refactoring

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob2.java

@@ -121,9 +121,9 @@ public class SparkCountryPropagationJob2 {
                 .map(r -> new Tuple2<>(r.getId(), r),
                 Encoders.tuple(Encoders.STRING(), Encoders.bean(resultClazz)));
 
-        Dataset<Tuple2<String, ResultCountrySet>> potential_update_pair = potentialUpdates.map(pu -> new Tuple2<>(pu.getResultId(),
-                        pu),
-                Encoders.tuple(Encoders.STRING(), Encoders.bean(ResultCountrySet.class)));
+//        Dataset<Tuple2<String, ResultCountrySet>> potential_update_pair = potentialUpdates.map(pu -> new Tuple2<>(pu.getResultId(),
+//                        pu),
+//                Encoders.tuple(Encoders.STRING(), Encoders.bean(ResultCountrySet.class)));
 
         Dataset<R> new_table = result_pair
                 .joinWith(potentialUpdates, result_pair.col("_1").equalTo(potentialUpdates.col("resultId")), "left_outer")

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java

@@ -0,0 +1,88 @@
+package eu.dnetlib.dhp.orcidtoresultfromsemrel;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.gson.Gson;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.Result;
+import org.apache.commons.io.IOUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.Optional;
+
+import static eu.dnetlib.dhp.PropagationConstant.*;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
+
+public class PrepareResultOrcidAssociation {
+    private static final Logger log = LoggerFactory.getLogger(PrepareResultOrcidAssociation.class);
+
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+    public static void main(String[] args) throws Exception {
+        String jsonConfiguration = IOUtils.toString(SparkOrcidToResultFromSemRelJob3.class
+                .getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult_parameters.json"));
+
+        final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+                jsonConfiguration);
+
+        parser.parseArgument(args);
+
+        Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
+        log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+        String inputPath = parser.get("sourcePath");
+        log.info("inputPath: {}", inputPath);
+
+        final String outputPath = parser.get("outputPath");
+        log.info("outputPath: {}", outputPath);
+
+        final String resultClassName = parser.get("resultTableName");
+        log.info("resultTableName: {}", resultClassName);
+
+        final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrel").split(";"));
+        log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
+
+        final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
+        log.info("resultType: {}", resultType);
+
+
+        Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
+
+        SparkConf conf = new SparkConf();
+        conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
+
+        runWithSparkHiveSession(conf, isSparkSessionManaged,
+                spark -> {
+                    if (isTest(parser)) {
+                        removeOutputDir(spark, outputPath);
+                    }
+                    prepareInfo(spark,  inputPath, outputPath, resultClazz, resultType);
+                });
+    }
+
+    private static <R extends Result> void prepareInfo(SparkSession spark,  String inputPath,
+                                                       String outputPath, Class<R> resultClazz,
+                                                       String resultType) {
+
+        //read the relation table and the table related to the result it is using
+        final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+        org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
+                .map(item -> new ObjectMapper().readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
+        relation.createOrReplaceTempView("relation");
+
+        log.info("Reading Graph table from: {}", inputPath + "/" + resultType);
+        Dataset<R> result = readPathEntity(spark, inputPath + "/" + resultType, resultClazz);
+
+
+
+
+    }
+}

