dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/SerializableSupplier.java

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

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

@@ -1,20 +1,27 @@
 package eu.dnetlib.dhp.countrypropagation;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.PropagationConstant;
 import eu.dnetlib.dhp.TypedRow;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.oaf.*;
-import eu.dnetlib.dhp.schema.oaf.Dataset;
+import net.sf.saxon.expr.ContextMappingFunction;
+import net.sf.saxon.expr.flwor.Tuple;
+import net.sf.saxon.om.Item;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.io.Text;
+import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaPairRDD;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.sql.*;
+import org.apache.spark.sql.Dataset;
 import scala.Tuple2;
 
+import javax.sql.DataSource;
+import java.beans.Encoder;
 import java.io.File;
 import java.io.IOException;
 import java.util.*;
@@ -22,42 +29,298 @@ import java.util.*;
 import static eu.dnetlib.dhp.PropagationConstant.*;
 
 public class SparkCountryPropagationJob {
+
     public static void main(String[] args) throws Exception {
 
         final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCountryPropagationJob.class.getResourceAsStream("/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_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(SparkCountryPropagationJob.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/countrytoresultfrominstitutionalrepositories";
 
         createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
 
-
         List<String> whitelist = Arrays.asList(parser.get("whitelist").split(";"));
         List<String> allowedtypes = Arrays.asList(parser.get("allowedtypes").split(";"));
 
