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Merge branch 'beta' into dblp_collection_plugin

This commit is contained in:
Alessia Bardi 2024-05-29 16:04:39 +02:00
parent e8a61d5dd5 fe9fb59c90
commit 05ee783c07
74 changed files with 2702 additions and 1365 deletions
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1
.gitignore vendored
View File

@ -27,3 +27,4 @@ spark-warehouse
/**/.factorypath
/**/.scalafmt.conf
/.java-version
/dhp-shade-package/dependency-reduced-pom.xml

10
dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectPropertiesTest.java
View File

@ -80,7 +80,15 @@ class WritePredefinedProjectPropertiesTest {
mojo.outputFile = testFolder;
// execute
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
try {
mojo.execute();
Assertions.assertTrue(false); // not reached
} catch (Exception e) {
Assertions
.assertTrue(
MojoExecutionException.class.isAssignableFrom(e.getClass()) ||
IllegalArgumentException.class.isAssignableFrom(e.getClass()));
}
}
@Test

26
dhp-common/pom.xml
View File

@ -70,10 +70,7 @@
<groupId>com.ibm.icu</groupId>
<artifactId>icu4j</artifactId>
</dependency>
<dependency>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-common</artifactId>
</dependency>
<dependency>
<groupId>com.github.sisyphsu</groupId>
<artifactId>dateparser</artifactId>
@ -163,7 +160,7 @@
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>${dhp-schemas.artifact}</artifactId>
<artifactId>dhp-schemas</artifactId>
</dependency>
<dependency>
@ -172,4 +169,23 @@
</dependency>
</dependencies>
<!-- dependencies required on JDK9+ because J2EE has been removed -->
<profiles>
<profile>
<id>spark-34</id>
<dependencies>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>2.2.11</version>
</dependency>
<dependency>
<groupId>com.sun.xml.ws</groupId>
<artifactId>jaxws-ri</artifactId>
<version>2.3.3</version>
<type>pom</type>
</dependency>
</dependencies>
</profile>
</profiles>
</project>

2
dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java
View File

@ -38,7 +38,7 @@ public class PacePerson {
PacePerson.class
.getResourceAsStream(
"/eu/dnetlib/dhp/common/name_particles.txt")));
} catch (IOException e) {
} catch (Exception e) {
throw new RuntimeException(e);
}
}

2
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java
View File

@ -217,8 +217,6 @@ public class ZenodoAPIClient implements Serializable {
* part of the url for the DOI Zenodo suggests to use to cite all versions: DOI: 10.xxx/zenodo.656930
* concept_rec_id = 656930
* @return response code
* @throws IOException
* @throws MissingConceptDoiException
*/
public int newVersion(String concept_rec_id) throws IOException, MissingConceptDoiException {
setDepositionId(concept_rec_id, 1);

2
dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpConnector2.java
View File

@ -12,9 +12,7 @@ import java.util.concurrent.TimeUnit;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.math.NumberUtils;
import org.apache.commons.lang3.time.DateUtils;
import org.apache.http.HttpHeaders;
import org.joda.time.Instant;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

8
dhp-common/src/main/resources/eu/dnetlib/scholexplorer/relation/relations.json
View File

@ -154,5 +154,13 @@
"unknown":{
"original":"Unknown",
"inverse":"Unknown"
},
"isamongtopnsimilardocuments": {
"original": "IsAmongTopNSimilarDocuments",
"inverse": "HasAmongTopNSimilarDocuments"
},
"hasamongtopnsimilardocuments": {
"original": "HasAmongTopNSimilarDocuments",
"inverse": "IsAmongTopNSimilarDocuments"
}
}

7
dhp-common/src/main/scala/eu/dnetlib/dhp/application/SparkScalaApplication.scala
View File

@ -65,12 +65,13 @@ abstract class AbstractScalaApplication(
val conf: SparkConf = new SparkConf()
val master = parser.get("master")
log.info(s"Creating Spark session: Master: $master")
SparkSession
val b = SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(master)
.getOrCreate()
if (master != null)
b.master(master)
b.getOrCreate()
}
def reportTotalSize(targetPath: String, outputBasePath: String): Unit = {

19
dhp-common/src/main/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala
View File

@ -65,7 +65,11 @@ object ScholixUtils extends Serializable {
}
def generateScholixResourceFromResult(r: Result): ScholixResource = {
generateScholixResourceFromSummary(ScholixUtils.resultToSummary(r))
val sum = ScholixUtils.resultToSummary(r)
if (sum != null)
generateScholixResourceFromSummary(ScholixUtils.resultToSummary(r))
else
null
}
val statsAggregator: Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] =
@ -153,6 +157,14 @@ object ScholixUtils extends Serializable {
}
def invRel(rel: String): String = {
val semanticRelation = relations.getOrElse(rel.toLowerCase, null)
if (semanticRelation != null)
semanticRelation.inverse
else
null
}
def extractCollectedFrom(summary: ScholixResource): List[ScholixEntityId] = {
if (summary.getCollectedFrom != null && !summary.getCollectedFrom.isEmpty) {
val l: List[ScholixEntityId] = summary.getCollectedFrom.asScala.map { d =>
@ -377,10 +389,7 @@ object ScholixUtils extends Serializable {
if (persistentIdentifiers.isEmpty)
return null
s.setLocalIdentifier(persistentIdentifiers.asJava)
if (r.isInstanceOf[Publication])
s.setTypology(Typology.publication)
else
s.setTypology(Typology.dataset)
// s.setTypology(r.getResulttype.getClassid)
s.setSubType(r.getInstance().get(0).getInstancetype.getClassname)

100
dhp-pace-core/pom.xml
View File

@ -24,7 +24,7 @@
<executions>
<execution>
<id>scala-compile-first</id>
<phase>initialize</phase>
<phase>process-resources</phase>
<goals>
<goal>add-source</goal>
<goal>compile</goal>
@ -59,14 +59,6 @@
<groupId>edu.cmu</groupId>
<artifactId>secondstring</artifactId>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
@ -91,10 +83,6 @@
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
</dependency>
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
@ -113,4 +101,90 @@
</dependency>
</dependencies>
<profiles>
<profile>
<id>spark-24</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.4.0</version>
<executions>
<execution>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>src/main/spark-2</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>spark-34</id>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.4.0</version>
<executions>
<execution>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>src/main/spark-2</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>spark-35</id>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.4.0</version>
<executions>
<execution>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>src/main/spark-35</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
</project>

13
dhp-pace-core/src/main/java/eu/dnetlib/pace/common/AbstractPaceFunctions.java
View File

@ -1,12 +1,6 @@
package eu.dnetlib.pace.common;
import com.google.common.base.Joiner;
import com.google.common.collect.Sets;
import com.ibm.icu.text.Transliterator;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import java.io.IOException;
import java.io.StringWriter;
import java.nio.charset.StandardCharsets;
@ -15,6 +9,13 @@ import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import com.google.common.base.Joiner;
import com.google.common.collect.Sets;
import com.ibm.icu.text.Transliterator;
/**
* Set of common functions for the framework
*

4
dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkModel.scala
View File

@ -3,7 +3,7 @@ package eu.dnetlib.pace.model
import com.jayway.jsonpath.{Configuration, JsonPath}
import eu.dnetlib.pace.common.AbstractPaceFunctions
import eu.dnetlib.pace.config.{DedupConfig, Type}
import eu.dnetlib.pace.util.MapDocumentUtil
import eu.dnetlib.pace.util.{MapDocumentUtil, SparkCompatUtils}
import org.apache.commons.lang3.StringUtils
import org.apache.spark.sql.catalyst.encoders.RowEncoder
import org.apache.spark.sql.catalyst.expressions.GenericRowWithSchema
@ -52,7 +52,7 @@ case class SparkModel(conf: DedupConfig) {
val orderingFieldPosition: Int = schema.fieldIndex(orderingFieldName)
val parseJsonDataset: (Dataset[String] => Dataset[Row]) = df => {
df.map(r => rowFromJson(r))(RowEncoder(schema))
df.map(r => rowFromJson(r))(SparkCompatUtils.encoderFor(schema))
}
def rowFromJson(json: String): Row = {

12
dhp-pace-core/src/main/spark-2/eu/dnetlib/pace/util/SparkCompatUtils.scala Normal file
View File

@ -0,0 +1,12 @@
package eu.dnetlib.pace.util
import org.apache.spark.sql.Row
import org.apache.spark.sql.catalyst.encoders.{ExpressionEncoder, RowEncoder}
import org.apache.spark.sql.types.StructType
object SparkCompatUtils {
def encoderFor(schema: StructType): ExpressionEncoder[Row] = {
RowEncoder(schema)
}
}

12
dhp-pace-core/src/main/spark-35/eu/dnetlib/pace/util/SparkCompatUtils.scala Normal file
View File

@ -0,0 +1,12 @@
package eu.dnetlib.pace.util
import org.apache.spark.sql.Row
import org.apache.spark.sql.catalyst.encoders.ExpressionEncoder
import org.apache.spark.sql.types.StructType
object SparkCompatUtils {
def encoderFor(schema: StructType): ExpressionEncoder[Row] = {
ExpressionEncoder(schema)
}
}

1
dhp-pace-core/src/test/java/eu/dnetlib/pace/util/UtilTest.java
View File

@ -11,6 +11,7 @@ import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import eu.dnetlib.pace.model.Person;
import jdk.nashorn.internal.ir.annotations.Ignore;
public class UtilTest {

169
dhp-shade-package/pom.xml Normal file
View File

@ -0,0 +1,169 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.2.5-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
<artifactId>dhp-shade-package</artifactId>
<packaging>jar</packaging>
<distributionManagement>
<site>
<id>DHPSite</id>
<url>${dhp.site.stage.path}/dhp-common</url>
</site>
</distributionManagement>
<description>This module create a jar of all module dependencies</description>
<dependencies>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-actionmanager</artifactId>
<version>${project.version}</version>
</dependency>
<!-- <dependency>-->
<!-- <groupId>eu.dnetlib.dhp</groupId>-->
<!-- <artifactId>dhp-aggregation</artifactId>-->
<!-- <version>${project.version}</version>-->
<!-- </dependency>-->
<!-- <dependency>-->
<!-- <groupId>eu.dnetlib.dhp</groupId>-->
<!-- <artifactId>dhp-blacklist</artifactId>-->
<!-- <version>${project.version}</version>-->
<!-- </dependency>-->
<!-- <dependency>-->
<!-- <groupId>eu.dnetlib.dhp</groupId>-->
<!-- <artifactId>dhp-broker-events</artifactId>-->
<!-- <version>${project.version}</version>-->
<!-- </dependency>-->
<!-- <dependency>-->
<!-- <groupId>eu.dnetlib.dhp</groupId>-->
<!-- <artifactId>dhp-dedup-openaire</artifactId>-->
<!-- <version>${project.version}</version>-->
<!-- </dependency>-->
<!-- <dependency>-->
<!-- <groupId>eu.dnetlib.dhp</groupId>-->
<!-- <artifactId>dhp-enrichment</artifactId>-->
<!-- <version>${project.version}</version>-->
<!-- </dependency>-->
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-graph-mapper</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-graph-provision</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-impact-indicators</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-stats-actionsets</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-stats-hist-snaps</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-stats-monitor-irish</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-stats-promote</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-stats-update</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-swh</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-usage-raw-data-update</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-usage-stats-build</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels</mainClass>
</transformer>
<!-- This is needed if you have dependencies that use Service Loader. Most Google Cloud client libraries do. -->
<transformer
implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
<transformer
implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
<resource>META-INF/cxf/bus-extensions.txt</resource>
</transformer>
</transformers>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/maven/**</exclude>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
<relocations>
<relocation>
<pattern>com</pattern>
<shadedPattern>repackaged.com.google.common</shadedPattern>
<includes>
<include>com.google.common.**</include>
</includes>
</relocation>
</relocations>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>

3
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
View File

@ -9,6 +9,7 @@ import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.BZip2Codec;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
@ -106,7 +107,7 @@ public class PrepareAffiliationRelations implements Serializable {
.union(openAPCRelations)
.union(dataciteRelations)
.saveAsHadoopFile(
outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
});
}

3
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java
View File

@ -10,6 +10,7 @@ import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.BZip2Codec;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
@ -83,7 +84,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
resultsRDD
.union(projectsRDD)
.saveAsHadoopFile(
outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
});
}

45
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
View File

@ -12,6 +12,7 @@ import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.sql.*;
import org.apache.spark.sql.types.StructType;
@ -70,6 +71,9 @@ public class CreateActionSetFromWebEntries implements Serializable {
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String blackListInputPath = parser.get("blackListPath");
log.info("blackListInputPath: {}", blackListInputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
@ -77,29 +81,35 @@ public class CreateActionSetFromWebEntries implements Serializable {
isSparkSessionManaged,
spark -> {
createActionSet(spark, inputPath, outputPath);
createActionSet(spark, inputPath, outputPath, blackListInputPath);
});
}
public static void createActionSet(SparkSession spark, String inputPath,
String outputPath) {
String outputPath, String blackListInputPath) {
final Dataset<Row> dataset = readWebCrawl(spark, inputPath)
.filter("publication_year <= 2020 or country_code=='IE'")
.filter("country_code=='IE'")
.drop("publication_year");
dataset.flatMap((FlatMapFunction<Row, Relation>) row -> {
List<Relation> ret = new ArrayList<>();
final String ror = ROR_PREFIX
+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror));
ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror));
final Dataset<Row> blackList = readBlackList(spark, blackListInputPath);
return ret
.iterator();
}, Encoders.bean(Relation.class))
dataset
.join(blackList, dataset.col("id").equalTo(blackList.col("OpenAlexId")), "left")
.filter((FilterFunction<Row>) r -> r.getAs("OpenAlexId") == null)
.drop("OpenAlexId")
.flatMap((FlatMapFunction<Row, Relation>) row -> {
List<Relation> ret = new ArrayList<>();
final String ror = ROR_PREFIX
+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror));
ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror));
return ret
.iterator();
}, Encoders.bean(Relation.class))
.toJavaRDD()
.map(p -> new AtomicAction(p.getClass(), p))
.mapToPair(
@ -136,6 +146,15 @@ public class CreateActionSetFromWebEntries implements Serializable {
}
private static Dataset<Row> readBlackList(SparkSession spark, String inputPath) {
return spark
.read()
.option("header", true)
.csv(inputPath)
.select("OpenAlexId");
}
private static List<Relation> createAffiliationRelationPairPMCID(String pmcid, String ror) {
if (pmcid == null)
return new ArrayList<>();

