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Merge remote-tracking branch 'origin/beta' into beta

This commit is contained in:
Miriam Baglioni 2024-06-11 10:28:51 +02:00
parent 9da006e98c 85c1eae7e0
commit 8fe934810f
45 changed files with 1568 additions and 250 deletions
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104
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeEntitiesComparator.java Normal file
View File

@ -0,0 +1,104 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static eu.dnetlib.dhp.schema.common.ModelConstants.CROSSREF_ID;
import java.util.*;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Result;
public class MergeEntitiesComparator implements Comparator<Oaf> {
static final List<String> PID_AUTHORITIES = Arrays
.asList(
ModelConstants.ARXIV_ID,
ModelConstants.PUBMED_CENTRAL_ID,
ModelConstants.EUROPE_PUBMED_CENTRAL_ID,
ModelConstants.DATACITE_ID,
ModelConstants.CROSSREF_ID);
static final List<String> RESULT_TYPES = Arrays
.asList(
ModelConstants.ORP_RESULTTYPE_CLASSID,
ModelConstants.SOFTWARE_RESULTTYPE_CLASSID,
ModelConstants.DATASET_RESULTTYPE_CLASSID,
ModelConstants.PUBLICATION_RESULTTYPE_CLASSID);
public static final Comparator<Oaf> INSTANCE = new MergeEntitiesComparator();
@Override
public int compare(Oaf left, Oaf right) {
if (left == null && right == null)
return 0;
if (left == null)
return -1;
if (right == null)
return 1;
int res = 0;
// pid authority
int cfp1 = left
.getCollectedfrom()
.stream()
.map(kv -> PID_AUTHORITIES.indexOf(kv.getKey()))
.max(Integer::compare)
.orElse(-1);
int cfp2 = right
.getCollectedfrom()
.stream()
.map(kv -> PID_AUTHORITIES.indexOf(kv.getKey()))
.max(Integer::compare)
.orElse(-1);
if (cfp1 >= 0 && cfp1 > cfp2) {
return 1;
} else if (cfp2 >= 0 && cfp2 > cfp1) {
return -1;
}
// trust
if (left.getDataInfo() != null && right.getDataInfo() != null) {
res = left.getDataInfo().getTrust().compareTo(right.getDataInfo().getTrust());
}
// result type
if (res == 0) {
if (left instanceof Result && right instanceof Result) {
Result r1 = (Result) left;
Result r2 = (Result) right;
if (r1.getResulttype() == null || r1.getResulttype().getClassid() == null) {
if (r2.getResulttype() != null && r2.getResulttype().getClassid() != null) {
return -1;
}
} else if (r2.getResulttype() == null || r2.getResulttype().getClassid() == null) {
return 1;
}
int rt1 = RESULT_TYPES.indexOf(r1.getResulttype().getClassid());
int rt2 = RESULT_TYPES.indexOf(r2.getResulttype().getClassid());
if (rt1 >= 0 && rt1 > rt2) {
return 1;
} else if (rt2 >= 0 && rt2 > rt1) {
return -1;
}
}
}
// id
if (res == 0) {
if (left instanceof OafEntity && right instanceof OafEntity) {
res = ((OafEntity) left).getId().compareTo(((OafEntity) right).getId());
}
}
return res;
}
}

53
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
View File

@ -40,27 +40,12 @@ public class MergeUtils {
public static <T extends Oaf> T mergeGroup(String s, Iterator<T> oafEntityIterator,
boolean checkDelegateAuthority) {
TreeSet<T> sortedEntities = new TreeSet<>((o1, o2) -> {
int res = 0;
if (o1.getDataInfo() != null && o2.getDataInfo() != null) {
res = o1.getDataInfo().getTrust().compareTo(o2.getDataInfo().getTrust());
}
ArrayList<T> sortedEntities = new ArrayList<>();
oafEntityIterator.forEachRemaining(sortedEntities::add);
sortedEntities.sort(MergeEntitiesComparator.INSTANCE.reversed());
if (res == 0) {
if (o1 instanceof Result && o2 instanceof Result) {
return ResultTypeComparator.INSTANCE.compare((Result) o1, (Result) o2);
}
}
return res;
});
while (oafEntityIterator.hasNext()) {
sortedEntities.add(oafEntityIterator.next());
}
Iterator<T> it = sortedEntities.descendingIterator();
Iterator<T> it = sortedEntities.iterator();
T merged = it.next();
while (it.hasNext()) {
@ -143,7 +128,7 @@ public class MergeUtils {
* https://graph.openaire.eu/docs/data-model/pids-and-identifiers#delegated-authorities and in that case it prefers
* such version.
* <p>
* Otherwise, it considers a resulttype priority order implemented in {@link ResultTypeComparator}
* Otherwise, it considers a resulttype priority order implemented in {@link MergeEntitiesComparator}
* and proceeds with the canonical property merging.
*
* @param left
@ -161,8 +146,9 @@ public class MergeUtils {
if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) {
return right;
}
// TODO: raise trust to have preferred fields from one or the other??
if (new ResultTypeComparator().compare(left, right) < 0) {
if (MergeEntitiesComparator.INSTANCE.compare(left, right) > 0) {
return mergeResultFields(left, right);
} else {
return mergeResultFields(right, left);
@ -225,9 +211,9 @@ public class MergeUtils {
private static <T, K> List<T> mergeLists(final List<T> left, final List<T> right, int trust,
Function<T, K> keyExtractor, BinaryOperator<T> merger) {
if (left == null) {
return right;
} else if (right == null) {
if (left == null || left.isEmpty()) {
return right != null ? right : new ArrayList<>();
} else if (right == null || right.isEmpty()) {
return left;
}
@ -405,7 +391,7 @@ public class MergeUtils {
}
// should be an instance attribute, get the first non-null value
merge.setLanguage(coalesce(merge.getLanguage(), enrich.getLanguage()));
merge.setLanguage(coalesceQualifier(merge.getLanguage(), enrich.getLanguage()));
// distinct countries, do not manage datainfo
merge.setCountry(mergeQualifiers(merge.getCountry(), enrich.getCountry(), trust));
@ -575,6 +561,13 @@ public class MergeUtils {
return m != null ? m : e;
}
private static Qualifier coalesceQualifier(Qualifier m, Qualifier e) {
if (m == null || m.getClassid() == null || StringUtils.isBlank(m.getClassid())) {
return e;
}
return m;
}
private static List<Author> mergeAuthors(List<Author> author, List<Author> author1, int trust) {
List<List<Author>> authors = new ArrayList<>();
if (author != null) {
@ -587,6 +580,10 @@ public class MergeUtils {
}
private static String instanceKeyExtractor(Instance i) {
// three levels of concatenating:
// 1. ::
// 2. @@
// 3. ||
return String
.join(
"::",
@ -594,10 +591,10 @@ public class MergeUtils {
kvKeyExtractor(i.getCollectedfrom()),
qualifierKeyExtractor(i.getAccessright()),
qualifierKeyExtractor(i.getInstancetype()),
Optional.ofNullable(i.getUrl()).map(u -> String.join("::", u)).orElse(null),
Optional.ofNullable(i.getUrl()).map(u -> String.join("@@", u)).orElse(null),
Optional
.ofNullable(i.getPid())
.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("::")))
.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("@@")))
.orElse(null));
}
@ -706,7 +703,7 @@ public class MergeUtils {
private static String spKeyExtractor(StructuredProperty sp) {
return Optional
.ofNullable(sp)
.map(s -> Joiner.on("::").join(s, qualifierKeyExtractor(s.getQualifier())))
.map(s -> Joiner.on("||").join(qualifierKeyExtractor(s.getQualifier()), s.getValue()))
.orElse(null);
}