 
-        JavaPairRDD<String, TypedRow> organizations = sc.textFile(inputPath + "/organization")
+        datasource(spark, whitelist, outputPath, inputPath);
+
+        //rdd(spark,whitelist,allowedtypes, outputPath, inputPath);
+
+    }
+
+    private static void datasource(SparkSession spark, List<String> whitelist, String outputPath, String inputPath){
+        String whitelisted = "";
+        for (String i : whitelist){
+            whitelisted += " OR id = '" + i + "'";
+        }
+
+        String query = "SELECT source ds, target org, country.classid country " +
+                       "FROM ( SELECT id " +
+                               "FROM openaire.datasource " +
+                               "WHERE datasourcetype.classid = 'pubsrepository::institutional' " +
+                               "AND (datainfo.deletedbyinference = false " + whitelisted + ") ) d " +
+                       "JOIN ( SELECT source, target " +
+                               "FROM openaire.relation " +
+                               "WHERE relclass = 'provides' " +
+                               "AND datainfo.deletedbyinference = false ) rel " +
+                       "ON d.id = rel.source " +
+                       "JOIN (SELECT id, country " +
+                              "FROM openaire.organization " +
+                              "WHERE datainfo.deletedbyinference = false ) o " +
+                       "ON o.id = rel.target";
+
+        Dataset<Row> rels = spark.sql(query);
+        rels.createOrReplaceTempView("rels");
+        
+        
+
+        final JavaRDD<Row> toupdateresultsoftware = propagateOnResult(spark, "openaire.software");
+        createUpdateForSoftwareDataset(toupdateresultsoftware, inputPath, spark)
+                .map(s -> new ObjectMapper().writeValueAsString(s))
+                .saveAsTextFile(outputPath + "/software");
+        createUpdateForResultDatasetWrite(toupdateresultsoftware, outputPath, "update_software");
+
+        JavaRDD<Row> toupdateresultdataset = propagateOnResult(spark, "openaire.dataset");
+        createUpdateForDatasetDataset(toupdateresultdataset,inputPath,spark)
+                .map(d -> new ObjectMapper().writeValueAsString(d))
+                .saveAsTextFile(outputPath + "/dataset");
+        createUpdateForResultDatasetWrite(toupdateresultdataset, outputPath, "update_dataset");
+
+        JavaRDD<Row> toupdateresultother = propagateOnResult(spark, "openaire.otherresearchproduct");
+        createUpdateForOtherDataset(toupdateresultother, inputPath, spark)
+                .map(o -> new ObjectMapper().writeValueAsString(o))
+                .saveAsTextFile(outputPath + "/otherresearchproduct");
+        createUpdateForResultDatasetWrite(toupdateresultother, outputPath, "update_other");
+
+        createUpdateForPublicationDataset(propagateOnResult(spark, "openaire.publication"), inputPath, spark)
+                .map(p -> new ObjectMapper().writeValueAsString(p))
+                .saveAsTextFile(outputPath + "/publication");
+
+    }
+
+    private static JavaRDD<OtherResearchProduct> createUpdateForOtherDataset(JavaRDD<Row> toupdateresult, String inputPath, SparkSession spark) {
+        final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+        return sc.textFile(inputPath + "/otherresearchproduct")
+                .map(item -> new ObjectMapper().readValue(item, OtherResearchProduct.class))
+                .mapToPair(s -> new Tuple2<>(s.getId(), s)).leftOuterJoin(getStringResultJavaPairRDD(toupdateresult))
+                .map(c -> {
+                    OtherResearchProduct oaf = c._2()._1();
+                    List<Country> countryList = oaf.getCountry();
+                    if (c._2()._2().isPresent()) {
+                        HashSet<String> countries = new HashSet<>();
+                        for (Qualifier country : countryList) {
+                            countries.add(country.getClassid());
+                        }
+                        Result r = c._2()._2().get();
+                        for (Country country : r.getCountry()) {
+                            if (!countries.contains(country.getClassid())) {
+                                countryList.add(country);
+                            }
+                        }
+                        oaf.setCountry(countryList);
+                    }
+                    return oaf;
+                });
+    }
+
+    private static JavaRDD<Publication> createUpdateForPublicationDataset(JavaRDD<Row> toupdateresult, String inputPath, SparkSession spark) {
+        final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+        return sc.textFile(inputPath + "/publication")
+                .map(item -> new ObjectMapper().readValue(item, Publication.class))
+                .mapToPair(s -> new Tuple2<>(s.getId(), s)).leftOuterJoin(getStringResultJavaPairRDD(toupdateresult))
+                .map(c -> {
+                    Publication oaf = c._2()._1();
+                    List<Country> countryList = oaf.getCountry();
+                    if (c._2()._2().isPresent()) {
+                        HashSet<String> countries = new HashSet<>();
+                        for (Qualifier country : countryList) {
+                            countries.add(country.getClassid());
+                        }
+                        Result r = c._2()._2().get();
+                        for (Country country : r.getCountry()) {
+                            if (!countries.contains(country.getClassid())) {
+                                countryList.add(country);
+                            }
+                        }
+                        oaf.setCountry(countryList);
+                    }
+                    return oaf;
+                });
+    }
+
+    private static JavaRDD<Software> createUpdateForSoftwareDataset(JavaRDD<Row> toupdateresult, String inputPath, SparkSession spark) {
+        final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+        return sc.textFile(inputPath + "/software")
+                .map(item -> new ObjectMapper().readValue(item, Software.class))
+                .mapToPair(s -> new Tuple2<>(s.getId(), s)).leftOuterJoin(getStringResultJavaPairRDD(toupdateresult))
+                .map(c -> {
+                    Software oaf = c._2()._1();
+                    List<Country> countryList = oaf.getCountry();
+                    if (c._2()._2().isPresent()) {
+                        HashSet<String> countries = new HashSet<>();
+                        for (Qualifier country : countryList) {
