Merge pull request '[Measures] added new measure (UsageCounts)' (#214) from eosc_dimitris into beta

Reviewed-on: D-Net/dnet-hadoop#214

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java

@@ -391,4 +391,19 @@ public class OafMapperUtils {
 		}
 		return null;
 	}
+
+	public static KeyValue newKeyValueInstance(String key, String value, DataInfo dataInfo) {
+		KeyValue kv = new KeyValue();
+		kv.setDataInfo(dataInfo);
+		kv.setKey(key);
+		kv.setValue(value);
+		return kv;
+	}
+
+	public static Measure newMeasureInstance(String id, String value, String key, DataInfo dataInfo) {
+		Measure m = new Measure();
+		m.setId(id);
+		m.setUnit(Arrays.asList(newKeyValueInstance(key, value, dataInfo)));
+		return m;
+	}
 }

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java

@@ -27,6 +27,8 @@ public class Constants {
 	public static final String UPDATE_CLASS_NAME = "Inferred by OpenAIRE";
 	public static final String UPDATE_MEASURE_BIP_CLASS_ID = "measure:bip";
 	public static final String UPDATE_SUBJECT_SDG_CLASS_ID = "subject:sdg";
+	public static final String UPDATE_MEASURE_USAGE_COUNTS_CLASS_ID = "measure:usage_counts";
+	public static final String UPDATE_KEY_USAGE_COUNTS = "count";
 
 	public static final String FOS_CLASS_ID = "FOS";
 	public static final String FOS_CLASS_NAME = "Fields of Science and Technology classification";

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java

@@ -0,0 +1,149 @@
+
+package eu.dnetlib.dhp.actionmanager.usagestats;
+
+import static eu.dnetlib.dhp.actionmanager.Constants.*;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
+
+import java.io.Serializable;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Optional;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.api.java.function.MapGroupsFunction;
+import org.apache.spark.sql.Dataset;
+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 com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.DataInfo;
+import eu.dnetlib.dhp.schema.oaf.Measure;
+import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
+
+/**
+ * created the Atomic Action for each type of results
+ */
+public class SparkAtomicActionUsageJob implements Serializable {
+
+	private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionUsageJob.class);
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	public static <I extends Result> void main(String[] args) throws Exception {
+
+		String jsonConfiguration = IOUtils
+			.toString(
+				SparkAtomicActionUsageJob.class
+					.getResourceAsStream(
+						"/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json"));
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
+
+		parser.parseArgument(args);
+
+		Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		final String outputPath = parser.get("outputPath");
+		log.info("outputPath {}: ", outputPath);
+
+		SparkConf conf = new SparkConf();
+		conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
+
+		final String dbname = parser.get("usagestatsdb");
+
+		final String workingPath = parser.get("workingPath");
+
+		runWithSparkHiveSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> {
+				removeOutputDir(spark, outputPath);
+				prepareResults(dbname, spark, workingPath);
+				prepareActionSet(spark, workingPath, outputPath);
+			});
+	}
+
+	public static void prepareResults(String db, SparkSession spark, String workingPath) {
+		spark
+			.sql(
+				"Select result_id, downloads, views " +
+					"from " + db + ".usage_stats")
+			.as(Encoders.bean(UsageStatsModel.class))
+			.write()
+			.mode(SaveMode.Overwrite)
+			.option("compression", "gzip")
+			.json(workingPath);
+	}
+
+	public static void prepareActionSet(SparkSession spark, String inputPath, String outputPath) {
+		readPath(spark, inputPath, UsageStatsModel.class)
+			.groupByKey((MapFunction<UsageStatsModel, String>) us -> us.getResult_id(), Encoders.STRING())
+			.mapGroups((MapGroupsFunction<String, UsageStatsModel, Result>) (k, it) -> {
+				UsageStatsModel first = it.next();
+				it.forEachRemaining(us -> {
+					first.setDownloads(first.getDownloads() + us.getDownloads());
+					first.setViews(first.getViews() + us.getViews());
+				});
+
+				Result res = new Result();
+				res.setId("50|" + k);
+
+				res.setMeasures(getMeasure(first.getDownloads(), first.getViews()));
+				return res;
+			}, Encoders.bean(Result.class))
+			.write()
+			.mode(SaveMode.Overwrite)
+			.option("compression", "gzip")
+			.json(outputPath);
+	}
+
+	private static List<Measure> getMeasure(Long downloads, Long views) {
+		DataInfo dataInfo = OafMapperUtils
+			.dataInfo(
+				false,
+				UPDATE_DATA_INFO_TYPE,
+				true,
+				false,
+				OafMapperUtils
+					.qualifier(
+						UPDATE_MEASURE_USAGE_COUNTS_CLASS_ID,
+						UPDATE_CLASS_NAME,
+						ModelConstants.DNET_PROVENANCE_ACTIONS,
+						ModelConstants.DNET_PROVENANCE_ACTIONS),
+				"");
+
+		return Arrays
+			.asList(
+				OafMapperUtils
+					.newMeasureInstance("downloads", String.valueOf(downloads), UPDATE_KEY_USAGE_COUNTS, dataInfo),
+				OafMapperUtils.newMeasureInstance("views", String.valueOf(views), UPDATE_KEY_USAGE_COUNTS, dataInfo));
+
+	}
+
+	private static void removeOutputDir(SparkSession spark, String path) {
+		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
+	}
+
+	public static <R> Dataset<R> readPath(
+		SparkSession spark, String inputPath, Class<R> clazz) {
+		return spark
+			.read()
+			.textFile(inputPath)
+			.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
+	}
+
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/UsageStatsModel.java