87
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultTypeComparator.java
View File

@ -1,87 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static eu.dnetlib.dhp.schema.common.ModelConstants.CROSSREF_ID;
import java.util.Comparator;
import java.util.HashSet;
import java.util.Optional;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Result;
public class ResultTypeComparator implements Comparator<Result> {
public static final ResultTypeComparator INSTANCE = new ResultTypeComparator();
@Override
public int compare(Result left, Result right) {
if (left == null && right == null)
return 0;
if (left == null)
return 1;
if (right == null)
return -1;
HashSet<String> lCf = getCollectedFromIds(left);
HashSet<String> rCf = getCollectedFromIds(right);
if (lCf.contains(CROSSREF_ID) && !rCf.contains(CROSSREF_ID)) {
return -1;
}
if (!lCf.contains(CROSSREF_ID) && rCf.contains(CROSSREF_ID)) {
return 1;
}
if (left.getResulttype() == null || left.getResulttype().getClassid() == null) {
if (right.getResulttype() == null || right.getResulttype().getClassid() == null) {
return 0;
}
return 1;
} else if (right.getResulttype() == null || right.getResulttype().getClassid() == null) {
return -1;
}
String lClass = left.getResulttype().getClassid();
String rClass = right.getResulttype().getClassid();
if (!lClass.equals(rClass)) {
if (lClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
return 1;
if (lClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
return 1;
if (lClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
return 1;
if (lClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
return 1;
}
// Else (but unlikely), lexicographical ordering will do.
return lClass.compareTo(rClass);
}
protected HashSet<String> getCollectedFromIds(Result left) {
return Optional
.ofNullable(left.getCollectedfrom())
.map(
cf -> cf
.stream()
.map(KeyValue::getKey)
.collect(Collectors.toCollection(HashSet::new)))
.orElse(new HashSet<>());
}
}

113
dhp-shade-package/dependency-reduced-pom.xml Normal file
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@ -0,0 +1,113 @@
<?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/maven-v4_0_0.xsd">
<parent>
<artifactId>dhp</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.5-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-shade-package</artifactId>
<description>This module create a jar of all module dependencies</description>
<build>
<plugins>
<plugin>
<artifactId>maven-shade-plugin</artifactId>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<transformer>
<mainClass>eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels</mainClass>
</transformer>
<transformer />
<transformer>
<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>
<dependencies>
<dependency>
<groupId>org.projectlombok</groupId>
<artifactId>lombok</artifactId>
<version>1.18.28</version>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
<version>5.6.1</version>
<scope>test</scope>
<exclusions>
<exclusion>
<artifactId>junit-jupiter-api</artifactId>
<groupId>org.junit.jupiter</groupId>
</exclusion>
<exclusion>
<artifactId>junit-jupiter-params</artifactId>
<groupId>org.junit.jupiter</groupId>
</exclusion>
<exclusion>
<artifactId>junit-jupiter-engine</artifactId>
<groupId>org.junit.jupiter</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>3.3.3</version>
<scope>test</scope>
<exclusions>
<exclusion>
<artifactId>byte-buddy</artifactId>
<groupId>net.bytebuddy</groupId>
</exclusion>
<exclusion>
<artifactId>byte-buddy-agent</artifactId>
<groupId>net.bytebuddy</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-junit-jupiter</artifactId>
<version>3.3.3</version>
<scope>test</scope>
</dependency>
</dependencies>
<distributionManagement>
<site>
<id>DHPSite</id>
<url>${dhp.site.stage.path}/dhp-common</url>
</site>
</distributionManagement>
</project>

2
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app/workflow.xml
View File

@ -103,6 +103,7 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@ -156,6 +157,7 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

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

@ -95,6 +95,7 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

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

@ -125,6 +125,7 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

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

@ -95,6 +95,7 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

4
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/otherresearchproduct/oozie_app/workflow.xml
View File

@ -103,6 +103,7 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@ -155,11 +156,12 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=2560
--conf spark.sql.shuffle.partitions=8000
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${workingDir}/otherresearchproduct</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>

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

@ -95,6 +95,7 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

6
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml
View File

@ -103,11 +103,12 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7000
--conf spark.sql.shuffle.partitions=15000
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/publication</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
@ -156,11 +157,12 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7000
--conf spark.sql.shuffle.partitions=15000
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${workingDir}/publication</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>

3
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml
View File

@ -95,11 +95,12 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=10000
--conf spark.sql.shuffle.partitions=15000
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/relation</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>

4
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/software/oozie_app/workflow.xml
View File

@ -103,6 +103,7 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@ -155,11 +156,12 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=2560
--conf spark.sql.shuffle.partitions=4000
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${workingDir}/software</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>

