generateNotificationsJob and indexNotificationsJob

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateNotificationsJob.java

@@ -0,0 +1,184 @@
+
+package eu.dnetlib.dhp.broker.oa;
+
+import java.util.Date;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+import org.apache.commons.codec.digest.DigestUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FlatMapFunction;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoder;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SparkSession;
+import org.apache.spark.util.LongAccumulator;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.broker.model.ConditionParams;
+import eu.dnetlib.dhp.broker.model.Event;
+import eu.dnetlib.dhp.broker.model.MappedFields;
+import eu.dnetlib.dhp.broker.model.Notification;
+import eu.dnetlib.dhp.broker.model.Subscription;
+import eu.dnetlib.dhp.broker.oa.util.ClusterUtils;
+import eu.dnetlib.dhp.broker.oa.util.NotificationGroup;
+import eu.dnetlib.dhp.broker.oa.util.SubscriptionUtils;
+
+public class GenerateNotificationsJob {
+
+	private static final Logger log = LoggerFactory.getLogger(GenerateNotificationsJob.class);
+
+	public static void main(final String[] args) throws Exception {
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(GenerateNotificationsJob.class
+					.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/generate_notifications.json")));
+		parser.parseArgument(args);
+
+		final SparkConf conf = new SparkConf();
+
+		final String eventsPath = parser.get("outputDir") + "/events";
+		log.info("eventsPath: {}", eventsPath);
+
+		final String notificationsPath = parser.get("outputDir") + "/notifications";
+		log.info("notificationsPath: {}", notificationsPath);
+
+		final String brokerApiBaseUrl = parser.get("brokerApiBaseUrl");
+		log.info("brokerApiBaseUrl: {}", brokerApiBaseUrl);
+
+		final SparkSession spark = SparkSession.builder().config(conf).getOrCreate();
+
+		final LongAccumulator total = spark.sparkContext().longAccumulator("total_notifications");
+
+		final long startTime = new Date().getTime();
+
+		final List<Subscription> subscriptions = listSubscriptions(brokerApiBaseUrl);
+
+		log.info("Number of subscriptions: " + subscriptions.size());
+
+		if (subscriptions.size() > 0) {
+			final Map<String, Map<String, List<ConditionParams>>> conditionsMap = prepareConditionsMap(subscriptions);
+
+			log.info("ConditionsMap: " + new ObjectMapper().writeValueAsString(conditionsMap));
+
+			final Encoder<NotificationGroup> ngEncoder = Encoders.bean(NotificationGroup.class);
+			final Encoder<Notification> nEncoder = Encoders.bean(Notification.class);
+			final Dataset<Notification> notifications = ClusterUtils
+				.readPath(spark, eventsPath, Event.class)
+				.map((MapFunction<Event, NotificationGroup>) e -> generateNotifications(e, subscriptions, conditionsMap, startTime), ngEncoder)
+				.flatMap((FlatMapFunction<NotificationGroup, Notification>) g -> g.getData().iterator(), nEncoder);
+
+			ClusterUtils.save(notifications, notificationsPath, Notification.class, total);
+		}
+	}
+
+	protected static Map<String, Map<String, List<ConditionParams>>> prepareConditionsMap(
+		final List<Subscription> subscriptions) {
+		final Map<String, Map<String, List<ConditionParams>>> map = new HashMap<>();
+		subscriptions.forEach(s -> map.put(s.getSubscriptionId(), s.conditionsAsMap()));
+		return map;
+	}
+
+	protected static NotificationGroup generateNotifications(final Event e,
+		final List<Subscription> subscriptions,
+		final Map<String, Map<String, List<ConditionParams>>> conditionsMap,
+		final long date) {
+		final List<Notification> list = subscriptions
+			.stream()
+			.filter(s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic()))
+			.filter(s -> verifyConditions(e.getMap(), conditionsMap.get(s.getSubscriptionId())))
+			.map(s -> generateNotification(s, e, date))
+			.collect(Collectors.toList());
+
+		return new NotificationGroup(list);
+	}
+
+	private static Notification generateNotification(final Subscription s, final Event e, final long date) {
+		final Notification n = new Notification();
+		n.setNotificationId("ntf-" + DigestUtils.md5Hex(s.getSubscriptionId() + "@@@" + e.getEventId()));
+		n.setSubscriptionId(s.getSubscriptionId());
+		n.setEventId(e.getEventId());
+		n.setProducerId(e.getProducerId());
+		n.setTopic(e.getTopic());
+		n.setPayload(e.getPayload());
+		n.setMap(e.getMap());
+		n.setDate(date);
+		return n;
+	}
+
+	private static boolean verifyConditions(final MappedFields map,
+		final Map<String, List<ConditionParams>> conditions) {
+		if (conditions.containsKey("targetDatasourceName")
+			&& !SubscriptionUtils
+				.verifyExact(map.getTargetDatasourceName(), conditions.get("targetDatasourceName").get(0).getValue())) {
+			return false;
+		}
+
+		if (conditions.containsKey("trust")
+			&& !SubscriptionUtils
+				.verifyFloatRange(map.getTrust(), conditions.get("trust").get(0).getValue(), conditions.get("trust").get(0).getOtherValue())) {
+			return false;
+		}
+
+		if (conditions.containsKey("targetDateofacceptance") && !conditions
+			.get("targetDateofacceptance")
+			.stream()
+			.anyMatch(c -> SubscriptionUtils
+				.verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) {
+			return false;
+		}
+
+		if (conditions.containsKey("targetResultTitle")
+			&& !conditions
+				.get("targetResultTitle")
+				.stream()
+				.anyMatch(c -> SubscriptionUtils.verifySimilar(map.getTargetResultTitle(), c.getValue()))) {
+			return false;
+		}
+
+		if (conditions.containsKey("targetAuthors")
+			&& !conditions
+				.get("targetAuthors")
+				.stream()
+				.allMatch(c -> SubscriptionUtils.verifyListSimilar(map.getTargetAuthors(), c.getValue()))) {
+			return false;
+		}
+
+		return !conditions.containsKey("targetSubjects")
+			|| conditions
+				.get("targetSubjects")
+				.stream()
+				.allMatch(c -> SubscriptionUtils.verifyListExact(map.getTargetSubjects(), c.getValue()));
+
+	}
+
+	private static List<Subscription> listSubscriptions(final String brokerApiBaseUrl) throws Exception {
+		final String url = brokerApiBaseUrl + "/api/subscriptions";
+		final HttpGet req = new HttpGet(url);
+
+		final ObjectMapper mapper = new ObjectMapper();
+
+		try (final CloseableHttpClient client = HttpClients.createDefault()) {
+			try (final CloseableHttpResponse response = client.execute(req)) {
+				final String s = IOUtils.toString(response.getEntity().getContent());
+				return mapper
+					.readValue(s, mapper.getTypeFactory().constructCollectionType(List.class, Subscription.class));
+			}
+		}
+	}
+
+}

