Merge pull request 'Context API update' (#379) from provision_community_api into beta

Reviewed-on: D-Net/dnet-hadoop#379

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/CategorySummary.java

@@ -0,0 +1,39 @@
+
+package eu.dnetlib.dhp.common.api.context;
+
+public class CategorySummary {
+
+	private String id;
+
+	private String label;
+
+	private boolean hasConcept;
+
+	public String getId() {
+		return id;
+	}
+
+	public String getLabel() {
+		return label;
+	}
+
+	public boolean isHasConcept() {
+		return hasConcept;
+	}
+
+	public CategorySummary setId(final String id) {
+		this.id = id;
+		return this;
+	}
+
+	public CategorySummary setLabel(final String label) {
+		this.label = label;
+		return this;
+	}
+
+	public CategorySummary setHasConcept(final boolean hasConcept) {
+		this.hasConcept = hasConcept;
+		return this;
+	}
+
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/CategorySummaryList.java

@@ -0,0 +1,7 @@
+
+package eu.dnetlib.dhp.common.api.context;
+
+import java.util.ArrayList;
+
+public class CategorySummaryList extends ArrayList<CategorySummary> {
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ConceptSummary.java

@@ -0,0 +1,52 @@
+
+package eu.dnetlib.dhp.common.api.context;
+
+import java.util.List;
+
+public class ConceptSummary {
+
+	private String id;
+
+	private String label;
+
+	public boolean hasSubConcept;
+
+	private List<ConceptSummary> concepts;
+
+	public String getId() {
+		return id;
+	}
+
+	public String getLabel() {
+		return label;
+	}
+
+	public List<ConceptSummary> getConcepts() {
+		return concepts;
+	}
+
+	public ConceptSummary setId(final String id) {
+		this.id = id;
+		return this;
+	}
+
+	public ConceptSummary setLabel(final String label) {
+		this.label = label;
+		return this;
+	}
+
+	public boolean isHasSubConcept() {
+		return hasSubConcept;
+	}
+
+	public ConceptSummary setHasSubConcept(final boolean hasSubConcept) {
+		this.hasSubConcept = hasSubConcept;
+		return this;
+	}
+
+	public ConceptSummary setConcept(final List<ConceptSummary> concepts) {
+		this.concepts = concepts;
+		return this;
+	}
+
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ConceptSummaryList.java

@@ -0,0 +1,7 @@
+
+package eu.dnetlib.dhp.common.api.context;
+
+import java.util.ArrayList;
+
+public class ConceptSummaryList extends ArrayList<ConceptSummary> {
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ContextSummary.java

@@ -0,0 +1,50 @@
+
+package eu.dnetlib.dhp.common.api.context;
+
+public class ContextSummary {
+
+	private String id;
+
+	private String label;
+
+	private String type;
+
+	private String status;
+
+	public String getId() {
+		return id;
+	}
+
+	public String getLabel() {
+		return label;
+	}
+
+	public String getType() {
+		return type;
+	}
+
+	public String getStatus() {
+		return status;
+	}
+
+	public ContextSummary setId(final String id) {
+		this.id = id;
+		return this;
+	}
+
+	public ContextSummary setLabel(final String label) {
+		this.label = label;
+		return this;
+	}
+
+	public ContextSummary setType(final String type) {
+		this.type = type;
+		return this;
+	}
+
+	public ContextSummary setStatus(final String status) {
+		this.status = status;
+		return this;
+	}
+
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ContextSummaryList.java

@@ -0,0 +1,7 @@
+
+package eu.dnetlib.dhp.common.api.context;
+
+import java.util.ArrayList;
+
+public class ContextSummaryList extends ArrayList<ContextSummary> {
+}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlConverterJob.java

@@ -62,8 +62,8 @@ public class XmlConverterJob {
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
-		final String isLookupUrl = parser.get("isLookupUrl");
+		final String contextApiBaseUrl = parser.get("contextApiBaseUrl");
-		log.info("isLookupUrl: {}", isLookupUrl);
+		log.info("contextApiBaseUrl: {}", contextApiBaseUrl);
 
 		final SparkConf conf = new SparkConf();
 		conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
@@ -71,7 +71,7 @@ public class XmlConverterJob {
 
 		runWithSparkSession(conf, isSparkSessionManaged, spark -> {
 			removeOutputDir(spark, outputPath);
-			convertToXml(spark, inputPath, outputPath, ContextMapper.fromIS(isLookupUrl));
+			convertToXml(spark, inputPath, outputPath, ContextMapper.fromAPI(contextApiBaseUrl));
 		});
 	}
 