@@ -0,0 +1,34 @@
+
+package eu.dnetlib.dhp.actionmanager.usagestats;
+
+import java.io.Serializable;
+
+public class UsageStatsModel implements Serializable {
+	private String result_id;
+	private Long downloads;
+	private Long views;
+
+	public String getResult_id() {
+		return result_id;
+	}
+
+	public void setResult_id(String result_id) {
+		this.result_id = result_id;
+	}
+
+	public Long getDownloads() {
+		return downloads;
+	}
+
+	public void setDownloads(Long downloads) {
+		this.downloads = downloads;
+	}
+
+	public Long getViews() {
+		return views;
+	}
+
+	public void setViews(Long views) {
+		this.views = views;
+	}
+}

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json

@@ -0,0 +1,32 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "hmu",
+    "paramLongName": "hive_metastore_uris",
+    "paramDescription": "the URI for the hive metastore",
+    "paramRequired": true
+  },
+  {
+    "paramName": "o",
+    "paramLongName": "outputPath",
+    "paramDescription": "the path of the new ActionSet",
+    "paramRequired": true
+  },
+  {
+    "paramName": "sdb",
+    "paramLongName": "usagestatsdb",
+    "paramDescription": "the name of the db to be used",
+    "paramRequired": true
+  },
+  {
+    "paramName": "wp",
+    "paramLongName": "workingPath",
+    "paramDescription": "the workingPath where to save the content of the usage_stats table",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/config-default.xml

@@ -0,0 +1,30 @@
+<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>hiveMetastoreUris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>hiveJdbcUrl</name>
+        <value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
+    </property>
+    <property>
+        <name>hiveDbName</name>
+        <value>openaire</value>
+    </property>
+    <property>
+        <name>oozie.launcher.mapreduce.user.classpath.first</name>
+        <value>true</value>
+    </property>
+</configuration>

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

@@ -0,0 +1,99 @@
+<workflow-app name="UsageStatsCounts" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>outputPath</name>
+            <description>the path where to store the actionset</description>
+        </property>
+        <property>
+            <name>usagestatsdb</name>
+            <description>the name of the db to be used</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>${oozieActionShareLibForSpark2}</value>
+            </property>
+
+        </configuration>
+    </global>
+    <start to="atomicactions"/>
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+
+    <action name="atomicactions">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Produces the atomic action with the usage stats count for results</name>
+            <class>eu.dnetlib.dhp.actionmanager.usagestats.SparkAtomicActionUsageJob</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${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}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--hive_metastore_uris</arg><arg>${hiveMetastoreUris}</arg>
+            <arg>--outputPath</arg><arg>${outputPath}</arg>
+            <arg>--usagestatsdb</arg><arg>${usagestatsdb}</arg>
+            <arg>--workingPath</arg><arg>${workingDir}/usageDb</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+</workflow-app>

