PromoteActionPayloadForGraphTableJob reads directly the content pointed by the input path, adjusted promote action tests (ISLookup mock)

dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java

@@ -29,17 +29,21 @@ public class ISClient implements Serializable {
 
 	private static final String INPUT_ACTION_SET_ID_SEPARATOR = ",";
 
-	public static List<String> getLatestRawsetPaths(String isLookupUrl, String setIds) {
+	private ISLookUpService isLookup;
+
+	public ISClient(String isLookupUrl) {
+		isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl);
+	}
+
+	public List<String> getLatestRawsetPaths(String setIds) {
 
-		ISLookUpService isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl);
-		ISClient isClient = new ISClient();
 		List<String> ids = Lists.newArrayList(Splitter.on(INPUT_ACTION_SET_ID_SEPARATOR)
 				.omitEmptyStrings()
 				.trimResults()
 				.split(setIds));
 
 		return ids.stream()
-				.map(id -> isClient.getSet(isLookup, id))
+				.map(id -> getSet(isLookup, id))
 				.map(as -> as.getPathToLatest())
 				.collect(Collectors.toCollection(ArrayList::new));
 	}

dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java

@@ -41,6 +41,15 @@ public class PartitionActionSetsByPayloadTypeJob {
                     StructField$.MODULE$.apply("payload", DataTypes.StringType, false, Metadata.empty())
             ));
 
+    private ISClient isClient;
+
+    public PartitionActionSetsByPayloadTypeJob(String isLookupUrl) {
+        this.isClient = new ISClient(isLookupUrl);
+    }
+
+    public PartitionActionSetsByPayloadTypeJob() {
+    }
+
     public static void main(String[] args) throws Exception {
         String jsonConfiguration = IOUtils.toString(
                 PromoteActionPayloadForGraphTableJob.class
@@ -63,7 +72,12 @@ public class PartitionActionSetsByPayloadTypeJob {
         String isLookupUrl = parser.get("isLookupUrl");
         logger.info("isLookupUrl: {}", isLookupUrl);
 
-        List<String> inputActionSetPaths = ISClient.getLatestRawsetPaths(isLookupUrl, inputActionSetIds);
+        new PartitionActionSetsByPayloadTypeJob(isLookupUrl).run(isSparkSessionManaged, inputActionSetIds, outputPath);
+    }
+
+    protected void run(Boolean isSparkSessionManaged, String inputActionSetIds, String outputPath) {
+
+        List<String> inputActionSetPaths = getIsClient().getLatestRawsetPaths(inputActionSetIds);
         logger.info("inputActionSetPaths: {}", String.join(",", inputActionSetPaths));
 
         SparkConf conf = new SparkConf();
@@ -95,21 +109,15 @@ public class PartitionActionSetsByPayloadTypeJob {
                                                       String path) {
         logger.info("Reading actions from path: {}", path);
 
-        List<String> files = HdfsSupport.listFiles(path, spark.sparkContext().hadoopConfiguration());
-        logger.info("Found files: {}", String.join(",", files));
-
         JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
-        return files
+
-                .stream()
+        JavaRDD<Row> rdd = sc
-                .map(file -> {
+                .sequenceFile(path, Text.class, Text.class)
-                    JavaRDD<Row> rdd = sc
+                .map(x -> RowFactory.create(x._1().toString(), x._2().toString()));
-                            .sequenceFile(file, Text.class, Text.class)
+
-                            .map(x -> RowFactory.create(x._1().toString(), x._2().toString()));
+        return spark.createDataFrame(rdd, KV_SCHEMA)
-                    return spark.createDataFrame(rdd, KV_SCHEMA)
+                .withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA))
-                            .withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA))
+                .select(expr("atomic_action.*"));
-                            .select(expr("atomic_action.*"));
-                })
-                .reduce(spark.createDataFrame(Collections.emptyList(), ATOMIC_ACTION_SCHEMA), Dataset::union);
     }
 
     private static void saveActions(Dataset<Row> actionDS,
@@ -121,4 +129,12 @@ public class PartitionActionSetsByPayloadTypeJob {
                 .mode(SaveMode.Append)
                 .parquet(path);
     }
+
+    public ISClient getIsClient() {
+        return isClient;
+    }
+
+    public void setIsClient(ISClient isClient) {
+        this.isClient = isClient;
+    }
 }

dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java

@@ -8,6 +8,7 @@ import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
@@ -119,10 +120,17 @@ public class PromoteActionPayloadForGraphTableJob {
                                                              String path,
                                                              Class<G> rowClazz) {
         logger.info("Reading graph table from path: {}", path);
+
+        return spark.read()
+                .textFile(path)
+                .map((MapFunction<String, G>) value -> OBJECT_MAPPER.readValue(value, rowClazz), Encoders.bean(rowClazz));
+
+        /*
         return spark
                 .read()
                 .parquet(path)
                 .as(Encoders.bean(rowClazz));
+         */
     }
 
