Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop

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

@@ -3,11 +3,16 @@ package eu.dnetlib.dhp.broker.oa;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
+import java.io.IOException;
 import java.util.Optional;
+import java.util.Properties;
 
 import org.apache.commons.io.IOUtils;
+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.sql.Dataset;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.TypedColumn;
 import org.slf4j.Logger;
@@ -29,7 +34,7 @@ public class GenerateStatsJob {
 			IOUtils
 				.toString(
 					GenerateStatsJob.class
-						.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json")));
+						.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/stats_params.json")));
 		parser.parseArgument(args);
 
 		final Boolean isSparkSessionManaged = Optional
@@ -43,21 +48,50 @@ public class GenerateStatsJob {
 		final String eventsPath = parser.get("workingPath") + "/events";
 		log.info("eventsPath: {}", eventsPath);
 
-		final String statsPath = parser.get("workingPath") + "/stats";
+		final String dbUrl = parser.get("dbUrl");
-		log.info("stats: {}", statsPath);
+		log.info("dbUrl: {}", dbUrl);
+
+		final String dbUser = parser.get("dbUser");
+		log.info("dbUser: {}", dbUser);
+
+		final String dbPassword = parser.get("dbPassword");
+		log.info("dbPassword: {}", "***");
+
+		final String brokerApiBaseUrl = parser.get("brokerApiBaseUrl");
+		log.info("brokerApiBaseUrl: {}", brokerApiBaseUrl);
 
 		final TypedColumn<Event, DatasourceStats> aggr = new StatsAggregator().toColumn();
 
+		final Properties connectionProperties = new Properties();
+		connectionProperties.put("user", dbUser);
+		connectionProperties.put("password", dbPassword);
+
 		runWithSparkSession(conf, isSparkSessionManaged, spark -> {
 
-			final Dataset<DatasourceStats> stats = ClusterUtils
+			ClusterUtils
 				.readPath(spark, eventsPath, Event.class)
-				.groupByKey(e -> e.getMap().getTargetDatasourceId(), Encoders.STRING())
+				.groupByKey(e -> e.getTopic() + "@@@" + e.getMap().getTargetDatasourceId(), Encoders.STRING())
 				.agg(aggr)
-				.map(t -> t._2, Encoders.bean(DatasourceStats.class));
+				.map(t -> t._2, Encoders.bean(DatasourceStats.class))
+				.write()
+				.jdbc(dbUrl, "oa_datasource_stats_temp", connectionProperties);
+
+			log.info("*** updateStats");
+			updateStats(brokerApiBaseUrl);
+			log.info("*** ALL done.");
 
-			ClusterUtils.save(stats, statsPath, DatasourceStats.class, null);
 		});
 	}
 
+	private static String updateStats(final String brokerApiBaseUrl) throws IOException {
+		final String url = brokerApiBaseUrl + "/api/openaireBroker/stats/update";
+		final HttpGet req = new HttpGet(url);
+
+		try (final CloseableHttpClient client = HttpClients.createDefault()) {
+			try (final CloseableHttpResponse response = client.execute(req)) {
+				return IOUtils.toString(response.getEntity().getContent());
+			}
+		}
+	}
+
 }