12
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestCollectorPlugin.java
View File

@ -1,6 +1,7 @@
package eu.dnetlib.dhp.collection.plugin.rest;
import java.util.Map;
import java.util.Optional;
import java.util.Spliterator;
import java.util.Spliterators;
@ -9,6 +10,8 @@ import java.util.stream.StreamSupport;
import org.apache.commons.lang3.StringUtils;
import com.google.gson.Gson;
import eu.dnetlib.dhp.collection.ApiDescriptor;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
@ -47,6 +50,9 @@ public class RestCollectorPlugin implements CollectorPlugin {
final String entityXpath = api.getParams().get("entityXpath");
final String authMethod = api.getParams().get("authMethod");
final String authToken = api.getParams().get("authToken");
final String requestHeaderMap = api.getParams().get("requestHeaderMap");
Gson gson = new Gson();
Map requestHeaders = gson.fromJson(requestHeaderMap, Map.class);
final String resultSizeValue = Optional
.ofNullable(api.getParams().get("resultSizeValue"))
.filter(StringUtils::isNotBlank)
@ -64,9 +70,6 @@ public class RestCollectorPlugin implements CollectorPlugin {
if (StringUtils.isBlank(resultFormatValue)) {
throw new CollectorException("Param 'resultFormatValue' is null or empty");
}
if (StringUtils.isBlank(queryParams)) {
throw new CollectorException("Param 'queryParams' is null or empty");
}
if (StringUtils.isBlank(entityXpath)) {
throw new CollectorException("Param 'entityXpath' is null or empty");
}
@ -92,7 +95,8 @@ public class RestCollectorPlugin implements CollectorPlugin {
entityXpath,
authMethod,
authToken,
resultOutputFormat);
resultOutputFormat,
requestHeaders);
return StreamSupport
.stream(

62
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java
View File

@ -9,6 +9,7 @@ import java.net.URL;
import java.net.URLEncoder;
import java.nio.charset.StandardCharsets;
import java.util.Iterator;
import java.util.Map;
import java.util.Queue;
import java.util.concurrent.PriorityBlockingQueue;
@ -34,6 +35,8 @@ import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import com.google.common.collect.Maps;
import eu.dnetlib.dhp.collection.plugin.utils.JsonUtils;
import eu.dnetlib.dhp.common.collection.CollectorException;
import eu.dnetlib.dhp.common.collection.HttpClientParams;
@ -55,7 +58,7 @@ public class RestIterator implements Iterator<String> {
private final HttpClientParams clientParams;
private final String BASIC = "basic";
private final String AUTHBASIC = "basic";
private final String baseUrl;
private final String resumptionType;
@ -89,6 +92,11 @@ public class RestIterator implements Iterator<String> {
*/
private final String resultOutputFormat;
/*
* Can be used to set additional request headers, like for content negotiation
*/
private Map<String, String> requestHeaders;
/**
* RestIterator class compatible to version 1.3.33
*/
@ -107,7 +115,8 @@ public class RestIterator implements Iterator<String> {
final String entityXpath,
final String authMethod,
final String authToken,
final String resultOutputFormat) {
final String resultOutputFormat,
final Map<String, String> requestHeaders) {
this.clientParams = clientParams;
this.baseUrl = baseUrl;
@ -119,6 +128,7 @@ public class RestIterator implements Iterator<String> {
this.authMethod = authMethod;
this.authToken = authToken;
this.resultOutputFormat = resultOutputFormat;
this.requestHeaders = requestHeaders != null ? requestHeaders : Maps.newHashMap();
this.queryFormat = StringUtils.isNotBlank(resultFormatParam) ? "&" + resultFormatParam + "=" + resultFormatValue
: "";
@ -231,25 +241,20 @@ public class RestIterator implements Iterator<String> {
final URL qUrl = new URL(query);
log.debug("authMethod: {}", this.authMethod);
if ("bearer".equalsIgnoreCase(this.authMethod)) {
log.trace("authMethod before inputStream: {}", resultXml);
final HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + this.authToken);
conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.getMimeType());
conn.setRequestMethod("GET");
theHttpInputStream = conn.getInputStream();
} else if (this.BASIC.equalsIgnoreCase(this.authMethod)) {
log.trace("authMethod before inputStream: {}", resultXml);
final HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Basic " + this.authToken);
conn.setRequestProperty(HttpHeaders.ACCEPT, ContentType.APPLICATION_XML.getMimeType());
conn.setRequestMethod("GET");
theHttpInputStream = conn.getInputStream();
} else {
theHttpInputStream = qUrl.openStream();
if (this.authMethod == "bearer") {
log.trace("RestIterator.downloadPage():: authMethod before inputStream: " + resultXml);
requestHeaders.put("Authorization", "Bearer " + authToken);
// requestHeaders.put("Content-Type", "application/json");
} else if (AUTHBASIC.equalsIgnoreCase(this.authMethod)) {
log.trace("RestIterator.downloadPage():: authMethod before inputStream: " + resultXml);
requestHeaders.put("Authorization", "Basic " + authToken);
// requestHeaders.put("accept", "application/xml");
}
HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
conn.setRequestMethod("GET");
this.setRequestHeader(conn);
resultStream = conn.getInputStream();
this.resultStream = theHttpInputStream;
if ("json".equals(this.resultOutputFormat)) {
resultJson = IOUtils.toString(this.resultStream, StandardCharsets.UTF_8);
resultXml = JsonUtils.convertToXML(resultJson);
@ -380,7 +385,8 @@ public class RestIterator implements Iterator<String> {
try {
if (this.resultTotal == -1) {
this.resultTotal = Integer.parseInt(this.xprResultTotalPath.evaluate(resultNode));
if ("page".equalsIgnoreCase(this.resumptionType) && !this.BASIC.equalsIgnoreCase(this.authMethod)) {
if ("page".equalsIgnoreCase(this.resumptionType)
&& !this.AUTHBASIC.equalsIgnoreCase(this.authMethod)) {
this.resultTotal += 1;
} // to correct the upper bound
log.info("resultTotal was -1 is now: " + this.resultTotal);
@ -433,6 +439,22 @@ public class RestIterator implements Iterator<String> {
}
}
/**
* setRequestHeader
*
* setRequestProperty: Sets the general request property. If a property with the key already exists, overwrite its value with the new value.
* @param conn
*/
private void setRequestHeader(HttpURLConnection conn) {
if (requestHeaders != null) {
for (String key : requestHeaders.keySet()) {
conn.setRequestProperty(key, requestHeaders.get(key));
}
log.debug("Set Request Header with: " + requestHeaders);
}
}
public String getResultFormatValue() {
return this.resultFormatValue;
}

7
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/as_parameters.json
View File

@ -16,5 +16,10 @@
"paramLongName": "isSparkSessionManaged",
"paramDescription": "the hdfs name node",
"paramRequired": false
}
},{
"paramName": "bl",
"paramLongName": "blackListPath",
"paramDescription": "the working path",
"paramRequired": true
}
]

1
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/job.properties
View File

@ -1,2 +1,3 @@
sourcePath=/user/miriam.baglioni/openalex-snapshot/data/works/
outputPath=/tmp/miriam/webcrawlComplete/
blackListPath=/user/miriam.baglioni/openalex-blackList

1
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/workflow.xml
View File

@ -45,6 +45,7 @@
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
<arg>--blackListPath</arg><arg>${blackListPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>

6
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json
View File

@ -625,12 +625,6 @@
"name": "Alimentary Health",
"synonym": []
},
{
"id": "501100011103",
"uri": "http://dx.doi.org/10.13039/501100011103",
"name": "Rann\u00eds",
"synonym": []
},
{
"id": "501100012354",
"uri": "http://dx.doi.org/10.13039/501100012354",

1
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
View File

@ -1025,6 +1025,7 @@ case object Crossref2Oaf {
tp._1 match {
case "electronic" => journal.setIssnOnline(tp._2)
case "print" => journal.setIssnPrinted(tp._2)
case _ =>
}
})
}

56
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/mag/MagUtility.scala
View File

@ -79,23 +79,6 @@ object MagUtility extends Serializable {
private val MAGCollectedFrom = keyValue(ModelConstants.MAG_ID, ModelConstants.MAG_NAME)
private val MAGDataInfo: DataInfo = {
val di = new DataInfo
di.setDeletedbyinference(false)
di.setInferred(false)
di.setInvisible(false)
di.setTrust("0.9")
di.setProvenanceaction(
OafMapperUtils.qualifier(
ModelConstants.SYSIMPORT_ACTIONSET,
ModelConstants.SYSIMPORT_ACTIONSET,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS
)
)
di
}
private val MAGDataInfoInvisible: DataInfo = {
val di = new DataInfo
di.setDeletedbyinference(false)
di.setInferred(false)
@ -453,7 +436,6 @@ object MagUtility extends Serializable {
case "repository" =>
result = new Publication()
result.setDataInfo(MAGDataInfoInvisible)
qualifier(
"0038",
"Other literature type",
@ -488,8 +470,7 @@ object MagUtility extends Serializable {
}
if (result != null) {
if (result.getDataInfo == null)
result.setDataInfo(MAGDataInfo)
result.setDataInfo(MAGDataInfo)
val i = new Instance
i.setInstancetype(tp)
i.setInstanceTypeMapping(
@ -512,7 +493,7 @@ object MagUtility extends Serializable {
return null
result.setCollectedfrom(List(MAGCollectedFrom).asJava)
val pidList = List(
var pidList = List(
structuredProperty(
paper.paperId.get.toString,
qualifier(
@ -525,8 +506,6 @@ object MagUtility extends Serializable {
)
)
result.setPid(pidList.asJava)
result.setOriginalId(pidList.map(s => s.getValue).asJava)
result.setId(s"50|mag_________::${DHPUtils.md5(paper.paperId.get.toString)}")
@ -618,22 +597,23 @@ object MagUtility extends Serializable {
}
val instance = result.getInstance().get(0)
instance.setPid(pidList.asJava)
if (paper.doi.orNull != null)
instance.setAlternateIdentifier(
List(
structuredProperty(
paper.doi.get,
qualifier(
PidType.doi.toString,
PidType.doi.toString,
ModelConstants.DNET_PID_TYPES,
ModelConstants.DNET_PID_TYPES
),
null
)
).asJava
if (paper.doi.orNull != null) {
pidList = pidList ::: List(
structuredProperty(
paper.doi.get,
qualifier(
PidType.doi.toString,
PidType.doi.toString,
ModelConstants.DNET_PID_TYPES,
ModelConstants.DNET_PID_TYPES
),
null
)
)
}
instance.setPid(pidList.asJava)
result.setPid(pidList.asJava)
instance.setUrl(paper.urls.get.asJava)
instance.setHostedby(ModelConstants.UNKNOWN_REPOSITORY)
instance.setCollectedfrom(MAGCollectedFrom)

1
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/mag/SparkMAGtoOAF.scala
View File

@ -38,6 +38,7 @@ class SparkMAGtoOAF(propertyPath: String, args: Array[String], log: Logger)
spark.read
.load(s"$magBasePath/mag_denormalized")
.as[MAGPaper]
.filter(col("doi").isNotNull)
.map(s => MagUtility.convertMAGtoOAF(s))
.filter(s => s != null)
.write