+                            countries.add(country.getClassid());
+                        }
+                        Result r = c._2()._2().get();
+                        for (Country country : r.getCountry()) {
+                            if (!countries.contains(country.getClassid())) {
+                                countryList.add(country);
+                            }
+                        }
+                        oaf.setCountry(countryList);
+                    }
+                    return oaf;
+                });
+    }
+
+    private static JavaRDD<eu.dnetlib.dhp.schema.oaf.Dataset> createUpdateForDatasetDataset(JavaRDD<Row> toupdateresult, String inputPath, SparkSession spark) {
+        final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+        return sc.textFile(inputPath + "/dataset")
+                .map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Dataset.class))
+                .mapToPair(d -> new Tuple2<>(d.getId(), d)).leftOuterJoin(getStringResultJavaPairRDD(toupdateresult))
+                .map(c -> {
+                    eu.dnetlib.dhp.schema.oaf.Dataset oaf = c._2()._1();
+                    List<Country> countryList = oaf.getCountry();
+                    if (c._2()._2().isPresent()) {
+                        HashSet<String> countries = new HashSet<>();
+                        for (Qualifier country : countryList) {
+                            countries.add(country.getClassid());
+                        }
+                        Result r = c._2()._2().get();
+                        for (Country country : r.getCountry()) {
+                            if (!countries.contains(country.getClassid())) {
+                                countryList.add(country);
+                            }
+                        }
+                        oaf.setCountry(countryList);
+                    }
+                    return oaf;
+                });
+    }
+
+    private static JavaRDD<Row> propagateOnResult(SparkSession spark, String table) {
+        String query;
+        query = "SELECT id, inst.collectedfrom.key cf , inst.hostedby.key hb " +
+                "FROM ( SELECT id, instance " +
+                       "FROM " + table +
+                       " WHERE datainfo.deletedbyinference = false)  ds " +
+                       "LATERAL VIEW EXPLODE(instance) i AS inst";
+        Dataset<Row> cfhb = spark.sql(query);
+        cfhb.createOrReplaceTempView("cfhb");
+
+        return countryPropagationAssoc(spark, "cfhb").toJavaRDD();
+
+    }
+
+    private static Dataset<Row> countryPropagationAssoc(SparkSession spark, String cfhbTable){
+        String  query = "SELECT id, collect_set(country) country "+
+                "FROM ( SELECT id, country " +
+                "FROM rels " +
+                "JOIN " + cfhbTable  +
+                " ON cf = ds     " +
+                "UNION ALL " +
+                "SELECT id , country     " +
+                "FROM rels " +
+                "JOIN " + cfhbTable  +
+                " ON hb = ds ) tmp " +
+                "GROUP BY id";
+        return spark.sql(query);
+    }
+
+    private static JavaPairRDD<String, Result> getStringResultJavaPairRDD(JavaRDD<Row> toupdateresult) {
+        return toupdateresult.map(c -> {
+            List<Country> countryList = new ArrayList<>();
+            List<String> tmp = c.getList(1);
+            for (String country : tmp) {
+                countryList.add(getCountry(country));
+            }
+            Result r = new Result();
+            r.setId(c.getString(0));
+            r.setCountry(countryList);
+            return r;
+        }).mapToPair(r -> new Tuple2<>(r.getId(), r));
+    }
+
+    private static void createUpdateForResultDatasetWrite(JavaRDD<Row> toupdateresult, String outputPath, String type){
+        toupdateresult.map(c -> {
+            List<Country> countryList = new ArrayList<>();
+            List<String> tmp = c.getList(1);
+            for (String country : tmp) {
+                countryList.add(getCountry(country));
+            }
+            Result r = new Result();
+            r.setId(c.getString(0));
+            r.setCountry(countryList);
+            return r;
+
+        }).map(r ->new ObjectMapper().writeValueAsString(r))
+                .saveAsTextFile(outputPath+"/"+type);
+    }
+
+    private static Dataset<Row> countryPropagation(SparkSession spark, String cfhbTable){
+       String  query = "SELECT id, collect_set(named_struct('classid', country, 'classname', country, " +
+                "'datainfo', named_struct( 'deletedbyinference', false, " +
+                "'inferenceprovenance','" + PROPAGATION_DATA_INFO_TYPE +"'," +
+                "'inferred',true,'invisible',false, " +
+                "'provenanceaction', named_struct('classid','" + PROPAGATION_COUNTRY_INSTREPO_CLASS_ID + "'," +
+                "'classname','" + PROPAGATION_COUNTRY_INSTREPO_CLASS_NAME +"'," +
+                "'schemeid','" + DNET_SCHEMA_ID +"'," +
+                "'schemename','" + DNET_SCHEMA_NAME +"')  , " +
+                "'trust','0.9') ,'schemeid','" + DNET_COUNTRY_SCHEMA +"','schemename','" + DNET_COUNTRY_SCHEMA + "')) country  " +
+                "FROM ( SELECT id, country " +
+                "FROM rels " +
+                "JOIN " + cfhbTable  +
+                " ON cf = ds     " +
+                "UNION ALL " +
+                "SELECT id , country     " +
+                "FROM rels " +
+                "JOIN " + cfhbTable  +
+                " ON hb = ds ) tmp " +
+                "GROUP BY id";
+        return spark.sql(query);
+    }
+
+    private static void rdd(SparkSession spark,  List<String> whitelist, List<String> allowedtypes, String outputPath, String inputPath) throws IOException {
+        final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+            JavaPairRDD<String, TypedRow> organizations = sc.textFile(inputPath + "/organization")
                 .map(item -> new ObjectMapper().readValue(item, Organization.class))
                 .filter(org -> !org.getDataInfo().getDeletedbyinference())
-                .map(org -> new TypedRow().setSourceId(org.getId()).setValue(org.getCountry().getClassid()))
+                .map(org -> {
+                    TypedRow tr = new TypedRow();
+                    tr.setSourceId(org.getId());
+                    tr.setValue(org.getCountry().getClassid());
+                    return tr;
+                })
                 .mapToPair(toPair());
 
