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merge branch with master

This commit is contained in:
Miriam Baglioni 2020-09-23 17:33:49 +02:00
parent 39eb8ab25b 9e681609fd
commit 0d83f47166
10 changed files with 393 additions and 38 deletions
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50
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java
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@ -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";
log.info("stats: {}", statsPath);
final String dbUrl = parser.get("dbUrl");
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());
}
}
}
}

17
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java
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@ -47,8 +47,9 @@ 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();
@ -116,7 +117,8 @@ public class IndexNotificationsJob {
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 -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic()))
.filter(s -> verifyConditions(e.getMap(), s.conditionsAsMap()))
.map(s -> generateNotification(s, e, date))
.collect(Collectors.toList());
@ -147,15 +149,18 @@ public class IndexNotificationsJob {
if (conditions.containsKey("trust")
&& !SubscriptionUtils
.verifyFloatRange(map.getTrust(), conditions.get("trust").get(0).getValue(), conditions.get("trust").get(0).getOtherValue())) {
.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()))) {
.anyMatch(
c -> SubscriptionUtils
.verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) {
return false;
}

113
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java Normal file
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@ -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;
}
}

28
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/stats/DatasourceStats.java
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@ -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() {
return topics;
public String getTopic() {
return topic;
}
public void setTopics(final Map<String, Long> topics) {
this.topics = topics;
public void setTopic(final String topic) {
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;
}
}

6
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/stats/StatsAggregator.java
View File

@ -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;
}

18
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/config-default.xml Normal file
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@ -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>

137
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/notifications_only/oozie_app/workflow.xml Normal file
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@ -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>

28
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml
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@ -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[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="index_notifications">
<action name="stats">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>IndexNotificationsOnESJob</name>
<class>eu.dnetlib.dhp.broker.oa.IndexNotificationsJob</class>
<name>GenerateStatsJob</name>
<class>eu.dnetlib.dhp.broker.oa.GenerateStatsJob</class>
<jar>dhp-broker-events-${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}
@ -123,14 +135,14 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--index</arg><arg>${esNotificationsIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg>
<arg>--dbUrl</arg><arg>${brokerDbUrl}</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"/>

32
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/stats_params.json Normal file
View File

@ -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
}
]

2
pom.xml
View File

@ -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>