36
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala
View File

@ -2,12 +2,9 @@ package eu.dnetlib.dhp.sx.bio.ebi
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.collection.CollectionUtils
import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH}
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion
import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
import eu.dnetlib.dhp.schema.oaf.Oaf
import eu.dnetlib.dhp.sx.bio.pubmed._
import eu.dnetlib.dhp.utils.DHPUtils.{MAPPER, writeHdfsFile}
import eu.dnetlib.dhp.utils.ISLookupClientFactory
import org.apache.commons.io.IOUtils
import org.apache.hadoop.conf.Configuration
@ -17,13 +14,13 @@ import org.apache.http.client.methods.HttpGet
import org.apache.http.impl.client.HttpClientBuilder
import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.expressions.Aggregator
import org.apache.spark.sql._
import org.apache.spark.sql.expressions.Aggregator
import org.slf4j.{Logger, LoggerFactory}
import java.io.InputStream
import scala.io.Source
import scala.xml.pull.XMLEventReader
import java.io.{ByteArrayInputStream, InputStream}
import java.nio.charset.Charset
import javax.xml.stream.XMLInputFactory
object SparkCreateBaselineDataFrame {
@ -86,7 +83,7 @@ object SparkCreateBaselineDataFrame {
if (response.getStatusLine.getStatusCode > 400) {
tries -= 1
} else
return IOUtils.toString(response.getEntity.getContent)
return IOUtils.toString(response.getEntity.getContent, Charset.defaultCharset())
} catch {
case e: Throwable =>
println(s"Error on requesting ${r.getURI}")
@ -158,7 +155,8 @@ object SparkCreateBaselineDataFrame {
IOUtils.toString(
SparkEBILinksToOaf.getClass.getResourceAsStream(
"/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json"
)
),
Charset.defaultCharset()
)
)
parser.parseArgument(args)
@ -167,15 +165,11 @@ object SparkCreateBaselineDataFrame {
val workingPath = parser.get("workingPath")
log.info("workingPath: {}", workingPath)
val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
log.info("mdstoreOutputVersion: {}", mdstoreOutputVersion)
val cleanedMdStoreVersion = MAPPER.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
val outputBasePath = cleanedMdStoreVersion.getHdfsPath
log.info("outputBasePath: {}", outputBasePath)
val targetPath = parser.get("targetPath")
log.info("targetPath: {}", targetPath)
val hdfsServerUri = parser.get("hdfsServerUri")
log.info("hdfsServerUri: {}", hdfsServerUri)
log.info("hdfsServerUri: {}", targetPath)
val skipUpdate = parser.get("skipUpdate")
log.info("skipUpdate: {}", skipUpdate)
@ -201,10 +195,11 @@ object SparkCreateBaselineDataFrame {
if (!"true".equalsIgnoreCase(skipUpdate)) {
downloadBaseLineUpdate(s"$workingPath/baseline", hdfsServerUri)
val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline", 2000)
val inputFactory = XMLInputFactory.newInstance
val ds: Dataset[PMArticle] = spark.createDataset(
k.filter(i => i._1.endsWith(".gz"))
.flatMap(i => {
val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes()))
val xml = inputFactory.createXMLEventReader(new ByteArrayInputStream(i._2.getBytes()))
new PMParser(xml)
})
)
@ -223,11 +218,8 @@ object SparkCreateBaselineDataFrame {
.map(a => PubMedToOaf.convert(a, vocabularies))
.as[Oaf]
.filter(p => p != null),
s"$outputBasePath/$MDSTORE_DATA_PATH"
targetPath
)
val df = spark.read.text(s"$outputBasePath/$MDSTORE_DATA_PATH")
val mdStoreSize = df.count
writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$mdStoreSize", s"$outputBasePath/$MDSTORE_SIZE_PATH")
}
}

3
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala
View File

@ -1,7 +1,8 @@
package eu.dnetlib.dhp.sx.bio.pubmed
import scala.xml.MetaData
import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader}
import javax.xml.stream.XMLEventReader
import scala.xml.pull.{EvElemEnd, EvElemStart, EvText}
/** @param xml
*/

5
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java
View File

@ -15,10 +15,7 @@ import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
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.junit.jupiter.api.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

4
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCITest.java
View File

@ -119,7 +119,9 @@ public class ReadCOCITest {
workingDir.toString() + "/COCI",
"-outputPath",
workingDir.toString() + "/COCI_json/",
"-inputFile", "input1;input2;input3;input4;input5"
"-inputFile", "input1;input2;input3;input4;input5",
"-format",
"COCI"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());

28
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java
View File

@ -75,7 +75,11 @@ public class CreateASTest {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/webcrawl/")
"/eu/dnetlib/dhp/actionmanager/webcrawl/input/")
.getPath();
String blackListPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/webcrawl/blackList/")
.getPath();
CreateActionSetFromWebEntries
@ -86,7 +90,8 @@ public class CreateASTest {
"-sourcePath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet1"
workingDir.toString() + "/actionSet1",
"-blackListPath", blackListPath
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
@ -96,7 +101,7 @@ public class CreateASTest {
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
Assertions.assertEquals(64, tmp.count());
Assertions.assertEquals(58, tmp.count());
}
@ -109,6 +114,10 @@ public class CreateASTest {
.getResource(
"/eu/dnetlib/dhp/actionmanager/webcrawl/")
.getPath();
String blackListPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/webcrawl/blackList/")
.getPath();
CreateActionSetFromWebEntries
.main(
@ -118,7 +127,8 @@ public class CreateASTest {
"-sourcePath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet1"
workingDir.toString() + "/actionSet1",
"-blackListPath", blackListPath
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
@ -184,7 +194,7 @@ public class CreateASTest {
Assertions
.assertEquals(
5, tmp
2, tmp
.filter(
r -> r
.getSource()
@ -197,7 +207,7 @@ public class CreateASTest {
Assertions
.assertEquals(
5, tmp
2, tmp
.filter(
r -> r
.getTarget()
@ -210,7 +220,7 @@ public class CreateASTest {
Assertions
.assertEquals(
2, tmp
1, tmp
.filter(
r -> r
.getTarget()
@ -224,7 +234,7 @@ public class CreateASTest {
Assertions
.assertEquals(
2, tmp
1, tmp
.filter(
r -> r
.getTarget()
@ -238,7 +248,7 @@ public class CreateASTest {
Assertions
.assertEquals(
1, tmp
0, tmp
.filter(
r -> r
.getTarget()

6
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/OsfPreprintCollectorTest.java
View File

@ -39,8 +39,8 @@ public class OsfPreprintCollectorTest {
private final String resumptionType = "page";
private final String resumptionXpath = "/*/*[local-name()='links']/*[local-name()='next']";
private final String resultSizeParam = "";
private final String resultSizeValue = "";
private final String resultSizeParam = "page[size]";
private final String resultSizeValue = "100";
private final String resultFormatParam = "format";
private final String resultFormatValue = "json";
@ -74,7 +74,7 @@ public class OsfPreprintCollectorTest {
final AtomicInteger i = new AtomicInteger(0);
final Stream<String> stream = this.rcp.collect(this.api, new AggregatorReport());
stream.limit(200).forEach(s -> {
stream.limit(2000).forEach(s -> {
Assertions.assertTrue(s.length() > 0);
i.incrementAndGet();
log.info(s);

41
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/RestCollectorPluginTest.java
View File

@ -4,6 +4,11 @@
package eu.dnetlib.dhp.collection.plugin.rest;
import java.io.IOException;
import java.io.InputStream;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.HashMap;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Stream;
@ -12,6 +17,8 @@ import org.junit.jupiter.api.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.gson.Gson;
import eu.dnetlib.dhp.collection.ApiDescriptor;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
import eu.dnetlib.dhp.common.collection.CollectorException;
@ -25,18 +32,18 @@ class RestCollectorPluginTest {
private static final Logger log = LoggerFactory.getLogger(RestCollectorPluginTest.class);
private final String baseUrl = "https://share.osf.io/api/v2/search/creativeworks/_search";
private final String resumptionType = "count";
private final String resumptionParam = "from";
private final String entityXpath = "//hits/hits";
private final String resumptionXpath = "//hits";
private final String resultTotalXpath = "//hits/total";
private final String resultFormatParam = "format";
private final String baseUrl = "https://ddh-openapi.worldbank.org/search";
private final String resumptionType = "discover";
private final String resumptionParam = "skip";
private final String entityXpath = "//*[local-name()='data']";
private final String resumptionXpath = "";
private final String resultTotalXpath = "//*[local-name()='count']";
private final String resultFormatParam = "";
private final String resultFormatValue = "json";
private final String resultSizeParam = "size";
private final String resultSizeParam = "top";
private final String resultSizeValue = "10";
// private String query = "q=%28sources%3ASocArXiv+AND+type%3Apreprint%29";
private final String query = "q=%28sources%3AengrXiv+AND+type%3Apreprint%29";
private final String query = "";
// private String query = "=(sources:engrXiv AND type:preprint)";
private final String protocolDescriptor = "rest_json2xml";
@ -56,6 +63,7 @@ class RestCollectorPluginTest {
params.put("resultSizeValue", resultSizeValue);
params.put("queryParams", query);
params.put("entityXpath", entityXpath);
params.put("requestHeaderMap", "{\"User-Agent\": \"OpenAIRE DEV\"}");
api.setBaseUrl(baseUrl);
api.setParams(params);
@ -78,4 +86,19 @@ class RestCollectorPluginTest {
log.info("{}", i.intValue());
Assertions.assertTrue(i.intValue() > 0);
}
@Disabled
@Test
void testUrl() throws IOException {
String url_s = "https://ddh-openapi.worldbank.org/search?&top=10";
URL url = new URL(url_s);
final HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestMethod("GET");
conn.setRequestProperty("User-Agent", "OpenAIRE");
Gson gson = new Gson();
System.out.println("Request header");
System.out.println(gson.toJson(conn.getHeaderFields()));
InputStream inputStream = conn.getInputStream();
}
}

2
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/RestIteratorTest.java
View File

@ -44,7 +44,7 @@ public class RestIteratorTest {
final RestIterator iterator = new RestIterator(clientParams, baseUrl, resumptionType, resumptionParam,
resumptionXpath, resultTotalXpath, resultFormatParam, resultFormatValue, resultSizeParam, resultSizeValue,
query, entityXpath, authMethod, authToken, resultOffsetParam);
query, entityXpath, authMethod, authToken, resultOffsetParam, null);
int i = 20;
while (iterator.hasNext() && i > 0) {
String result = iterator.next();

0
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/part-00000 → dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/input/part-00000
View File

0
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/part-00001 → dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/input/part-00001
View File

0
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/part-00002 → dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/input/part-00002
View File

4
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/crossref/issn_pub.json
View File

@ -789,10 +789,6 @@
"value": "2227-9717",
"type": "electronic"
},
{
"value": "VALUE",
"type": "PIPPO"
},
{
"value": "1063-4584",
"type": "pu"

13
dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala
View File

@ -2,7 +2,9 @@ package eu.dnetlib.dhp.collection.crossref
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
import org.junit.jupiter.api.BeforeEach
import eu.dnetlib.dhp.collection.crossref.Crossref2Oaf.TransformationType
import org.apache.commons.io.IOUtils
import org.junit.jupiter.api.{BeforeEach, Test}
import org.junit.jupiter.api.extension.ExtendWith
import org.mockito.junit.jupiter.MockitoExtension
import org.slf4j.{Logger, LoggerFactory}
@ -18,4 +20,13 @@ class CrossrefMappingTest extends AbstractVocabularyTest {
super.setUpVocabulary()
}
@Test
def mappingRecord(): Unit = {
val input =
IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/issn_pub.json"), "utf-8")
println(Crossref2Oaf.convert(input, vocabularies, TransformationType.All))
}
}

7
dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/mag/MAGMappingTest.scala
View File

@ -3,6 +3,7 @@ package eu.dnetlib.dhp.collection.mag
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.schema.oaf.{Dataset, Publication, Result}
import org.apache.spark.sql.SparkSession
import org.apache.spark.sql.functions.col
import org.junit.jupiter.api.Assertions._
import org.junit.jupiter.api.Test
@ -18,10 +19,8 @@ class MAGMappingTest {
.master("local[*]")
.getOrCreate()
val s = new SparkMagOrganizationAS(null, null, null)
s.generateAS(spark, "/home/sandro/Downloads/mag_test", "/home/sandro/Downloads/mag_AS")
val s = new SparkMAGtoOAF(null, null, null)
s.convertMAG(spark, "/Users/sandro/Downloads/", "/Users/sandro/Downloads/mag_OAF")
}
@Test

20
dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
View File

@ -16,6 +16,7 @@ import org.mockito.junit.jupiter.MockitoExtension
import java.io.{BufferedReader, InputStream, InputStreamReader}
import java.util.zip.GZIPInputStream
import javax.xml.stream.XMLInputFactory
import scala.collection.JavaConverters._
import scala.collection.mutable.ListBuffer
import scala.io.Source
@ -49,10 +50,8 @@ class BioScholixTest extends AbstractVocabularyTest {
@Test
def testEBIData() = {
val inputXML = Source
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
.mkString
val xml = new XMLEventReader(Source.fromBytes(inputXML.getBytes()))
val inputFactory = XMLInputFactory.newInstance
val xml = inputFactory.createXMLEventReader(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
new PMParser(xml).foreach(s => println(mapper.writeValueAsString(s)))
}
@ -91,9 +90,10 @@ class BioScholixTest extends AbstractVocabularyTest {
@Test
def testParsingPubmedXML(): Unit = {
val xml = new XMLEventReader(
Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
)
val inputFactory = XMLInputFactory.newInstance
val xml = inputFactory.createXMLEventReader(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
val parser = new PMParser(xml)
parser.foreach(checkPMArticle)
}
@ -156,9 +156,9 @@ class BioScholixTest extends AbstractVocabularyTest {
@Test
def testPubmedMapping(): Unit = {
val xml = new XMLEventReader(
Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
)
val inputFactory = XMLInputFactory.newInstance
val xml = inputFactory.createXMLEventReader(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
val parser = new PMParser(xml)
val results = ListBuffer[Oaf]()
parser.foreach(x => results += PubMedToOaf.convert(x, vocabularies))

24
dhp-workflows/dhp-dedup-openaire/pom.xml
View File

@ -53,24 +53,10 @@
<artifactId>dhp-pace-core</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</dependency>
<dependency>
<groupId>org.scala-lang.modules</groupId>
<artifactId>scala-java8-compat_${scala.binary.version}</artifactId>
<version>1.0.2</version>
</dependency>
<dependency>
<groupId>org.scala-lang.modules</groupId>
<artifactId>scala-collection-compat_${scala.binary.version}</artifactId>
<version>2.11.0</version>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_${scala.binary.version}</artifactId>
@ -79,16 +65,10 @@
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_${scala.binary.version}</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-graphx_${scala.binary.version}</artifactId>
</dependency>
<dependency>
<groupId>com.arakelian</groupId>
<artifactId>java-jq</artifactId>
</dependency>
<dependency>
<groupId>dom4j</groupId>
<artifactId>dom4j</artifactId>
@ -101,10 +81,6 @@
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>