         JavaPairRDD<String, TypedRow> organization_datasource =
                 sc.textFile(inputPath + "/relation")
-                .map(item -> new ObjectMapper().readValue(item, Relation.class))
-                .filter(r -> !r.getDataInfo().getDeletedbyinference())
-                .filter(r -> RELATION_DATASOURCEORGANIZATION_REL_TYPE.equals(r.getRelClass()) && RELATION_ORGANIZATION_DATASOURCE_REL_CLASS.equals(r.getRelType()))
-                .map(r -> new TypedRow().setSourceId(r.getSource()).setTargetId(r.getTarget()))
-                .mapToPair(toPair()); //id is the organization identifier
-
+                        .map(item -> new ObjectMapper().readValue(item, Relation.class))
+                        .filter(r -> !r.getDataInfo().getDeletedbyinference())
+                        .filter(r -> RELATION_DATASOURCEORGANIZATION_REL_TYPE.equals(r.getRelType()) &&
+                                RELATION_ORGANIZATION_DATASOURCE_REL_CLASS.equals(r.getRelClass()))
+                        .map(r -> {
+                            TypedRow tp = new TypedRow(); tp.setSourceId(r.getSource()); tp.setTargetId(r.getTarget());
+                            return tp;
+                        })
+                        .mapToPair(toPair()); //id is the organization identifier
 