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java

@@ -2,28 +2,22 @@
 package eu.dnetlib.dhp.broker.oa;
 
 import java.io.IOException;
-import java.util.Date;
 import java.util.HashMap;
-import java.util.List;
 import java.util.Map;
-import java.util.stream.Collectors;
 
-import org.apache.commons.codec.digest.DigestUtils;
 import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
 import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpDelete;
 import org.apache.http.client.methods.HttpGet;
 import org.apache.http.impl.client.CloseableHttpClient;
 import org.apache.http.impl.client.HttpClients;
 import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.function.FlatMapFunction;
+import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.sql.Dataset;
-import org.apache.spark.sql.Encoder;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SparkSession;
 import org.apache.spark.util.LongAccumulator;
+import org.elasticsearch.spark.rdd.api.java.JavaEsSpark;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -31,14 +25,8 @@ import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.broker.model.ConditionParams;
-import eu.dnetlib.dhp.broker.model.Event;
-import eu.dnetlib.dhp.broker.model.MappedFields;
 import eu.dnetlib.dhp.broker.model.Notification;
-import eu.dnetlib.dhp.broker.model.Subscription;
 import eu.dnetlib.dhp.broker.oa.util.ClusterUtils;
-import eu.dnetlib.dhp.broker.oa.util.NotificationGroup;
-import eu.dnetlib.dhp.broker.oa.util.SubscriptionUtils;
 
 public class IndexNotificationsJob {
 
@@ -48,15 +36,14 @@ public class IndexNotificationsJob {
 
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			IOUtils
-				.toString(
-					IndexNotificationsJob.class
-						.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json")));
+				.toString(IndexNotificationsJob.class
+					.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json")));
 		parser.parseArgument(args);
 
 		final SparkConf conf = new SparkConf();
 
-		final String eventsPath = parser.get("outputDir") + "/events";
-		log.info("eventsPath: {}", eventsPath);
+		final String notificationsPath = parser.get("outputDir") + "/notifications";
+		log.info("notificationsPath: {}", notificationsPath);
 
 		final String index = parser.get("index");
 		log.info("index: {}", index);
@@ -83,131 +70,38 @@ public class IndexNotificationsJob {
 
 		final LongAccumulator total = spark.sparkContext().longAccumulator("total_indexed");
 