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(

120
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java
View File

@ -9,8 +9,11 @@ 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;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.xml.transform.OutputKeys;
import javax.xml.transform.Transformer;
@ -18,22 +21,18 @@ import javax.xml.transform.TransformerConfigurationException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import javax.xml.xpath.XPath;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpression;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
import javax.xml.xpath.*;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.HttpHeaders;
import org.apache.http.entity.ContentType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
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;
@ -48,20 +47,23 @@ import eu.dnetlib.dhp.common.collection.HttpClientParams;
*
*/
public class RestIterator implements Iterator<String> {
private static final Logger log = LoggerFactory.getLogger(RestIterator.class);
public static final String UTF_8 = "UTF-8";
private static final int MAX_ATTEMPTS = 5;
private final HttpClientParams clientParams;
private final String BASIC = "basic";
private final String AUTHBASIC = "basic";
private static final String XML_HEADER = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
private static final String EMPTY_XML = XML_HEADER + "<" + JsonUtils.XML_WRAP_TAG + "></" + JsonUtils.XML_WRAP_TAG
+ ">";
private final String baseUrl;
private final String resumptionType;
private final String resumptionParam;
private final String resultFormatValue;
private String queryParams;
private String queryParams = "";
private final int resultSizeValue;
private int resumptionInt = 0; // integer resumption token (first record to harvest)
private int resultTotal = -1;
@ -89,6 +91,11 @@ 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 +114,8 @@ 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 +127,7 @@ 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
: "";
@ -148,7 +157,12 @@ public class RestIterator implements Iterator<String> {
}
private void initQueue() {
this.query = this.baseUrl + "?" + this.queryParams + this.querySize + this.queryFormat;
if (queryParams.equals("") && querySize.equals("") && queryFormat.equals("")) {
query = baseUrl;
} else {
query = baseUrl + "?" + queryParams + querySize + queryFormat;
}
log.info("REST calls starting with {}", this.query);
}
@ -209,9 +223,8 @@ public class RestIterator implements Iterator<String> {
try {
String resultJson;
String resultXml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
String resultXml = XML_HEADER;
String nextQuery = "";
final String emptyXml = resultXml + "<" + JsonUtils.XML_WRAP_TAG + "></" + JsonUtils.XML_WRAP_TAG + ">";
Node resultNode = null;
NodeList nodeList = null;
String qUrlArgument = "";
@ -226,37 +239,47 @@ public class RestIterator implements Iterator<String> {
}
}
// find pagination page start number in queryParam and remove before start the first query
if ((resumptionType.toLowerCase().equals("pagination") || resumptionType.toLowerCase().equals("page"))
&& (query.contains("paginationStart="))) {
final Matcher m = Pattern.compile("paginationStart=([0-9]+)").matcher(query);
m.find(); // guaranteed to be true for this regex
String[] pageVal = m.group(0).split("=");
pagination = Integer.parseInt(pageVal[1]);
// remove page start number from queryParams
query = query.replaceFirst("&?paginationStart=[0-9]+", "");
}
try {
log.info("requesting URL [{}]", query);
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);
this.resultStream = IOUtils.toInputStream(resultXml, UTF_8);
}
if (!(emptyXml).equalsIgnoreCase(resultXml)) {
if (!isEmptyXml(resultXml)) {
resultNode = (Node) this.xpath
.evaluate("/", new InputSource(this.resultStream), XPathConstants.NODE);
nodeList = (NodeList) this.xprEntity.evaluate(resultNode, XPathConstants.NODESET);
@ -265,8 +288,7 @@ public class RestIterator implements Iterator<String> {
final StringWriter sw = new StringWriter();
this.transformer.transform(new DOMSource(nodeList.item(i)), new StreamResult(sw));
final String toEnqueue = sw.toString();
if ((toEnqueue == null) || StringUtils.isBlank(toEnqueue)
|| emptyXml.equalsIgnoreCase(toEnqueue)) {
if ((toEnqueue == null) || StringUtils.isBlank(toEnqueue) || isEmptyXml(toEnqueue)) {
log
.warn(
"The following record resulted in empty item for the feeding queue: {}", resultXml);
@ -294,6 +316,7 @@ public class RestIterator implements Iterator<String> {
throw new CollectorException("Mode: discover, Param 'resultSizeValue' is less than 2");
}
qUrlArgument = qUrl.getQuery();
final String[] arrayQUrlArgument = qUrlArgument.split("&");
for (final String arrayUrlArgStr : arrayQUrlArgument) {
if (arrayUrlArgStr.startsWith(this.resumptionParam)) {
@ -307,7 +330,7 @@ public class RestIterator implements Iterator<String> {
}
}
if (((emptyXml).equalsIgnoreCase(resultXml))
if (isEmptyXml(resultXml)
|| ((nodeList != null) && (nodeList.getLength() < this.resultSizeValue))) {
// resumptionStr = "";
if (nodeList != null) {
@ -326,13 +349,13 @@ public class RestIterator implements Iterator<String> {
case "pagination":
case "page": // pagination, iterate over page numbers
this.pagination += 1;
if (nodeList != null) {
if (nodeList != null && nodeList.getLength() > 0) {
this.discoverResultSize += nodeList.getLength();
} else {
this.resultTotal = this.discoverResultSize;
this.pagination = this.discoverResultSize;
}
this.pagination += 1;
this.resumptionInt = this.pagination;
this.resumptionStr = Integer.toString(this.resumptionInt);
break;
@ -380,7 +403,8 @@ 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);
@ -409,6 +433,10 @@ public class RestIterator implements Iterator<String> {
}
private boolean isEmptyXml(String s) {
return EMPTY_XML.equalsIgnoreCase(s);
}
private boolean isInteger(final String s) {
boolean isValidInteger = false;
try {
@ -433,6 +461,22 @@ 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;
}

45
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XMLIterator.java
View File

@ -8,7 +8,10 @@ import java.io.StringWriter;
import java.nio.charset.Charset;
import java.nio.charset.CharsetDecoder;
import java.nio.charset.CodingErrorAction;
import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
import java.util.stream.Collectors;
import javax.xml.stream.XMLEventFactory;
import javax.xml.stream.XMLEventReader;
@ -19,6 +22,7 @@ import javax.xml.stream.XMLStreamException;
import javax.xml.stream.events.StartElement;
import javax.xml.stream.events.XMLEvent;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -58,13 +62,23 @@ public class XMLIterator implements Iterator<String> {
private String element;
private List<String> elements;
private InputStream inputStream;
public XMLIterator(final String element, final InputStream inputStream) {
super();
this.element = element;
if (element.contains(",")) {
elements = Arrays
.stream(element.split(","))
.filter(StringUtils::isNoneBlank)
.map(String::toLowerCase)
.collect(Collectors.toList());
}
this.inputStream = inputStream;
this.parser = getParser();
try {
this.current = findElement(parser);
} catch (XMLStreamException e) {
@ -113,7 +127,7 @@ public class XMLIterator implements Iterator<String> {
final XMLEvent event = parser.nextEvent();
// TODO: replace with depth tracking instead of close tag tracking.
if (event.isEndElement() && event.asEndElement().getName().getLocalPart().equals(element)) {
if (event.isEndElement() && isCheckTag(event.asEndElement().getName().getLocalPart())) {
writer.add(event);
break;
}
@ -142,18 +156,16 @@ public class XMLIterator implements Iterator<String> {
XMLEvent peek = parser.peek();
if (peek != null && peek.isStartElement()) {
String name = peek.asStartElement().getName().getLocalPart();
if (element.equals(name)) {
if (isCheckTag(name))
return peek;
}
}
while (parser.hasNext()) {
final XMLEvent event = parser.nextEvent();
XMLEvent event = parser.nextEvent();
if (event != null && event.isStartElement()) {
String name = event.asStartElement().getName().getLocalPart();
if (element.equals(name)) {
if (isCheckTag(name))
return event;
}
}
}
return null;
@ -161,12 +173,31 @@ public class XMLIterator implements Iterator<String> {
private XMLEventReader getParser() {
try {
return inputFactory.get().createXMLEventReader(sanitize(inputStream));
XMLInputFactory xif = inputFactory.get();
xif.setProperty(XMLInputFactory.SUPPORT_DTD, false);
return xif.createXMLEventReader(sanitize(inputStream));
} catch (XMLStreamException e) {
throw new RuntimeException(e);
}
}
private boolean isCheckTag(final String tagName) {
if (elements != null) {
final String found = elements
.stream()
.filter(e -> e.equalsIgnoreCase(tagName))
.findFirst()
.orElse(null);
if (found != null)
return true;
} else {
if (element.equalsIgnoreCase(tagName)) {
return true;
}
}
return false;
}
private Reader sanitize(final InputStream in) {
final CharsetDecoder charsetDecoder = Charset.forName(UTF_8).newDecoder();
charsetDecoder.onMalformedInput(CodingErrorAction.REPLACE);