4
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java
View File

@ -42,6 +42,7 @@ import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.util.SparkCompatUtils;
import scala.Tuple3;
import scala.collection.JavaConversions;
@ -148,8 +149,7 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
Dataset<Row> pivotHistory = spark
.createDataset(
Collections.emptyList(),
RowEncoder
.apply(StructType.fromDDL("id STRING, lastUsage STRING")));
SparkCompatUtils.encoderFor(StructType.fromDDL("id STRING, lastUsage STRING")));
if (StringUtils.isNotBlank(pivotHistoryDatabase)) {
pivotHistory = spark

14
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPrepareNewOrgs.java
View File

@ -22,7 +22,9 @@ import eu.dnetlib.dhp.oa.dedup.model.OrgSimRel;
import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ -164,12 +166,12 @@ public class SparkPrepareNewOrgs extends AbstractSparkAction {
.map(
(MapFunction<Tuple2<Tuple2<String, Organization>, Tuple2<String, String>>, OrgSimRel>) r -> new OrgSimRel(
"",
r._1()._2().getOriginalId().get(0),
r._1()._2().getLegalname() != null ? r._1()._2().getLegalname().getValue() : "",
r._1()._2().getLegalshortname() != null ? r._1()._2().getLegalshortname().getValue() : "",
r._1()._2().getCountry() != null ? r._1()._2().getCountry().getClassid() : "",
r._1()._2().getWebsiteurl() != null ? r._1()._2().getWebsiteurl().getValue() : "",
r._1()._2().getCollectedfrom().get(0).getValue(),
Optional.ofNullable(r._1()._2().getOriginalId()).map(oid -> oid.get(0)).orElse(null),
Optional.ofNullable(r._1()._2().getLegalname()).map(Field::getValue).orElse(""),
Optional.ofNullable(r._1()._2().getLegalshortname()).map(Field::getValue).orElse(""),
Optional.ofNullable(r._1()._2().getCountry()).map(Qualifier::getClassid).orElse(""),
Optional.ofNullable(r._1()._2().getWebsiteurl()).map(Field::getValue).orElse(""),
Optional.ofNullable(r._1()._2().getCollectedfrom()).map(cf -> cf.get(0).getValue()).orElse(null),
"",
structuredPropertyListToString(r._1()._2().getPid()),
parseECField(r._1()._2().getEclegalbody()),

6
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPrepareOrgRels.java
View File

@ -217,7 +217,7 @@ public class SparkPrepareOrgRels extends AbstractSparkAction {
final Organization o = r._2()._2();
return new OrgSimRel(
r._1()._1(),
o.getOriginalId().get(0),
Optional.ofNullable(o.getOriginalId()).map(oid -> oid.get(0)).orElse(null),
Optional.ofNullable(o.getLegalname()).map(Field::getValue).orElse(""),
Optional.ofNullable(o.getLegalshortname()).map(Field::getValue).orElse(""),
Optional.ofNullable(o.getCountry()).map(Qualifier::getClassid).orElse(""),
@ -249,7 +249,9 @@ public class SparkPrepareOrgRels extends AbstractSparkAction {
.map(
(MapFunction<Tuple2<Tuple2<String, OrgSimRel>, Tuple2<String, Organization>>, OrgSimRel>) r -> {
OrgSimRel orgSimRel = r._1()._2();
orgSimRel.setLocal_id(r._2()._2().getOriginalId().get(0));
orgSimRel
.setLocal_id(
Optional.ofNullable(r._2()._2().getOriginalId()).map(oid -> oid.get(0)).orElse(null));
return orgSimRel;
},
Encoders.bean(OrgSimRel.class));

4
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java
View File

@ -8,7 +8,6 @@ import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.ReduceFunction;
import org.apache.spark.sql.*;
import org.apache.spark.sql.catalyst.encoders.RowEncoder;
import org.apache.spark.sql.types.StructType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -23,6 +22,7 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import eu.dnetlib.pace.util.SparkCompatUtils;
import scala.Tuple2;
import scala.Tuple3;
@ -145,7 +145,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
StructType idsSchema = StructType
.fromDDL("`id` STRING, `dataInfo` STRUCT<`deletedbyinference`:BOOLEAN,`invisible`:BOOLEAN>");
Dataset<Row> allIds = spark.emptyDataset(RowEncoder.apply(idsSchema));
Dataset<Row> allIds = spark.emptyDataset(SparkCompatUtils.encoderFor(idsSchema));
for (EntityType entityType : ModelSupport.entityTypes.keySet()) {
String entityPath = graphBasePath + '/' + entityType.name();

13
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java
View File

@ -50,7 +50,7 @@ public class CleaningRuleMap extends HashMap<Class<?>, SerializableConsumer<Obje
* @param subject
*/
private static void cleanSubjectForVocabulary(String vocabularyId, VocabularyGroup vocabularies,
Subject subject) {
Subject subject) {
vocabularies.find(vocabularyId).ifPresent(vocabulary -> {
if (ModelConstants.DNET_SUBJECT_KEYWORD.equalsIgnoreCase(subject.getQualifier().getClassid())) {
@ -61,13 +61,14 @@ public class CleaningRuleMap extends HashMap<Class<?>, SerializableConsumer<Obje
subject.getQualifier().setClassname(vocabulary.getName());
}
} else {
final String provenanceActionClassId = Optional.ofNullable(subject.getDataInfo())
.map(DataInfo::getProvenanceaction)
.map(Qualifier::getClassid)
.orElse(null);
final String provenanceActionClassId = Optional
.ofNullable(subject.getDataInfo())
.map(DataInfo::getProvenanceaction)
.map(Qualifier::getClassid)
.orElse(null);
if (vocabularyId.equals(subject.getQualifier().getClassid()) &&
!"subject:fos".equals(provenanceActionClassId)) {
!"subject:fos".equals(provenanceActionClassId)) {
Qualifier syn = vocabulary.getSynonymAsQualifier(subject.getValue());
VocabularyTerm term = vocabulary.getTerm(subject.getValue());

5
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/create_scholix_dump_params.json Normal file
View File

@ -0,0 +1,5 @@
[
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": false},
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true},
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the scholix dump", "paramRequired": true}
]

166
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/relation/relations.json Normal file
View File

@ -0,0 +1,166 @@
{
"cites":{
"original":"Cites",
"inverse":"IsCitedBy"
},
"compiles":{
"original":"Compiles",
"inverse":"IsCompiledBy"
},
"continues":{
"original":"Continues",
"inverse":"IsContinuedBy"
},
"derives":{
"original":"IsSourceOf",
"inverse":"IsDerivedFrom"
},
"describes":{
"original":"Describes",
"inverse":"IsDescribedBy"
},
"documents":{
"original":"Documents",
"inverse":"IsDocumentedBy"
},
"hasmetadata":{
"original":"HasMetadata",
"inverse":"IsMetadataOf"
},
"hasassociationwith":{
"original":"HasAssociationWith",
"inverse":"HasAssociationWith"
},
"haspart":{
"original":"HasPart",
"inverse":"IsPartOf"
},
"hasversion":{
"original":"HasVersion",
"inverse":"IsVersionOf"
},
"iscitedby":{
"original":"IsCitedBy",
"inverse":"Cites"
},
"iscompiledby":{
"original":"IsCompiledBy",
"inverse":"Compiles"
},
"iscontinuedby":{
"original":"IsContinuedBy",
"inverse":"Continues"
},
"isderivedfrom":{
"original":"IsDerivedFrom",
"inverse":"IsSourceOf"
},
"isdescribedby":{
"original":"IsDescribedBy",
"inverse":"Describes"
},
"isdocumentedby":{
"original":"IsDocumentedBy",
"inverse":"Documents"
},
"isidenticalto":{
"original":"IsIdenticalTo",
"inverse":"IsIdenticalTo"
},
"ismetadatafor":{
"original":"IsMetadataFor",
"inverse":"IsMetadataOf"
},
"ismetadataof":{
"original":"IsMetadataOf",
"inverse":"IsMetadataFor"
},
"isnewversionof":{
"original":"IsNewVersionOf",
"inverse":"IsPreviousVersionOf"
},
"isobsoletedby":{
"original":"IsObsoletedBy",
"inverse":"Obsoletes"
},
"isoriginalformof":{
"original":"IsOriginalFormOf",
"inverse":"IsVariantFormOf"
},
"ispartof":{
"original":"IsPartOf",
"inverse":"HasPart"
},
"ispreviousversionof":{
"original":"IsPreviousVersionOf",
"inverse":"IsNewVersionOf"
},
"isreferencedby":{
"original":"IsReferencedBy",
"inverse":"References"
},
"isrelatedto":{
"original":"IsRelatedTo",
"inverse":"IsRelatedTo"
},
"isrequiredby":{
"original":"IsRequiredBy",
"inverse":"Requires"
},
"isreviewedby":{
"original":"IsReviewedBy",
"inverse":"Reviews"
},
"issourceof":{
"original":"IsSourceOf",
"inverse":"IsDerivedFrom"
},
"issupplementedby":{
"original":"IsSupplementedBy",
"inverse":"IsSupplementTo"
},
"issupplementto":{
"original":"IsSupplementTo",
"inverse":"IsSupplementedBy"
},
"isvariantformof":{
"original":"IsVariantFormOf",
"inverse":"IsOriginalFormOf"
},
"isversionof":{
"original":"IsVersionOf",
"inverse":"HasVersion"
},
"obsoletes":{
"original":"Obsoletes",
"inverse":"IsObsoletedBy"
},
"references":{
"original":"References",
"inverse":"IsReferencedBy"
},
"requires":{
"original":"Requires",
"inverse":"IsRequiredBy"
},
"related":{
"original":"IsRelatedTo",
"inverse":"IsRelatedTo"
},
"reviews":{
"original":"Reviews",
"inverse":"IsReviewedBy"
},
"unknown":{
"original":"Unknown",
"inverse":"Unknown"
},
"isamongtopnsimilardocuments": {
"original": "IsAmongTopNSimilarDocuments",
"inverse": "HasAmongTopNSimilarDocuments"
},
"hasamongtopnsimilardocuments": {
"original": "HasAmongTopNSimilarDocuments",
"inverse": "IsAmongTopNSimilarDocuments"
}
}

258
dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/ScholexplorerUtils.scala Normal file
View File