-		final long startTime = new Date().getTime();
+		final Long date = ClusterUtils
+			.readPath(spark, notificationsPath, Notification.class)
+			.first()
+			.getDate();
 
-		final List<Subscription> subscriptions = listSubscriptions(brokerApiBaseUrl);
+		final JavaRDD<String> toIndexRdd = ClusterUtils
+			.readPath(spark, notificationsPath, Notification.class)
+			.map((MapFunction<Notification, String>) n -> prepareForIndexing(n, total), Encoders.STRING())
+			.javaRDD();
 
-		log.info("Number of subscriptions: " + subscriptions.size());
+		final Map<String, String> esCfg = new HashMap<>();
 
-		if (subscriptions.size() > 0) {
-			final Map<String, Map<String, List<ConditionParams>>> conditionsMap = prepareConditionsMap(subscriptions);
+		esCfg.put("es.index.auto.create", "false");
+		esCfg.put("es.nodes", indexHost);
+		esCfg.put("es.mapping.id", "notificationId"); // THE PRIMARY KEY
+		esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount);
+		esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait);
+		esCfg.put("es.batch.size.entries", esBatchSizeEntries);
+		esCfg.put("es.nodes.wan.only", esNodesWanOnly);
 
-			log.info("ConditionsMap: " + new ObjectMapper().writeValueAsString(conditionsMap));
+		log.info("*** Start indexing");
+		JavaEsSpark.saveJsonToEs(toIndexRdd, index, esCfg);
+		log.info("*** End indexing");
 
-			final Encoder<NotificationGroup> ngEncoder = Encoders.bean(NotificationGroup.class);
-			final Encoder<Notification> nEncoder = Encoders.bean(Notification.class);
-			final Dataset<Notification> notifications = ClusterUtils
-				.readPath(spark, eventsPath, Event.class)
-				.map(
-					(MapFunction<Event, NotificationGroup>) e -> generateNotifications(
-						e, subscriptions, conditionsMap, startTime),
-					ngEncoder)
-				.flatMap((FlatMapFunction<NotificationGroup, Notification>) g -> g.getData().iterator(), nEncoder);
+		log.info("*** Deleting old notifications");
+		final String message = deleteOldNotifications(brokerApiBaseUrl, date - 1000);
+		log.info("*** Deleted notifications: {}", message);
 
-			notifications
-				.map((MapFunction<Notification, String>) n -> prepareForIndexing(n, total), Encoders.STRING())
-				.javaRDD()
-				.saveAsTextFile("/tmp/IndexNotificationsJob_test_6504");
-		}
-	}
+		log.info("*** sendNotifications (emails, ...)");
+		sendNotifications(brokerApiBaseUrl, date - 1000);
+		log.info("*** ALL done.");
 
