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Merge branch 'beta' into 7096-fileGZip-collector-plugin

This commit is contained in:
Claudio Atzori 2022-04-22 11:22:21 +02:00
parent eabb40fccc a82ec3aaaf
commit 30105f0722
12 changed files with 1016 additions and 247 deletions
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15
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java
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@ -391,4 +391,19 @@ public class OafMapperUtils {
} }
return null; 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;
}
} }

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
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@ -27,6 +27,8 @@ public class Constants {
public static final String UPDATE_CLASS_NAME = "Inferred by OpenAIRE"; 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_MEASURE_BIP_CLASS_ID = "measure:bip";
public static final String UPDATE_SUBJECT_SDG_CLASS_ID = "subject:sdg"; 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_ID = "FOS";
public static final String FOS_CLASS_NAME = "Fields of Science and Technology classification"; public static final String FOS_CLASS_NAME = "Fields of Science and Technology classification";

149
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java Normal file
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@ -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));
}
}

34
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/UsageStatsModel.java Normal file
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@ -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;
}
}

32
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json Normal file
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@ -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
}
]

30
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/config-default.xml Normal file
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@ -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>

99
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml Normal file
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@ -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>

259
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java Normal file
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@ -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());
}
}

12
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb Normal file
View File

@ -0,0 +1,12 @@
{"result_id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":4}
{"result_id":"dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6","downloads":0,"views":1}
{"result_id":"doi_________::17eda2ff77407538fbe5d3d719b9d1c0","downloads":0,"views":1}
{"result_id":"doi_________::1d4dc08605fd0a2be1105d30c63bfea1","downloads":1,"views":3}
{"result_id":"doi_________::2e3527822854ca9816f6dfea5bff61a8","downloads":1,"views":1}
{"result_id":"doi_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":2,"views":3}
{"result_id":"doi_________::3085e4c6e051378ca6157fe7f0430c1f","downloads":0,"views":3}
{"result_id":"doi_________::33f710e6dd30cc5e67e35b371ddc33cf","downloads":0,"views":1}
{"result_id":"doi_________::39738ebf10654732dd3a7af9f24655f8","downloads":1,"views":3}
{"result_id":"doi_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":1,"views":8}
{"result_id":"doi_________::3c3b65f07c1a06c7894397eda1d11bbf","downloads":0,"views":2}
{"result_id":"doi_________::4938a71a884dd481d329657aa543b850","downloads":0,"views":3}

75
dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala
View File

@ -59,52 +59,6 @@ object SparkGenerateDoiBoost {
val workingDirPath = parser.get("workingPath") val workingDirPath = parser.get("workingPath")
val openaireOrganizationPath = parser.get("openaireOrganizationPath") val openaireOrganizationPath = parser.get("openaireOrganizationPath")
val crossrefAggregator = new Aggregator[(String, Publication), Publication, Publication] with Serializable {
override def zero: Publication = new Publication
override def reduce(b: Publication, a: (String, Publication)): Publication = {
if (b == null) {
if (a != null && a._2 != null) {
a._2.setId(a._1)
return a._2
}
} else {
if (a != null && a._2 != null) {
b.mergeFrom(a._2)
b.setId(a._1)
val authors = AuthorMerger.mergeAuthor(b.getAuthor, a._2.getAuthor)
b.setAuthor(authors)
return b
}
}
new Publication
}
override def merge(b1: Publication, b2: Publication): Publication = {
if (b1 == null) {
if (b2 != null)
return b2
} else {
if (b2 != null) {
b1.mergeFrom(b2)
val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor)
b1.setAuthor(authors)
if (b2.getId != null && b2.getId.nonEmpty)
b1.setId(b2.getId)
return b1
}
}
new Publication
}
override def finish(reduction: Publication): Publication = reduction
override def bufferEncoder: Encoder[Publication] = Encoders.kryo[Publication]
override def outputEncoder: Encoder[Publication] = Encoders.kryo[Publication]
}
implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication] implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
implicit val mapEncoderOrg: Encoder[Organization] = Encoders.kryo[Organization] implicit val mapEncoderOrg: Encoder[Organization] = Encoders.kryo[Organization]
implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset] implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset]
@ -175,8 +129,33 @@ object SparkGenerateDoiBoost {
.map(DoiBoostMappingUtil.fixPublication) .map(DoiBoostMappingUtil.fixPublication)
.map(p => (p.getId, p)) .map(p => (p.getId, p))
.groupByKey(_._1) .groupByKey(_._1)
.agg(crossrefAggregator.toColumn) .reduceGroups((left, right) => {
.map(p => p._2) //Check left is not null
if (left != null && left._1 != null) {
//If right is null then return left
if (right == null || right._2 == null)
left
else {
// Here Left and Right are not null
// So we have to merge
val b1 = left._2
val b2 = right._2
b1.mergeFrom(b2)
b1.mergeOAFDataInfo(b2)
val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor)
b1.setAuthor(authors)
if (b2.getId != null && b2.getId.nonEmpty)
b1.setId(b2.getId)
//Return publication Merged
(b1.getId, b1)
}
} else {
// Left is Null so we return right
right
}
})
.filter(s => s != null && s._2 != null)
.map(s => s._2._2)
.write .write
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.save(s"$workingDirPath/doiBoostPublicationFiltered") .save(s"$workingDirPath/doiBoostPublicationFiltered")