@ -0,0 +1,258 @@
package eu.dnetlib.dhp.sx.graph
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.schema.oaf.{KeyValue, Result, StructuredProperty}
import eu.dnetlib.dhp.schema.sx.scholix.{
Scholix,
ScholixCollectedFrom,
ScholixEntityId,
ScholixIdentifier,
ScholixRelationship,
ScholixResource
}
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import scala.collection.JavaConverters._
import scala.io.Source
case class RelationInfo(
source: String,
target: String,
relclass: String,
id: String,
collectedfrom: Seq[RelKeyValue]
) {}
case class RelKeyValue(key: String, value: String) {}
object ScholexplorerUtils {
val OPENAIRE_IDENTIFIER_SCHEMA: String = "OpenAIRE Identifier"
val mapper = new ObjectMapper()
case class RelationVocabulary(original: String, inverse: String) {}
val relations: Map[String, RelationVocabulary] = {
val input = Source
.fromInputStream(
getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/relation/relations.json")
)
.mkString
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input)
json.extract[Map[String, RelationVocabulary]]
}
def invRel(rel: String): String = {
val semanticRelation = relations.getOrElse(rel.toLowerCase, null)
if (semanticRelation != null)
semanticRelation.inverse
else
null
}
def generateDatasourceOpenAIREURLS(id: String): String = {
if (id != null && id.length > 12)
s"https://explore.openaire.eu/search/dataprovider?datasourceId=${id.substring(3)}"
else
null
}
def findURLForPID(
pidValue: List[StructuredProperty],
urls: List[String]
): List[(StructuredProperty, String)] = {
pidValue.map { p =>
val pv = p.getValue
val r = urls.find(u => u.toLowerCase.contains(pv.toLowerCase))
(p, r.orNull)
}
}
def extractTypedIdentifierFromInstance(r: Result): List[ScholixIdentifier] = {
if (r.getInstance() == null || r.getInstance().isEmpty)
return List()
r.getInstance()
.asScala
.filter(i => i.getUrl != null && !i.getUrl.isEmpty)
.filter(i => i.getPid != null && i.getUrl != null)
.flatMap(i => findURLForPID(i.getPid.asScala.toList, i.getUrl.asScala.toList))
.map(i => new ScholixIdentifier(i._1.getValue, i._1.getQualifier.getClassid, i._2))
.distinct
.toList
}
def generateScholixResourceFromResult(result: Result): ScholixResource = {
if (result.getInstance() == null || result.getInstance().size() == 0)
return null
if (result.getPid == null || result.getPid.isEmpty)
return null
val r = new ScholixResource
r.setDnetIdentifier(result.getId)
val persistentIdentifiers: List[ScholixIdentifier] = extractTypedIdentifierFromInstance(result)
if (persistentIdentifiers.isEmpty)
return null
r.setIdentifier(persistentIdentifiers.asJava)
r.setObjectType(result.getResulttype.getClassid)
r.setObjectSubType(
result
.getInstance()
.asScala
.filter(i => i != null && i.getInstancetype != null)
.map(i => i.getInstancetype.getClassname)
.distinct
.head
)
if (result.getTitle != null && result.getTitle.asScala.nonEmpty) {
val titles: List[String] = result.getTitle.asScala.map(t => t.getValue).toList
if (titles.nonEmpty)
r.setTitle(titles.head)
else
return null
}
if (result.getAuthor != null && !result.getAuthor.isEmpty) {
val authors: List[ScholixEntityId] =
result.getAuthor.asScala
.map(a => {
val entity = new ScholixEntityId()
entity.setName(a.getFullname)
if (a.getPid != null && a.getPid.size() > 0)
entity.setIdentifiers(
a.getPid.asScala
.map(sp => {
val id = new ScholixIdentifier()
id.setIdentifier(sp.getValue)
id.setSchema(sp.getQualifier.getClassid)
id
})
.take(3)
.toList
.asJava
)
entity
})
.toList
if (authors.nonEmpty)
r.setCreator(authors.asJava)
}
val dt: List[String] = result
.getInstance()
.asScala
.filter(i => i.getDateofacceptance != null)
.map(i => i.getDateofacceptance.getValue)
.toList
if (dt.nonEmpty)
r.setPublicationDate(dt.distinct.head)
r.setPublisher(
result
.getInstance()
.asScala
.map(i => i.getHostedby)
.filter(h => !"unknown".equalsIgnoreCase(h.getValue))
.map(h => {
val eid = new ScholixEntityId()
eid.setName(h.getValue)
val id = new ScholixIdentifier()
id.setIdentifier(h.getKey)
id.setSchema(OPENAIRE_IDENTIFIER_SCHEMA)
id.setUrl(generateDatasourceOpenAIREURLS(h.getKey))
eid.setIdentifiers(List(id).asJava)
eid
})
.distinct
.asJava
)
r.setCollectedFrom(
result.getCollectedfrom.asScala
.map(cf => {
val scf = new ScholixCollectedFrom()
scf.setProvisionMode("collected")
scf.setCompletionStatus("complete")
val eid = new ScholixEntityId()
eid.setName(cf.getValue)
val id = new ScholixIdentifier()
id.setIdentifier(cf.getKey)
id.setSchema(OPENAIRE_IDENTIFIER_SCHEMA)
id.setUrl(generateDatasourceOpenAIREURLS(cf.getKey))
eid.setIdentifiers(List(id).asJava)
scf.setProvider(eid)
scf
})
.asJava
)
r
}
def generateScholix(relation: RelationInfo, source: ScholixResource): Scholix = {
val s: Scholix = new Scholix
s.setSource(source)
if (relation.collectedfrom != null && relation.collectedfrom.nonEmpty)
s.setLinkprovider(
relation.collectedfrom
.map(cf => {
val eid = new ScholixEntityId()
eid.setName(cf.value)
val id = new ScholixIdentifier()
id.setIdentifier(cf.key)
id.setSchema(OPENAIRE_IDENTIFIER_SCHEMA)
id.setUrl(generateDatasourceOpenAIREURLS(cf.key))
eid.setIdentifiers(List(id).asJava)
eid
})
.toList
.asJava
)
else {
val eid = new ScholixEntityId()
eid.setName("OpenAIRE")
val id = new ScholixIdentifier()
id.setIdentifier("10|infrastruct_::f66f1bd369679b5b077dcdf006089556")
id.setSchema(OPENAIRE_IDENTIFIER_SCHEMA)
id.setUrl(generateDatasourceOpenAIREURLS(id.getIdentifier))
eid.setIdentifiers(List(id).asJava)
s.setLinkprovider(List(eid).asJava)
}
s.setIdentifier(relation.id)
val semanticRelation = relations.getOrElse(relation.relclass.toLowerCase, null)
if (semanticRelation == null)
return null
s.setRelationship(
new ScholixRelationship(semanticRelation.original, "datacite", semanticRelation.inverse)
)
s.setPublicationDate(source.getPublicationDate)
s.setPublisher(source.getPublisher)
val mockTarget = new ScholixResource
mockTarget.setDnetIdentifier(relation.target)
s.setTarget(mockTarget)
s
}
def updateTarget(s: Scholix, t: ScholixResource): String = {
s.setTarget(t)
val spublishers: Seq[ScholixEntityId] =
if (s.getPublisher != null && !s.getPublisher.isEmpty) s.getPublisher.asScala else List()
val tpublishers: Seq[ScholixEntityId] =
if (t.getPublisher != null && !t.getPublisher.isEmpty) t.getPublisher.asScala else List()
val mergedPublishers = spublishers.union(tpublishers).distinct.take(10).toList
s.setPublisher(mergedPublishers.asJava)
mapper.writeValueAsString(s)
}
}

141
dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateScholexplorerDump.scala Normal file
View File

@ -0,0 +1,141 @@
package eu.dnetlib.dhp.sx.graph
import eu.dnetlib.dhp.application.AbstractScalaApplication
import eu.dnetlib.dhp.schema.oaf.{
KeyValue,
OtherResearchProduct,
Publication,
Relation,
Result,
Software,
Dataset => OafDataset
}
import eu.dnetlib.dhp.schema.sx.scholix.{Scholix, ScholixResource}
import org.apache.spark.sql.functions.{col, concat, expr, first, md5}
import org.apache.spark.sql.types.StructType
import org.apache.spark.sql._
import org.slf4j.{Logger, LoggerFactory}
class SparkCreateScholexplorerDump(propertyPath: String, args: Array[String], log: Logger)
extends AbstractScalaApplication(propertyPath, args, log: Logger) {
/** Here all the spark applications runs this method
* where the whole logic of the spark node is defined
*/
override def run(): Unit = {
val sourcePath = parser.get("sourcePath")
log.info("sourcePath: {}", sourcePath)
val targetPath = parser.get("targetPath")
log.info("targetPath: {}", targetPath)
generateBidirectionalRelations(sourcePath, targetPath, spark)
generateScholixResource(sourcePath, targetPath, spark)
generateScholix(targetPath, spark)
}
def generateScholixResource(inputPath: String, outputPath: String, spark: SparkSession): Unit = {
val entityMap: Map[String, StructType] = Map(
"publication" -> Encoders.bean(classOf[Publication]).schema,
"dataset" -> Encoders.bean(classOf[OafDataset]).schema,
"software" -> Encoders.bean(classOf[Software]).schema,
"otherresearchproduct" -> Encoders.bean(classOf[OtherResearchProduct]).schema
)
implicit val scholixResourceEncoder: Encoder[ScholixResource] = Encoders.bean(classOf[ScholixResource])
implicit val resultEncoder: Encoder[Result] = Encoders.bean(classOf[Result])
val resDs = spark.emptyDataset[ScholixResource]
val scholixResourceDS = entityMap.foldLeft[Dataset[ScholixResource]](resDs)((res, item) => {
println(s"adding ${item._1}")
res.union(
spark.read
.schema(item._2)
.json(s"$inputPath/${item._1}")
.as[Result]
.map(r => ScholexplorerUtils.generateScholixResourceFromResult(r))
.filter(s => s != null)
)
})
scholixResourceDS.write.mode(SaveMode.Overwrite).save(s"$outputPath/resource")
}
def generateBidirectionalRelations(inputPath: String, otuputPath: String, spark: SparkSession): Unit = {
val relSchema = Encoders.bean(classOf[Relation]).schema
val relDF = spark.read
.schema(relSchema)
.json(s"$inputPath/relation")
.where(
"datainfo.deletedbyinference is false and source like '50%' and target like '50%' " +
"and relClass <> 'merges' and relClass <> 'isMergedIn'"
)
.select("source", "target", "collectedfrom", "relClass")
def invRel: String => String = { s =>
ScholexplorerUtils.invRel(s)
}
import org.apache.spark.sql.functions.udf
val inverseRelationUDF = udf(invRel)
val inverseRelation = relDF.select(
col("target").alias("source"),
col("source").alias("target"),
col("collectedfrom"),
inverseRelationUDF(col("relClass")).alias("relClass")
)
val bidRel = inverseRelation
.union(relDF)
.withColumn("id", md5(concat(col("source"), col("relClass"), col("target"))))
.withColumn("cf", expr("transform(collectedfrom, x -> struct(x.key, x.value))"))
.drop("collectedfrom")
.withColumnRenamed("cf", "collectedfrom")
.groupBy(col("id"))
.agg(
first("source").alias("source"),
first("target").alias("target"),
first("relClass").alias("relClass"),
first("collectedfrom").alias("collectedfrom")
)
bidRel.write.mode(SaveMode.Overwrite).save(s"$otuputPath/relation")
}
def generateScholix(outputPath: String, spark: SparkSession): Unit = {
implicit val scholixResourceEncoder: Encoder[ScholixResource] = Encoders.bean(classOf[ScholixResource])
implicit val scholixEncoder: Encoder[Scholix] = Encoders.kryo(classOf[Scholix])
import spark.implicits._
val relations = spark.read.load(s"$outputPath/relation").as[RelationInfo]
val resource = spark.read.load(s"$outputPath/resource").as[ScholixResource]
val scholix_one_verse = relations
.joinWith(resource, relations("source") === resource("dnetIdentifier"), "inner")
.map(res => ScholexplorerUtils.generateScholix(res._1, res._2))
.map(s => (s.getIdentifier, s))(Encoders.tuple(Encoders.STRING, Encoders.kryo(classOf[Scholix])))
val resourceTarget = relations
.joinWith(resource, relations("target") === resource("dnetIdentifier"), "inner")
.map(res => (res._1.id, res._2))(Encoders.tuple(Encoders.STRING, Encoders.kryo(classOf[ScholixResource])))
scholix_one_verse
.joinWith(resourceTarget, scholix_one_verse("_1") === resourceTarget("_1"), "inner")
.map(k => ScholexplorerUtils.updateTarget(k._1._2, k._2._2))
.write
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.text(s"$outputPath/scholix")
}
}
object SparkCreateScholexplorerDump {
val logger: Logger = LoggerFactory.getLogger(SparkCreateScholexplorerDump.getClass)
def main(args: Array[String]): Unit = {
new SparkCreateScholexplorerDump(
log = logger,
args = args,
propertyPath = "/eu/dnetlib/dhp/sx/create_scholix_dump_params.json"
).initialize().run()
}
}

26
dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGenerationTest.scala Normal file
View File

@ -0,0 +1,26 @@
package eu.dnetlib.dhp.sx.graph.scholix
import eu.dnetlib.dhp.schema.sx.scholix.ScholixResource
import eu.dnetlib.dhp.sx.graph.SparkCreateScholexplorerDump
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
import org.junit.jupiter.api.Test
import org.objenesis.strategy.StdInstantiatorStrategy
class ScholixGenerationTest {
@Test
def generateScholix(): Unit = {
val spark: SparkSession = SparkSession.builder().master("local[*]").getOrCreate()
val app = new SparkCreateScholexplorerDump(null, null, null)
// app.generateScholixResource("/home/sandro/Downloads/scholix_sample/", "/home/sandro/Downloads/scholix/", spark)
// app.generateBidirectionalRelations(
// "/home/sandro/Downloads/scholix_sample/",
// "/home/sandro/Downloads/scholix/",
// spark
// )
app.generateScholix("/home/sandro/Downloads/scholix/", spark)
}
}

113
dhp-workflows/dhp-graph-provision/pom.xml
View File

@ -18,7 +18,7 @@
<executions>
<execution>
<id>scala-compile-first</id>
<phase>initialize</phase>
<phase>process-resources</phase>
<goals>
<goal>add-source</goal>
<goal>compile</goal>
@ -59,12 +59,6 @@
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>dom4j</groupId>
@ -160,6 +154,26 @@
<groupId>org.apache.zookeeper</groupId>
<artifactId>zookeeper</artifactId>
</exclusion>
<exclusion>
<artifactId>ant</artifactId>
<groupId>org.apache.ant</groupId>
</exclusion>
<exclusion>
<artifactId>antlr4-runtime</artifactId>
<groupId>org.antlr</groupId>
</exclusion>
<exclusion>
<artifactId>woodstox-core</artifactId>
<groupId>com.fasterxml.woodstox</groupId>
</exclusion>
<exclusion>
<artifactId>log4j</artifactId>
<groupId>*</groupId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
@ -206,5 +220,90 @@
</dependencies>
<profiles>
<profile>
<id>spark-24</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.4.0</version>
<executions>
<execution>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>src/main/sparksolr-3</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>spark-34</id>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.4.0</version>
<executions>
<execution>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>src/main/sparksolr-4</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>spark-35</id>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.4.0</version>
<executions>
<execution>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>src/main/sparksolr-4</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
</project>

3
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java
View File

@ -25,6 +25,7 @@ import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
import eu.dnetlib.dhp.oa.provision.model.TupleWrapper;
import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
import eu.dnetlib.dhp.oa.provision.utils.StreamingInputDocumentFactory;
import eu.dnetlib.dhp.sparksolr.DHPSolrSupport;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
@ -129,7 +130,7 @@ public class XmlIndexingJob extends AbstractSolrRecordTransformJob {
.javaRDD()
.map(
t -> new StreamingInputDocumentFactory().parseDocument(t.getXml(), t.getJson()));
SolrSupport.indexDocs(zkHost, collection, batchSize, docs.rdd());
DHPSolrSupport.indexDocs(zkHost, collection, batchSize, docs.rdd());
}
}

3
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java
View File

@ -5,14 +5,11 @@ import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.removePrefix;
import static eu.dnetlib.dhp.oa.provision.utils.XmlSerializationUtils.escapeXml;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import javax.swing.text.html.Option;
import org.apache.commons.lang3.StringUtils;
import org.stringtemplate.v4.ST;