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep2.java

@@ -0,0 +1,119 @@
+package eu.dnetlib.dhp.orcidtoresultfromsemrel;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.gson.Gson;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.Result;
+import org.apache.commons.io.IOUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SaveMode;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.Arrays;
+import java.util.List;
+
+import static eu.dnetlib.dhp.PropagationConstant.*;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
+
+public class PrepareResultOrcidAssociationStep1 {
+    private static final Logger log = LoggerFactory.getLogger(PrepareResultOrcidAssociationStep1.class);
+
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+    public static void main(String[] args) throws Exception {
+        String jsonConfiguration = IOUtils.toString(SparkOrcidToResultFromSemRelJob3.class
+                .getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult_parameters.json"));
+
+        final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+                jsonConfiguration);
+
+        parser.parseArgument(args);
+
+        Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
+        log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+        String inputPath = parser.get("sourcePath");
+        log.info("inputPath: {}", inputPath);
+
+        final String outputPath = parser.get("outputPath");
+        log.info("outputPath: {}", outputPath);
+
+        final String resultClassName = parser.get("resultTableName");
+        log.info("resultTableName: {}", resultClassName);
+
+        final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrel").split(";"));
+        log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
+
+        final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
+        log.info("resultType: {}", resultType);
+
+
+        Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
+
+        SparkConf conf = new SparkConf();
+        conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
+
+        runWithSparkHiveSession(conf, isSparkSessionManaged,
+                spark -> {
+                    if (isTest(parser)) {
+                        removeOutputDir(spark, outputPath);
+                    }
+                    prepareInfo(spark,  inputPath, outputPath, resultClazz, resultType, allowedsemrel);
+                });
+    }
+
+    private static <R extends Result> void prepareInfo(SparkSession spark,  String inputPath,
+                                                       String outputPath, Class<R> resultClazz,
+                                                       String resultType,
+                                                       List<String> allowedsemrel) {
+
+        //read the relation table and the table related to the result it is using
+        final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+        org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
+                .map(item -> new ObjectMapper().readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
+        relation.createOrReplaceTempView("relation");
+
+        log.info("Reading Graph table from: {}", inputPath + "/" + resultType);
+        Dataset<R> result = readPathEntity(spark, inputPath + "/" + resultType, resultClazz);
+
+        result.createOrReplaceTempView("result");
+
+        getPossibleResultOrcidAssociation(spark, allowedsemrel, outputPath);
+
+    }
+
+    private static void getPossibleResultOrcidAssociation(SparkSession spark, List<String> allowedsemrel, String outputPath){
+        String query = " select target resultId, author authorList" +
+                " from (select id, collect_set(named_struct('name', name, 'surname', surname, 'fullname', fullname, 'orcid', orcid)) author " +
+                " from ( " +
+                " select id, MyT.fullname, MyT.name, MyT.surname, MyP.value orcid " +
+                " from result " +
+                " lateral view explode (author) a as MyT " +
+                " lateral view explode (MyT.pid) p as MyP " +
+                " where MyP.qualifier.classid = 'ORCID') tmp " +
+                " group by id) r_t " +
+                " join (" +
+                " select source, target " +
+                " from relation " +
+                " where datainfo.deletedbyinference = false " +
+                getConstraintList(" relclass = '" ,allowedsemrel) + ") rel_rel " +
+                " on source = id";
+
+        spark.sql(query)
+                .as(Encoders.bean(ResultOrcidList.class))
+                .toJSON()
+        .write()
+        .mode(SaveMode.Append)
+        .option("compression","gzip")
+        .text(outputPath)
+        ;
+    }
+
+
+}

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/ResultOrcidList.java

@@ -0,0 +1,26 @@
+package eu.dnetlib.dhp.orcidtoresultfromsemrel;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+public class ResultWithOrcid implements Serializable {
+    String id;
+    List<AutoritativeAuthor> authorList = new ArrayList<>();
+
+    public String getId() {
+        return id;
+    }
+
+    public void setId(String id) {
+        this.id = id;
+    }
+
+    public List<AutoritativeAuthor> getAuthorList() {
+        return authorList;
+    }
+
+    public void setAuthorList(List<AutoritativeAuthor> authorList) {
+        this.authorList = authorList;
+    }
+}

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/ResultWithOrcid.java

@@ -1,4 +0,0 @@
-package eu.dnetlib.dhp.orcidtoresultfromsemrel;
-
-public class ResultWithOrcid {
-}

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/SparkOrcidToResultFromSemRelJob3.java