-	protected static Map<String, Map<String, List<ConditionParams>>> prepareConditionsMap(
-		final List<Subscription> subscriptions) {
-		final Map<String, Map<String, List<ConditionParams>>> map = new HashMap<>();
-		subscriptions.forEach(s -> map.put(s.getSubscriptionId(), s.conditionsAsMap()));
-		return map;
-	}
-
-	protected static NotificationGroup generateNotifications(final Event e,
-		final List<Subscription> subscriptions,
-		final Map<String, Map<String, List<ConditionParams>>> conditionsMap,
-		final long date) {
-		final List<Notification> list = subscriptions
-			.stream()
-			.filter(
-				s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic()))
-			.filter(s -> verifyConditions(e.getMap(), conditionsMap.get(s.getSubscriptionId())))
-			.map(s -> generateNotification(s, e, date))
-			.collect(Collectors.toList());
-
-		return new NotificationGroup(list);
-	}
-
-	private static Notification generateNotification(final Subscription s, final Event e, final long date) {
-		final Notification n = new Notification();
-		n.setNotificationId("ntf-" + DigestUtils.md5Hex(s.getSubscriptionId() + "@@@" + e.getEventId()));
-		n.setSubscriptionId(s.getSubscriptionId());
-		n.setEventId(e.getEventId());
-		n.setProducerId(e.getProducerId());
-		n.setTopic(e.getTopic());
-		n.setPayload(e.getPayload());
-		n.setMap(e.getMap());
-		n.setDate(date);
-		return n;
-	}
-
-	private static boolean verifyConditions(final MappedFields map,
-		final Map<String, List<ConditionParams>> conditions) {
-		if (conditions.containsKey("targetDatasourceName")
-			&& !SubscriptionUtils
-				.verifyExact(map.getTargetDatasourceName(), conditions.get("targetDatasourceName").get(0).getValue())) {
-			return false;
-		}
-
-		if (conditions.containsKey("trust")
-			&& !SubscriptionUtils
-				.verifyFloatRange(
-					map.getTrust(), conditions.get("trust").get(0).getValue(),
-					conditions.get("trust").get(0).getOtherValue())) {
-			return false;
-		}
-
-		if (conditions.containsKey("targetDateofacceptance") && !conditions
-			.get("targetDateofacceptance")
-			.stream()
-			.anyMatch(
-				c -> SubscriptionUtils
-					.verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) {
-			return false;
-		}
-
-		if (conditions.containsKey("targetResultTitle")
-			&& !conditions
-				.get("targetResultTitle")
-				.stream()
-				.anyMatch(c -> SubscriptionUtils.verifySimilar(map.getTargetResultTitle(), c.getValue()))) {
-			return false;
-		}
-
-		if (conditions.containsKey("targetAuthors")
-			&& !conditions
-				.get("targetAuthors")
-				.stream()
-				.allMatch(c -> SubscriptionUtils.verifyListSimilar(map.getTargetAuthors(), c.getValue()))) {
-			return false;
-		}
-
-		return !conditions.containsKey("targetSubjects")
-			|| conditions
-				.get("targetSubjects")
-				.stream()
-				.allMatch(c -> SubscriptionUtils.verifyListExact(map.getTargetSubjects(), c.getValue()));
-
-	}
-
-	private static List<Subscription> listSubscriptions(final String brokerApiBaseUrl) throws Exception {
-		final String url = brokerApiBaseUrl + "/api/subscriptions";
-		final HttpGet req = new HttpGet(url);
-
-		final ObjectMapper mapper = new ObjectMapper();
-
-		try (final CloseableHttpClient client = HttpClients.createDefault()) {
-			try (final CloseableHttpResponse response = client.execute(req)) {
-				final String s = IOUtils.toString(response.getEntity().getContent());
-				return mapper
-					.readValue(s, mapper.getTypeFactory().constructCollectionType(List.class, Subscription.class));
-			}
-		}
 	}
 
 	private static String deleteOldNotifications(final String brokerApiBaseUrl, final long l) throws Exception {

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml

@@ -542,6 +542,30 @@
             <arg>--dbPassword</arg><arg>${brokerDbPassword}</arg>
             <arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
         </spark>
+        <ok to="generate_notifications"/>
+        <error to="Kill"/>
+    </action>
+    
+    <action name="generate_notifications">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>GenerateNotificationsJob</name>
+            <class>eu.dnetlib.dhp.broker.oa.GenerateNotificationsJob</class>
+            <jar>dhp-broker-events-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCores}
+                --executor-memory=${sparkExecutorMemory}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=3840
+            </spark-opts>
+            <arg>--outputDir</arg><arg>${outputDir}</arg>
+            <arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
+        </spark>
         <ok to="index_notifications"/>
         <error to="Kill"/>
     </action>

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_notifications.json

@@ -0,0 +1,14 @@
+[
+	{
+		"paramName": "o",
+		"paramLongName": "outputDir",
+		"paramDescription": "the dir that contains the events folder",
+		"paramRequired": true
+	},
+	{
+		"paramName": "broker",
+		"paramLongName": "brokerApiBaseUrl",
+		"paramDescription": "the url of the broker service api",
+		"paramRequired": true
+	}
+]

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml

@@ -119,12 +119,36 @@
         </configuration>
     </global>
 
-    <start to="index_notifications"/>
+    <start to="generate_notifications"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
     
+     <action name="generate_notifications">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>GenerateNotificationsJob</name>
+            <class>eu.dnetlib.dhp.broker.oa.GenerateNotificationsJob</class>
+            <jar>dhp-broker-events-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCores}
+                --executor-memory=${sparkExecutorMemory}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=3840
+            </spark-opts>
+            <arg>--outputDir</arg><arg>${outputDir}</arg>
+            <arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
+        </spark>
+        <ok to="index_notifications"/>
+        <error to="Kill"/>
+    </action>
+    
     <action name="index_notifications">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
@@ -135,6 +159,7 @@
             <spark-opts>
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.dynamicAllocation.maxExecutors="8" 
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}