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

@@ -0,0 +1,113 @@
+
+package eu.dnetlib.dhp.broker.oa;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.io.IOException;
+import java.util.Optional;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileStatus;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.spark.SparkConf;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SaveMode;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.google.gson.Gson;
+
+import eu.dnetlib.broker.api.ShortEventMessage;
+import eu.dnetlib.broker.objects.OaBrokerEventPayload;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.broker.model.Event;
+import eu.dnetlib.dhp.broker.oa.util.ClusterUtils;
+import scala.Tuple2;
+
+public class PartitionEventsByDsIdJob {
+
+	private static final Logger log = LoggerFactory.getLogger(PartitionEventsByDsIdJob.class);
+	private static final String OPENDOAR_NSPREFIX = "opendoar____::";
+
+	public static void main(final String[] args) throws Exception {
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					PartitionEventsByDsIdJob.class
+						.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json")));
+		parser.parseArgument(args);
+
+		final Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		final SparkConf conf = new SparkConf();
+
+		final String eventsPath = parser.get("workingPath") + "/events";
+		log.info("eventsPath: {}", eventsPath);
+
+		final String partitionPath = parser.get("workingPath") + "/eventsByOpendoarId";
+		log.info("partitionPath: {}", partitionPath);
+
+		runWithSparkSession(conf, isSparkSessionManaged, spark -> {
+
+			ClusterUtils
+				.readPath(spark, eventsPath, Event.class)
+				.filter(e -> StringUtils.isNotBlank(e.getMap().getTargetDatasourceId()))
+				.filter(e -> e.getMap().getTargetDatasourceId().contains(OPENDOAR_NSPREFIX))
+				.map(
+					e -> new Tuple2<>(
+						StringUtils.substringAfter(e.getMap().getTargetDatasourceId(), OPENDOAR_NSPREFIX),
+						messageFromNotification(e)),
+					Encoders.tuple(Encoders.STRING(), Encoders.bean(ShortEventMessage.class)))
+				.write()
+				.partitionBy("_1")
+				.mode(SaveMode.Overwrite)
+				.json(partitionPath);
+
+		});
+		renameSubDirs(partitionPath);
+
+	}
+
+	private static void renameSubDirs(final String path) throws IOException {
+		final String prefix = "_1=";
+		final FileSystem fs = FileSystem.get(new Configuration());
+
+		log.info("** Renaming subdirs of " + path);
+		for (final FileStatus fileStatus : fs.listStatus(new Path(path))) {
+			if (fileStatus.isDirectory()) {
+				final Path oldPath = fileStatus.getPath();
+				final String oldName = oldPath.getName();
+				if (oldName.startsWith(prefix)) {
+					final Path newPath = new Path(path + "/" + StringUtils.substringAfter(oldName, prefix));
+					log.info(" * " + oldPath.getName() + " -> " + newPath.getName());
+					fs.rename(oldPath, newPath);
+				}
+			}
+		}
+	}
+
+	private static ShortEventMessage messageFromNotification(final Event e) {
+		final Gson gson = new Gson();
+
+		final OaBrokerEventPayload payload = gson.fromJson(e.getPayload(), OaBrokerEventPayload.class);
+
+		final ShortEventMessage res = new ShortEventMessage();
+
+		res.setOriginalId(payload.getResult().getOriginalId());
+		res.setTitle(payload.getResult().getTitles().stream().filter(StringUtils::isNotBlank).findFirst().orElse(null));
+		res.setTopic(e.getTopic());
+		res.setTrust(payload.getTrust());
+		res.generateMessageFromObject(payload.getHighlight());
+
+		return res;
+	}
+
+}

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/stats/DatasourceStats.java

@@ -2,8 +2,6 @@
 package eu.dnetlib.dhp.broker.oa.util.aggregators.stats;
 
 import java.io.Serializable;
-import java.util.HashMap;
-import java.util.Map;
 
 public class DatasourceStats implements Serializable {
 
@@ -15,7 +13,8 @@ public class DatasourceStats implements Serializable {
 	private String id;
 	private String name;
 	private String type;
-	private Map<String, Long> topics = new HashMap<>();
+	private String topic;
+	private long size = 0l;
 
 	public String getId() {
 		return id;
@@ -41,21 +40,24 @@ public class DatasourceStats implements Serializable {
 		this.type = type;
 	}
 
-	public Map<String, Long> getTopics() {
+	public String getTopic() {
-		return topics;
+		return topic;
 	}
 
-	public void setTopics(final Map<String, Long> topics) {
+	public void setTopic(final String topic) {
-		this.topics = topics;
+		this.topic = topic;
-	}
-
-	public void incrementTopic(final String topic, final long inc) {
-		if (topics.containsKey(topic)) {
-			topics.put(topic, topics.get(topic) + inc);
-		} else {
-			topics.put(topic, inc);
 	}
 
+	public long getSize() {
+		return size;
+	}
+
+	public void setSize(final long size) {
+		this.size = size;
+	}
+
+	public void incrementSize(final long inc) {
+		this.size = this.size + inc;
 	}
 
