code formatting

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

@@ -1,16 +1,13 @@
+
 package eu.dnetlib.dhp.oa.graph.clean;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+
-import eu.dnetlib.dhp.common.HdfsSupport;
+import java.io.Serializable;
-import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
+import java.util.List;
-import eu.dnetlib.dhp.schema.common.ModelConstants;
+import java.util.Optional;
-import eu.dnetlib.dhp.schema.oaf.Context;
+import java.util.stream.Collectors;
-import eu.dnetlib.dhp.schema.oaf.Oaf;
+
-import eu.dnetlib.dhp.schema.oaf.OafEntity;
-import eu.dnetlib.dhp.schema.oaf.Result;
-import eu.dnetlib.dhp.utils.ISLookupClientFactory;
-import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.MapFunction;
@@ -21,12 +18,18 @@ import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.Serializable;
+import com.fasterxml.jackson.databind.ObjectMapper;
-import java.util.List;
-import java.util.Optional;
-import java.util.stream.Collectors;
 
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Context;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
+import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.utils.ISLookupClientFactory;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 
 public class CleanContextSparkJob implements Serializable {
 	private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class);
@@ -61,13 +64,11 @@ public class CleanContextSparkJob implements Serializable {
 		String verifyParam = parser.get("verifyParam");
 		log.info("verifyParam: {}", verifyParam);
 
-
 		String graphTableClassName = parser.get("graphTableClassName");
 		log.info("graphTableClassName: {}", graphTableClassName);
 
 		Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName);
 
-
 		SparkConf conf = new SparkConf();
 		runWithSparkSession(
 			conf,
@@ -78,7 +79,8 @@ public class CleanContextSparkJob implements Serializable {
 			});
 	}
 
-    private static <T extends Result> void  cleanContext(SparkSession spark, String contextId, String verifyParam, String inputPath, Class<T> entityClazz, String workingPath) {
+	private static <T extends Result> void cleanContext(SparkSession spark, String contextId, String verifyParam,
+		String inputPath, Class<T> entityClazz, String workingPath) {
 		Dataset<T> res = spark
 			.read()
 			.textFile(inputPath)
@@ -87,27 +89,42 @@ public class CleanContextSparkJob implements Serializable {
 				Encoders.bean(entityClazz));
 
 		res.map((MapFunction<T, T>) r -> {
-            if(!r.getTitle()
+			if (!r
+				.getTitle()
 				.stream()
-                    .filter(t -> t.getQualifier().getClassid()
+				.filter(
+					t -> t
+						.getQualifier()
+						.getClassid()
 						.equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid()))
-                    .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))){
+				.anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))) {
 				return r;
 			}
-            r.setContext(r.getContext().stream().filter(c -> !c.getId().split("::")[0]
+			r
-                    .equalsIgnoreCase(contextId)).collect(Collectors.toList()));
+				.setContext(
+					r
+						.getContext()
+						.stream()
+						.filter(
+							c -> !c.getId().split("::")[0]
+								.equalsIgnoreCase(contextId))
+						.collect(Collectors.toList()));
 			return r;
-        } ,Encoders.bean(entityClazz))
+		}, Encoders.bean(entityClazz))
 			.write()
 			.mode(SaveMode.Overwrite)
-                .option("compression","gzip")
+			.option("compression", "gzip")
 			.json(workingPath);
 
-        spark.read().textFile(workingPath).map((MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
+		spark
+			.read()
+			.textFile(workingPath)
+			.map(
+				(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
 				Encoders.bean(entityClazz))
 			.write()
 			.mode(SaveMode.Overwrite)
-                .option("compression","gzip")
+			.option("compression", "gzip")
 			.json(inputPath);
 	}
 }

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

@@ -1,18 +1,12 @@
+
 package eu.dnetlib.dhp.oa.graph.clean;
 
