Merge remote-tracking branch 'origin/master' into doiboost

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java

@@ -25,6 +25,7 @@ public class DedupRecordFactory {
 
     public static <T extends OafEntity> Dataset<T> createDedupRecord(
             final SparkSession spark,
+            final DataInfo dataInfo,
             final String mergeRelsInputPath,
             final String entitiesInputPath,
             final Class<T> clazz) {
@@ -67,41 +68,39 @@ public class DedupRecordFactory {
                         Encoders.STRING())
                 .mapGroups(
                         (MapGroupsFunction<String, Tuple2<String, T>, T>)
-                                (key, values) -> entityMerger(key, values, ts, clazz),
+                                (key, values) -> entityMerger(key, values, ts, dataInfo),
                         Encoders.bean(clazz));
     }
 
     private static <T extends OafEntity> T entityMerger(
-            String id, Iterator<Tuple2<String, T>> entities, long ts, Class<T> clazz) {
+            String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo) {
-        try {
-            T entity = clazz.newInstance();
-            entity.setId(id);
-            entity.setDataInfo(new DataInfo());
-            entity.getDataInfo().setTrust("0.9");
-            entity.setLastupdatetimestamp(ts);
 
-            final Collection<String> dates = Lists.newArrayList();
+        T entity = entities.next()._2();
-            entities.forEachRemaining(
-                    t -> {
-                        T duplicate = t._2();
-                        entity.mergeFrom(duplicate);
-                        if (ModelSupport.isSubClass(duplicate, Result.class)) {
-                            Result r1 = (Result) duplicate;
-                            Result er = (Result) entity;
-                            er.setAuthor(DedupUtility.mergeAuthor(er.getAuthor(), r1.getAuthor()));
 
-                            if (er.getDateofacceptance() != null) {
+        final Collection<String> dates = Lists.newArrayList();
-                                dates.add(r1.getDateofacceptance().getValue());
+        entities.forEachRemaining(
-                            }
+                t -> {
+                    T duplicate = t._2();
+                    entity.mergeFrom(duplicate);
+                    if (ModelSupport.isSubClass(duplicate, Result.class)) {
+                        Result r1 = (Result) duplicate;
+                        Result er = (Result) entity;
+                        er.setAuthor(DedupUtility.mergeAuthor(er.getAuthor(), r1.getAuthor()));
+
+                        if (r1.getDateofacceptance() != null) {
+                            dates.add(r1.getDateofacceptance().getValue());
                         }
-                    });
+                    }
+                });
 
-            if (ModelSupport.isSubClass(entity, Result.class)) {
+        if (ModelSupport.isSubClass(entity, Result.class)) {
-                ((Result) entity).setDateofacceptance(DatePicker.pick(dates));
+            ((Result) entity).setDateofacceptance(DatePicker.pick(dates));
-            }
-            return entity;
-        } catch (IllegalAccessException | InstantiationException e) {
-            throw new RuntimeException(e);
         }
+
+        entity.setId(id);
+        entity.setLastupdatetimestamp(ts);
+        entity.setDataInfo(dataInfo);
+
+        return entity;
     }
 }

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java

@@ -3,7 +3,9 @@ package eu.dnetlib.dhp.oa.dedup;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.common.EntityType;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.DataInfo;
 import eu.dnetlib.dhp.schema.oaf.OafEntity;
+import eu.dnetlib.dhp.schema.oaf.Qualifier;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@@ -21,6 +23,10 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
 
     private static final Logger log = LoggerFactory.getLogger(SparkCreateDedupRecord.class);
 
+    public static final String ROOT_TRUST = "0.8";
+    public static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup";
+    public static final String PROVENANCE_ACTIONS = "dnet:provenanceActions";
+
     public SparkCreateDedupRecord(ArgumentApplicationParser parser, SparkSession spark) {
         super(parser, spark);
     }
@@ -67,13 +73,30 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
                     DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity);
             final String entityPath = DedupUtility.createEntityPath(graphBasePath, subEntity);
 