         JavaPairRDD<String, TypedRow> datasources = sc.textFile(inputPath + "/datasource")
                 .map(item -> new ObjectMapper().readValue(item, Datasource.class))
@@ -65,6 +328,97 @@ public class SparkCountryPropagationJob {
                 .map(ds -> new TypedRow().setSourceId(ds.getId()))
                 .mapToPair(toPair());
 
+        JavaPairRDD<String, TypedRow> datasource_country = organizations.join(organization_datasource)
+                .map(x -> x._2()._1().setSourceId(x._2()._2().getTargetId())) // (OrganizationId,(TypedRow for Organization, TypedRow for Relation)
+                .mapToPair(toPair()); //(DatasourceId, TypedRowforOrganziation)
+
+
+        JavaPairRDD<String, TypedRow> alloweddatasources_country = datasources.join(datasource_country)
+                .mapToPair(ds -> new Tuple2<>(ds._1(), ds._2()._2())).cache();
+
+//        System.out.println("OUTPUT  *** ORGANIZATION COUNT *** " + organizations.count());
+//        System.out.println("OUTPUT  *** ORGANIZATION DATASOURCE RELATIONS COUNT *** " + organization_datasource.count());
+//        System.out.println("OUTPUT  ***  DATASOURCE COUNT *** " + datasources.count());
+//        System.out.println("OUTPUT  ***  ALLOWED_DATASOURCE-COUNTRY COUNT *** " + alloweddatasources_country.count());
+
+//        alloweddatasources_country.map(p -> new ObjectMapper().writeValueAsString(p))
+//                .saveAsTextFile(outputPath+"/datasource_country");
+
+       JavaRDD<Software> software = sc.textFile(inputPath + "/software")
+                .map(item -> new ObjectMapper().readValue(item, Software.class));
+
+        JavaPairRDD<String, TypedRow> datasource_software = software
+                .map(oaf -> getTypedRowsDatasourceResult(oaf))
+                .flatMapToPair(f -> {
+                    ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
+                    for (TypedRow t : f) {
+                        ret.add(new Tuple2<>(t.getSourceId(), t));
+                    }
+                    return ret.iterator();
+                });
+
+        datasource_software.map(p -> new ObjectMapper().writeValueAsString(p))
+                .saveAsTextFile(outputPath+"/datasource_software");
+
+        JavaPairRDD<String, Result> sfw = software.mapToPair(p -> new Tuple2<>(p.getId(),p));
+
+        JavaPairRDD<String,TypedRow> toupdateresult = alloweddatasources_country.join(datasource_software)
+                .map(u -> {
+                    TypedRow tp = u._2()._2();
+                    tp.setValue(u._2()._1().getValue());
+                    return tp;
+                })
+                .mapToPair(toPair())
+                .reduceByKey((a, p) -> {
+                    if (a == null) {
+                        return p;
+                    }
+                    if (p == null) {
+                        return a;
+                    }
+                    a.addAll(p.getAccumulator());
+                    return a;
+                });
+        toupdateresult.map(p -> new ObjectMapper().writeValueAsString(p))
+                .saveAsTextFile(outputPath+"/toupdateresult");
+        //updateResult(sfw, toupdateresult, outputPath, "software");
+       // createUpdateForResult(toupdateresult, outputPath, "software");
+
+
+
+     /*  JavaRDD<Publication> publications = sc.textFile(inputPath + "/publication")
+                .map(item -> new ObjectMapper().readValue(item, Publication.class));
+
+        JavaPairRDD<String, TypedRow> datasource_publication = publications
+                .map(oaf -> getTypedRowsDatasourceResult(oaf))
+                .flatMapToPair(f -> {
+                    ArrayList<Tuple2<String, TypedRow>> ret = new ArrayList<>();
+                    for (TypedRow t : f) {
+                        ret.add(new Tuple2<>(t.getSourceId(), t));
+                    }
+                    return ret.iterator();
+                });
+
+        JavaPairRDD<String,TypedRow> toupdateresult = alloweddatasources_country.join(datasource_publication)
+                .map(u -> u._2()._2().setValue(u._2()._1().getValue()))
+                .mapToPair(toPair())
+                .reduceByKey((a, p) -> {
+                    if (a == null) {
+                        return p;
+                    }
+                    if (p == null) {
+                        return a;
+                    }
+                    a.addAll(p.getAccumulator());
+                    return a;
+                });
+
+
+
+
+
+
+
 
         JavaRDD<Publication> publications = sc.textFile(inputPath + "/publication")
                 .map(item -> new ObjectMapper().readValue(item, Publication.class));
@@ -75,6 +429,9 @@ public class SparkCountryPropagationJob {
         JavaRDD<OtherResearchProduct> other = sc.textFile(inputPath + "/otherresearchproduct")
                 .map(item -> new ObjectMapper().readValue(item, OtherResearchProduct.class));
 