-import com.fasterxml.jackson.core.JsonProcessingException;
+import java.io.IOException;
-import com.fasterxml.jackson.databind.ObjectMapper;
+import java.nio.file.Files;
-import eu.dnetlib.dhp.oa.graph.dump.Constants;
+import java.nio.file.Path;
-import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest;
+import java.util.List;
-import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
+import java.util.Locale;
-import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
+
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.dump.oaf.Instance;
-import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute;
-import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult;
-import eu.dnetlib.dhp.schema.oaf.Publication;
-import eu.dnetlib.dhp.schema.oaf.Software;
-import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 import org.apache.commons.io.FileUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
@@ -27,11 +21,20 @@ import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.IOException;
+import com.fasterxml.jackson.core.JsonProcessingException;
-import java.nio.file.Files;
+import com.fasterxml.jackson.databind.ObjectMapper;
-import java.nio.file.Path;
+
-import java.util.List;
+import eu.dnetlib.dhp.oa.graph.dump.Constants;
-import java.util.Locale;
+import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest;
+import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
+import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.dump.oaf.Instance;
+import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute;
+import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult;
+import eu.dnetlib.dhp.schema.oaf.Publication;
+import eu.dnetlib.dhp.schema.oaf.Software;
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 
 public class CleanContextTest {
 
@@ -78,18 +81,22 @@ public class CleanContextTest {
 			.getPath();
 		final String prefix = "gcube ";
 
-
+		spark
-        spark.read().textFile(sourcePath).map((MapFunction<String, Publication>)  r -> OBJECT_MAPPER.readValue(r, Publication.class), Encoders.bean(Publication.class))
+			.read()
-                        .write().json(workingDir.toString() + "/publication");
+			.textFile(sourcePath)
-
+			.map(
+				(MapFunction<String, Publication>) r -> OBJECT_MAPPER.readValue(r, Publication.class),
+				Encoders.bean(Publication.class))
+			.write()
+			.json(workingDir.toString() + "/publication");
 
 		CleanContextSparkJob.main(new String[] {
 			"--isSparkSessionManaged", Boolean.FALSE.toString(),
 			"--inputPath", workingDir.toString() + "/publication",
 			"-graphTableClassName", Publication.class.getCanonicalName(),
 			"-workingPath", workingDir.toString() + "/working",
-                "-contextId","sobigdata",
+			"-contextId", "sobigdata",
-                "-verifyParam","gCube "
+			"-verifyParam", "gCube "
 		});
 
 		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@@ -99,61 +106,195 @@ public class CleanContextTest {
 
 		Assertions.assertEquals(7, tmp.count());
 
-        //original result with sobigdata context and gcube as starting string in the main title for the publication
+		// original result with sobigdata context and gcube as starting string in the main title for the publication
-        Assertions.assertEquals(0,
+		Assertions
-                tmp.filter(p->p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")).collect().get(0).getContext().size());
+			.assertEquals(
+				0,
+				tmp
+					.filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))
+					.collect()
+					.get(0)
+					.getContext()
+					.size());
 
-        //original result with sobigdata context without gcube as starting string in the main title for the publication
+		// original result with sobigdata context without gcube as starting string in the main title for the publication
-        Assertions.assertEquals(1,
+		Assertions
-                tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().size());
+			.assertEquals(
-        Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().get(0).getId() );
+				1,
+				tmp
+					.filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
+					.collect()
+					.get(0)
+					.getContext()
+					.size());
+		Assertions
+			.assertEquals(
+				"sobigdata::projects::2",
+				tmp
+					.filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
+					.collect()
+					.get(0)
+					.getContext()
+					.get(0)
+					.getId());
 
-        //original result with sobigdata context with gcube as starting string in the subtitle
+		// original result with sobigdata context with gcube as starting string in the subtitle
-        Assertions.assertEquals(1,
+		Assertions
-                tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().size());
+			.assertEquals(
-        Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().get(0).getId() );
+				1,
-        List<StructuredProperty> titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getTitle();
+				tmp
+					.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
+					.collect()
+					.get(0)
+					.getContext()
+					.size());
+		Assertions
+			.assertEquals(
+				"sobigdata::projects::2",
+				tmp
+					.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
+					.collect()
+					.get(0)
+					.getContext()
+					.get(0)
+					.getId());
+		List<StructuredProperty> titles = tmp
+			.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
+			.collect()
+			.get(0)
+			.getTitle();
 		Assertions.assertEquals(1, titles.size());
-        Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) );
+		Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix));
 		Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid());
 