-            Class<OafEntity> clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity));
+            final Class<OafEntity> clazz =
-
+                    ModelSupport.entityTypes.get(EntityType.valueOf(subEntity));
-            DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz)
+            final DataInfo dataInfo = getDataInfo(dedupConf);
+            DedupRecordFactory.createDedupRecord(spark, dataInfo, mergeRelPath, entityPath, clazz)
                     .write()
                     .mode(SaveMode.Overwrite)
                     .option("compression", "gzip")
                     .json(outputPath);
         }
     }
+
+    private static DataInfo getDataInfo(DedupConfig dedupConf) {
+        DataInfo info = new DataInfo();
+        info.setDeletedbyinference(false);
+        info.setInferred(true);
+        info.setInvisible(false);
+        info.setTrust(ROOT_TRUST);
+        info.setInferenceprovenance(dedupConf.getWf().getConfigurationId());
+        Qualifier provenance = new Qualifier();
+        provenance.setClassid(PROVENANCE_ACTION_CLASS);
+        provenance.setClassname(PROVENANCE_ACTION_CLASS);
+        provenance.setSchemeid(PROVENANCE_ACTIONS);
+        provenance.setSchemename(PROVENANCE_ACTIONS);
+        info.setProvenanceaction(provenance);
+        return info;
+    }
 }

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/graph/ConnectedComponent.java

@@ -25,7 +25,7 @@ public class ConnectedComponent implements Serializable {
         if (docIds.size() > 1) {
             final String s = getMin();
             String prefix = s.split("\\|")[0];
-            ccId = prefix + "|dedup_______::" + DedupUtility.md5(s);
+            ccId = prefix + "|dedup_wf_001::" + DedupUtility.md5(s);
             return ccId;
         } else {
             return docIds.iterator().next();

dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/graph/ConnectedComponent.java

@@ -25,7 +25,7 @@ public class ConnectedComponent implements Serializable {
         if (docIds.size() > 1) {
             final String s = getMin();
             String prefix = s.split("\\|")[0];
-            ccId = prefix + "|dedup_______::" + DedupUtility.md5(s);
+            ccId = prefix + "|dedup_wf_001::" + DedupUtility.md5(s);
             return ccId;
         } else {
             return docIds.iterator().next();

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

@@ -19,6 +19,8 @@ public class GraphHiveImporterJob {
 
     private static final Logger log = LoggerFactory.getLogger(GraphHiveImporterJob.class);
 
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
     public static void main(String[] args) throws Exception {
 
         final ArgumentApplicationParser parser =
@@ -37,12 +39,12 @@ public class GraphHiveImporterJob {
         String inputPath = parser.get("inputPath");
         log.info("inputPath: {}", inputPath);
 
-        String hiveMetastoreUris = parser.get("hiveMetastoreUris");
-        log.info("hiveMetastoreUris: {}", hiveMetastoreUris);
-
         String hiveDbName = parser.get("hiveDbName");
         log.info("hiveDbName: {}", hiveDbName);
 
+        String hiveMetastoreUris = parser.get("hiveMetastoreUris");
+        log.info("hiveMetastoreUris: {}", hiveMetastoreUris);
+
         SparkConf conf = new SparkConf();
         conf.set("hive.metastore.uris", hiveMetastoreUris);
 
@@ -58,13 +60,13 @@ public class GraphHiveImporterJob {
         spark.sql(String.format("DROP DATABASE IF EXISTS %s CASCADE", hiveDbName));
         spark.sql(String.format("CREATE DATABASE IF NOT EXISTS %s", hiveDbName));
 
-        final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+        final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
         // Read the input file and convert it into RDD of serializable object
         ModelSupport.oafTypes.forEach(
                 (name, clazz) ->
                         spark.createDataset(
                                         sc.textFile(inputPath + "/" + name)
-                                                .map(s -> new ObjectMapper().readValue(s, clazz))
+                                                .map(s -> OBJECT_MAPPER.readValue(s, clazz))
                                                 .rdd(),
                                         Encoders.bean(clazz))
                                 .write()