     private static <A extends Oaf> Dataset<A> readActionPayload(SparkSession spark,

dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJobTest.java

@@ -1,6 +1,8 @@
 package eu.dnetlib.dhp.actionmanager.partition;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.common.collect.Lists;
+import eu.dnetlib.dhp.actionmanager.ISClient;
 import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest;
 import eu.dnetlib.dhp.schema.oaf.*;
 import org.apache.hadoop.conf.Configuration;
@@ -15,7 +17,11 @@ import org.apache.spark.sql.Row;
 import org.apache.spark.sql.SparkSession;
 import org.apache.spark.sql.types.*;
 import org.junit.jupiter.api.*;
+import org.junit.jupiter.api.extension.ExtendWith;
 import org.junit.jupiter.api.io.TempDir;
+import org.mockito.Mock;
+import org.mockito.Mockito;
+import org.mockito.junit.jupiter.MockitoExtension;
 import scala.Tuple2;
 import scala.collection.mutable.Seq;
 
@@ -31,6 +37,7 @@ import static org.apache.spark.sql.functions.*;
 import static org.junit.jupiter.api.Assertions.assertIterableEquals;
 import static scala.collection.JavaConversions.mutableSeqAsJavaList;
 
+@ExtendWith(MockitoExtension.class)
 public class PartitionActionSetsByPayloadTypeJobTest {
     private static final ClassLoader cl = PartitionActionSetsByPayloadTypeJobTest.class.getClassLoader();
 
@@ -64,20 +71,29 @@ public class PartitionActionSetsByPayloadTypeJobTest {
     @Nested
     class Main {
 
+        @Mock
+        private ISClient isClient;
+
         @Test
         public void shouldPartitionActionSetsByPayloadType(@TempDir Path workingDir) throws Exception {
             // given
-            Path inputActionSetsDir = workingDir.resolve("input").resolve("action_sets");
+            Path inputActionSetsBaseDir = workingDir.resolve("input").resolve("action_sets");
             Path outputDir = workingDir.resolve("output");
 
-            Map<String, List<String>> oafsByClassName = createActionSets(inputActionSetsDir);
+            Map<String, List<String>> oafsByClassName = createActionSets(inputActionSetsBaseDir);
+
+            List<String> inputActionSetsPaths = resolveInputActionSetPaths(inputActionSetsBaseDir);
 
             // when
-            PartitionActionSetsByPayloadTypeJob.main(new String[]{
+            Mockito.when(isClient.getLatestRawsetPaths(Mockito.anyString())).thenReturn(inputActionSetsPaths);
-                    "-isSparkSessionManaged", Boolean.FALSE.toString(),
+
-                    "-inputActionSetPaths", inputActionSetsDir.toString(),
+            PartitionActionSetsByPayloadTypeJob job = new PartitionActionSetsByPayloadTypeJob();
-                    "-outputPath", outputDir.toString()
+            job.setIsClient(isClient);
-            });
+            job.run(
+                    Boolean.FALSE,
+                    "", // it can be empty we're mocking the response from isClient to resolve the paths
+                    outputDir.toString()
+            );
 
             // then
             Files.exists(outputDir);
@@ -94,10 +110,19 @@ public class PartitionActionSetsByPayloadTypeJobTest {
         }
     }
 
+    private List<String> resolveInputActionSetPaths(Path inputActionSetsBaseDir) throws IOException {
+        Path inputActionSetJsonDumpsDir = getInputActionSetJsonDumpsDir();
+        return Files
+                .list(inputActionSetJsonDumpsDir)
+                .map(path -> {
+                    String inputActionSetId = path.getFileName().toString();
+                    return inputActionSetsBaseDir.resolve(inputActionSetId).toString();
+                })
+                .collect(Collectors.toCollection(ArrayList::new));
+    }
+
     private static Map<String, List<String>> createActionSets(Path inputActionSetsDir) throws IOException {
-        Path inputActionSetJsonDumpsDir = Paths
+        Path inputActionSetJsonDumpsDir = getInputActionSetJsonDumpsDir();
-                .get(Objects.requireNonNull(cl.getResource("eu/dnetlib/dhp/actionmanager/partition/input/"))
-                        .getFile());
 
         Map<String, List<String>> oafsByType = new HashMap<>();
         Files
@@ -138,6 +163,12 @@ public class PartitionActionSetsByPayloadTypeJobTest {
         return oafsByType;
     }
 
+    private static Path getInputActionSetJsonDumpsDir() {
+        return Paths
+                .get(Objects.requireNonNull(cl.getResource("eu/dnetlib/dhp/actionmanager/partition/input/"))
+                        .getFile());
+    }
+
     private static Dataset<String> readActionsFromJsonDump(String path) {
         return spark
                 .read()