27
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java
View File

@ -170,30 +170,19 @@ public class XmlSerializationUtils {
return sb.toString();
}
// <measure downloads="0" views="0">infrastruct_::f66f1bd369679b5b077dcdf006089556||OpenAIRE</measure>
// <measure views="0" datasource="infrastruct_::f66f1bd369679b5b077dcdf006089556||OpenAIRE" />
// <measure downloads="0" datasource="infrastruct_::f66f1bd369679b5b077dcdf006089556||OpenAIRE" />
public static String usageMeasureAsXmlElement(String name, Measure measure) {
HashSet<String> dsIds = Optional
.ofNullable(measure.getUnit())
.map(
m -> m
.stream()
.map(KeyValue::getKey)
.collect(Collectors.toCollection(HashSet::new)))
.orElse(new HashSet<>());
StringBuilder sb = new StringBuilder();
dsIds.forEach(dsId -> {
for (KeyValue kv : measure.getUnit()) {
sb
.append("<")
.append(name);
for (KeyValue kv : measure.getUnit()) {
sb.append(" ").append(attr(measure.getId(), kv.getValue()));
}
sb
.append(name)
.append(" ")
.append(attr("datasource", dsId))
.append("/>");
});
.append(attr(measure.getId(), kv.getValue()))
.append(attr("datasource", kv.getKey()))
.append(" />");
}
return sb.toString();
}

2
dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml
View File

@ -15,8 +15,8 @@
</property>
<property>
<name>validateXML</name>
<description>should the payload converter validate the XMLs</description>
<value>false</value>
<description>should the payload converter validate the XMLs</description>
</property>
<property>
<name>relPartitions</name>

12
dhp-workflows/dhp-graph-provision/src/main/sparksolr-3/eu/dnetlib/dhp/sparksolr/DHPSolrSupport.java Normal file
View File

@ -0,0 +1,12 @@
package eu.dnetlib.dhp.sparksolr;
import com.lucidworks.spark.util.SolrSupport;
import org.apache.solr.common.SolrInputDocument;
import org.apache.spark.rdd.RDD;
public class DHPSolrSupport {
static public void indexDocs(String zkhost, String collection, int batchSize, RDD<SolrInputDocument> docs) {
SolrSupport.indexDocs(zkhost, collection, batchSize, docs);
}
}

12
dhp-workflows/dhp-graph-provision/src/main/sparksolr-4/eu/dnetlib/dhp/sparksolr/DHPSolrSupport.java Normal file
View File

@ -0,0 +1,12 @@
package eu.dnetlib.dhp.sparksolr;
import com.lucidworks.spark.util.SolrSupport;
import org.apache.solr.common.SolrInputDocument;
import org.apache.spark.rdd.RDD;
public class DHPSolrSupport {
static public void indexDocs(String zkhost, String collection, int batchSize, RDD<SolrInputDocument> docs) {
SolrSupport.indexDocs(zkhost, collection, batchSize, com.lucidworks.spark.BatchSizeType.NUM_DOCS, docs);
}
}

4
dhp-workflows/dhp-stats-actionsets/pom.xml
View File

@ -16,11 +16,11 @@
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
<artifactId>spark-core_${scala.binary.version}</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.11</artifactId>
<artifactId>spark-sql_${scala.binary.version}</artifactId>
</dependency>
<dependency>

4
dhp-workflows/dhp-stats-hist-snaps/pom.xml
View File

@ -10,11 +10,11 @@
<dependencies>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
<artifactId>spark-core_${scala.binary.version}</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.11</artifactId>
<artifactId>spark-sql_${scala.binary.version}</artifactId>
</dependency>
</dependencies>
<build>

90
dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh
View File

@ -8,6 +8,8 @@ fi
export HADOOP_USER_NAME=$2
SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR=0
# Set the active HDFS node of OCEAN and IMPALA cluster.
OCEAN_HDFS_NODE='hdfs://nameservice1'
@ -30,7 +32,9 @@ while [ $COUNTER -lt 3 ]; do
done
if [ -z "$IMPALA_HDFS_NODE" ]; then
echo -e "\n\nERROR: PROBLEM WHEN SETTING THE HDFS-NODE FOR IMPALA CLUSTER! | AFTER ${COUNTER} RETRIES.\n\n"
exit 1
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 1
fi
fi
echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
@ -39,26 +43,25 @@ IMPALA_CONFIG_FILE='/etc/impala_cluster/hdfs-site.xml'
IMPALA_HDFS_DB_BASE_PATH="${IMPALA_HDFS_NODE}/user/hive/warehouse"
# Set sed arguments.
LOCATION_HDFS_NODE_SED_ARG="s|${OCEAN_HDFS_NODE}|${IMPALA_HDFS_NODE}|g" # This requires to be used with "sed -e" in order to have the "|" delimiter (as the "/" conflicts with the URIs)
# Set the SED command arguments for column-names with reserved words:
DATE_SED_ARG_1='s/[[:space:]]\date[[:space:]]/\`date\`/g'
DATE_SED_ARG_2='s/\.date,/\.\`date\`,/g' # the "date" may be part of a larger field name like "datestamp" or "date_aggregated", so we need to be careful with what we are replacing.
DATE_SED_ARG_3='s/\.date[[:space:]]/\.\`date\` /g'
HASH_SED_ARG_1='s/[[:space:]]\hash[[:space:]]/\`hash\`/g'
HASH_SED_ARG_2='s/\.hash,/\.\`hash\`,/g'
HASH_SED_ARG_3='s/\.hash[[:space:]]/\.\`hash\` /g'
LOCATION_SED_ARG_1='s/[[:space:]]\location[[:space:]]/\`location\`/g'
LOCATION_SED_ARG_2='s/\.location,/\.\`location\`,/g'
LOCATION_SED_ARG_3='s/\.location[[:space:]]/\.\`location\` /g'
function print_elapsed_time()
{
start_time=$1
end_time=$(date +%s)
elapsed_time=$(($end_time-$start_time))
hours=$((elapsed_time / 3600))
minutes=$(((elapsed_time % 3600) / 60))
seconds=$((elapsed_time % 60))
printf "\nElapsed time: %02d:%02d:%02d\n\n" $hours $minutes $seconds
}
function copydb() {
db=$1
start_db_time=$(date +%s)
echo -e "\nStart processing db: '${db}'..\n"
# Delete the old DB from Impala cluster (if exists).
@ -67,7 +70,11 @@ function copydb() {
if [ -n "$log_errors" ]; then
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
rm -f error.log
exit 2
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 2
else
return 2
fi
fi
echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
@ -85,17 +92,30 @@ function copydb() {
-pb \
${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
# Check the exit status of the "hadoop distcp" command.
if [ $? -eq 0 ]; then
echo -e "\nSuccessfully copied the files of '${db}'.\n"
if [ $? -eq 0 ]; then # Check the exit status of the "hadoop distcp" command.
echo -e "\nSuccessfully copied the files of '${db}' from Ocean to Impala cluster.\n"
else
echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
rm -f error.log
exit 3
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 3
else
return 3
fi
fi
# In case we ever use this script for a writable DB (using inserts/updates), we should perform the following costly operation as well..
#hdfs dfs -conf ${IMPALA_CONFIG_FILE} -chmod -R 777 ${TEMP_SUBDIR_FULLPATH}/${db}.db
# Give WRITE and EXECUTE permissions to the DBs' directory only, in order to be able to create more tables later, on top of that DB.
hdfs dfs -conf ${IMPALA_CONFIG_FILE} -chmod u+wx ${IMPALA_HDFS_DB_BASE_PATH}/${db}.db
# In case we ever use this script for a writable DB (using inserts/updates), we should perform the costly recursive operation as well, using the "-R" param.
if [ $? -ne 0 ]; then # Check the exit status..
echo -e "\n\nERROR: FAILED TO ASSIGN WRITE AND EXECUTE PERMISSIONS TO THE DIRECTORY OF DB: '${db}'. GOT EXIT STATUS: $?\n\n"
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 4
else
return 4
fi
fi
echo -e "\nCreating schema for db: '${db}'\n"
@ -109,17 +129,13 @@ function copydb() {
num_tables=0
entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'` # Get the tables and views without any potential the "WARN" logs.
for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elemetns are single-words.
for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elements are single-words.
# Check if this is a view by showing the create-statement where it should print "create view" for a view, not the "create table". Unfortunately, there is no "show views" command.
create_entity_statement=`hive -e "show create table ${db}.${i};"` # It needs to happen in two stages, otherwise the "grep" is not able to match multi-line statement.
create_view_statement_test=`echo -e "$create_entity_statement" | grep 'CREATE VIEW'`
create_entity_statement=`hive --database ${db} -e "show create table ${i};"` # We need to use the "--database", instead of including it inside the query, in order to return the statements with the '`' chars being in the right place to be used by impala-shell. However, we need to add the db-name in the "CREATE VIEW view_name" statement.
create_view_statement_test=`echo -e "$create_entity_statement" | grep 'CREATE VIEW'` # It needs to happen in two stages, otherwise the "grep" is not able to match multi-line statement.
if [ -n "$create_view_statement_test" ]; then
echo -e "\n'${i}' is a view, so we will save its 'create view' statement and execute it on Impala, after all tables have been created.\n"
create_view_statement=`echo -e "$create_entity_statement" | sed 's/WARN:.*//g' | sed 's/\`//g' \
| sed 's/"$/;/' | sed 's/^"//' | sed 's/\\"\\"/\"/g' | sed -e "${LOCATION_HDFS_NODE_SED_ARG}" | sed "${DATE_SED_ARG_1}" | sed "${HASH_SED_ARG_1}" | sed "${LOCATION_SED_ARG_1}" \
| sed "${DATE_SED_ARG_2}" | sed "${HASH_SED_ARG_2}" | sed "${LOCATION_SED_ARG_2}" \
| sed "${DATE_SED_ARG_3}" | sed "${HASH_SED_ARG_3}" | sed "${LOCATION_SED_ARG_3}"`
create_view_statement=`echo -e "$create_entity_statement" | sed 's/WARN:.*//g' | sed 's/"$/;/' | sed 's/^"//' | sed 's/\\"\\"/\"/g' | sed -e "${LOCATION_HDFS_NODE_SED_ARG}" | sed "s/CREATE VIEW /CREATE VIEW ${db}./"`
all_create_view_statements+=("$create_view_statement")
else
echo -e "\n'${i}' is a table, so we will check for its parquet files and create the table on Impala cluster.\n"
@ -127,12 +143,17 @@ function copydb() {
CURRENT_PRQ_FILE=`hdfs dfs -conf ${IMPALA_CONFIG_FILE} -ls -C "${IMPALA_HDFS_DB_BASE_PATH}/${db}.db/${i}/" | grep -v 'Found' | grep -v '_impala_insert_staging' | head -1`
if [ -z "$CURRENT_PRQ_FILE" ]; then # If there is not parquet-file inside.
echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
exit 4 # Comment out when testing a DB which has such a table, just for performing this exact test-check.
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 5
fi
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
if [ -n "$log_errors" ]; then
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN CREATING TABLE '${i}'!\n\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 6
fi
fi
fi
fi
@ -176,7 +197,9 @@ function copydb() {
if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
exit 5
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 7
fi
elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
else
@ -204,11 +227,14 @@ function copydb() {
else
echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
rm -f error.log
exit 6
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 8
fi
fi
rm -f error.log
echo -e "\n\nFinished processing db: ${db}\n\n"
echo -e "\n\nFinished processing db: ${db}\n"
print_elapsed_time start_db_time
}

4
dhp-workflows/dhp-stats-monitor-irish/pom.xml
View File

@ -10,11 +10,11 @@
<dependencies>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
<artifactId>spark-core_${scala.binary.version}</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.11</artifactId>
<artifactId>spark-sql_${scala.binary.version}</artifactId>
</dependency>
</dependencies>
<build>