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/ContextMapper.java

@@ -1,18 +1,22 @@
 
 package eu.dnetlib.dhp.oa.provision.utils;
 
-import java.io.Serializable;
+import java.io.*;
-import java.io.StringReader;
+import java.net.HttpURLConnection;
+import java.net.URL;
 import java.util.HashMap;
 
 import org.dom4j.Document;
 import org.dom4j.DocumentException;
 import org.dom4j.Node;
 import org.dom4j.io.SAXReader;
+import org.jetbrains.annotations.NotNull;
 import org.xml.sax.SAXException;
 
 import com.google.common.base.Joiner;
 
+import eu.dnetlib.dhp.common.api.context.*;
+import eu.dnetlib.dhp.common.rest.DNetRestClient;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@@ -23,6 +27,42 @@ public class ContextMapper extends HashMap<String, ContextDef> implements Serial
 
 	private static final String XQUERY = "for $x in //RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ContextDSResourceType']//*[name()='context' or name()='category' or name()='concept'] return <entry id=\"{$x/@id}\" label=\"{$x/@label|$x/@name}\" name=\"{$x/name()}\" type=\"{$x/@type}\"/>";
 
+	public static ContextMapper fromAPI(final String baseURL) throws Exception {
+
+		final ContextMapper contextMapper = new ContextMapper();
+
+		for (ContextSummary ctx : DNetRestClient.doGET(baseURL + "/contexts", ContextSummaryList.class)) {
+
+			contextMapper.put(ctx.getId(), new ContextDef(ctx.getId(), ctx.getLabel(), "context", ctx.getType()));
+
+			for (CategorySummary cat : DNetRestClient
+				.doGET(baseURL + "/context/" + ctx.getId(), CategorySummaryList.class)) {
+				contextMapper.put(cat.getId(), new ContextDef(cat.getId(), cat.getLabel(), "category", ""));
+				if (cat.isHasConcept()) {
+					for (ConceptSummary c : DNetRestClient
+						.doGET(baseURL + "/context/category/" + cat.getId(), ConceptSummaryList.class)) {
+						contextMapper.put(c.getId(), new ContextDef(c.getId(), c.getLabel(), "concept", ""));
+						if (c.isHasSubConcept()) {
+							for (ConceptSummary cs : c.getConcepts()) {
+								contextMapper.put(cs.getId(), new ContextDef(cs.getId(), cs.getLabel(), "concept", ""));
+								if (cs.isHasSubConcept()) {
+									for (ConceptSummary css : cs.getConcepts()) {
+										contextMapper
+											.put(
+												css.getId(),
+												new ContextDef(css.getId(), css.getLabel(), "concept", ""));
+									}
+								}
+							}
+						}
+					}
+				}
+			}
+		}
+		return contextMapper;
+	}
+
+	@Deprecated
 	public static ContextMapper fromIS(final String isLookupUrl)
 		throws DocumentException, ISLookUpException, SAXException {
 		ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
@@ -32,6 +72,7 @@ public class ContextMapper extends HashMap<String, ContextDef> implements Serial
 		return fromXml(sb.toString());
 	}
 
+	@Deprecated
 	public static ContextMapper fromXml(final String xml) throws DocumentException, SAXException {
 		final ContextMapper contextMapper = new ContextMapper();
 

dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml

@@ -9,6 +9,10 @@
             <name>isLookupUrl</name>
             <description>URL for the isLookup service</description>
         </property>
+        <property>
+            <name>contextApiBaseUrl</name>
+            <description>context API URL</description>
+        </property>
         <property>
             <name>relPartitions</name>
             <description>number or partitions for the relations Dataset</description>
@@ -589,7 +593,7 @@
             </spark-opts>
             <arg>--inputPath</arg><arg>${workingDir}/join_entities</arg>
             <arg>--outputPath</arg><arg>${workingDir}/xml</arg>
-            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--contextApiBaseUrl</arg><arg>${contextApiBaseUrl}</arg>
         </spark>
         <ok to="should_index"/>
         <error to="Kill"/>