64
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipMultipleNodeTest.java Normal file
View File

@ -0,0 +1,64 @@
package eu.dnetlib.dhp.collection.plugin.file;
import java.io.IOException;
import java.util.HashMap;
import java.util.Objects;
import java.util.stream.Stream;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.junit.jupiter.api.*;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.junit.jupiter.MockitoExtension;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.collection.ApiDescriptor;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
import eu.dnetlib.dhp.common.collection.CollectorException;
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
@ExtendWith(MockitoExtension.class)
public class FileGZipMultipleNodeTest {
private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPluginTest.class);
private final ApiDescriptor api = new ApiDescriptor();
private FileGZipCollectorPlugin plugin;
private static final String SPLIT_ON_ELEMENT = "incollection,article";
@BeforeEach
public void setUp() throws IOException {
final String gzipFile = Objects
.requireNonNull(
this
.getClass()
.getResource("/eu/dnetlib/dhp/collection/plugin/file/dblp.gz"))
.getFile();
api.setBaseUrl(gzipFile);
HashMap<String, String> params = new HashMap<>();
params.put("splitOnElement", SPLIT_ON_ELEMENT);
api.setParams(params);
FileSystem fs = FileSystem.get(new Configuration());
plugin = new FileGZipCollectorPlugin(fs);
}
@Test
void test() throws CollectorException {
final Stream<String> stream = plugin.collect(api, new AggregatorReport());
stream.limit(10).forEach(s -> {
Assertions.assertTrue(s.length() > 0);
log.info(s);
});
}
}

10
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/OsfPreprintCollectorTest.java
View File

@ -36,11 +36,11 @@ public class OsfPreprintCollectorTest {
private final String resultTotalXpath = "/*/*[local-name()='links']/*[local-name()='meta']/*[local-name()='total']";
private final String resumptionParam = "page";
private final String resumptionType = "page";
private final String resumptionXpath = "/*/*[local-name()='links']/*[local-name()='next']";
private final String resumptionType = "scan";
private final String resumptionXpath = "substring-before(substring-after(/*/*[local-name()='links']/*[local-name()='next'], 'page='), '&')";
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();

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dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/file/dblp.gz Normal file
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103
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DatasetMergerTest.java Normal file
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@ -0,0 +1,103 @@
package eu.dnetlib.dhp.oa.dedup;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.io.Serializable;
import java.lang.reflect.InvocationTargetException;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import org.codehaus.jackson.map.ObjectMapper;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import eu.dnetlib.pace.util.MapDocumentUtil;
import scala.Tuple2;
class DatasetMergerTest implements Serializable {
private List<Tuple2<String, Dataset>> datasets;
private String testEntityBasePath;
private DataInfo dataInfo;
private final String dedupId = "50|doi_________::3d18564ef27ebe9ef3bd8b4dec67e148";
private Dataset dataset_top;
@BeforeEach
public void setUp() throws Exception {
testEntityBasePath = Paths
.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/json").toURI())
.toFile()
.getAbsolutePath();
datasets = readSample(testEntityBasePath + "/dataset_merge.json", Dataset.class);
dataset_top = getTopPub(datasets);
dataInfo = setDI();
}
@Test
void datasetMergerTest() throws InstantiationException, IllegalAccessException, InvocationTargetException {
Dataset pub_merged = MergeUtils.mergeGroup(dedupId, datasets.stream().map(Tuple2::_2).iterator());
// verify id
assertEquals(dedupId, pub_merged.getId());
assertEquals(2, pub_merged.getInstance().size());
}
public DataInfo setDI() {
DataInfo dataInfo = new DataInfo();
dataInfo.setTrust("0.9");
dataInfo.setDeletedbyinference(false);
dataInfo.setInferenceprovenance("testing");
dataInfo.setInferred(true);
return dataInfo;
}
public Dataset getTopPub(List<Tuple2<String, Dataset>> publications) {
Double maxTrust = 0.0;
Dataset maxPub = new Dataset();
for (Tuple2<String, Dataset> publication : publications) {
Double pubTrust = Double.parseDouble(publication._2().getDataInfo().getTrust());
if (pubTrust > maxTrust) {
maxTrust = pubTrust;
maxPub = publication._2();
}
}
return maxPub;
}
public <T> List<Tuple2<String, T>> readSample(String path, Class<T> clazz) {
List<Tuple2<String, T>> res = new ArrayList<>();
BufferedReader reader;
try {
reader = new BufferedReader(new FileReader(path));
String line = reader.readLine();
while (line != null) {
res
.add(
new Tuple2<>(
MapDocumentUtil.getJPathString("$.id", line),
new ObjectMapper().readValue(line, clazz)));
// read next line
line = reader.readLine();
}
reader.close();
} catch (IOException e) {
e.printStackTrace();
}
return res;
}
}

10
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java
View File

@ -93,14 +93,14 @@ class EntityMergerTest implements Serializable {
assertEquals(pub_top.getJournal().getConferencedate(), pub_merged.getJournal().getConferencedate());
assertEquals(pub_top.getJournal().getConferenceplace(), pub_merged.getJournal().getConferenceplace());
assertEquals("OPEN", pub_merged.getBestaccessright().getClassid());
assertEquals(pub_top.getResulttype(), pub_merged.getResulttype());
assertEquals(pub_top.getLanguage(), pub_merged.getLanguage());
assertEquals(pub_top.getPublisher(), pub_merged.getPublisher());
assertEquals(pub_top.getEmbargoenddate(), pub_merged.getEmbargoenddate());
assertEquals(pub_top.getResulttype().getClassid(), pub_merged.getResulttype().getClassid());
assertEquals(pub_top.getLanguage().getClassid(), pub_merged.getLanguage().getClassid());
assertEquals("Elsevier BV", pub_merged.getPublisher().getValue());
assertEquals(pub_top.getEmbargoenddate().getValue(), pub_merged.getEmbargoenddate().getValue());
assertEquals(pub_top.getResourcetype().getClassid(), "");
assertEquals(pub_top.getDateoftransformation(), pub_merged.getDateoftransformation());
assertEquals(pub_top.getOaiprovenance(), pub_merged.getOaiprovenance());
assertEquals(pub_top.getDateofcollection(), pub_merged.getDateofcollection());
// assertEquals(pub_top.getDateofcollection(), pub_merged.getDateofcollection());
assertEquals(3, pub_merged.getInstance().size());
assertEquals(2, pub_merged.getCountry().size());
assertEquals(0, pub_merged.getSubject().size());

2
dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/dataset_merge.json Normal file
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File diff suppressed because one or more lines are too long