91
dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh
View File

@ -8,6 +8,9 @@ fi
export HADOOP_USER_NAME=$2
SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR=0
# Set the active HDFS node of OCEAN and IMPALA cluster.
OCEAN_HDFS_NODE='hdfs://nameservice1'
echo -e "\nOCEAN HDFS virtual-name which resolves automatically to the active-node: ${OCEAN_HDFS_NODE}"
@ -29,7 +32,9 @@ while [ $COUNTER -lt 3 ]; do
done
if [ -z "$IMPALA_HDFS_NODE" ]; then
echo -e "\n\nERROR: PROBLEM WHEN SETTING THE HDFS-NODE FOR IMPALA CLUSTER! | AFTER ${COUNTER} RETRIES.\n\n"
exit 1
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 1
fi
fi
echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
@ -38,26 +43,25 @@ IMPALA_CONFIG_FILE='/etc/impala_cluster/hdfs-site.xml'
IMPALA_HDFS_DB_BASE_PATH="${IMPALA_HDFS_NODE}/user/hive/warehouse"
# Set sed arguments.
LOCATION_HDFS_NODE_SED_ARG="s|${OCEAN_HDFS_NODE}|${IMPALA_HDFS_NODE}|g" # This requires to be used with "sed -e" in order to have the "|" delimiter (as the "/" conflicts with the URIs)
# Set the SED command arguments for column-names with reserved words:
DATE_SED_ARG_1='s/[[:space:]]\date[[:space:]]/\`date\`/g'
DATE_SED_ARG_2='s/\.date,/\.\`date\`,/g' # the "date" may be part of a larger field name like "datestamp" or "date_aggregated", so we need to be careful with what we are replacing.
DATE_SED_ARG_3='s/\.date[[:space:]]/\.\`date\` /g'
HASH_SED_ARG_1='s/[[:space:]]\hash[[:space:]]/\`hash\`/g'
HASH_SED_ARG_2='s/\.hash,/\.\`hash\`,/g'
HASH_SED_ARG_3='s/\.hash[[:space:]]/\.\`hash\` /g'
LOCATION_SED_ARG_1='s/[[:space:]]\location[[:space:]]/\`location\`/g'
LOCATION_SED_ARG_2='s/\.location,/\.\`location\`,/g'
LOCATION_SED_ARG_3='s/\.location[[:space:]]/\.\`location\` /g'
function print_elapsed_time()
{
start_time=$1
end_time=$(date +%s)
elapsed_time=$(($end_time-$start_time))
hours=$((elapsed_time / 3600))
minutes=$(((elapsed_time % 3600) / 60))
seconds=$((elapsed_time % 60))
printf "\nElapsed time: %02d:%02d:%02d\n\n" $hours $minutes $seconds
}
function copydb() {
db=$1
start_db_time=$(date +%s)
echo -e "\nStart processing db: '${db}'..\n"
# Delete the old DB from Impala cluster (if exists).
@ -66,7 +70,11 @@ function copydb() {
if [ -n "$log_errors" ]; then
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
rm -f error.log
exit 2
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 2
else
return 2
fi
fi
echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
@ -84,17 +92,30 @@ function copydb() {
-pb \
${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
# Check the exit status of the "hadoop distcp" command.
if [ $? -eq 0 ]; then
echo -e "\nSuccessfully copied the files of '${db}'.\n"
if [ $? -eq 0 ]; then # Check the exit status of the "hadoop distcp" command.
echo -e "\nSuccessfully copied the files of '${db}' from Ocean to Impala cluster.\n"
else
echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
rm -f error.log
exit 3
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 3
else
return 3
fi
fi
# In case we ever use this script for a writable DB (using inserts/updates), we should perform the following costly operation as well..
#hdfs dfs -conf ${IMPALA_CONFIG_FILE} -chmod -R 777 ${TEMP_SUBDIR_FULLPATH}/${db}.db
# Give WRITE and EXECUTE permissions to the DBs' directory only, in order to be able to create more tables later, on top of that DB.
hdfs dfs -conf ${IMPALA_CONFIG_FILE} -chmod u+wx ${IMPALA_HDFS_DB_BASE_PATH}/${db}.db
# In case we ever use this script for a writable DB (using inserts/updates), we should perform the costly recursive operation as well, using the "-R" param.
if [ $? -ne 0 ]; then # Check the exit status..
echo -e "\n\nERROR: FAILED TO ASSIGN WRITE AND EXECUTE PERMISSIONS TO THE DIRECTORY OF DB: '${db}'. GOT EXIT STATUS: $?\n\n"
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 4
else
return 4
fi
fi
echo -e "\nCreating schema for db: '${db}'\n"
@ -108,17 +129,13 @@ function copydb() {
num_tables=0
entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'` # Get the tables and views without any potential the "WARN" logs.
for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elemetns are single-words.
for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elements are single-words.
# Check if this is a view by showing the create-statement where it should print "create view" for a view, not the "create table". Unfortunately, there is no "show views" command.
create_entity_statement=`hive -e "show create table ${db}.${i};"` # It needs to happen in two stages, otherwise the "grep" is not able to match multi-line statement.
create_view_statement_test=`echo -e "$create_entity_statement" | grep 'CREATE VIEW'`
create_entity_statement=`hive --database ${db} -e "show create table ${i};"` # We need to use the "--database", instead of including it inside the query, in order to return the statements with the '`' chars being in the right place to be used by impala-shell. However, we need to add the db-name in the "CREATE VIEW view_name" statement.
create_view_statement_test=`echo -e "$create_entity_statement" | grep 'CREATE VIEW'` # It needs to happen in two stages, otherwise the "grep" is not able to match multi-line statement.
if [ -n "$create_view_statement_test" ]; then
echo -e "\n'${i}' is a view, so we will save its 'create view' statement and execute it on Impala, after all tables have been created.\n"
create_view_statement=`echo -e "$create_entity_statement" | sed 's/WARN:.*//g' | sed 's/\`//g' \
| sed 's/"$/;/' | sed 's/^"//' | sed 's/\\"\\"/\"/g' | sed -e "${LOCATION_HDFS_NODE_SED_ARG}" | sed "${DATE_SED_ARG_1}" | sed "${HASH_SED_ARG_1}" | sed "${LOCATION_SED_ARG_1}" \
| sed "${DATE_SED_ARG_2}" | sed "${HASH_SED_ARG_2}" | sed "${LOCATION_SED_ARG_2}" \
| sed "${DATE_SED_ARG_3}" | sed "${HASH_SED_ARG_3}" | sed "${LOCATION_SED_ARG_3}"`
create_view_statement=`echo -e "$create_entity_statement" | sed 's/WARN:.*//g' | sed 's/"$/;/' | sed 's/^"//' | sed 's/\\"\\"/\"/g' | sed -e "${LOCATION_HDFS_NODE_SED_ARG}" | sed "s/CREATE VIEW /CREATE VIEW ${db}./"`
all_create_view_statements+=("$create_view_statement")
else
echo -e "\n'${i}' is a table, so we will check for its parquet files and create the table on Impala cluster.\n"
@ -126,12 +143,17 @@ function copydb() {
CURRENT_PRQ_FILE=`hdfs dfs -conf ${IMPALA_CONFIG_FILE} -ls -C "${IMPALA_HDFS_DB_BASE_PATH}/${db}.db/${i}/" | grep -v 'Found' | grep -v '_impala_insert_staging' | head -1`
if [ -z "$CURRENT_PRQ_FILE" ]; then # If there is not parquet-file inside.
echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
exit 4 # Comment out when testing a DB which has such a table, just for performing this exact test-check.
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 5
fi
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
if [ -n "$log_errors" ]; then
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN CREATING TABLE '${i}'!\n\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 6
fi
fi
fi
fi
@ -175,7 +197,9 @@ function copydb() {
if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
exit 5
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 7
fi
elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
else
@ -203,11 +227,14 @@ function copydb() {
else
echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
rm -f error.log
exit 6
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 8
fi
fi
rm -f error.log
echo -e "\n\nFinished processing db: ${db}\n\n"
echo -e "\n\nFinished processing db: ${db}\n"
print_elapsed_time start_db_time
}

4
dhp-workflows/dhp-stats-monitor-update/pom.xml
View File

@ -10,11 +10,11 @@
<dependencies>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
<artifactId>spark-core_${scala.binary.version}</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.11</artifactId>
<artifactId>spark-sql_${scala.binary.version}</artifactId>
</dependency>
</dependencies>
<build>

91
dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh
View File

@ -8,6 +8,9 @@ fi
export HADOOP_USER_NAME=$2
SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR=0
# Set the active HDFS node of OCEAN and IMPALA cluster.
OCEAN_HDFS_NODE='hdfs://nameservice1'
echo -e "\nOCEAN HDFS virtual-name which resolves automatically to the active-node: ${OCEAN_HDFS_NODE}"
@ -29,7 +32,9 @@ while [ $COUNTER -lt 3 ]; do
done
if [ -z "$IMPALA_HDFS_NODE" ]; then
echo -e "\n\nERROR: PROBLEM WHEN SETTING THE HDFS-NODE FOR IMPALA CLUSTER! | AFTER ${COUNTER} RETRIES.\n\n"
exit 1
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 1
fi
fi
echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
@ -38,26 +43,25 @@ IMPALA_CONFIG_FILE='/etc/impala_cluster/hdfs-site.xml'
IMPALA_HDFS_DB_BASE_PATH="${IMPALA_HDFS_NODE}/user/hive/warehouse"
# Set sed arguments.
LOCATION_HDFS_NODE_SED_ARG="s|${OCEAN_HDFS_NODE}|${IMPALA_HDFS_NODE}|g" # This requires to be used with "sed -e" in order to have the "|" delimiter (as the "/" conflicts with the URIs)
# Set the SED command arguments for column-names with reserved words:
DATE_SED_ARG_1='s/[[:space:]]\date[[:space:]]/\`date\`/g'
DATE_SED_ARG_2='s/\.date,/\.\`date\`,/g' # the "date" may be part of a larger field name like "datestamp" or "date_aggregated", so we need to be careful with what we are replacing.
DATE_SED_ARG_3='s/\.date[[:space:]]/\.\`date\` /g'
HASH_SED_ARG_1='s/[[:space:]]\hash[[:space:]]/\`hash\`/g'
HASH_SED_ARG_2='s/\.hash,/\.\`hash\`,/g'
HASH_SED_ARG_3='s/\.hash[[:space:]]/\.\`hash\` /g'
LOCATION_SED_ARG_1='s/[[:space:]]\location[[:space:]]/\`location\`/g'
LOCATION_SED_ARG_2='s/\.location,/\.\`location\`,/g'
LOCATION_SED_ARG_3='s/\.location[[:space:]]/\.\`location\` /g'
function print_elapsed_time()
{
start_time=$1
end_time=$(date +%s)
elapsed_time=$(($end_time-$start_time))
hours=$((elapsed_time / 3600))
minutes=$(((elapsed_time % 3600) / 60))
seconds=$((elapsed_time % 60))
printf "\nElapsed time: %02d:%02d:%02d\n\n" $hours $minutes $seconds
}
function copydb() {
db=$1
start_db_time=$(date +%s)
echo -e "\nStart processing db: '${db}'..\n"
# Delete the old DB from Impala cluster (if exists).
@ -66,7 +70,11 @@ function copydb() {
if [ -n "$log_errors" ]; then
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
rm -f error.log
exit 2
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 2
else
return 2
fi
fi
echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
@ -84,17 +92,30 @@ function copydb() {
-pb \
${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
# Check the exit status of the "hadoop distcp" command.
if [ $? -eq 0 ]; then
echo -e "\nSuccessfully copied the files of '${db}'.\n"
if [ $? -eq 0 ]; then # Check the exit status of the "hadoop distcp" command.
echo -e "\nSuccessfully copied the files of '${db}' from Ocean to Impala cluster.\n"
else
echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
rm -f error.log
exit 3
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 3
else
return 3
fi
fi
# In case we ever use this script for a writable DB (using inserts/updates), we should perform the following costly operation as well..
#hdfs dfs -conf ${IMPALA_CONFIG_FILE} -chmod -R 777 ${TEMP_SUBDIR_FULLPATH}/${db}.db
# Give WRITE and EXECUTE permissions to the DBs' directory only, in order to be able to create more tables later, on top of that DB.
hdfs dfs -conf ${IMPALA_CONFIG_FILE} -chmod u+wx ${IMPALA_HDFS_DB_BASE_PATH}/${db}.db
# In case we ever use this script for a writable DB (using inserts/updates), we should perform the costly recursive operation as well, using the "-R" param.
if [ $? -ne 0 ]; then # Check the exit status..
echo -e "\n\nERROR: FAILED TO ASSIGN WRITE AND EXECUTE PERMISSIONS TO THE DIRECTORY OF DB: '${db}'. GOT EXIT STATUS: $?\n\n"
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 4
else
return 4
fi
fi
echo -e "\nCreating schema for db: '${db}'\n"
@ -108,17 +129,13 @@ function copydb() {
num_tables=0
entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'` # Get the tables and views without any potential the "WARN" logs.
for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elemetns are single-words.
for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elements are single-words.
# Check if this is a view by showing the create-statement where it should print "create view" for a view, not the "create table". Unfortunately, there is no "show views" command.
create_entity_statement=`hive -e "show create table ${db}.${i};"` # It needs to happen in two stages, otherwise the "grep" is not able to match multi-line statement.
create_view_statement_test=`echo -e "$create_entity_statement" | grep 'CREATE VIEW'`
create_entity_statement=`hive --database ${db} -e "show create table ${i};"` # We need to use the "--database", instead of including it inside the query, in order to return the statements with the '`' chars being in the right place to be used by impala-shell. However, we need to add the db-name in the "CREATE VIEW view_name" statement.
create_view_statement_test=`echo -e "$create_entity_statement" | grep 'CREATE VIEW'` # It needs to happen in two stages, otherwise the "grep" is not able to match multi-line statement.
if [ -n "$create_view_statement_test" ]; then
echo -e "\n'${i}' is a view, so we will save its 'create view' statement and execute it on Impala, after all tables have been created.\n"
create_view_statement=`echo -e "$create_entity_statement" | sed 's/WARN:.*//g' | sed 's/\`//g' \
| sed 's/"$/;/' | sed 's/^"//' | sed 's/\\"\\"/\"/g' | sed -e "${LOCATION_HDFS_NODE_SED_ARG}" | sed "${DATE_SED_ARG_1}" | sed "${HASH_SED_ARG_1}" | sed "${LOCATION_SED_ARG_1}" \
| sed "${DATE_SED_ARG_2}" | sed "${HASH_SED_ARG_2}" | sed "${LOCATION_SED_ARG_2}" \
| sed "${DATE_SED_ARG_3}" | sed "${HASH_SED_ARG_3}" | sed "${LOCATION_SED_ARG_3}"`
create_view_statement=`echo -e "$create_entity_statement" | sed 's/WARN:.*//g' | sed 's/"$/;/' | sed 's/^"//' | sed 's/\\"\\"/\"/g' | sed -e "${LOCATION_HDFS_NODE_SED_ARG}" | sed "s/CREATE VIEW /CREATE VIEW ${db}./"`
all_create_view_statements+=("$create_view_statement")
else
echo -e "\n'${i}' is a table, so we will check for its parquet files and create the table on Impala cluster.\n"
@ -126,12 +143,17 @@ function copydb() {
CURRENT_PRQ_FILE=`hdfs dfs -conf ${IMPALA_CONFIG_FILE} -ls -C "${IMPALA_HDFS_DB_BASE_PATH}/${db}.db/${i}/" | grep -v 'Found' | grep -v '_impala_insert_staging' | head -1`
if [ -z "$CURRENT_PRQ_FILE" ]; then # If there is not parquet-file inside.
echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
exit 4 # Comment out when testing a DB which has such a table, just for performing this exact test-check.
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 5
fi
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
if [ -n "$log_errors" ]; then
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN CREATING TABLE '${i}'!\n\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 6
fi
fi
fi
fi
@ -175,7 +197,9 @@ function copydb() {
if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
exit 5
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 7
fi
elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
else
@ -203,11 +227,14 @@ function copydb() {
else
echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
rm -f error.log
exit 6
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 8
fi
fi
rm -f error.log
echo -e "\n\nFinished processing db: ${db}\n\n"
echo -e "\n\nFinished processing db: ${db}\n"
print_elapsed_time start_db_time
}

