seconf phase of data preparation. Groups all the possible updates by id

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

@@ -1,34 +1,27 @@
 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.hadoop.io.compress.GzipCodec;
 import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.*;
-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 scala.Tuple2;
-import java.util.Arrays;
+import java.util.HashSet;
-import java.util.List;
+import java.util.Set;
-
 import static eu.dnetlib.dhp.PropagationConstant.*;
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
-public class PrepareResultOrcidAssociationStep1 {
+public class PrepareResultOrcidAssociationStep2 {
-    private static final Logger log = LoggerFactory.getLogger(PrepareResultOrcidAssociationStep1.class);
+    private static final Logger log = LoggerFactory.getLogger(PrepareResultOrcidAssociationStep2.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"));
+                .getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult2_parameters.json"));
 
         final ArgumentApplicationParser parser = new ArgumentApplicationParser(
                 jsonConfiguration);
@@ -44,76 +37,55 @@ public class PrepareResultOrcidAssociationStep1 {
         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,
+        runWithSparkSession(conf, isSparkSessionManaged,
                 spark -> {
                     if (isTest(parser)) {
                         removeOutputDir(spark, outputPath);
                     }
-                    prepareInfo(spark,  inputPath, outputPath, resultClazz, resultType, allowedsemrel);
+                    mergeInfo(spark,  inputPath, outputPath);
                 });
     }
 
-    private static <R extends Result> void prepareInfo(SparkSession spark,  String inputPath,
+    private static void mergeInfo(SparkSession spark, String inputPath, String outputPath) {
-                                                       String outputPath, Class<R> resultClazz,
-                                                       String resultType,
-                                                       List<String> allowedsemrel) {
 
-        //read the relation table and the table related to the result it is using
+        Dataset<ResultOrcidList> resultOrcidAssoc = readAssocResultOrcidList(spark, inputPath);
-        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);
+        resultOrcidAssoc
-        Dataset<R> result = readPathEntity(spark, inputPath + "/" + resultType, resultClazz);
+                .toJavaRDD()
-
+                .mapToPair(r -> new Tuple2<>(r.getResultId(), r))
-        result.createOrReplaceTempView("result");
+                .reduceByKey((a, b) -> {
-
+                    if (a == null) {
-        getPossibleResultOrcidAssociation(spark, allowedsemrel, outputPath);
+                        return b;
+                    }
+                    if (b == null) {
+                        return a;
+                    }
+                    Set<String> orcid_set = new HashSet<>();
+                    a.getAuthorList().stream().forEach(aa -> orcid_set.add(aa.getOrcid()));
 
+                    b.getAuthorList().stream().forEach(aa -> {
+                        if (!orcid_set.contains(aa.getOrcid())) {
+                            a.getAuthorList().add(aa);
+                            orcid_set.add(aa.getOrcid());
+                        }
+                    });
+                    return a;
+                })
+                .map(c -> c._2())
+                .map(r -> OBJECT_MAPPER.writeValueAsString(r))
+                .saveAsTextFile(outputPath, GzipCodec.class);
     }
 
-    private static void getPossibleResultOrcidAssociation(SparkSession spark, List<String> allowedsemrel, String outputPath){
+    private static Dataset<ResultOrcidList> readAssocResultOrcidList(SparkSession spark, String relationPath) {
-        String query = " select target resultId, author authorList" +
+        return spark
-                " from (select id, collect_set(named_struct('name', name, 'surname', surname, 'fullname', fullname, 'orcid', orcid)) author " +
+                .read()
-                " from ( " +
+                .textFile(relationPath)
-                " select id, MyT.fullname, MyT.name, MyT.surname, MyP.value orcid " +
+                .map(value -> OBJECT_MAPPER.readValue(value, ResultOrcidList.class), Encoders.bean(ResultOrcidList.class));
-                " 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)
-        ;
     }
 
 
+
+
 }