[aggregator graph] save invalid records aside for further inspection

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java

@@ -79,9 +79,6 @@ public class GenerateEntitiesApplication {
 		final String targetPath = parser.get("targetPath");
 		log.info("targetPath: {}", targetPath);
 
-		final String invalidPath = parser.get("invalidPath");
-		log.info("invalidPath: {}", invalidPath);
-
 		final String isLookupUrl = parser.get("isLookupUrl");
 		log.info("isLookupUrl: {}", isLookupUrl);
 
@@ -103,8 +100,7 @@ public class GenerateEntitiesApplication {
 		final SparkConf conf = new SparkConf();
 		runWithSparkSession(conf, isSparkSessionManaged, spark -> {
 			HdfsSupport.remove(targetPath, spark.sparkContext().hadoopConfiguration());
-			HdfsSupport.remove(invalidPath, spark.sparkContext().hadoopConfiguration());
-			generateEntities(spark, vocs, sourcePaths, targetPath, invalidPath, shouldHashId, mode);
+			generateEntities(spark, vocs, sourcePaths, targetPath, shouldHashId, mode);
 		});
 	}
 
@@ -113,7 +109,6 @@ public class GenerateEntitiesApplication {
 		final VocabularyGroup vocs,
 		final String sourcePaths,
 		final String targetPath,
-		final String invalidPath,
 		final boolean shouldHashId,
 		final Mode mode) {
 
@@ -126,21 +121,6 @@ public class GenerateEntitiesApplication {
 		log.info("Generate entities from files:");
 		existingSourcePaths.forEach(log::info);
 
-		for (final String sp : existingSourcePaths) {
-			RDD<String> invalidRecords = sc
-				.sequenceFile(sp, Text.class, Text.class)
-				.map(k -> new Tuple2<>(k._1().toString(), k._2().toString()))
-				.map(k -> tryApplyMapping(k._1(), k._2(), shouldHashId, vocs))
-				.filter(Objects::nonNull)
-				.rdd();
-			spark
-				.createDataset(invalidRecords, Encoders.STRING())
-				.write()
-				.mode(SaveMode.Append)
-				.option("compression", "gzip")
-				.text(invalidPath);
-		}
-
 		JavaRDD<Oaf> inputRdd = sc.emptyRDD();
 
 		for (final String sp : existingSourcePaths) {
@@ -178,7 +158,7 @@ public class GenerateEntitiesApplication {
 			.saveAsTextFile(targetPath, GzipCodec.class);
 	}
 
-	private static List<Oaf> convertToListOaf(
+	public static List<Oaf> convertToListOaf(
 		final String id,
 		final String s,
 		final boolean shouldHashId,
@@ -219,19 +199,6 @@ public class GenerateEntitiesApplication {
 		}
 	}
 
-	private static String tryApplyMapping(
-		final String id,
-		final String s,
-		final boolean shouldHashId,
-		final VocabularyGroup vocs) {
-
-		final List<Oaf> oaf = convertToListOaf(id, s, shouldHashId, vocs);
-		if (Optional.ofNullable(oaf).map(List::isEmpty).orElse(false)) {
-			return s;
-		}
-		return null;
-	}
-
 	private static Oaf convertFromJson(final String s, final Class<? extends Oaf> clazz) {
 		try {
 			return OBJECT_MAPPER.readValue(s, clazz);

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/VerifyRecordsApplication.java

@@ -0,0 +1,108 @@
+
+package eu.dnetlib.dhp.oa.graph.raw;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.stream.Collectors;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.rdd.RDD;
+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 eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.utils.ISLookupClientFactory;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+import scala.Tuple2;
+
+public class VerifyRecordsApplication {
+
+	private static final Logger log = LoggerFactory.getLogger(VerifyRecordsApplication.class);
+
+	public static void main(final String[] args) throws Exception {
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					VerifyRecordsApplication.class
+						.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/verify_records_parameters.json")));
+
+		parser.parseArgument(args);
+
+		final Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		final String sourcePaths = parser.get("sourcePaths");
+		log.info("sourcePaths: {}", sourcePaths);
+
+		final String invalidPath = parser.get("invalidPath");
+		log.info("invalidPath: {}", invalidPath);
+
+		final String isLookupUrl = parser.get("isLookupUrl");
+		log.info("isLookupUrl: {}", isLookupUrl);
+
+		final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl);
+		final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService);
+
+		final SparkConf conf = new SparkConf();
+		runWithSparkSession(conf, isSparkSessionManaged, spark -> {
+			HdfsSupport.remove(invalidPath, spark.sparkContext().hadoopConfiguration());
+			validateRecords(spark, sourcePaths, invalidPath, vocs);
+		});
+	}
+
+	private static void validateRecords(SparkSession spark, String sourcePaths, String invalidPath,
+		VocabularyGroup vocs) {
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+		final List<String> existingSourcePaths = Arrays
+			.stream(sourcePaths.split(","))
+			.filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration()))
+			.collect(Collectors.toList());
+
+		log.info("Verify records in files:");
+		existingSourcePaths.forEach(log::info);
+
+		for (final String sp : existingSourcePaths) {
+			RDD<String> invalidRecords = sc
+				.sequenceFile(sp, Text.class, Text.class)
+				.map(k -> tryApplyMapping(k._1().toString(), k._2().toString(), true, vocs))
+				.filter(Objects::nonNull)
+				.rdd();
+			spark
+				.createDataset(invalidRecords, Encoders.STRING())
+				.write()
+				.mode(SaveMode.Append)
+				.option("compression", "gzip")
+				.text(invalidPath);
+		}
+	}
+
+	private static String tryApplyMapping(
+		final String id,
+		final String xmlRecord,
+		final boolean shouldHashId,
+		final VocabularyGroup vocs) {
+
+		final List<Oaf> oaf = GenerateEntitiesApplication.convertToListOaf(id, xmlRecord, shouldHashId, vocs);
+		if (Optional.ofNullable(oaf).map(List::isEmpty).orElse(false)) {
+			return xmlRecord;
+		}
+		return null;
+	}
+}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java