73
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java
View File

@ -1,16 +1,13 @@
package eu.dnetlib.dhp.oa.graph.clean; package eu.dnetlib.dhp.oa.graph.clean;
import com.fasterxml.jackson.databind.ObjectMapper; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport; import java.io.Serializable;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import java.util.List;
import eu.dnetlib.dhp.schema.common.ModelConstants; import java.util.Optional;
import eu.dnetlib.dhp.schema.oaf.Context; import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapFunction;
@ -21,12 +18,18 @@ import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import java.io.Serializable; import com.fasterxml.jackson.databind.ObjectMapper;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Context;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class CleanContextSparkJob implements Serializable { public class CleanContextSparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class); private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class);
@ -61,13 +64,11 @@ public class CleanContextSparkJob implements Serializable {
String verifyParam = parser.get("verifyParam"); String verifyParam = parser.get("verifyParam");
log.info("verifyParam: {}", verifyParam); log.info("verifyParam: {}", verifyParam);
String graphTableClassName = parser.get("graphTableClassName"); String graphTableClassName = parser.get("graphTableClassName");
log.info("graphTableClassName: {}", graphTableClassName); log.info("graphTableClassName: {}", graphTableClassName);
Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName); Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
runWithSparkSession( runWithSparkSession(
conf, conf,
@ -78,7 +79,8 @@ public class CleanContextSparkJob implements Serializable {
}); });
} }
private static <T extends Result> void cleanContext(SparkSession spark, String contextId, String verifyParam, String inputPath, Class<T> entityClazz, String workingPath) { private static <T extends Result> void cleanContext(SparkSession spark, String contextId, String verifyParam,
String inputPath, Class<T> entityClazz, String workingPath) {
Dataset<T> res = spark Dataset<T> res = spark
.read() .read()
.textFile(inputPath) .textFile(inputPath)
@ -87,27 +89,42 @@ public class CleanContextSparkJob implements Serializable {
Encoders.bean(entityClazz)); Encoders.bean(entityClazz));
res.map((MapFunction<T, T>) r -> { res.map((MapFunction<T, T>) r -> {
if(!r.getTitle() if (!r
.getTitle()
.stream() .stream()
.filter(t -> t.getQualifier().getClassid() .filter(
t -> t
.getQualifier()
.getClassid()
.equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid()))
.anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))){ .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))) {
return r; return r;
} }
r.setContext(r.getContext().stream().filter(c -> !c.getId().split("::")[0] r
.equalsIgnoreCase(contextId)).collect(Collectors.toList())); .setContext(
r
.getContext()
.stream()
.filter(
c -> !c.getId().split("::")[0]
.equalsIgnoreCase(contextId))
.collect(Collectors.toList()));
return r; return r;
} ,Encoders.bean(entityClazz)) }, Encoders.bean(entityClazz))
.write() .write()
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.option("compression","gzip") .option("compression", "gzip")
.json(workingPath); .json(workingPath);
spark.read().textFile(workingPath).map((MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz), spark
.read()
.textFile(workingPath)
.map(
(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
Encoders.bean(entityClazz)) Encoders.bean(entityClazz))
.write() .write()
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.option("compression","gzip") .option("compression", "gzip")
.json(inputPath); .json(inputPath);
} }
} }