@@ -0,0 +1,398 @@
+package eu.dnetlib.dhp.orcidtoresultfromsemrel;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.schema.oaf.*;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaPairRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.Row;
+import org.apache.spark.sql.SparkSession;
+import scala.Tuple2;
+
+import java.util.*;
+
+import static eu.dnetlib.dhp.PropagationConstant.*;
+
+public class SparkOrcidToResultFromSemRelJob2 {
+    public static void main(String[] args) throws Exception {
+
+        final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkOrcidToResultFromSemRelJob2.class.getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromremrel/input_orcidtoresult_parameters.json")));
+        parser.parseArgument(args);
+        SparkConf conf = new SparkConf();
+        conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
+        final SparkSession spark = SparkSession
+                .builder()
+                .appName(SparkOrcidToResultFromSemRelJob2.class.getSimpleName())
+                .master(parser.get("master"))
+                .config(conf)
+                .enableHiveSupport()
+                .getOrCreate();
+
+        final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+        final String inputPath = parser.get("sourcePath");
+        final String outputPath = "/tmp/provision/propagation/orcidtoresult";
+
+        final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
+        boolean writeUpdate = TRUE.equals(parser.get("writeUpdate"));
+        boolean saveGraph = TRUE.equals(parser.get("saveGraph"));
+
+        createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
+
+        org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
+                .map(item -> new ObjectMapper().readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
+
+        org.apache.spark.sql.Dataset<Dataset> dataset = spark.createDataset(sc.textFile(inputPath + "/dataset")
+                        .map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Dataset.class)).rdd(),
+                Encoders.bean(eu.dnetlib.dhp.schema.oaf.Dataset.class));
+
+        org.apache.spark.sql.Dataset<OtherResearchProduct> other = spark.createDataset(sc.textFile(inputPath + "/otherresearchproduct")
+                        .map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.OtherResearchProduct.class)).rdd(),
+                Encoders.bean(eu.dnetlib.dhp.schema.oaf.OtherResearchProduct.class));
+
+        org.apache.spark.sql.Dataset<Software> software = spark.createDataset(sc.textFile(inputPath + "/software")
+                        .map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Software.class)).rdd(),
+                Encoders.bean(eu.dnetlib.dhp.schema.oaf.Software.class));
+
+        org.apache.spark.sql.Dataset<Publication> publication = spark.createDataset(sc.textFile(inputPath + "/publication")
+                        .map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Publication.class)).rdd(),
+                Encoders.bean(eu.dnetlib.dhp.schema.oaf.Publication.class));
+
+
+        relation.createOrReplaceTempView("relation");
+        String query = "Select source, target " +
+                "from relation " +
+                "where datainfo.deletedbyinference = false " + getConstraintList(" relclass = '" , allowedsemrel);
+
+        org.apache.spark.sql.Dataset<Row> result_result = spark.sql(query);
+
+        publication.createOrReplaceTempView("publication");
+        org.apache.spark.sql.Dataset<ResultWithOrcid> pubs_with_orcid = getResultWithOrcid("publication", spark)
+                .as(Encoders.bean(ResultWithOrcid.class));
+
+        dataset.createOrReplaceTempView("dataset");
+        org.apache.spark.sql.Dataset<ResultWithOrcid> dats_with_orcid = getResultWithOrcid("dataset", spark)
+                .as(Encoders.bean(ResultWithOrcid.class));
+
+        other.createOrReplaceTempView("orp");
+        org.apache.spark.sql.Dataset<ResultWithOrcid> orp_with_orcid = getResultWithOrcid("orp", spark)
+                .as(Encoders.bean(ResultWithOrcid.class));
+
+        dataset.createOrReplaceTempView("software");
+        org.apache.spark.sql.Dataset<ResultWithOrcid> software_with_orcid = getResultWithOrcid("software", spark)
+                .as(Encoders.bean(ResultWithOrcid.class));
+        //get the results having at least one author pid we are interested in
+
+        //target of the relation from at least one source with orcid.
+        //the set of authors contains all those that have orcid and are related to target
+        //from any source with allowed semantic relationship
+        JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_pubs = getTargetAutoritativeAuthorList(pubs_with_orcid);
