first phase of data preparation. For each result type (parallel) it produces the possible updates

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

@@ -10,19 +10,19 @@ 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 java.util.Optional;
 
 import static eu.dnetlib.dhp.PropagationConstant.*;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
 
-public class PrepareResultOrcidAssociation {
+public class PrepareResultOrcidAssociationStep1 {
-    private static final Logger log = LoggerFactory.getLogger(PrepareResultOrcidAssociation.class);
+    private static final Logger log = LoggerFactory.getLogger(PrepareResultOrcidAssociationStep1.class);
 
     private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
@@ -64,13 +64,14 @@ public class PrepareResultOrcidAssociation {
                     if (isTest(parser)) {
                         removeOutputDir(spark, outputPath);
                     }
-                    prepareInfo(spark,  inputPath, outputPath, resultClazz, resultType);
+                    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) {
+                                                       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());
@@ -81,8 +82,38 @@ public class PrepareResultOrcidAssociation {
         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)
+        ;
+    }
+
+
 }