269
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java
View File

@ -1,18 +1,12 @@
package eu.dnetlib.dhp.oa.graph.clean; package eu.dnetlib.dhp.oa.graph.clean;
import com.fasterxml.jackson.core.JsonProcessingException; import java.io.IOException;
import com.fasterxml.jackson.databind.ObjectMapper; import java.nio.file.Files;
import eu.dnetlib.dhp.oa.graph.dump.Constants; import java.nio.file.Path;
import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; import java.util.List;
import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; import java.util.Locale;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.dump.oaf.Instance;
import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute;
import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaRDD;
@ -27,11 +21,20 @@ import org.junit.jupiter.api.Test;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import java.io.IOException; import com.fasterxml.jackson.core.JsonProcessingException;
import java.nio.file.Files; import com.fasterxml.jackson.databind.ObjectMapper;
import java.nio.file.Path;
import java.util.List; import eu.dnetlib.dhp.oa.graph.dump.Constants;
import java.util.Locale; import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest;
import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.dump.oaf.Instance;
import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute;
import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class CleanContextTest { public class CleanContextTest {
@ -78,18 +81,22 @@ public class CleanContextTest {
.getPath(); .getPath();
final String prefix = "gcube "; final String prefix = "gcube ";
spark
spark.read().textFile(sourcePath).map((MapFunction<String, Publication>) r -> OBJECT_MAPPER.readValue(r, Publication.class), Encoders.bean(Publication.class)) .read()
.write().json(workingDir.toString() + "/publication"); .textFile(sourcePath)
.map(
(MapFunction<String, Publication>) r -> OBJECT_MAPPER.readValue(r, Publication.class),
Encoders.bean(Publication.class))
.write()
.json(workingDir.toString() + "/publication");
CleanContextSparkJob.main(new String[] { CleanContextSparkJob.main(new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(), "--isSparkSessionManaged", Boolean.FALSE.toString(),
"--inputPath", workingDir.toString() + "/publication", "--inputPath", workingDir.toString() + "/publication",
"-graphTableClassName", Publication.class.getCanonicalName(), "-graphTableClassName", Publication.class.getCanonicalName(),
"-workingPath", workingDir.toString() + "/working", "-workingPath", workingDir.toString() + "/working",
"-contextId","sobigdata", "-contextId", "sobigdata",
"-verifyParam","gCube " "-verifyParam", "gCube "
}); });
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@ -99,61 +106,195 @@ public class CleanContextTest {
Assertions.assertEquals(7, tmp.count()); Assertions.assertEquals(7, tmp.count());
//original result with sobigdata context and gcube as starting string in the main title for the publication // original result with sobigdata context and gcube as starting string in the main title for the publication
Assertions.assertEquals(0, Assertions
tmp.filter(p->p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")).collect().get(0).getContext().size()); .assertEquals(
0,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))
.collect()
.get(0)
.getContext()
.size());
//original result with sobigdata context without gcube as starting string in the main title for the publication // original result with sobigdata context without gcube as starting string in the main title for the publication
Assertions.assertEquals(1, Assertions
tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().size()); .assertEquals(
Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().get(0).getId() ); 1,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
.collect()
.get(0)
.getContext()
.size());
Assertions
.assertEquals(
"sobigdata::projects::2",
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
.collect()
.get(0)
.getContext()
.get(0)
.getId());
//original result with sobigdata context with gcube as starting string in the subtitle // original result with sobigdata context with gcube as starting string in the subtitle
Assertions.assertEquals(1, Assertions
tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().size()); .assertEquals(
Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().get(0).getId() ); 1,
List<StructuredProperty> titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getTitle(); tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
.collect()
.get(0)
.getContext()
.size());
Assertions
.assertEquals(
"sobigdata::projects::2",
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
.collect()
.get(0)
.getContext()
.get(0)
.getId());
List<StructuredProperty> titles = tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