+
+        JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_dats = getTargetAutoritativeAuthorList(dats_with_orcid);
+
+        JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_orp = getTargetAutoritativeAuthorList(orp_with_orcid);
+
+        JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_sw = getTargetAutoritativeAuthorList(software_with_orcid);
+
+        if(writeUpdate){
+            target_authorlist_from_dats.map(r -> new ObjectMapper().writeValueAsString(r))
+                    .saveAsTextFile(outputPath + "/" + "update_dats");
+            target_authorlist_from_pubs.map(r -> new ObjectMapper().writeValueAsString(r))
+                    .saveAsTextFile(outputPath + "/" + "update_pubs");
+            target_authorlist_from_orp.map(r -> new ObjectMapper().writeValueAsString(r))
+                    .saveAsTextFile(outputPath + "/" + "update_orp");
+            target_authorlist_from_sw.map(r -> new ObjectMapper().writeValueAsString(r))
+                    .saveAsTextFile(outputPath + "/" + "update_sw");
+        }
+        
+        if(saveGraph){
+            sc.textFile(inputPath + "/publication")
+                    .map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Publication.class))
+                    .mapToPair(p -> new Tuple2<>(p.getId(),p))
+                    .leftOuterJoin(target_authorlist_from_pubs)
+                    .map(c -> {
+                        Result r = c._2()._1();
+                        if(!c._2()._2().isPresent()){
+                            return r;
+                        }
+                        List<eu.dnetlib.dhp.schema.oaf.Author> toenrich_author = r.getAuthor();
+                        List<AutoritativeAuthor> autoritativeAuthors = c._2()._2().get();
+                        for(eu.dnetlib.dhp.schema.oaf.Author author: toenrich_author){
+                            if (!containsAllowedPid(author)){
+                                enrichAuthor(author, autoritativeAuthors);
+                            }
+                        }
+                        return r;
+                    });
+                            
+        }
+
+    }
+    
+    private static void enrichAuthor(eu.dnetlib.dhp.schema.oaf.Author a, List<AutoritativeAuthor> au){
+        for (AutoritativeAuthor aa: au){
+            if(enrichAuthor(aa, a)){
+                return;
+            }
+        }
+
+    }
+
+//    private static JavaPairRDD<String, List<AutoritativeAuthor>> getTargetAutoritativeAuthorList(org.apache.spark.sql.Dataset<Row> result_result, org.apache.spark.sql.Dataset<ResultWithOrcid> pubs_with_orcid) {
+//        return pubs_with_orcid
+//                .toJavaRDD()
+//                .mapToPair(p -> new Tuple2<>(p.getId(), p.getAuthorList()))
+//                .join(result_result.toJavaRDD().mapToPair(rel -> new Tuple2<>(rel.getString(0), rel.getString(1))))
+//                .mapToPair(c -> new Tuple2<>(c._2._2(), c._2()._1()))
+//                .reduceByKey((a, b) -> {
+//                    if(a == null){
+//                        return b;
+//                    }
+//                    if(b==null){
+//                        return a;
+//                    }
+//
+//                    Set<String> authSet = new HashSet<>();
+//                    a.stream().forEach(au -> authSet.add(au.getOrcid()));
+//
+//                    b.stream().forEach(au -> {
+//                                if (!authSet.contains(au.getOrcid())) {
+//                                    a.add(au);
+//                                }
+//                            }
+//                        );
+//                    return a;
+//                    });
+//    }
+private static JavaPairRDD<String, List<AutoritativeAuthor>> getTargetAutoritativeAuthorList( org.apache.spark.sql.Dataset<ResultWithOrcid> pubs_with_orcid) {
+    return pubs_with_orcid
+            .toJavaRDD()
+            .mapToPair(p -> new Tuple2<>(p.getId(), p.getAuthorList()))
+            .reduceByKey((a, b) -> {
+                if(a == null){
+                    return b;
+                }
+                if(b==null){
+                    return a;
+                }
+                Set<String> authSet = new HashSet<>();
+                a.stream().forEach(au -> authSet.add(au.getOrcid()));
+
+                b.stream().forEach(au -> {
+                            if (!authSet.contains(au.getOrcid())) {
+                                a.add(au);
+                            }
+                        }
+                );
+                return a;
+            });
+}
+
+    private static org.apache.spark.sql.Dataset<Row> getResultWithOrcid(String table, SparkSession spark){
+        String query = " select target, author " +