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java
View File

@ -172,7 +172,7 @@ public class SparkBulkTagJob {
.option("compression", "gzip")
.json(outputPath + "project");
readPath(spark, outputPath + "project", Datasource.class)
readPath(spark, outputPath + "project", Project.class)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")

1
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
View File

@ -398,6 +398,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
o.setEcsmevalidated(field(Boolean.toString(rs.getBoolean("ecsmevalidated")), info));
o.setEcnutscode(field(Boolean.toString(rs.getBoolean("ecnutscode")), info));
o.setCountry(prepareQualifierSplitting(rs.getString("country")));
o.setOrganizationType(Organization.OrganizationType.valueOf(rs.getString("typology")));
o.setDataInfo(info);
o.setLastupdatetimestamp(lastUpdateTimestamp);

8
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml
View File

@ -156,6 +156,7 @@
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@ -190,6 +191,7 @@
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@ -224,6 +226,7 @@
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@ -258,6 +261,7 @@
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@ -292,6 +296,7 @@
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@ -326,6 +331,7 @@
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@ -360,6 +366,7 @@
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@ -394,6 +401,7 @@
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

30
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml
View File

@ -116,17 +116,19 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
--conf spark.sql.shuffle.partitions=10000
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/publication</arg>
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
<arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
<arg>--numPartitions</arg><arg>8000</arg>
<arg>--numPartitions</arg><arg>10000</arg>
</spark>
<ok to="join_import"/>
<error to="Kill"/>
@ -143,17 +145,19 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
--conf spark.sql.shuffle.partitions=4000
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/dataset</arg>
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
<arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
<arg>--numPartitions</arg><arg>4000</arg>
<arg>--numPartitions</arg><arg>8000</arg>
</spark>
<ok to="join_import"/>
<error to="Kill"/>
@ -170,11 +174,13 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
--conf spark.sql.shuffle.partitions=8000
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/otherresearchproduct</arg>
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
@ -197,17 +203,19 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
--conf spark.sql.shuffle.partitions=1000
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/software</arg>
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
<arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
<arg>--numPartitions</arg><arg>300</arg>
<arg>--numPartitions</arg><arg>1000</arg>
</spark>
<ok to="join_import"/>
<error to="Kill"/>
@ -224,17 +232,19 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
--conf spark.sql.shuffle.partitions=200
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/datasource</arg>
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
<arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
<arg>--numPartitions</arg><arg>100</arg>
<arg>--numPartitions</arg><arg>200</arg>
</spark>
<ok to="join_import"/>
<error to="Kill"/>
@ -251,17 +261,19 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
--conf spark.sql.shuffle.partitions=1000
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/organization</arg>
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
<arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
<arg>--numPartitions</arg><arg>400</arg>
<arg>--numPartitions</arg><arg>1000</arg>
</spark>
<ok to="join_import"/>
<error to="Kill"/>
@ -278,17 +290,19 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
--conf spark.sql.shuffle.partitions=1000
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/project</arg>
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
<arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
<arg>--numPartitions</arg><arg>100</arg>
<arg>--numPartitions</arg><arg>1000</arg>
</spark>
<ok to="join_import"/>
<error to="Kill"/>
@ -305,17 +319,19 @@
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
--conf spark.sql.shuffle.partitions=15000
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/relation</arg>
<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
<arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>
<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
<arg>--numPartitions</arg><arg>10000</arg>
<arg>--numPartitions</arg><arg>15000</arg>
</spark>
<ok to="join_import"/>
<error to="Kill"/>

7
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOpenOrgsForProvision.sql
View File

@ -28,7 +28,8 @@ SELECT
(array_remove(array_cat(ARRAY[o.ec_internationalorganization], array_agg(od.ec_internationalorganization)), NULL))[1] AS ecinternationalorganization,
(array_remove(array_cat(ARRAY[o.ec_enterprise], array_agg(od.ec_enterprise)), NULL))[1] AS ecenterprise,
(array_remove(array_cat(ARRAY[o.ec_smevalidated], array_agg(od.ec_smevalidated)), NULL))[1] AS ecsmevalidated,
(array_remove(array_cat(ARRAY[o.ec_nutscode], array_agg(od.ec_nutscode)), NULL))[1] AS ecnutscode
(array_remove(array_cat(ARRAY[o.ec_nutscode], array_agg(od.ec_nutscode)), NULL))[1] AS ecnutscode,
org_types.name AS typology
FROM organizations o
LEFT OUTER JOIN acronyms a ON (a.id = o.id)
LEFT OUTER JOIN urls u ON (u.id = o.id)
@ -37,6 +38,7 @@ FROM organizations o
LEFT OUTER JOIN oa_duplicates d ON (o.id = d.local_id AND d.reltype != 'is_different')
LEFT OUTER JOIN organizations od ON (d.oa_original_id = od.id)
LEFT OUTER JOIN other_ids idup ON (od.id = idup.id)
LEFT OUTER JOIN org_types ON (org_types.val = o.type)
WHERE
o.status = 'approved' OR o.status = 'suggested'
GROUP BY
@ -44,4 +46,5 @@ GROUP BY
o.name,
o.creation_date,
o.modification_date,
o.country;
o.country,
org_types.name;

39
dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala
View File

@ -25,27 +25,38 @@ object SparkApplyHostedByMapToResult {
val i = p.getInstance().asScala
if (i.size == 1) {
val inst: Instance = i.head
inst.getHostedby.setKey(ei.getHostedById)
inst.getHostedby.setValue(ei.getName)
if (ei.getOpenAccess) {
inst.setAccessright(
OafMapperUtils.accessRight(
ModelConstants.ACCESS_RIGHT_OPEN,
"Open Access",
ModelConstants.DNET_ACCESS_MODES,
ModelConstants.DNET_ACCESS_MODES
)
)
inst.getAccessright.setOpenAccessRoute(OpenAccessRoute.gold)
p.setBestaccessright(OafMapperUtils.createBestAccessRights(p.getInstance()));
}
patchInstance(p, ei, inst)
} else {
val cf = i.map(ii => ii.getCollectedfrom.getValue)
if (cf.contains("Crossref")) {
i.foreach(ii => {
patchInstance(p, ei, ii)
})
}
}
}
p
})(Encoders.bean(classOf[Publication]))
}
private def patchInstance(p: Publication, ei: EntityInfo, inst: Instance): Unit = {
inst.getHostedby.setKey(ei.getHostedById)
inst.getHostedby.setValue(ei.getName)
if (ei.getOpenAccess) {
inst.setAccessright(
OafMapperUtils.accessRight(
ModelConstants.ACCESS_RIGHT_OPEN,
"Open Access",
ModelConstants.DNET_ACCESS_MODES,
ModelConstants.DNET_ACCESS_MODES
)
)
inst.getAccessright.setOpenAccessRoute(OpenAccessRoute.gold)
p.setBestaccessright(OafMapperUtils.createBestAccessRights(p.getInstance()));
}
}
def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(getClass)

186
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java Normal file
View File