@@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.graph.raw.common;
 import java.io.Closeable;
 import java.io.IOException;
 import java.util.Arrays;
+import java.util.List;
 import java.util.Set;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Collectors;
@@ -24,8 +25,11 @@ import org.apache.http.impl.client.HttpClients;
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
+import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
+import eu.dnetlib.dhp.oa.graph.raw.OafToOafMapper;
+import eu.dnetlib.dhp.oa.graph.raw.OdfToOafMapper;
 import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo;
-import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.utils.DHPUtils;
 
 public class AbstractMigrationApplication implements Closeable {

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json

@@ -17,12 +17,6 @@
 		"paramDescription": "the path of the target file",
 		"paramRequired": true
 	},
-	{
-		"paramName": "i",
-		"paramLongName": "invalidPath",
-		"paramDescription": "the path of the invalid records file",
-		"paramRequired": false
-	},
 	{
 		"paramName": "isu",
 		"paramLongName": "isLookupUrl",

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml

@@ -446,10 +446,34 @@
     <join name="wait_import" to="fork_generate_entities"/>
 
     <fork name="fork_generate_entities">
-        <path start="GenerateEntities_claim"/>
-        <path start="GenerateEntities"/>
+        <path start="VerifyRecords_claim"/>
+        <path start="VerifyRecords"/>
     </fork>
 
+    <action name="VerifyRecords_claim">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>VerifyRecords_claim</name>
+            <class>eu.dnetlib.dhp.oa.graph.raw.VerifyRecordsApplication</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --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}${spark2EventLogDir}
+            </spark-opts>
+            <arg>--sourcePaths</arg><arg>${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims</arg>
+            <arg>--invalidPath</arg><arg>${workingDir}/invalid_records_claim</arg>
+            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+        </spark>
+        <ok to="GenerateEntities_claim"/>
+        <error to="Kill"/>
+    </action>
+
     <action name="GenerateEntities_claim">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
@@ -468,7 +492,6 @@
             </spark-opts>
             <arg>--sourcePaths</arg><arg>${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims</arg>
             <arg>--targetPath</arg><arg>${workingDir}/entities_claim</arg>
-            <arg>--invalidPath</arg><arg>${workingDir}/invalid_records_claim</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
             <arg>--shouldHashId</arg><arg>${shouldHashId}</arg>
             <arg>--mode</arg><arg>claim</arg>
@@ -500,6 +523,30 @@
         <error to="Kill"/>
     </action>
 
+    <action name="VerifyRecords">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>VerifyRecords</name>
+            <class>eu.dnetlib.dhp.oa.graph.raw.VerifyRecordsApplication</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --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}${spark2EventLogDir}
+            </spark-opts>
+            <arg>--sourcePaths</arg><arg>${contentPath}/db_openaire,${contentPath}/db_openorgs,${contentPath}/oaf_records,${contentPath}/odf_records,${contentPath}/oaf_records_hdfs,${contentPath}/odf_records_hdfs,${contentPath}/oaf_records_invisible</arg>
+            <arg>--invalidPath</arg><arg>${workingDir}/invalid_records</arg>
+            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+        </spark>
+        <ok to="GenerateEntities"/>
+        <error to="Kill"/>
+    </action>
+
     <action name="GenerateEntities">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
@@ -518,7 +565,6 @@
             </spark-opts>
             <arg>--sourcePaths</arg><arg>${contentPath}/db_openaire,${contentPath}/db_openorgs,${contentPath}/oaf_records,${contentPath}/odf_records,${contentPath}/oaf_records_hdfs,${contentPath}/odf_records_hdfs,${contentPath}/oaf_records_invisible</arg>
             <arg>--targetPath</arg><arg>${workingDir}/entities</arg>
-            <arg>--invalidPath</arg><arg>${workingDir}/invalid_records</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
             <arg>--shouldHashId</arg><arg>${shouldHashId}</arg>
         </spark>

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/verify_records_parameters.json

@@ -0,0 +1,26 @@
+[
+	{
+		"paramName": "issm",
+		"paramLongName": "isSparkSessionManaged",
+		"paramDescription": "when true will stop SparkSession after job execution",
+		"paramRequired": false
+	},
+	{
+		"paramName": "s",
+		"paramLongName": "sourcePaths",
+		"paramDescription": "the HDFS source paths which contains the sequential file (comma separated)",
+		"paramRequired": true
+	},
+	{
+		"paramName": "i",
+		"paramLongName": "invalidPath",
+		"paramDescription": "the path of the invalid records file",
+		"paramRequired": false
+	},
+	{
+		"paramName": "isu",
+		"paramLongName": "isLookupUrl",
+		"paramDescription": "the url of the ISLookupService",
+		"paramRequired": true
+	}
+]