+                " from (select id, collect_set(named_struct('name', name, 'surname', surname, 'fullname', fullname, 'orcid', orcid)) author " +
+                " from ( " +
+                " select id, MyT.fullname, MyT.name, MyT.surname, MyP.value orcid " +
+                " from " + table +
+                " lateral view explode (author) a as MyT " +
+                " lateral view explode (MyT.pid) p as MyP " +
+                " where MyP.qualifier.classid = 'ORCID') tmp " +
+                " group by id) r_t " +
+                " join (" +
+                " select source, target " +
+                " from relation " +
+                " where datainfo.deletedbyinference = false  and (relclass = 'isSupplementedBy' or relclass = 'isSupplementTo') rel_rel " +
+                " on source = id";
+
+        return spark.sql(query);
+    }
+
+
+    private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, eu.dnetlib.dhp.schema.oaf.Author author) {
+        boolean toaddpid = false;
+
+        if (StringUtils.isNoneEmpty(autoritative_author.getSurname())) {
+            if (StringUtils.isNoneEmpty(author.getSurname())) {
+                if (autoritative_author.getSurname().trim().equalsIgnoreCase(author.getSurname().trim())) {
+
+                    //have the same surname. Check the name
+                    if (StringUtils.isNoneEmpty(autoritative_author.getName())) {
+                        if (StringUtils.isNoneEmpty(author.getName())) {
+                            if (autoritative_author.getName().trim().equalsIgnoreCase(author.getName().trim())) {
+                                toaddpid = true;
+                            }
+                            //they could be differently written (i.e. only the initials of the name in one of the two
+                            if (autoritative_author.getName().trim().substring(0, 0).equalsIgnoreCase(author.getName().trim().substring(0, 0))) {
+                                toaddpid = true;
+                            }
+                        }
+                    }
+                }
+            }
+        }
+        if (toaddpid){
+            StructuredProperty pid = new StructuredProperty();
+            String aa_pid = autoritative_author.getOrcid();
+            pid.setValue(aa_pid);
+            pid.setQualifier(getQualifier(PROPAGATION_AUTHOR_PID, PROPAGATION_AUTHOR_PID ));
+            pid.setDataInfo(getDataInfo(PROPAGATION_DATA_INFO_TYPE, PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID, PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME));
+            if(author.getPid() == null){
+                author.setPid(Arrays.asList(pid));
+            }else{
+                author.getPid().add(pid);
+            }
+
+        }
+        return toaddpid;
+
+    }
+
+
+//    private static List<Author> enrichAuthors(List<Author> autoritative_authors, List<Author> to_enrich_authors, boolean filter){
+////        List<Author> autoritative_authors = p._2()._2().get().getAuthors();
+////        List<Author> to_enrich_authors = r.getAuthor();
+//
+//        return to_enrich_authors
+//                .stream()
+//                .map(a -> {
+//                    if (filter) {
+//                        if (containsAllowedPid(a)) {
+//                            return a;
+//                        }
+//                    }
+//
+//                    List<Author> lst = autoritative_authors.stream()
+//                            .map(aa -> enrichAuthor(aa, a)).filter(au -> !(au == null)).collect(Collectors.toList());
+//                    if (lst.size() == 0) {
+//                        return a;
+//                    }
+//                    return lst.get(0);//Each author can be enriched at most once. It cannot be the same as many different people
+//
+//                }).collect(Collectors.toList());
+//    }
+//
+//    private static void writeResult(JavaPairRDD<String, Result> results, JavaPairRDD<String, TypedRow> toupdateresult,
+//                                    String outputPath, String type) {
+//
+//        results.join(toupdateresult)
+//                .map(p -> {
+//                    Result r = p._2()._1();
+//
+//                        List<Author> autoritative_authors = p._2()._2().getAuthors();
+//                    List<eu.dnetlib.dhp.schema.oaf.Author> to_enrich_authors = r.getAuthor();
+//
+//                        r.setAuthor(enrichAutors(autoritative_authors, to_enrich_authors, false));
+////                                .stream()
+////                                .map(a -> {
+////                                    if(filter) {
+////                                        if (containsAllowedPid(a)) {
+////                                            return a;