@ -0,0 +1,186 @@
package eu.dnetlib.dhp.oa.oaipmh;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.nio.charset.Charset;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.Statement;
import java.time.LocalDateTime;
import java.util.ArrayList;
import java.util.Optional;
import java.util.Properties;
import java.util.zip.GZIPOutputStream;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoder;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.dom4j.Document;
import org.dom4j.DocumentHelper;
import org.dom4j.Node;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
import eu.dnetlib.dhp.oa.provision.model.TupleWrapper;
public class IrishOaiExporterJob {
private static final Logger log = LoggerFactory.getLogger(IrishOaiExporterJob.class);
protected static final int NUM_CONNECTIONS = 20;
public static final String TMP_OAI_TABLE = "temp_oai_data";
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
IrishOaiExporterJob.class
.getResourceAsStream("/eu/dnetlib/dhp/oa/oaipmh/input_params_irish_oai_exporter.json")));
parser.parseArgument(args);
final Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
final String dbUrl = parser.get("dbUrl");
final String dbUser = parser.get("dbUser");
final String dbPwd = parser.get("dbPwd");
final int numConnections = Optional
.ofNullable(parser.get("numConnections"))
.map(Integer::valueOf)
.orElse(NUM_CONNECTIONS);
log.info("inputPath: '{}'", inputPath);
log.info("dbUrl: '{}'", dbUrl);
log.info("dbUser: '{}'", dbUser);
log.info("dbPwd: '{}'", "xxx");
log.info("numPartitions: '{}'", numConnections);
final Properties connectionProperties = new Properties();
connectionProperties.put("user", dbUser);
connectionProperties.put("password", dbPwd);
final SparkConf conf = new SparkConf();
conf.registerKryoClasses(new Class[] {
SerializableSolrInputDocument.class
});
final Encoder<TupleWrapper> encoderTuple = Encoders.bean(TupleWrapper.class);
final Encoder<OaiRecordWrapper> encoderOaiRecord = Encoders.bean(OaiRecordWrapper.class);
final String date = LocalDateTime.now().toString();
log.info("Creating temporary table...");
runWithSparkSession(conf, isSparkSessionManaged, spark -> {
final Dataset<OaiRecordWrapper> docs = spark
.read()
.schema(encoderTuple.schema())
.json(inputPath)
.as(encoderTuple)
.map((MapFunction<TupleWrapper, String>) TupleWrapper::getXml, Encoders.STRING())
.map((MapFunction<String, OaiRecordWrapper>) r -> asIrishOaiResult(r, date), encoderOaiRecord)
.filter((FilterFunction<OaiRecordWrapper>) obj -> (obj != null) && StringUtils.isNotBlank(obj.getId()));
docs
.repartition(numConnections)
.write()
.mode(SaveMode.Overwrite)
.jdbc(dbUrl, TMP_OAI_TABLE, connectionProperties);
});
log.info("Temporary table created.");
log.info("Updating OAI records...");
try (final Connection con = DriverManager.getConnection(dbUrl, dbUser, dbPwd)) {
try (final Statement st = con.createStatement()) {
final String query = IOUtils
.toString(IrishOaiExporterJob.class.getResourceAsStream("oai-finalize.sql"));
st.execute(query);
}
}
log.info("DONE.");
}
protected static OaiRecordWrapper asIrishOaiResult(final String xml, final String date) {
try {
final Document doc = DocumentHelper.parseText(xml);
final OaiRecordWrapper r = new OaiRecordWrapper();
if (isValid(doc)) {
r.setId(doc.valueOf("//*[local-name()='objIdentifier']").trim());
r.setBody(gzip(doc.selectSingleNode("//*[local-name()='entity']").asXML()));
r.setDate(date);
r.setSets(new ArrayList<>());
}
return r;
} catch (final Exception e) {
log.error("Error parsing record: " + xml, e);
throw new RuntimeException("Error parsing record: " + xml, e);
}
}
protected static boolean isValid(final Document doc) {
final Node n = doc.selectSingleNode("//*[local-name()='entity']/*[local-name()='result']");
if (n != null) {
for (final Object o : n.selectNodes(".//*[local-name()='datainfo']/*[local-name()='deletedbyinference']")) {
if ("true".equals(((Node) o).getText().trim())) {
return false;
}
}
// verify the main country of the result
for (final Object o : n.selectNodes("./*[local-name()='country']")) {
if ("IE".equals(((Node) o).valueOf("@classid").trim())) {
return true;
}
}
// verify the countries of the related organizations
for (final Object o : n.selectNodes(".//*[local-name()='rel']")) {
final String relType = ((Node) o).valueOf("./*[local-name() = 'to']/@type").trim();
final String relCountry = ((Node) o).valueOf("./*[local-name() = 'country']/@classid").trim();
if ("organization".equals(relType) && "IE".equals(relCountry)) {
return true;
}
}
}
return false;
}
protected static byte[] gzip(final String str) {
if (StringUtils.isBlank(str)) {
return null;
}
try (final ByteArrayOutputStream baos = new ByteArrayOutputStream()) {
try (final GZIPOutputStream gzip = new GZIPOutputStream(baos)) {
IOUtils.write(str.getBytes(Charset.defaultCharset()), gzip);
}
return baos.toByteArray();
} catch (final IOException e) {
throw new RuntimeException("error in gzip", e);
}
}
}

51
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/OaiRecordWrapper.java Normal file
View File

@ -0,0 +1,51 @@
package eu.dnetlib.dhp.oa.oaipmh;
import java.io.Serializable;
import java.util.List;
public class OaiRecordWrapper implements Serializable {
private static final long serialVersionUID = 8997046455575004880L;
private String id;
private byte[] body;
private String date;
private List<String> sets;
public OaiRecordWrapper() {
}
public String getId() {
return this.id;
}
public void setId(final String id) {
this.id = id;
}
public byte[] getBody() {
return this.body;
}
public void setBody(final byte[] body) {
this.body = body;
}
public String getDate() {
return this.date;
}
public void setDate(final String date) {
this.date = date;
}
public List<String> getSets() {
return this.sets;
}
public void setSets(final List<String> sets) {
this.sets = sets;
}
}

32
dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/input_params_irish_oai_exporter.json Normal file
View File

@ -0,0 +1,32 @@
[
{
"paramName": "i",
"paramLongName": "inputPath",
"paramDescription": "The path of the input records on HDFS",
"paramRequired": true
},
{
"paramName": "nc",
"paramLongName": "numConnections",
"paramDescription": "number of connections to the postgres db (for the write operation)",
"paramRequired": false
},
{
"paramName": "du",
"paramLongName": "dbUrl",
"paramDescription": "the url of the database",
"paramRequired": true
},
{
"paramName": "dusr",
"paramLongName": "dbUser",
"paramDescription": "the user of the database",
"paramRequired": true
},
{
"paramName": "dpwd",
"paramLongName": "dbPwd",
"paramDescription": "the password for the user of the database",
"paramRequired": true
}
]

12
dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/oai-finalize.sql Normal file
View File

