job execution now based on file last_update.txt on hdfs

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java

@@ -28,13 +28,14 @@ import org.slf4j.LoggerFactory;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.doiboost.orcid.model.DownloadedRecordData;
+import eu.dnetlib.doiboost.orcid.util.HDFSUtil;
 import scala.Tuple2;
 
 public class SparkDownloadOrcidAuthors {
 
 	static Logger logger = LoggerFactory.getLogger(SparkDownloadOrcidAuthors.class);
 	static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss";
-	static final String lastUpdate = "2020-11-18 00:00:05";
+	static String lastUpdate;
 
 	public static void main(String[] args) throws IOException, Exception {
 
@@ -58,6 +59,8 @@ public class SparkDownloadOrcidAuthors {
 		final String lambdaFileName = parser.get("lambdaFileName");
 		logger.info("lambdaFileName: ", lambdaFileName);
 
+		lastUpdate = HDFSUtil.readFromTextFile(workingPath.concat("last_update.txt"));
+
 		SparkConf conf = new SparkConf();
 		runWithSparkSession(
 			conf,
@@ -182,6 +185,9 @@ public class SparkDownloadOrcidAuthors {
 			if (modifiedDate.length() != 19) {
 				modifiedDate = modifiedDate.substring(0, 19);
 			}
+			if (lastUpdate.length() != 19) {
+				lastUpdate = lastUpdate.substring(0, 19);
+			}
 			modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate);
 			lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate);
 		} catch (Exception e) {

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidWorks.java

@@ -31,6 +31,7 @@ import com.google.gson.JsonParser;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.doiboost.orcid.model.DownloadedRecordData;
+import eu.dnetlib.doiboost.orcid.util.HDFSUtil;
 import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser;
 import scala.Tuple2;
 
@@ -43,7 +44,7 @@ public class SparkDownloadOrcidWorks {
 	public static final String ORCID_XML_DATETIME_FORMAT = "yyyy-MM-dd'T'HH:mm:ss.SSS'Z'";
 	public static final DateTimeFormatter ORCID_XML_DATETIMEFORMATTER = DateTimeFormatter
 		.ofPattern(ORCID_XML_DATETIME_FORMAT);
-	public static final String lastUpdateValue = "2020-11-18 00:00:05";
+	public static String lastUpdateValue;
 
 	public static void main(String[] args) throws IOException, Exception {
 
@@ -64,6 +65,11 @@ public class SparkDownloadOrcidWorks {
 		final String outputPath = parser.get("outputPath");
 		final String token = parser.get("token");
 
+		lastUpdateValue = HDFSUtil.readFromTextFile(workingPath.concat("last_update.txt"));
+		if (lastUpdateValue.length() != 19) {
+			lastUpdateValue = lastUpdateValue.substring(0, 19);
+		}
+
 		SparkConf conf = new SparkConf();
 		runWithSparkSession(
 			conf,

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkGenLastModifiedSeq.java

@@ -3,9 +3,7 @@ package eu.dnetlib.doiboost.orcid;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
-import java.io.BufferedReader;
+import java.io.*;
-import java.io.IOException;
-import java.io.InputStreamReader;
 import java.net.URI;
 import java.util.Arrays;
 import java.util.List;
@@ -17,6 +15,7 @@ import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FSDataInputStream;
+import org.apache.hadoop.fs.FSDataOutputStream;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.io.SequenceFile;
@@ -26,6 +25,7 @@ import org.apache.spark.SparkConf;
 import org.mortbay.log.Log;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.doiboost.orcid.util.HDFSUtil;
 
 public class SparkGenLastModifiedSeq {
 	private static String hdfsServerUri;
@@ -50,6 +50,9 @@ public class SparkGenLastModifiedSeq {
 		outputPath = parser.get("outputPath");
 		lambdaFileName = parser.get("lambdaFileName");
 		String lambdaFileUri = hdfsServerUri.concat(workingPath).concat(lambdaFileName);
+		String lastModifiedDateFromLambdaFileUri = hdfsServerUri
+			.concat(workingPath)
+			.concat("last_modified_date_from_lambda_file.txt");
 