-        //original result with sobigdata context with gcube not as starting string in the main title
+		// original result with sobigdata context with gcube not as starting string in the main title
-        Assertions.assertEquals(1,
+		Assertions
-                tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().size());
+			.assertEquals(
-        Assertions.assertEquals("sobigdata::projects::1",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().get(0).getId() );
+				1,
-        titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getTitle();
+				tmp
+					.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f"))
+					.collect()
+					.get(0)
+					.getContext()
+					.size());
+		Assertions
+			.assertEquals(
+				"sobigdata::projects::1",
+				tmp
+					.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f"))
+					.collect()
+					.get(0)
+					.getContext()
+					.get(0)
+					.getId());
+		titles = tmp
+			.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f"))
+			.collect()
+			.get(0)
+			.getTitle();
 		Assertions.assertEquals(1, titles.size());
-        Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix) );
+		Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix));
-        Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()) );
+		Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()));
 		Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid());
 
-        //original result with sobigdata in context and also other contexts with gcube as starting string for the main title
+		// original result with sobigdata in context and also other contexts with gcube as starting string for the main
-        Assertions.assertEquals(1,
+		// title
-                tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().size());
+		Assertions
-        Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().get(0).getId() );
+			.assertEquals(
-        titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getTitle();
+				1,
+				tmp
+					.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53"))
+					.collect()
+					.get(0)
+					.getContext()
+					.size());
+		Assertions
+			.assertEquals(
+				"dh-ch",
+				tmp
+					.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53"))
+					.collect()
+					.get(0)
+					.getContext()
+					.get(0)
+					.getId());
+		titles = tmp
+			.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53"))
+			.collect()
+			.get(0)
+			.getTitle();
 		Assertions.assertEquals(1, titles.size());
-        Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) );
+		Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix));
 		Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid());
 
-        //original result with multiple main title one of which whith gcube as starting string and with 2 contextes
+		// original result with multiple main title one of which whith gcube as starting string and with 2 contextes
-        Assertions.assertEquals(1,
+		Assertions
-                tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().size());
+			.assertEquals(
-        Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().get(0).getId() );
+				1,
-        titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getTitle();
+				tmp
+					.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff"))
+					.collect()
+					.get(0)
+					.getContext()
+					.size());
+		Assertions
+			.assertEquals(
+				"dh-ch",
+				tmp
+					.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff"))
+					.collect()
+					.get(0)
+					.getContext()
+					.get(0)
+					.getId());
+		titles = tmp
+			.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff"))
+			.collect()
+			.get(0)
+			.getTitle();
 		Assertions.assertEquals(2, titles.size());
-        Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix)) );
+		Assertions
+			.assertTrue(
+				titles
+					.stream()
+					.anyMatch(
+						t -> t.getQualifier().getClassid().equals("main title")
+							&& t.getValue().toLowerCase().startsWith(prefix)));
 
-
+		// original result without sobigdata in context with gcube as starting string for the main title
-        //original result without sobigdata in context with gcube as starting string for the main title
+		Assertions
-        Assertions.assertEquals(1,
+			.assertEquals(
-                tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().size());
+				1,
-        Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().get(0).getId() );
+				tmp
-        titles = tmp.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getTitle();
+					.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8"))
+					.collect()
+					.get(0)
+					.getContext()
+					.size());
+		Assertions
+			.assertEquals(
+				"dh-ch",
+				tmp
+					.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8"))
+					.collect()
+					.get(0)
+					.getContext()
+					.get(0)
+					.getId());
+		titles = tmp
+			.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8"))
+			.collect()
+			.get(0)
+			.getTitle();
 		Assertions.assertEquals(2, titles.size());
 
-        Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix)));
+		Assertions
-
+			.assertTrue(
+				titles
+					.stream()
+					.anyMatch(
+						t -> t.getQualifier().getClassid().equals("main title")
+							&& t.getValue().toLowerCase().startsWith(prefix)));
 
 	}
 }