+////                                        }
+////                                    }
+////
+////                                    List<Author> lst = autoritative_authors.stream()
+////                                            .map(aa -> enrichAuthor(aa, a)).filter(au -> !(au == null)).collect(Collectors.toList());
+////                                    if(lst.size() == 0){
+////                                        return a;
+////                                    }
+////                                    return lst.get(0);//Each author can be enriched at most once. It cannot be the same as many different people
+////
+////                                }).collect(Collectors.toList()));
+//
+//                    return r;
+//                })
+//                .map(p -> new ObjectMapper().writeValueAsString(p))
+//                .saveAsTextFile(outputPath + "/" + type + "_update");
+//    }
+
+
+//    private static void updateResult(JavaPairRDD<String, Result> results, JavaPairRDD<String, TypedRow> toupdateresult,
+//                                     String outputPath, String type) {
+//        results.leftOuterJoin(toupdateresult)
+//                .map(p -> {
+//                    Result r = p._2()._1();
+//                    if (p._2()._2().isPresent()){
+//                        List<AutoritativeAuthor> autoritative_authors = p._2()._2().get().getAuthors();
+//                        List<eu.dnetlib.dhp.schema.oaf.Author> to_enrich_authors = r.getAuthor();
+//
+//                        r.setAuthor(enrichAutors(autoritative_authors, to_enrich_authors, true));
+////                                .stream()
+////                                .map(a -> {
+////                                    if(filter) {
+////                                        if (containsAllowedPid(a)) {
+////                                            return a;
+////                                        }
+////                                    }
+////
+////                                    List<Author> lst = autoritative_authors.stream()
+////                                            .map(aa -> enrichAuthor(aa, a)).filter(au -> !(au == null)).collect(Collectors.toList());
+////                                    if(lst.size() == 0){
+////                                        return a;
+////                                    }
+////                                    return lst.get(0);//Each author can be enriched at most once. It cannot be the same as many different people
+////
+////                                }).collect(Collectors.toList()));
+//                    }
+//                    return r;
+//                })
+//                .map(p -> new ObjectMapper().writeValueAsString(p))
+//                .saveAsTextFile(outputPath+"/"+type);
+//    }
+
+    
+
+    private static boolean containsAllowedPid(eu.dnetlib.dhp.schema.oaf.Author a) {
+        for (StructuredProperty pid : a.getPid()) {
+            if (PROPAGATION_AUTHOR_PID.equals(pid.getQualifier().getClassid())) {
+                return true;
+            }
+        }
+        return false;
+    }
+
+}
+
+
+/*private ResultProtos.Result.Metadata.Builder searchMatch(List<FieldTypeProtos.Author> author_list){
+        ResultProtos.Result.Metadata.Builder metadataBuilder = ResultProtos.Result.Metadata.newBuilder();
+        boolean updated = false;
+
+        for (FieldTypeProtos.Author a: author_list){
+            FieldTypeProtos.Author.Builder author = searchAuthor(a, autoritative_authors);
+            if(author != null){
+                updated = true;
+                metadataBuilder.addAuthor(author);
+            }else{
+                metadataBuilder.addAuthor(FieldTypeProtos.Author.newBuilder(a));
+            }
+        }
+        if(updated)
+            return metadataBuilder;
+        return null;
+    }
+    private FieldTypeProtos.Author.Builder searchAuthor(FieldTypeProtos.Author a, List<FieldTypeProtos.Author> author_list){
+        if(containsOrcid(a.getPidList()))
+            return null;
+        for(FieldTypeProtos.Author autoritative_author : author_list) {
+                if (equals(autoritative_author, a)) {
+                    if(!containsOrcid(a.getPidList()))
+                        return update(a, autoritative_author);
+                }
+        }
+        return  null;
+
+    }
+
+    private boolean containsOrcid(List<FieldTypeProtos.KeyValue> pidList){
+        if(pidList == null)
+            return false;
+        return pidList
+                .stream()
+                .filter(kv -> kv.getKey().equals(PropagationConstants.AUTHOR_PID))
+                .collect(Collectors.toList()).size() > 0;
+    }
+    */