 		SparkConf sparkConf = new SparkConf();
 		runWithSparkSession(
@@ -57,6 +60,7 @@ public class SparkGenLastModifiedSeq {
 			isSparkSessionManaged,
 			spark -> {
 				int rowsNum = 0;
+				String lastModifiedAuthorDate = "";
 				Path output = new Path(
 					hdfsServerUri
 						.concat(workingPath)
@@ -89,10 +93,15 @@ public class SparkGenLastModifiedSeq {
 								final Text value = new Text(recordInfo.get(3));
 								writer.append(key, value);
 								rowsNum++;
+								if (rowsNum == 2) {
+									lastModifiedAuthorDate = value.toString();
+								}
+							}
+
 						}
 					}
 				}
-				}
+				HDFSUtil.writeToTextFile(lastModifiedDateFromLambdaFileUri, lastModifiedAuthorDate);
 				Log.info("Saved rows from lamda csv tar file: " + rowsNum);
 			});
 	}

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkUpdateOrcidAuthors.java

@@ -95,7 +95,7 @@ public class SparkUpdateOrcidAuthors {
 								authorSummary = XMLRecordParser
 									.VTDParseAuthorSummary(xmlAuthor.getBytes());
 								authorSummary.setStatusCode(statusCode);
-								authorSummary.setDownloadDate("2020-12-15 00:00:01.000000");
+								authorSummary.setDownloadDate(Long.toString(System.currentTimeMillis()));
 								authorSummary.setBase64CompressData(compressedData);
 								return authorSummary;
 							} catch (Exception e) {
@@ -105,7 +105,7 @@ public class SparkUpdateOrcidAuthors {
 						}
 					} else {
 						authorSummary.setStatusCode(statusCode);
-						authorSummary.setDownloadDate("2020-12-15 00:00:01.000000");
+						authorSummary.setDownloadDate(Long.toString(System.currentTimeMillis()));
 						errorCodeAuthorsFoundAcc.add(1);
 					}
 					return authorSummary;

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkUpdateOrcidWorks.java

@@ -27,6 +27,7 @@ import com.google.gson.JsonParser;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.orcid.Work;
 import eu.dnetlib.dhp.schema.orcid.WorkDetail;
+import eu.dnetlib.doiboost.orcid.util.HDFSUtil;
 import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi;
 
 public class SparkUpdateOrcidWorks {
@@ -83,7 +84,7 @@ public class SparkUpdateOrcidWorks {
 					String statusCode = getJsonValue(jElement, "statusCode");
 					work.setStatusCode(statusCode);
 					String downloadDate = getJsonValue(jElement, "lastModifiedDate");
-					work.setDownloadDate("2020-12-15 00:00:01.000000");
+					work.setDownloadDate(Long.toString(System.currentTimeMillis()));
 					if (statusCode.equals("200")) {
 						String compressedData = getJsonValue(jElement, "compressedData");
 						if (StringUtils.isEmpty(compressedData)) {
@@ -165,6 +166,10 @@ public class SparkUpdateOrcidWorks {
 				logger.info("errorLoadingJsonWorksFoundAcc: " + errorLoadingWorksJsonFoundAcc.value().toString());
 				logger.info("errorParsingXMLWorksFoundAcc: " + errorParsingWorksXMLFoundAcc.value().toString());
 
+				String lastModifiedDateFromLambdaFile = HDFSUtil
+					.readFromTextFile(workingPath.concat("last_modified_date_from_lambda_file.txt"));
+				HDFSUtil.writeToTextFile(workingPath.concat("last_update.txt"), lastModifiedDateFromLambdaFile);
+				logger.info("last_update file updated");
 			});
 	}
 

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/util/HDFSUtil.java

@@ -0,0 +1,38 @@
+
+package eu.dnetlib.doiboost.orcid.util;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.nio.charset.StandardCharsets;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FSDataInputStream;
+import org.apache.hadoop.fs.FSDataOutputStream;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+
+public class HDFSUtil {
+
+	public static String readFromTextFile(String path) throws IOException {
+		Configuration conf = new Configuration();
+		FileSystem fileSystem = FileSystem.get(conf);
+		FSDataInputStream inputStream = new FSDataInputStream(fileSystem.open(new Path(path)));
+		return IOUtils.toString(inputStream, StandardCharsets.UTF_8.name());
+	}
+
+	public static void writeToTextFile(String pathValue, String text) throws IOException {
+		Configuration conf = new Configuration();
+		FileSystem fileSystem = FileSystem.get(conf);
+		Path path = new Path(pathValue);
+		if (fileSystem.exists(path)) {
+			fileSystem.delete(path, true);
+		}
+		FSDataOutputStream os = fileSystem.create(path);
+		BufferedWriter br = new BufferedWriter(new OutputStreamWriter(os, "UTF-8"));
+		br.write(text);
+		br.close();
+		fileSystem.close();
+	}
+}