 }

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/stats/StatsAggregator.java

@@ -25,7 +25,8 @@ public class StatsAggregator extends Aggregator<Event, DatasourceStats, Datasour
 		stats.setId(e.getMap().getTargetDatasourceId());
 		stats.setName(e.getMap().getTargetDatasourceName());
 		stats.setType(e.getMap().getTargetDatasourceType());
-		stats.incrementTopic(e.getTopic(), 1l);
+		stats.setTopic(e.getTopic());
+		stats.incrementSize(1l);
 		return stats;
 	}
 
@@ -35,8 +36,9 @@ public class StatsAggregator extends Aggregator<Event, DatasourceStats, Datasour
 			stats0.setId(stats1.getId());
 			stats0.setName(stats1.getName());
 			stats0.setType(stats1.getType());
+			stats0.setTopic(stats1.getTopic());
 		}
-		stats1.getTopics().entrySet().forEach(e -> stats0.incrementTopic(e.getKey(), e.getValue()));
+		stats0.incrementSize(stats1.getSize());
 		return stats0;
 	}
 

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

@@ -0,0 +1,18 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>oozie.action.sharelib.for.spark</name>
+        <value>spark2</value>
+    </property>
+</configuration>

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

@@ -0,0 +1,137 @@
+<workflow-app name="create broker events - partial" xmlns="uri:oozie:workflow:0.5">
+
+    <parameters>
+        <property>
+            <name>graphInputPath</name>
+            <description>the path where the graph is stored</description>
+        </property>
+        <property>
+            <name>workingPath</name>
+            <description>the path where the the generated data will be stored</description>
+        </property>
+		<property>
+            <name>datasourceIdWhitelist</name>
+            <value>-</value>
+            <description>a white list (comma separeted, - for empty list) of datasource ids</description>
+        </property>
+		<property>
+            <name>datasourceTypeWhitelist</name>
+            <value>-</value>
+            <description>a white list (comma separeted, - for empty list) of datasource types</description>
+        </property>
+		<property>
+            <name>datasourceIdBlacklist</name>
+            <value>-</value>
+            <description>a black list (comma separeted, - for empty list) of datasource ids</description>
+        </property>
+        <property>
+            <name>esEventIndexName</name>
+            <description>the elasticsearch index name for events</description>
+        </property>
+        <property>
+            <name>esNotificationsIndexName</name>
+            <description>the elasticsearch index name for notifications</description>
+        </property>
+        <property>
+            <name>esIndexHost</name>
+            <description>the elasticsearch host</description>
+        </property>
+        <property>
+        	<name>maxIndexedEventsForDsAndTopic</name>
+        	<description>the max number of events for each couple (ds/topic)</description>
+        </property>
+        <property>
+        	<name>brokerApiBaseUrl</name>
+        	<description>the url of the broker service api</description>
+        </property>
+        <property>
+            <name>sparkDriverMemory</name>
+            <description>memory for driver process</description>
+        </property>
+        <property>
+            <name>sparkExecutorMemory</name>
+            <description>memory for individual executor</description>
+        </property>
+        <property>
+            <name>sparkExecutorCores</name>
+            <description>number of cores used by single executor</description>
+        </property>
+        <property>
+            <name>oozieActionShareLibForSpark2</name>
+            <description>oozie action sharelib for spark 2.*</description>
+        </property>
+        <property>
+            <name>spark2ExtraListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+            <description>spark 2.* extra listeners classname</description>
+        </property>
+        <property>
+            <name>spark2SqlQueryExecutionListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+            <description>spark 2.* sql query execution listeners classname</description>
+        </property>
+        <property>
+            <name>spark2YarnHistoryServerAddress</name>
+            <description>spark 2.* yarn history server address</description>
+        </property>
+        <property>
+            <name>spark2EventLogDir</name>
+            <description>spark 2.* event log dir location</description>
+        </property>
+    </parameters>
+
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>mapreduce.job.queuename</name>
+                <value>${queueName}</value>
+            </property>
+            <property>
+                <name>oozie.launcher.mapred.job.queue.name</name>
+                <value>${oozieLauncherQueueName}</value>
+            </property>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+        </configuration>
+    </global>
+
+    <start to="index_notifications"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+    
+    <action name="index_notifications">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>IndexNotificationsOnESJob</name>
+            <class>eu.dnetlib.dhp.broker.oa.IndexNotificationsJob</class>
+            <jar>dhp-broker-events-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.dynamicAllocation.maxExecutors="8" 
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=3840
+            </spark-opts>
+            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--index</arg><arg>${esNotificationsIndexName}</arg>
+            <arg>--esHost</arg><arg>${esIndexHost}</arg>
+            <arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+    
+    	
+    <end name="End"/>
+
+</workflow-app>