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java

@@ -0,0 +1,259 @@
+
+package eu.dnetlib.dhp.actionmanager.usagestats;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.stream.Collectors;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.Row;
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.oaf.Result;
+
+public class SparkAtomicActionCountJobTest {
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	private static SparkSession spark;
+
+	private static Path workingDir;
+	private static final Logger log = LoggerFactory
+		.getLogger(SparkAtomicActionCountJobTest.class);
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		workingDir = Files
+			.createTempDirectory(SparkAtomicActionCountJobTest.class.getSimpleName());
+		log.info("using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(SparkAtomicActionCountJobTest.class.getSimpleName());
+
+		conf.setMaster("local[*]");
+		conf.set("spark.driver.host", "localhost");
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+		conf.set("spark.sql.warehouse.dir", workingDir.toString());
+		conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
+
+		spark = SparkSession
+			.builder()
+			.appName(SparkAtomicActionCountJobTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	@Test
+	void testMatch() {
+		String usageScoresPath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb")
+			.getPath();
+
+		SparkAtomicActionUsageJob.prepareActionSet(spark, usageScoresPath, workingDir.toString() + "/actionSet");
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Result> tmp = sc
+			.textFile(workingDir.toString() + "/actionSet")
+			.map(usm -> OBJECT_MAPPER.readValue(usm, Result.class));
+
+		Assertions.assertEquals(9, tmp.count());
+
+		tmp.foreach(r -> Assertions.assertEquals(2, r.getMeasures().size()));
+		tmp
+			.foreach(
+				r -> r
+					.getMeasures()
+					.stream()
+					.forEach(
+						m -> m
+							.getUnit()
+							.stream()
+							.forEach(u -> Assertions.assertFalse(u.getDataInfo().getDeletedbyinference()))));
+		tmp
+			.foreach(
+				r -> r
+					.getMeasures()
+					.stream()
+					.forEach(
+						m -> m.getUnit().stream().forEach(u -> Assertions.assertTrue(u.getDataInfo().getInferred()))));
+		tmp
+			.foreach(
+				r -> r
+					.getMeasures()
+					.stream()
+					.forEach(
+						m -> m
+							.getUnit()
+							.stream()
+							.forEach(u -> Assertions.assertFalse(u.getDataInfo().getInvisible()))));
+
+		tmp
+			.foreach(
+				r -> r
+					.getMeasures()
+					.stream()
+					.forEach(
+						m -> m
+							.getUnit()
+							.stream()
+							.forEach(
+								u -> Assertions
+									.assertEquals(
+										"measure:usage_counts",
+										u.getDataInfo().getProvenanceaction().getClassid()))));
+		tmp
+			.foreach(
+				r -> r
+					.getMeasures()
+					.stream()
+					.forEach(
+						m -> m
+							.getUnit()
+							.stream()
+							.forEach(
+								u -> Assertions
+									.assertEquals(
+										"Inferred by OpenAIRE",
+										u.getDataInfo().getProvenanceaction().getClassname()))));
+
+		tmp
+			.foreach(
+				r -> r
+					.getMeasures()
+					.stream()
+					.forEach(
+						m -> m
+							.getUnit()
+							.stream()
+							.forEach(
+								u -> Assertions
+									.assertEquals(
+										"count",
+										u.getKey()))));
+
+		Assertions
+			.assertEquals(
+				1, tmp.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).count());
+
+		Assertions
+			.assertEquals(
+				"0",
+				tmp
+					.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(m -> m.getId().equals("downloads"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+		Assertions
+			.assertEquals(
+				"5",
+				tmp
+					.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(m -> m.getId().equals("views"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+
+		Assertions
+			.assertEquals(
+				"0",
+				tmp
+					.filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(m -> m.getId().equals("downloads"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+		Assertions
+			.assertEquals(
+				"1",
+				tmp
+					.filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(m -> m.getId().equals("views"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+
+		Assertions
+			.assertEquals(
+				"2",
+				tmp
+					.filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(m -> m.getId().equals("downloads"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+		Assertions
+			.assertEquals(
+				"6",
+				tmp
+					.filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(m -> m.getId().equals("views"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+	}
+
+}

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb

@@ -0,0 +1,12 @@
+{"result_id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":4}
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