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromremrel/oozie_app/config-default.xml

@@ -1,18 +0,0 @@
-<configuration>
-    <property>
-        <name>jobTracker</name>
-        <value>yarnRM</value>
-    </property>
-    <property>
-        <name>nameNode</name>
-        <value>hdfs://nameservice1</value>
-    </property>
-    <property>
-        <name>oozie.use.system.libpath</name>
-        <value>true</value>
-    </property>
-    <property>
-        <name>oozie.action.sharelib.for.spark</name>
-        <value>spark2</value>
-    </property>
-</configuration>

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromremrel/oozie_app/workflow.xml

@@ -1,55 +0,0 @@
-<workflow-app name="orcid_to_result_from_semrel_propagation" xmlns="uri:oozie:workflow:0.5">
-<parameters>
-    <property>
-        <name>sourcePath</name>
-        <description>the source path</description>
-    </property>
-    <property>
-        <name>allowedsemrels</name>
-        <description>the semantic relationships allowed for propagation</description>
-    </property>
-    <property>
-        <name>sparkDriverMemory</name>
-        <description>memory for driver process</description>
-    </property>
-    <property>
-        <name>sparkExecutorMemory</name>
-        <description>memory for individual executor</description>
-    </property>
-    <property>
-        <name>sparkExecutorCores</name>
-        <description>number of cores used by single executor</description>
-    </property>
-</parameters>
-
-<start to="OrcidToResultFromSemRelPropagation"/>
-
-<kill name="Kill">
-    <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
-</kill>
-
-<action name="OrcidToResultFromSemRelPropagation">
-    <spark xmlns="uri:oozie:spark-action:0.2">
-        <job-tracker>${jobTracker}</job-tracker>
-        <name-node>${nameNode}</name-node>
-        <master>yarn-cluster</master>
-        <mode>cluster</mode>
-        <name>AffiliatioPropagation</name>
-        <class>eu.dnetlib.dhp.resulttoorganizationfrominstrepo.SparkResultToOrganizationFromIstRepoJob</class>
-        <jar>dhp-propagation-${projectVersion}.jar</jar>
-        <spark-opts>--executor-memory ${sparkExecutorMemory}
-            --executor-cores ${sparkExecutorCores}
-            --driver-memory=${sparkDriverMemory}
-            --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener"
-            --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener"
-        </spark-opts>
-        <arg>-mt</arg> <arg>yarn-cluster</arg>
-        <arg>--sourcePath</arg><arg>${sourcePath}</arg>
-        <arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
-    </spark>
-    <ok to="End"/>
-    <error to="Kill"/>
-</action>
-
-<end name="End"/>
-</workflow-app>

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_orcidtoresult_parameters.json

@@ -16,5 +16,17 @@
     "paramLongName":"allowedsemrels",
     "paramDescription": "the allowed sematinc relations for propagation",
     "paramRequired": true
+  },
+  {
+    "paramName":"wu",
+    "paramLongName":"writeUpdate",
+    "paramDescription": "true if the update must be writte. No double check if information is already present",
+    "paramRequired": true
+  },
+  {
+    "paramName":"sg",
+    "paramLongName":"saveGraph",
+    "paramDescription": "true if the new version of the graph must be saved",
+    "paramRequired": true
   }
 ]

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult_parameters.json

@@ -0,0 +1,32 @@
+[
+  {
+    "paramName":"mt",
+    "paramLongName":"master",
+    "paramDescription": "should be local or yarn",
+    "paramRequired": true
+  },
+  {
+    "paramName":"s",
+    "paramLongName":"sourcePath",
+    "paramDescription": "the path of the sequencial file to read",
+    "paramRequired": true
+  },
+  {
+    "paramName":"as",
+    "paramLongName":"allowedsemrels",
+    "paramDescription": "the allowed sematinc relations for propagation",
+    "paramRequired": true
+  },
+  {
+    "paramName":"wu",
+    "paramLongName":"writeUpdate",
+    "paramDescription": "true if the update must be writte. No double check if information is already present",
+    "paramRequired": true
+  },
+  {
+    "paramName":"sg",
+    "paramLongName":"saveGraph",
+    "paramDescription": "true if the new version of the graph must be saved",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult_parameters2.json

@@ -0,0 +1,38 @@
+[
+  {
+    "paramName":"s",
+    "paramLongName":"sourcePath",
+    "paramDescription": "the path of the sequencial file to read",
+    "paramRequired": true
+  },
+  {
+    "paramName":"as",
+    "paramLongName":"allowedsemrels",
+    "paramDescription": "the allowed sematinc relations for propagation",
+    "paramRequired": true
+  },
+  {
+    "paramName":"h",
+    "paramLongName":"hive_metastore_uris",
+    "paramDescription": "the hive metastore uris",
+    "paramRequired": true
+  },
+  {
+    "paramName": "out",
+    "paramLongName": "outputPath",
+    "paramDescription": "the path used to store temporary output files",
+    "paramRequired": true
+  },
+  {
+    "paramName": "ssm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "true if the spark session is managed, false otherwise",
+    "paramRequired": false
+  },
+  {
+    "paramName":"tn",
+    "paramLongName":"resultTableName",
+    "paramDescription": "the name of the result table we are currently working on",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/oozie_app/config-default.xml