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_update/oozie_app/workflow.xml

@@ -1,163 +0,0 @@
-<workflow-app name="update_orcid_datasets" xmlns="uri:oozie:workflow:0.5">
-    <parameters>
-        <property>
-            <name>spark2MaxExecutors</name>
-            <value>50</value>
-        </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>
-        <property>
-            <name>workingPath</name>
-            <description>the working dir base path</description>
-        </property>
-    </parameters>
-
-    <global>
-        <job-tracker>${jobTracker}</job-tracker>
-        <name-node>${nameNode}</name-node>
-        <configuration>
-            <property>
-                <name>oozie.action.sharelib.for.spark</name>
-                <value>${oozieActionShareLibForSpark2}</value>
-            </property>
-        </configuration>
-    </global>
-
-    <start to="promoteOrcidAuthorsDataset"/>
-
-    <kill name="Kill">
-        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
-    </kill>
-
-    <action name="ResetWorkingPath">
-        <fs>
-            <delete path='${workingPath}/orcid_dataset/new_authors'/>
-            <delete path='${workingPath}/orcid_dataset/new_works'/>
-        </fs>
-        <ok to="UpdateOrcidAuthors"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="UpdateOrcidAuthors">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn-cluster</master>
-            <mode>cluster</mode>
-            <name>UpdateOrcidAuthors</name>
-            <class>eu.dnetlib.doiboost.orcid.SparkUpdateOrcidAuthors</class>
-            <jar>dhp-doiboost-${projectVersion}.jar</jar>
-            <spark-opts>
-                --conf spark.dynamicAllocation.enabled=true
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-            </spark-opts>
-            <arg>-w</arg><arg>${workingPath}/</arg>
-            <arg>-n</arg><arg>${nameNode}</arg>
-            <arg>-f</arg><arg>-</arg>
-            <arg>-o</arg><arg>-</arg>
-            <arg>-t</arg><arg>-</arg>
-        </spark>
-        <ok to="UpdateOrcidWorks"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="UpdateOrcidWorks">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn-cluster</master>
-            <mode>cluster</mode>
-            <name>UpdateOrcidWorks</name>
-            <class>eu.dnetlib.doiboost.orcid.SparkUpdateOrcidWorks</class>
-            <jar>dhp-doiboost-${projectVersion}.jar</jar>
-            <spark-opts>
-                --conf spark.dynamicAllocation.enabled=true
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-            </spark-opts>
-            <arg>-w</arg><arg>${workingPath}/</arg>
-            <arg>-n</arg><arg>${nameNode}</arg>
-            <arg>-f</arg><arg>-</arg>
-            <arg>-o</arg><arg>-</arg>
-            <arg>-t</arg><arg>-</arg>
-        </spark>
-        <ok to="End"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="promoteOrcidAuthorsDataset">
-        <distcp xmlns="uri:oozie:distcp-action:0.2">
-            <prepare>
-                <delete path="${workingPath}/orcid_dataset/authors"/>
-                <mkdir path="${workingPath}/orcid_dataset/authors"/>
-            </prepare>
-            <arg>${workingPath}/orcid_dataset/new_authors/*</arg>
-            <arg>${workingPath}/orcid_dataset/authors</arg>
-        </distcp>
-        <ok to="promoteOrcidWorksDataset"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="promoteOrcidWorksDataset">
-        <distcp xmlns="uri:oozie:distcp-action:0.2">
-            <prepare>
-                <delete path="${workingPath}/orcid_dataset/works"/>
-                <mkdir path="${workingPath}/orcid_dataset/works"/>
-            </prepare>
-            <arg>${workingPath}/orcid_dataset/new_works/*</arg>
-            <arg>${workingPath}/orcid_dataset/works</arg>
-        </distcp>
-        <ok to="CleanWorkingPath"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="CleanWorkingPath">
-        <fs>
-            <delete path='${workingPath}/orcid_dataset/new_authors'/>
-            <delete path='${workingPath}/orcid_dataset/new_works'/>
-        </fs>
-        <ok to="End"/>
-        <error to="Kill"/>
-    </action>
-
-    <end name="End"/>
-</workflow-app>