@ -0,0 +1,12 @@
BEGIN;
DELETE FROM oai_data;
INSERT INTO oai_data(id, body, date, sets) SELECT
id,
body,
date::timestamp,
sets
FROM temp_oai_data;
COMMIT;

106
dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/oozie_app/workflow.xml Normal file
View File

@ -0,0 +1,106 @@
<workflow-app name="irish-oaipmh-provision" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>inputPath</name>
<description>The path of the input records on HDFS</description>
</property>
<property>
<name>numConnections</name>
<description>number of connections to the postgres db (for the write operation)</description>
</property>
<property>
<name>dbUrl</name>
<description>the url of the database</description>
</property>
<property>
<name>dbUser</name>
<description>the user of the database</description>
</property>
<property>
<name>dbPwd</name>
<description>the password for the user of the database</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="oaiphm_provision"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="irish_oaiphm_provision">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Irish OAI-PHM provision</name>
<class>eu.dnetlib.dhp.oa.oaipmh.IrishOaiExporterJob</class>
<jar>dhp-graph-provision-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=8000
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}</arg>
<arg>--numConnections</arg><arg>${numConnections}</arg>
<arg>--dbUrl</arg><arg>${dbUrl}</arg>
<arg>--dbUser</arg><arg>${dbUser}</arg>
<arg>--dbPwd</arg><arg>${dbPwd}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

97
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/DbSerializationTest.java Normal file
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package eu.dnetlib.dhp.oa.oaipmh;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.Statement;
import java.time.LocalDateTime;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Properties;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@Disabled
public class DbSerializationTest {
private static SparkSession spark;
public static final String dbUrl = "jdbc:postgresql://localhost:5432/db_test";
public static final String dbUser = null;
public static final String dbPwd = null;
@BeforeAll
public static void beforeAll() throws IOException {
final SparkConf conf = new SparkConf();
conf.setAppName("TEST");
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
spark = SparkSession
.builder()
.appName("TEST")
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
spark.stop();
}
@Test
public void testDatabaseSerialization() throws Exception {
final Properties connectionProperties = new Properties();
if (dbUser != null) {
connectionProperties.put("user", dbUser);
}
if (dbPwd != null) {
connectionProperties.put("password", dbPwd);
}
runWithSparkSession(new SparkConf(), false, spark -> {
final List<OaiRecordWrapper> list = new ArrayList<>();
for (int i = 0; i < 10; i++) {
final OaiRecordWrapper r = new OaiRecordWrapper();
r.setId("record_" + i);
r.setBody("jsahdjkahdjahdajad".getBytes());
r.setDate(LocalDateTime.now().toString());
r.setSets(Arrays.asList());
list.add(r);
}
final Dataset<OaiRecordWrapper> docs = spark.createDataset(list, Encoders.bean(OaiRecordWrapper.class));
docs
.write()
.mode(SaveMode.Overwrite)
.jdbc(dbUrl, IrishOaiExporterJob.TMP_OAI_TABLE, connectionProperties);
});
try (final Connection con = DriverManager.getConnection(dbUrl, dbUser, dbPwd)) {
try (final Statement st = con.createStatement()) {
final String query = IOUtils.toString(getClass().getResourceAsStream("oai-finalize.sql"));
st.execute(query);
}
}
}
}

88
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJobTest.java Normal file
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package eu.dnetlib.dhp.oa.oaipmh;
import static org.junit.Assert.assertNull;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.nio.charset.Charset;
import java.time.LocalDateTime;
import java.util.zip.GZIPInputStream;
import org.apache.commons.io.IOUtils;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.io.SAXReader;
import org.junit.jupiter.api.Test;
public class IrishOaiExporterJobTest {
@Test
void testAsIrishOaiResult() throws Exception {
final String xml = IOUtils.toString(getClass().getResourceAsStream("record_IE.xml"));
final OaiRecordWrapper res = IrishOaiExporterJob.asIrishOaiResult(xml, LocalDateTime.now().toString());
assertNotNull(res.getId());
assertNotNull(res.getBody());
assertNotNull(res.getSets());
assertNotNull(res.getDate());
assertEquals("dedup_wf_002::532be02f990b479a1da46d71f1a4c3f0", res.getId());
assertTrue(res.getBody().length > 0);
assertTrue(res.getSets().isEmpty());
}
@Test
void testIsValid_IE() throws DocumentException {
final Document doc = new SAXReader().read(getClass().getResourceAsStream("record_IE.xml"));
assertTrue(IrishOaiExporterJob.isValid(doc));
}
@Test
void testIsValid_invalid_country() throws DocumentException {
final Document doc = new SAXReader().read(getClass().getResourceAsStream("record_IT.xml"));
assertFalse(IrishOaiExporterJob.isValid(doc));
}
@Test
void testIsValid_deleted() throws DocumentException {
final Document doc = new SAXReader().read(getClass().getResourceAsStream("record_IE_deleted.xml"));
assertFalse(IrishOaiExporterJob.isValid(doc));
}
@Test
void testGzip_simple() {
final String message = "<test />";
final byte[] bytes = IrishOaiExporterJob.gzip(message);
assertNotNull(bytes);
assertTrue(bytes.length > 0);
assertEquals(message, gunzip(bytes));
}
@Test
void testGzip_empty() {
assertNull(IrishOaiExporterJob.gzip(""));
assertNull(IrishOaiExporterJob.gzip(null));
}
public static String gunzip(final byte[] compressed) {
if ((compressed == null) || (compressed.length == 0)) {
return null;
}
if (!isCompressed(compressed)) {
return new String(compressed);
}
try (final GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream(compressed))) {
return IOUtils.toString(gis, Charset.defaultCharset());
} catch (final IOException e) {
throw new RuntimeException("error in gunzip", e);
}
}
private static boolean isCompressed(final byte[] compressed) {
return (compressed[0] == (byte) GZIPInputStream.GZIP_MAGIC)
&& (compressed[1] == (byte) (GZIPInputStream.GZIP_MAGIC >> 8));
}
}

89
dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/oaipmh/record_IE.xml Normal file
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<dateOfTransformation>2023-03-31T18:45:52.701Z</dateOfTransformation>
</header>
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89
dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/oaipmh/record_IE_deleted.xml Normal file
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<result objidentifier="od_______934::55a12e2e0fee45ce8005633c6c17fe9f">
<title classid="main title" classname="main title" schemeid="dnet:dataCite_title" schemename="dnet:dataCite_title" inferred="false" provenanceaction="sysimport:crosswalk:repository" trust="0.9">A service innovation capability maturity model for SMEs</title>
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<refereed classid="0002" classname="nonPeerReviewed" schemeid="dnet:review_levels" schemename="dnet:review_levels" />
<fulltext>http://repository.wit.ie/3029/1/Research%20Day%202015%20-%20Poster%20Tadhg%20Blommerde.pdf</fulltext>
<webresource>
<url>http://repository.wit.ie/3029/</url>
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66
dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/oaipmh/record_IT.xml Normal file
View File

