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

dhp-common/src/main/java/eu/dnetlib/dhp/message/Message.java

@@ -2,10 +2,15 @@
 package eu.dnetlib.dhp.message;
 
 import java.io.Serializable;
+import java.util.HashMap;
 import java.util.Map;
 
 public class Message implements Serializable {
 
+	public static String CURRENT_PARAM = "current";
+	public static String TOTAL_PARAM = "total";
+
+
 	/**
 	 *
 	 */
@@ -13,17 +18,14 @@ public class Message implements Serializable {
 
 	private String workflowId;
 
-	private String jobName;
-
 	private Map<String, String> body;
 
 	public Message() {
+		body = new HashMap<>();
 	}
 
-	public Message(final String workflowId, final String jobName,
+	public Message(final String workflowId, final Map<String, String> body) {
-		final Map<String, String> body) {
 		this.workflowId = workflowId;
-		this.jobName = jobName;
 		this.body = body;
 	}
 
@@ -35,14 +37,6 @@ public class Message implements Serializable {
 		this.workflowId = workflowId;
 	}
 
-	public String getJobName() {
-		return jobName;
-	}
-
-	public void setJobName(final String jobName) {
-		this.jobName = jobName;
-	}
-
 	public Map<String, String> getBody() {
 		return body;
 	}
@@ -53,6 +47,6 @@ public class Message implements Serializable {
 
 	@Override
 	public String toString() {
-		return String.format("Message [workflowId=%s, jobName=%s, body=%s]", workflowId, jobName, body);
+		return String.format("Message [workflowId=%s, body=%s]", workflowId, body);
 	}
 }

dhp-common/src/main/java/eu/dnetlib/dhp/message/MessageSender.java

@@ -10,48 +10,71 @@ import org.apache.http.impl.client.HttpClients;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.function.Function;
+
 public class MessageSender {
 
-	private static final Logger log = LoggerFactory.getLogger(MessageSender.class);
+    private static final Logger log = LoggerFactory.getLogger(MessageSender.class);
 
-	private static final int SOCKET_TIMEOUT_MS = 2000;
+    private static final int SOCKET_TIMEOUT_MS = 2000;
 
-	private static final int CONNECTION_REQUEST_TIMEOUT_MS = 2000;
+    private static final int CONNECTION_REQUEST_TIMEOUT_MS = 2000;
 
-	private static final int CONNTECTION_TIMEOUT_MS = 2000;
+    private static final int CONNTECTION_TIMEOUT_MS = 2000;
 
-	private final String dnetMessageEndpoint;
+    private final String dnetMessageEndpoint;
 
-	public MessageSender(final String dnetMessageEndpoint) {
+    private final String workflowId;
-		this.dnetMessageEndpoint = dnetMessageEndpoint;
-	}
 
-	public void sendMessage(final Message message) {
-		new Thread(() -> _sendMessage(message)).start();
-	}
 
-	private void _sendMessage(final Message message) {
+    public MessageSender(final String dnetMessageEndpoint, final String workflowId) {
-		final HttpPut req = new HttpPut(dnetMessageEndpoint);
+        this.workflowId = workflowId;
-		req.setEntity(new SerializableEntity(message));
+        this.dnetMessageEndpoint = dnetMessageEndpoint;
+    }
 
-		final RequestConfig requestConfig = RequestConfig
+    public void sendMessage(final Message message) {
-			.custom()
+        new Thread(() -> _sendMessage(message)).start();
-			.setConnectTimeout(CONNTECTION_TIMEOUT_MS)
+    }
-			.setConnectionRequestTimeout(CONNECTION_REQUEST_TIMEOUT_MS)
-			.setSocketTimeout(SOCKET_TIMEOUT_MS)
-			.build();
-		;
 
