> <https://schema.org/identifier> "https://identifiers.org/ped:PED00014" <https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1> .
+<https://proteinensemble.org/PED00014> <https://schema.org/includedInDataset> "https://proteinensemble.org/#2021-02-12" <https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1> .
+<https://proteinensemble.org/PED00014> <https://schema.org/mainEntity> <https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1/proteinensemble.org/PED00014/23786852> <https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1> .
+<https://proteinensemble.org/PED00014> <https://schema.org/name> "Structural ensemble of pSic1 (1-90) phosphorylated at Thr5, Thr33, Thr45, Ser69, Ser76 and Ser80, in complex with SKP1 (4-186) and CDC4 (270-744)" <https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1> .
+<https://identifiers.org/pubmed:20399186> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <https://schema.org/ScholarlyArticle> <https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1> .
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+<https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1/proteinensemble.org/PED00014/23786852> <https://schema.org/itemListElement> <https://proteinensemble.org/PED00014#P52286_C_0> <https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1> .
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+<https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1/proteinensemble.org/PED00014/23786852> <https://schema.org/numberOfItems> "3" <https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1> .
+<https://proteinensemble.org/PED00014#P07834_D_0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <https://schema.org/Protein> <https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1> .
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+<https://proteinensemble.org/PED00014#P07834_D_0> <https://schema.org/hasSequenceAnnotation> <https://proteinensemble.org/PED00014#P07834_D_0_270_744> <https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1> .
+<https://proteinensemble.org/PED00014#P07834_D_0> <https://schema.org/identifier> "https://identifiers.org/uniprot:P07834" <https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1> .
+<https://proteinensemble.org/PED00014#P07834_D_0> <https://schema.org/name> "Cell division control protein 4" <https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1> .
+<https://proteinensemble.org/PED00014#P07834_D_0> <https://schema.org/sameAs> <http://purl.uniprot.org/uniprot/P07834> <https://bioschemas.org/crawl/v1/proteinensemble/PED00014/20211206/1> .
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diff --git a/dhp-workflows/dhp-rdfconverter/src/test/resources/log4j.properties b/dhp-workflows/dhp-rdfconverter/src/test/resources/log4j.properties
new file mode 100644
index 000000000..20f56e38d
--- /dev/null
+++ b/dhp-workflows/dhp-rdfconverter/src/test/resources/log4j.properties
@@ -0,0 +1,11 @@
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=INFO, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.logger.org = ERROR
+log4j.logger.eu.dnetlib = DEBUG
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
\ No newline at end of file