@ -0,0 +1,66 @@
<record rank="null">
<result>
<header>
<objIdentifier>od_______310::02365c51a0ed7cbb54b2bbc7c0426d1b</objIdentifier>
<dateOfCollection>2024-04-06T06:05:16+0000</dateOfCollection>
<dateOfTransformation>2024-04-06T06:56:01.776Z</dateOfTransformation>
</header>
<metadata>
<entity schemaLocation="http://namespace.openaire.eu/oaf https://www.openaire.eu/schema/1.0/oaf-1.0.xsd">
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<originalId>oai:flore.unifi.it:2158/608965</originalId>
<pid classid="handle" classname="Handle" schemeid="dnet:pid_types" schemename="dnet:pid_types" inferred="false" provenanceaction="sysimport:crosswalk:repository" trust="0.9">2158/608965</pid>
<measure id="influence" score="3.1177596E-9" class="C5" />
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<measure id="popularity_alt" score="0.0" class="C5" />
<measure id="impulse" score="0" class="C5" />
<title classid="main title" classname="main title" schemeid="dnet:dataCite_title" schemename="dnet:dataCite_title" inferred="false" provenanceaction="sysimport:crosswalk:repository" trust="0.9">Estorsione (art. 629)</title>
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<creator rank="1" name="Francesco" surname="Macri" orcid_pending="0000-0001-7658-6173">MACRI', FRANCESCO</creator>
<country classid="IT" classname="Italy" schemeid="dnet:countries" schemename="dnet:countries" />
<dateofacceptance>2011-01-01</dateofacceptance>
<language classid="und" classname="Undetermined" schemeid="dnet:languages" schemename="dnet:languages" />
<relevantdate classid="Accepted" classname="Accepted" schemeid="dnet:dataCite_date" schemename="dnet:dataCite_date" inferred="false" provenanceaction="sysimport:crosswalk:repository" trust="0.9">2011-01-01</relevantdate>
<relevantdate classid="issued" classname="issued" schemeid="dnet:dataCite_date" schemename="dnet:dataCite_date" inferred="false" provenanceaction="sysimport:crosswalk:repository" trust="0.9">2011-01-01</relevantdate>
<relevantdate classid="available" classname="available" schemeid="dnet:dataCite_date" schemename="dnet:dataCite_date" inferred="false" provenanceaction="sysimport:crosswalk:repository" trust="0.9">2015-04-28</relevantdate>
<publisher>UTET</publisher>
<resulttype classid="publication" classname="publication" schemeid="dnet:result_typologies" schemename="dnet:result_typologies" />
<resourcetype classid="book part" classname="book part" schemeid="dnet:dataCite_resource" schemename="dnet:dataCite_resource" />
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<inferred>false</inferred>
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<trust>0.9</trust>
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<to class="hasAuthorInstitution" scheme="dnet:result_organization_relations" type="organization">openorgs____::41406edad82942e9e0b29317b8a847e2</to>
<legalshortname>University of Florence</legalshortname>
<country classid="IT" classname="Italy" schemeid="dnet:countries" schemename="dnet:countries" />
<legalname>University of Florence</legalname>
</rel>
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<collectedfrom name="Flore (Florence Research Repository)" id="opendoar____::06eb61b839a0cefee4967c67ccb099dc" />
<hostedby name="Flore (Florence Research Repository)" id="opendoar____::06eb61b839a0cefee4967c67ccb099dc" />
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<instancetype classid="0013" classname="Part of book or chapter of book" schemeid="dnet:publication_resource" schemename="dnet:publication_resource" />
<pid classid="handle" classname="Handle" schemeid="dnet:pid_types" schemename="dnet:pid_types" inferred="false" provenanceaction="sysimport:crosswalk:repository" trust="0.9">2158/608965</pid>
<alternateidentifier classid="urn" classname="urn" schemeid="dnet:pid_types" schemename="dnet:pid_types" inferred="false" provenanceaction="sysimport:crosswalk:repository" trust="0.9">http://hdl.handle.net/2158/608965</alternateidentifier>
<refereed classid="0002" classname="nonPeerReviewed" schemeid="dnet:review_levels" schemename="dnet:review_levels" />
<webresource>
<url>https://hdl.handle.net/2158/608965</url>
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31
dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh
View File

@ -72,6 +72,8 @@ function copydb() {
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 2
else
return 2
fi
fi
@ -90,19 +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
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"
@ -131,7 +144,7 @@ function copydb() {
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"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 4
exit 5
fi
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
@ -139,7 +152,7 @@ function copydb() {
if [ -n "$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 5
exit 6
fi
fi
fi
@ -185,7 +198,7 @@ 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"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 6
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${all_create_view_statements[@]}\n"
@ -215,7 +228,7 @@ function copydb() {
echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 7
exit 8
fi
fi

31
dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh
View File

@ -72,6 +72,8 @@ function copydb() {
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 2
else
return 2
fi
fi
@ -90,19 +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
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"
@ -131,7 +144,7 @@ function copydb() {
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"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 4
exit 5
fi
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
@ -139,7 +152,7 @@ function copydb() {
if [ -n "$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 5
exit 6
fi
fi
fi
@ -185,7 +198,7 @@ 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"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 6
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${all_create_view_statements[@]}\n"
@ -215,7 +228,7 @@ function copydb() {
echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 7
exit 8
fi
fi

31
dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh
View File

@ -72,6 +72,8 @@ function copydb() {
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 2
else
return 2
fi
fi
@ -90,19 +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
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"
@ -131,7 +144,7 @@ function copydb() {
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"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 4
exit 5
fi
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
@ -139,7 +152,7 @@ function copydb() {
if [ -n "$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 5
exit 6
fi
fi
fi
@ -185,7 +198,7 @@ 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"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 6
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${all_create_view_statements[@]}\n"
@ -215,7 +228,7 @@ function copydb() {
echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 7
exit 8
fi
fi

31
dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh
View File

@ -74,6 +74,8 @@ function copydb() {
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 2
else
return 2
fi
fi
@ -92,19 +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
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"
@ -133,7 +146,7 @@ function copydb() {
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"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 4
exit 5
fi
else
impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
@ -141,7 +154,7 @@ function copydb() {
if [ -n "$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 5
exit 6
fi
fi
fi
@ -187,7 +200,7 @@ 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"
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 6
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${all_create_view_statements[@]}\n"
@ -217,7 +230,7 @@ function copydb() {
echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
rm -f error.log
if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
exit 7
exit 8
fi
fi

2
pom.xml
View File

@ -960,7 +960,7 @@
<commons.logging.version>1.1.3</commons.logging.version>
<commons-validator.version>1.7</commons-validator.version>
<dateparser.version>1.0.7</dateparser.version>
<dhp-schemas.version>[6.1.2]</dhp-schemas.version>
<dhp-schemas.version>[6.1.3-SNAPSHOT]</dhp-schemas.version>
<dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
<dhp.commons.lang.version>3.5</dhp.commons.lang.version>
<dhp.guava.version>11.0.2</dhp.guava.version>