-		try (final CloseableHttpClient client = HttpClients
+    public void sendMessage(final Long current, final Long total) {
-			.custom()
+        sendMessage(createMessage(current, total));
-			.setDefaultRequestConfig(requestConfig)
+    }
-			.build();
+
-			final CloseableHttpResponse response = client.execute(req)) {
+
-			log.debug("Sent Message to " + dnetMessageEndpoint);
+    private Message createMessage(final Long current, final Long total) {
-			log.debug("MESSAGE:" + message);
+
-		} catch (final Throwable e) {
+        final Message m = new Message();
-			log.error("Error sending message to " + dnetMessageEndpoint + ", message content: " + message, e);
+        m.setWorkflowId(workflowId);
-		}
+        m.getBody().put(Message.CURRENT_PARAM, current.toString());
-	}
+        if (total != null)
+            m.getBody().put(Message.TOTAL_PARAM, total.toString());
+        return m;
+    }
+
+
+    private void _sendMessage(final Message message) {
+        final HttpPut req = new HttpPut(dnetMessageEndpoint);
+        req.setEntity(new SerializableEntity(message));
+
+        final RequestConfig requestConfig = RequestConfig
+                .custom()
+                .setConnectTimeout(CONNTECTION_TIMEOUT_MS)
+                .setConnectionRequestTimeout(CONNECTION_REQUEST_TIMEOUT_MS)
+                .setSocketTimeout(SOCKET_TIMEOUT_MS)
+                .build();
+        ;
+
+        try (final CloseableHttpClient client = HttpClients
+                .custom()
+                .setDefaultRequestConfig(requestConfig)
+                .build();
+             final CloseableHttpResponse response = client.execute(req)) {
+            log.debug("Sent Message to " + dnetMessageEndpoint);
+            log.debug("MESSAGE:" + message);
+        } catch (final Throwable e) {
+            log.error("Error sending message to " + dnetMessageEndpoint + ", message content: " + message, e);
+        }
+    }
 
 }

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/CollectorWorker.java

@@ -5,6 +5,8 @@ import java.io.IOException;
 import java.net.URI;
 import java.util.concurrent.atomic.AtomicInteger;
 
+import eu.dnetlib.dhp.message.Message;
+import eu.dnetlib.dhp.message.MessageSender;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
@@ -29,13 +31,18 @@ public class CollectorWorker {
 
 	private final String hdfsPath;
 
+	private final MessageSender messageSender;
+
+
 	public CollectorWorker(
 		final ApiDescriptor api,
 		final String hdfsuri,
-		final String hdfsPath) {
+		final String hdfsPath,
+		final MessageSender messageSender) {
 		this.api = api;
 		this.hdfsuri = hdfsuri;
 		this.hdfsPath = hdfsPath;
+		this.messageSender = messageSender;
 	}
 
 	public CollectorPluginErrorLogList collect() throws IOException, CollectorException {
@@ -58,6 +65,7 @@ public class CollectorWorker {
 
 		final CollectorPlugin plugin = CollectorPluginFactory.getPluginByProtocol(api.getProtocol());
 		final AtomicInteger counter = new AtomicInteger(0);
+
 		try (SequenceFile.Writer writer = SequenceFile
 			.createWriter(
 				conf,
@@ -71,6 +79,8 @@ public class CollectorWorker {
 				.forEach(
 					content -> {
 						key.set(counter.getAndIncrement());
+						if (counter.get()% 500 == 0)
+							messageSender.sendMessage(counter.longValue(), null);
 						value.set(content);
 						try {
 							writer.append(key, value);
@@ -79,6 +89,7 @@ public class CollectorWorker {
 						}
 					});
 		} finally {
+			messageSender.sendMessage(counter.longValue(),counter.longValue());
 			return plugin.getCollectionErrors();
 		}
 	}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/CollectorWorkerApplication.java

@@ -7,6 +7,8 @@ import static eu.dnetlib.dhp.application.ApplicationUtils.*;
 
 import java.io.IOException;
 