+
+
+
         JavaPairRDD<String, TypedRow> datasource_results = publications
                 .map(oaf -> getTypedRowsDatasourceResult(oaf))
                 .flatMapToPair(f -> {
@@ -112,18 +469,8 @@ public class SparkCountryPropagationJob {
                             return ret.iterator();
                         }));
 
-        JavaPairRDD<String, Result> pubs = publications.mapToPair(p -> new Tuple2<>(p.getId(),p));
-        JavaPairRDD<String, Result> dss = datasets.mapToPair(p -> new Tuple2<>(p.getId(),p));
-        JavaPairRDD<String, Result> sfw = software.mapToPair(p -> new Tuple2<>(p.getId(),p));
-        JavaPairRDD<String, Result> orp = other.mapToPair(p -> new Tuple2<>(p.getId(),p));
-
-        JavaPairRDD<String, TypedRow> datasource_country = organizations.join(organization_datasource)
-                .map(x -> x._2()._1().setSourceId(x._2()._2().getTargetId())) // (OrganizationId,(TypedRow for Organization, TypedRow for Relation)
-                .mapToPair(toPair()); //(DatasourceId, TypedRowforOrganziation)
 
 
-        JavaPairRDD<String, TypedRow> alloweddatasources_country = datasources.join(datasource_country)
-                .mapToPair(ds -> new Tuple2<>(ds._1(), ds._2()._2()));
 
 
         JavaPairRDD<String,TypedRow> toupdateresult = alloweddatasources_country.join(datasource_results)
@@ -140,15 +487,48 @@ public class SparkCountryPropagationJob {
                     return a;
                 });
 
+
+        JavaPairRDD<String, Result> pubs = publications.mapToPair(p -> new Tuple2<>(p.getId(),p));
+        JavaPairRDD<String, Result> dss = datasets.mapToPair(p -> new Tuple2<>(p.getId(),p));
+        JavaPairRDD<String, Result> sfw = software.mapToPair(p -> new Tuple2<>(p.getId(),p));
+        JavaPairRDD<String, Result> orp = other.mapToPair(p -> new Tuple2<>(p.getId(),p));
+
         updateResult(pubs, toupdateresult, outputPath, "publication");
         updateResult(dss, toupdateresult, outputPath, "dataset");
         updateResult(sfw, toupdateresult, outputPath, "software");
         updateResult(orp, toupdateresult, outputPath, "otherresearchproduct");
         //we use leftOuterJoin because we want to rebuild the entire structure
 
+*/
+
     }
 
 
+    
+    private static void createUpdateForResult(JavaPairRDD<String, TypedRow> toupdateresult, String outputPath, String type){
+        toupdateresult.map(c -> {
+            List<Country> countryList = new ArrayList<>();
+            for (String country : c._2.getAccumulator()) {
+                countryList.add(getCountry(country));
+            }
+            switch(type                ){
+                case  "software":
+                    Software s = new Software();
+                    s.setId(c._1());
+                    s.setCountry(countryList);
+                    return s;
+                case "publication":
+                    break;
+                case "dataset":
+                    break;
+                case "otherresearchproduct":
+                    break;
+
+            }
+            return null;
+        }).map(r ->new ObjectMapper().writeValueAsString(r))
+                .saveAsTextFile(outputPath+"/"+type);
+    }
 
     private static void updateResult(JavaPairRDD<String, Result> results, JavaPairRDD<String, TypedRow> toupdateresult, String outputPath, String type) {
         results.leftOuterJoin(toupdateresult)
@@ -176,13 +556,7 @@ public class SparkCountryPropagationJob {
                 .map(p -> new ObjectMapper().writeValueAsString(p))
                 .saveAsTextFile(outputPath+"/"+type);
     }
-
-
-
-
-
-
-
+    
 
 }