95
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh
View File

@ -6,6 +6,8 @@ then
ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder}
fi
SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR=0
# Set the active HDFS node of OCEAN and IMPALA cluster.
OCEAN_HDFS_NODE='hdfs://nameservice1'
@ -28,7 +30,9 @@ while [ $COUNTER -lt 3 ]; do
done
if [ -z "$IMPALA_HDFS_NODE" ]; then
echo -e "\n\nERROR: PROBLEM WHEN SETTING THE HDFS-NODE FOR IMPALA CLUSTER! | AFTER ${COUNTER} RETRIES.\n\n"
exit 1
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 1
fi
fi
echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
@ -40,26 +44,26 @@ IMPALA_HDFS_DB_BASE_PATH="${IMPALA_HDFS_NODE}/user/hive/warehouse"
# Set sed arguments.
LOCATION_HDFS_NODE_SED_ARG="s|${OCEAN_HDFS_NODE}|${IMPALA_HDFS_NODE}|g" # This requires to be used with "sed -e" in order to have the "|" delimiter (as the "/" conflicts with the URIs)
# Set the SED command arguments for column-names with reserved words:
DATE_SED_ARG_1='s/[[:space:]]\date[[:space:]]/\`date\`/g'
DATE_SED_ARG_2='s/\.date,/\.\`date\`,/g' # the "date" may be part of a larger field name like "datestamp" or "date_aggregated", so we need to be careful with what we are replacing.
DATE_SED_ARG_3='s/\.date[[:space:]]/\.\`date\` /g'
HASH_SED_ARG_1='s/[[:space:]]\hash[[:space:]]/\`hash\`/g'
HASH_SED_ARG_2='s/\.hash,/\.\`hash\`,/g'
HASH_SED_ARG_3='s/\.hash[[:space:]]/\.\`hash\` /g'
LOCATION_SED_ARG_1='s/[[:space:]]\location[[:space:]]/\`location\`/g'
LOCATION_SED_ARG_2='s/\.location,/\.\`location\`,/g'
LOCATION_SED_ARG_3='s/\.location[[:space:]]/\.\`location\` /g'
export HADOOP_USER_NAME=$6
export PROD_USAGE_STATS_DB="openaire_prod_usage_stats"
function print_elapsed_time()
{
start_time=$1
end_time=$(date +%s)
elapsed_time=$(($end_time-$start_time))
hours=$((elapsed_time / 3600))
minutes=$(((elapsed_time % 3600) / 60))
seconds=$((elapsed_time % 60))
printf "\nElapsed time: %02d:%02d:%02d\n\n" $hours $minutes $seconds
}
function copydb() {
db=$1
start_db_time=$(date +%s)
echo -e "\nStart processing db: '${db}'..\n"
# Delete the old DB from Impala cluster (if exists).
@ -68,7 +72,11 @@ function copydb() {
if [ -n "$log_errors" ]; then
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
rm -f error.log
exit 2
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 2
else
return 2
fi
fi
echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
@ -86,17 +94,30 @@ function copydb() {
-pb \
${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
# Check the exit status of the "hadoop distcp" command.
if [ $? -eq 0 ]; then
echo -e "\nSuccessfully copied the files of '${db}'.\n"
if [ $? -eq 0 ]; then # Check the exit status of the "hadoop distcp" command.
echo -e "\nSuccessfully copied the files of '${db}' from Ocean to Impala cluster.\n"
else
echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
rm -f error.log
exit 3
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 3
else
return 3
fi
fi
# In case we ever use this script for a writable DB (using inserts/updates), we should perform the following costly operation as well..
#hdfs dfs -conf ${IMPALA_CONFIG_FILE} -chmod -R 777 ${TEMP_SUBDIR_FULLPATH}/${db}.db
# Give WRITE and EXECUTE permissions to the DBs' directory only, in order to be able to create more tables later, on top of that DB.
hdfs dfs -conf ${IMPALA_CONFIG_FILE} -chmod u+wx ${IMPALA_HDFS_DB_BASE_PATH}/${db}.db
# In case we ever use this script for a writable DB (using inserts/updates), we should perform the costly recursive operation as well, using the "-R" param.
if [ $? -ne 0 ]; then # Check the exit status..
echo -e "\n\nERROR: FAILED TO ASSIGN WRITE AND EXECUTE PERMISSIONS TO THE DIRECTORY OF DB: '${db}'. GOT EXIT STATUS: $?\n\n"
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 4
else
return 4
fi
fi
echo -e "\nCreating schema for db: '${db}'\n"
@ -110,17 +131,13 @@ function copydb() {
num_tables=0
entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'` # Get the tables and views without any potential the "WARN" logs.
for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elemetns are single-words.
for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elements are single-words.
# Check if this is a view by showing the create-statement where it should print "create view" for a view, not the "create table". Unfortunately, there is no "show views" command.
create_entity_statement=`hive -e "show create table ${db}.${i};"` # It needs to happen in two stages, otherwise the "grep" is not able to match multi-line statement.
create_view_statement_test=`echo -e "$create_entity_statement" | grep 'CREATE VIEW'`
create_entity_statement=`hive --database ${db} -e "show create table ${i};"` # We need to use the "--database", instead of including it inside the query, in order to return the statements with the '`' chars being in the right place to be used by impala-shell. However, we need to add the db-name in the "CREATE VIEW view_name" statement.
create_view_statement_test=`echo -e "$create_entity_statement" | grep 'CREATE VIEW'` # It needs to happen in two stages, otherwise the "grep" is not able to match multi-line statement.
if [ -n "$create_view_statement_test" ]; then
echo -e "\n'${i}' is a view, so we will save its 'create view' statement and execute it on Impala, after all tables have been created.\n"
create_view_statement=`echo -e "$create_entity_statement" | sed 's/WARN:.*//g' | sed 's/\`//g' \
| sed 's/"$/;/' | sed 's/^"//' | sed 's/\\"\\"/\"/g' | sed -e "${LOCATION_HDFS_NODE_SED_ARG}" | sed "${DATE_SED_ARG_1}" | sed "${HASH_SED_ARG_1}" | sed "${LOCATION_SED_ARG_1}" \
| sed "${DATE_SED_ARG_2}" | sed "${HASH_SED_ARG_2}" | sed "${LOCATION_SED_ARG_2}" \
| sed "${DATE_SED_ARG_3}" | sed "${HASH_SED_ARG_3}" | sed "${LOCATION_SED_ARG_3}"`
create_view_statement=`echo -e "$create_entity_statement" | sed 's/WARN:.*//g' | sed 's/"$/;/' | sed 's/^"//' | sed 's/\\"\\"/\"/g' | sed -e "${LOCATION_HDFS_NODE_SED_ARG}" | sed "s/CREATE VIEW /CREATE VIEW ${db}./"`
all_create_view_statements+=("$create_view_statement")
else
echo -e "\n'${i}' is a table, so we will check for its parquet files and create the table on Impala cluster.\n"
@ -128,12 +145,17 @@ function copydb() {
CURRENT_PRQ_FILE=`hdfs dfs -conf ${IMPALA_CONFIG_FILE} -ls -C "${IMPALA_HDFS_DB_BASE_PATH}/${db}.db/${i}/" | grep -v 'Found' | grep -v '_impala_insert_staging' | head -1`
if [ -z "$CURRENT_PRQ_FILE" ]; then # If there is not parquet-file inside.
echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
exit 4 # Comment out when testing a DB which has such a table, just for performing this exact test-check.
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 5
fi
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
if [ -n "$log_errors" ]; then
echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN CREATING TABLE '${i}'!\n\n"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 6
fi
fi
fi
fi
@ -177,7 +199,9 @@ function copydb() {
if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
exit 5
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 7
fi
elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
else
@ -205,11 +229,14 @@ function copydb() {
else
echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
rm -f error.log
exit 6
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 8
fi
fi
rm -f error.log
echo -e "\n\nFinished processing db: ${db}\n\n"
echo -e "\n\nFinished processing db: ${db}\n"
print_elapsed_time start_db_time
}
STATS_DB=$1
@ -233,6 +260,6 @@ copydb $MONITOR_DB'_ris_tail'
contexts="knowmad::other dh-ch::other enermaps::other gotriple::other neanias-atmospheric::other rural-digital-europe::other covid-19::other aurora::other neanias-space::other north-america-studies::other north-american-studies::other eutopia::other"
for i in ${contexts}
do
tmp=`echo "$i" | sed 's/'-'/'_'/g' | sed 's/'::'/'_'/g'`
tmp=`echo "$i" | sed 's/'-'/'_'/g' | sed 's/'::'/'_'/g'`
copydb ${MONITOR_DB}'_'${tmp}
done

9
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
View File

@ -129,11 +129,14 @@ create table ${stats_db_name}.result_fos stored as parquet as
with
lvl1 as (select id, topic from ${stats_db_name}.result_topics where topic like '__ %' and type='Fields of Science and Technology classification'),
lvl2 as (select id, topic from ${stats_db_name}.result_topics where topic like '____ %' and type='Fields of Science and Technology classification'),
lvl3 as (select id, topic from ${stats_db_name}.result_topics where topic like '______ %' and type='Fields of Science and Technology classification')
select lvl1.id, lvl1.topic as lvl1, lvl2.topic as lvl2, lvl3.topic as lvl3
lvl3 as (select id, topic from ${stats_db_name}.result_topics where topic like '______ %' and type='Fields of Science and Technology classification'),
lvl4 as (select id, topic from ${stats_db_name}.result_topics where topic like '________ %' and type='Fields of Science and Technology classification')
select lvl1.id, lvl1.topic as lvl1, lvl2.topic as lvl2, lvl3.topic as lvl3, lvl4.topic as lvl4
from lvl1
join lvl2 on lvl1.id=lvl2.id and substr(lvl2.topic, 1, 2)=substr(lvl1.topic, 1, 2)
join lvl3 on lvl3.id=lvl1.id and substr(lvl3.topic, 1, 4)=substr(lvl2.topic, 1, 4);
join lvl3 on lvl3.id=lvl1.id and substr(lvl3.topic, 1, 4)=substr(lvl2.topic, 1, 4)
join lvl4 on lvl4.id=lvl1.id and substr(lvl4.topic, 1, 6)=substr(lvl3.topic, 1, 6);
DROP TABLE IF EXISTS ${stats_db_name}.result_organization purge;

3
dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/PrepareSWHActionsets.java
View File

@ -17,6 +17,7 @@ import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
import org.apache.spark.sql.Dataset;
@ -117,7 +118,7 @@ public class PrepareSWHActionsets {
.map(
(MapFunction<String, Software>) t -> OBJECT_MAPPER.readValue(t, Software.class),
Encoders.bean(Software.class))
.filter(t -> t.getCodeRepositoryUrl() != null)
.filter((FilterFunction<Software>) t -> t.getCodeRepositoryUrl() != null)
.select(col("id"), col("codeRepositoryUrl.value").as("repoUrl"));
}

12
dhp-workflows/dhp-usage-raw-data-update/pom.xml
View File

@ -39,8 +39,8 @@
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<cdh.hive.version>0.13.1-cdh5.2.1</cdh.hive.version>
<cdh.hadoop.version>2.5.0-cdh5.2.1</cdh.hadoop.version>
<cdh.hive.version>1.1.0-cdh5.16.2</cdh.hive.version>
<cdh.hadoop.version>2.6.0-cdh5.16.2</cdh.hadoop.version>
</properties>
<dependencies>
@ -72,7 +72,13 @@
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-common</artifactId>
<version>${cdh.hadoop.version}</version>
</dependency>
<exclusions>
<exclusion>
<groupId>jdk.tools</groupId>
<artifactId>jdk.tools</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-common</artifactId>

18
dhp-workflows/dhp-usage-stats-build/pom.xml
View File

@ -39,8 +39,8 @@
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<cdh.hive.version>0.13.1-cdh5.2.1</cdh.hive.version>
<cdh.hadoop.version>2.5.0-cdh5.2.1</cdh.hadoop.version>
<cdh.hive.version>1.1.0-cdh5.16.2</cdh.hive.version>
<cdh.hadoop.version>2.6.0-cdh5.16.2</cdh.hadoop.version>
</properties>
<dependencies>
@ -67,11 +67,23 @@
<groupId>org.apache.hive</groupId>
<artifactId>hive-jdbc</artifactId>
<version>${cdh.hive.version}</version>
</dependency>
<exclusions>
<exclusion>
<groupId>jdk.tools</groupId>
<artifactId>jdk.tools</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-common</artifactId>
<version>${cdh.hadoop.version}</version>
<exclusions>
<exclusion>
<groupId>jdk.tools</groupId>
<artifactId>jdk.tools</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>

2054
pom.xml
View File

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