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/config-default.xml

@@ -12,19 +12,15 @@
         <value>true</value>
     </property>
     <property>
-        <name>oozie.action.sharelib.for.spark</name>
+        <name>hiveMetastoreUris</name>
-        <value>spark2</value>
-    </property>
-    <property>
-        <name>hive_metastore_uris</name>
         <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
     </property>
     <property>
-        <name>hive_jdbc_url</name>
+        <name>hiveJdbcUrl</name>
         <value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
     </property>
     <property>
-        <name>hive_db_name</name>
+        <name>hiveDbName</name>
         <value>openaire</value>
     </property>
 </configuration>

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/lib/scripts/postprocessing.sql

@@ -1,10 +1,10 @@
-DROP VIEW IF EXISTS ${hive_db_name}.result;
+DROP VIEW IF EXISTS ${hiveDbName}.result;
 
 CREATE VIEW IF NOT EXISTS result as
-    select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hive_db_name}.publication p
+    select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hiveDbName}.publication p
     union all
-    select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hive_db_name}.dataset d
+    select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hiveDbName}.dataset d
     union all
-    select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hive_db_name}.software s
+    select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hiveDbName}.software s
     union all
-    select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hive_db_name}.otherresearchproduct o;
+    select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hiveDbName}.otherresearchproduct o;

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

@@ -2,13 +2,21 @@
 
     <parameters>
         <property>
-            <name>sourcePath</name>
+            <name>inputPath</name>
             <description>the source path</description>
         </property>
         <property>
-            <name>hive_db_name</name>
+            <name>hiveDbName</name>
             <description>the target hive database name</description>
         </property>
+        <property>
+            <name>hiveJdbcUrl</name>
+            <description>hive server jdbc url</description>
+        </property>
+        <property>
+            <name>hiveMetastoreUris</name>
+            <description>hive server metastore URIs</description>
+        </property>
         <property>
             <name>sparkDriverMemory</name>
             <description>memory for driver process</description>
@@ -87,9 +95,9 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
             </spark-opts>
-            <arg>--sourcePath</arg><arg>${sourcePath}</arg>
+            <arg>--inputPath</arg><arg>${inputPath}</arg>
-            <arg>--hive_db_name</arg><arg>${hive_db_name}</arg>
+            <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
-            <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
         </spark>
         <ok to="PostProcessing"/>
         <error to="Kill"/>
@@ -102,12 +110,12 @@
             <configuration>
                 <property>
                     <name>hive.metastore.uris</name>
-                    <value>${hive_metastore_uris}</value>
+                    <value>${hiveMetastoreUris}</value>
                 </property>
             </configuration>
-            <jdbc-url>${hive_jdbc_url}/${hive_db_name}</jdbc-url>
+            <jdbc-url>${hiveJdbcUrl}/${hiveDbName}</jdbc-url>
             <script>lib/scripts/postprocessing.sql</script>
-            <param>hive_db_name=${hive_db_name}</param>
+            <param>hiveDbName=${hiveDbName}</param>
         </hive2>
         <ok to="End"/>
         <error to="Kill"/>

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java

@@ -216,6 +216,7 @@ public class CreateRelatedEntitiesJob_phase2 {
                         (MapFunction<String, E>)
                                 value -> OBJECT_MAPPER.readValue(value, entityClazz),
                         Encoders.bean(entityClazz))
+                .filter("dataInfo.invisible == false")
                 .map(
                         (MapFunction<E, TypedRow>)
                                 value ->

pom.xml

@@ -292,6 +292,12 @@
 				<groupId>eu.dnetlib</groupId>
 				<artifactId>dnet-actionmanager-common</artifactId>
 				<version>6.0.5</version>
+				<exclusions>
+					<exclusion>
+						<groupId>org.apache.hadoop</groupId>
+						<artifactId>hadoop-common</artifactId>
+					</exclusion>
+				</exclusions>
 			</dependency>
 			<dependency>
 				<groupId>eu.dnetlib</groupId>