.collect()
.get(0)
.getTitle();
Assertions.assertEquals(1, titles.size()); Assertions.assertEquals(1, titles.size());
Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix));
Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid());
//original result with sobigdata context with gcube not as starting string in the main title // original result with sobigdata context with gcube not as starting string in the main title
Assertions.assertEquals(1, Assertions
tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().size()); .assertEquals(
Assertions.assertEquals("sobigdata::projects::1",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().get(0).getId() ); 1,
titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getTitle(); tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f"))
.collect()
.get(0)
.getContext()
.size());
Assertions
.assertEquals(
"sobigdata::projects::1",
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f"))
.collect()
.get(0)
.getContext()
.get(0)
.getId());
titles = tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f"))
.collect()
.get(0)
.getTitle();
Assertions.assertEquals(1, titles.size()); Assertions.assertEquals(1, titles.size());
Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix));
Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()) ); Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()));
Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid());
//original result with sobigdata in context and also other contexts with gcube as starting string for the main title // original result with sobigdata in context and also other contexts with gcube as starting string for the main
Assertions.assertEquals(1, // title
tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().size()); Assertions
Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().get(0).getId() ); .assertEquals(
titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getTitle(); 1,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53"))
.collect()
.get(0)
.getContext()
.size());
Assertions
.assertEquals(
"dh-ch",
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53"))
.collect()
.get(0)
.getContext()
.get(0)
.getId());
titles = tmp
.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53"))
.collect()
.get(0)
.getTitle();
Assertions.assertEquals(1, titles.size()); Assertions.assertEquals(1, titles.size());
Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) ); Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix));
Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid());
//original result with multiple main title one of which whith gcube as starting string and with 2 contextes // original result with multiple main title one of which whith gcube as starting string and with 2 contextes
Assertions.assertEquals(1, Assertions
tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().size()); .assertEquals(
Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().get(0).getId() ); 1,
titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getTitle(); tmp
.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff"))
.collect()
.get(0)
.getContext()
.size());
Assertions
.assertEquals(
"dh-ch",
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff"))
.collect()
.get(0)
.getContext()
.get(0)
.getId());
titles = tmp
.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff"))
.collect()
.get(0)
.getTitle();
Assertions.assertEquals(2, titles.size()); Assertions.assertEquals(2, titles.size());
Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix)) ); Assertions
.assertTrue(
titles
.stream()
.anyMatch(
t -> t.getQualifier().getClassid().equals("main title")
&& t.getValue().toLowerCase().startsWith(prefix)));
// original result without sobigdata in context with gcube as starting string for the main title
//original result without sobigdata in context with gcube as starting string for the main title Assertions
Assertions.assertEquals(1, .assertEquals(
tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().size()); 1,
Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().get(0).getId() ); tmp
titles = tmp.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getTitle(); .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8"))
.collect()
.get(0)
.getContext()
.size());
Assertions
.assertEquals(
"dh-ch",
tmp
.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8"))
.collect()
.get(0)
.getContext()
.get(0)
.getId());
titles = tmp
.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8"))
.collect()
.get(0)
.getTitle();
Assertions.assertEquals(2, titles.size()); Assertions.assertEquals(2, titles.size());
Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix))); Assertions
.assertTrue(
titles
.stream()
.anyMatch(
t -> t.getQualifier().getClassid().equals("main title")
&& t.getValue().toLowerCase().startsWith(prefix)));
} }
} }