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

@@ -44,6 +44,18 @@
         	<name>brokerApiBaseUrl</name>
         	<description>the url of the broker service api</description>
         </property>
+        <property>
+        	<name>brokerDbUrl</name>
+        	<description>the url of the broker database</description>
+        </property>
+        <property>
+        	<name>brokerDbUser</name>
+        	<description>the user of the broker database</description>
+        </property>
+        <property>
+        	<name>brokerDbPassword</name>
+        	<description>the password of the broker database</description>
+        </property>
         <property>
             <name>sparkDriverMemory</name>
             <description>memory for driver process</description>
@@ -99,23 +111,23 @@
         </configuration>
     </global>
 
-    <start to="index_notifications"/>
+    <start to="stats"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
     
-    <action name="index_notifications">
+    <action name="stats">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
             <mode>cluster</mode>
-            <name>IndexNotificationsOnESJob</name>
+            <name>GenerateStatsJob</name>
-            <class>eu.dnetlib.dhp.broker.oa.IndexNotificationsJob</class>
+            <class>eu.dnetlib.dhp.broker.oa.GenerateStatsJob</class>
             <jar>dhp-broker-events-${projectVersion}.jar</jar>
             <spark-opts>
+                --executor-cores=${sparkExecutorCores}
                 --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=${spark2YarnHistoryServerAddress}
@@ -123,15 +135,15 @@
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--workingPath</arg><arg>${workingPath}</arg>
-            <arg>--index</arg><arg>${esNotificationsIndexName}</arg>
+            <arg>--dbUrl</arg><arg>${brokerDbUrl}</arg>
-            <arg>--esHost</arg><arg>${esIndexHost}</arg>
+            <arg>--dbUser</arg><arg>${brokerDbUser}</arg>
+            <arg>--dbPassword</arg><arg>${brokerDbPassword}</arg>
             <arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
         </spark>
         <ok to="End"/>
         <error to="Kill"/>
     </action>
     	
-    	
     <end name="End"/>
 
 </workflow-app>

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

@@ -0,0 +1,32 @@
+[
+	{
+		"paramName": "wp",
+		"paramLongName": "workingPath",
+		"paramDescription": "the working path",
+		"paramRequired": true
+	},
+	{
+		"paramName": "dburl",
+		"paramLongName": "dbUrl",
+		"paramDescription": "the broker database url",
+		"paramRequired": true
+	},
+	{
+		"paramName": "u",
+		"paramLongName": "dbUser",
+		"paramDescription": "the broker database user",
+		"paramRequired": true
+	},
+	{
+		"paramName": "p",
+		"paramLongName": "dbPassword",
+		"paramDescription": "the broker database password",
+		"paramRequired": true
+	},
+	{
+		"paramName": "broker",
+		"paramLongName": "brokerApiBaseUrl",
+		"paramDescription": "the url of the broker service api",
+		"paramRequired": true
+	}
+]

pom.xml

@@ -663,7 +663,7 @@
 		<mockito-core.version>3.3.3</mockito-core.version>
 		<mongodb.driver.version>3.4.2</mongodb.driver.version>
 		<vtd.version>[2.12,3.0)</vtd.version>
-		<dnet.openaire.broker.common>3.1.0</dnet.openaire.broker.common>
+		<dnet.openaire.broker.common>3.1.1</dnet.openaire.broker.common>
 		<solr.version>7.5.0</solr.version>
 		<okhttp.version>4.7.2</okhttp.version>
 		<common.compress.version>1.1</common.compress.version>