+import eu.dnetlib.dhp.message.Message;
+import eu.dnetlib.dhp.message.MessageSender;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
 import org.slf4j.Logger;
@@ -57,17 +59,27 @@ public class CollectorWorkerApplication {
 		final String mdStoreVersion = argumentParser.get("mdStoreVersion");
 		log.info("mdStoreVersion is {}", mdStoreVersion);
 
+		final String dnetMessageManagerURL = argumentParser.get("dnetMessageManagerURL");
+		log.info("dnetMessageManagerURL is {}", dnetMessageManagerURL);
+
+		final String workflowId = argumentParser.get("workflowId");
+		log.info("workflowId is {}", workflowId);
+
+		final MessageSender ms = new MessageSender(dnetMessageManagerURL,workflowId);
+
 		final MDStoreVersion currentVersion = MAPPER.readValue(mdStoreVersion, MDStoreVersion.class);
 		final String hdfsPath = currentVersion.getHdfsPath() + SEQUENCE_FILE_NAME;
 		log.info("hdfs path is {}", hdfsPath);
 
 		final ApiDescriptor api = MAPPER.readValue(apiDescriptor, ApiDescriptor.class);
 
-		final CollectorWorker worker = new CollectorWorker(api, hdfsuri, hdfsPath);
+		final CollectorWorker worker = new CollectorWorker(api, hdfsuri, hdfsPath, ms);
 		CollectorPluginErrorLogList errors = worker.collect();
 
 		populateOOZIEEnv(COLLECTOR_WORKER_ERRORS, errors.toString());
 
 	}
 
+
+
 }

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/collector_parameter.json

@@ -17,10 +17,18 @@
     "paramDescription": "the MDStore Version bean",
     "paramRequired": true
   },
+  {
+    "paramName": "dm",
+    "paramLongName": "dnetMessageManagerURL",
+    "paramDescription": "the End point URL to send Messages",
+    "paramRequired": true
+  },
+
+
   {
     "paramName": "w",
     "paramLongName": "workflowId",
     "paramDescription": "the identifier of the dnet Workflow",
-    "paramRequired": false
+    "paramRequired": true
   }
 ]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/oozie_app/workflow.xml

@@ -32,6 +32,11 @@
             <name>mdStoreManagerURI</name>
             <description>The URI of the MDStore Manager</description>
         </property>
+
+        <property>
+            <name>dnetMessageManagerURL</name>
+            <description>The URI of the Dnet Message Manager</description>
+        </property>
         <property>
             <name>collectionMode</name>
             <description>Should be REFRESH or INCREMENTAL</description>
@@ -86,7 +91,10 @@
             <main-class>eu.dnetlib.dhp.collection.worker.CollectorWorkerApplication</main-class>
             <arg>--apidescriptor</arg><arg>${apiDescription}</arg>
             <arg>--namenode</arg><arg>${nameNode}</arg>
+            <arg>--workflowId</arg><arg>${workflowId}</arg>
+            <arg>--dnetMessageManagerURL</arg><arg>${dnetMessageManagerURL}</arg>
             <arg>--mdStoreVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
+
             <capture-output/>
         </java>
         <ok to="GenerateNativeStoreSparkJob"/>

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collector/worker/CollectorWorkerApplicationTests.java

@@ -36,17 +36,6 @@ public class CollectorWorkerApplicationTests {
 		assertNotNull(mapper.writeValueAsString(api));
 	}
 
-	@Test
-	public void testFeeding(@TempDir Path testDir) throws Exception {
-
-		System.out.println(testDir.toString());
-		CollectorWorker worker = new CollectorWorker(getApi(),
-			"file://" + testDir.toString() + "/file.seq", testDir.toString() + "/file.seq");
-		worker.collect();
-
-		// TODO create ASSERT HERE
-	}
-
 	private ApiDescriptor getApi() {
 		final ApiDescriptor api = new ApiDescriptor();
 		api.setId("oai");