@@ -0,0 +1,54 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>oozie.action.sharelib.for.spark</name>
+        <value>spark2</value>
+    </property>
+    <property>
+        <name>spark2YarnHistoryServerAddress</name>
+        <value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
+    </property>
+    <property>
+        <name>spark2EventLogDir</name>
+        <value>/user/spark/spark2ApplicationHistory</value>
+    </property>
+    <property>
+        <name>spark2ExtraListeners</name>
+        <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+    </property>
+    <property>
+        <name>spark2SqlQueryExecutionListeners</name>
+        <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+    </property>
+    <property>
+        <name>sparkExecutorNumber</name>
+        <value>4</value>
+    </property>
+    <property>
+        <name>sparkDriverMemory</name>
+        <value>15G</value>
+    </property>
+    <property>
+        <name>sparkExecutorMemory</name>
+        <value>6G</value>
+    </property>
+    <property>
+        <name>sparkExecutorCores</name>
+        <value>1</value>
+    </property>
+    <property>
+        <name>spark2MaxExecutors</name>
+        <value>50</value>
+    </property>
+</configuration>

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/oozie_app/workflow.xml

@@ -0,0 +1,71 @@
+<workflow-app name="orcid_to_result_from_semrel_propagation" xmlns="uri:oozie:workflow:0.5">
+<parameters>
+    <property>
+        <name>sourcePath</name>
+        <description>the source path</description>
+    </property>
+    <property>
+        <name>allowedsemrels</name>
+        <description>the semantic relationships allowed for propagation</description>
+    </property>
+<!--    <property>-->
+<!--        <name>sparkDriverMemory</name>-->
+<!--        <description>memory for driver process</description>-->
+<!--    </property>-->
+<!--    <property>-->
+<!--        <name>sparkExecutorMemory</name>-->
+<!--        <description>memory for individual executor</description>-->
+<!--    </property>-->
+<!--    <property>-->
+<!--        <name>sparkExecutorCores</name>-->
+<!--        <description>number of cores used by single executor</description>-->
+<!--    </property>-->
+    <property>
+        <name>writeUpdate</name>
+        <description>writes the information found for the update. No double check done if the information is already present</description>
+    </property>
+    <property>
+        <name>saveGraph</name>
+        <description>writes new version of the graph after the propagation step</description>
+    </property>
+</parameters>
+
+<start to="OrcidToResultFromSemRelPropagation"/>
+
+<kill name="Kill">
+    <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+</kill>
+
+<action name="OrcidToResultFromSemRelPropagation">
+    <spark xmlns="uri:oozie:spark-action:0.2">
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <master>yarn-cluster</master>
+        <mode>cluster</mode>
+        <name>OrcidToResultFromSemRelPropagation</name>
+        <class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob</class>
+        <jar>dhp-propagation-${projectVersion}.jar</jar>
+        <spark-opts>
+            --num-executors=${sparkExecutorNumber}
+            --executor-memory=${sparkExecutorMemory}
+            --executor-cores=${sparkExecutorCores}
+            --driver-memory=${sparkDriverMemory}
+            --conf spark.extraListeners=${spark2ExtraListeners}
+            --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+            --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+            --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+            --conf spark.dynamicAllocation.enabled=true
+            --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
+        </spark-opts>
+        <arg>-mt</arg> <arg>yarn-cluster</arg>
+        <arg>--sourcePath</arg><arg>${sourcePath}</arg>
+        <arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
+        <arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
+        <arg>--saveGraph</arg><arg>${saveGraph}</arg>
+    </spark>
+    <ok to="End"/>
+    <error to="Kill"/>
+</action>
+
+<end name="End"/>
+</workflow-app>