Merge pull request 'Open Citations' (#158) from openCitations into beta

Reviewed-on: #158
This commit is contained in:
Claudio Atzori 2021-11-15 10:59:19 +01:00
commit 1ecceea788
12 changed files with 838 additions and 0 deletions

View File

@ -0,0 +1,181 @@
package eu.dnetlib.dhp.actionmanager.opencitations;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.io.Serializable;
import java.util.*;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
import scala.Tuple2;
public class CreateActionSetSparkJob implements Serializable {
public static final String OPENCITATIONS_CLASSID = "sysimport:crosswalk:opencitations";
public static final String OPENCITATIONS_CLASSNAME = "Imported from OpenCitations";
private static final String ID_PREFIX = "50|doi_________::";
private static final String TRUST = "0.91";
private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(final String[] args) throws IOException, ParseException {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
Objects
.requireNonNull(
CreateActionSetSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/opencitations/as_parameters.json"))));
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}", inputPath.toString());
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
final boolean shouldDuplicateRels =
Optional.ofNullable(parser.get("shouldDuplicateRels"))
.map(Boolean::valueOf)
.orElse(Boolean.FALSE);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
extractContent(spark, inputPath, outputPath, shouldDuplicateRels);
});
}
private static void extractContent(SparkSession spark, String inputPath, String outputPath,
boolean shouldDuplicateRels) {
spark
.sqlContext()
.createDataset(spark.sparkContext().textFile(inputPath + "/*", 6000), Encoders.STRING())
.flatMap(
(FlatMapFunction<String, Relation>) value -> createRelation(value, shouldDuplicateRels).iterator(),
Encoders.bean(Relation.class))
.filter((FilterFunction<Relation>) value -> value != null)
.toJavaRDD()
.map(p -> new AtomicAction(p.getClass(), p))
.mapToPair(
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
new Text(OBJECT_MAPPER.writeValueAsString(aa))))
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
}
private static List<Relation> createRelation(String value, boolean duplicate) {
String[] line = value.split(",");
if (!line[1].startsWith("10.")) {
return new ArrayList<>();
}
List<Relation> relationList = new ArrayList<>();
String citing = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", line[1]));
final String cited = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", line[2]));
relationList
.addAll(
getRelations(
citing,
cited));
if (duplicate && line[1].endsWith(".refs")) {
citing = ID_PREFIX + IdentifierFactory
.md5(CleaningFunctions.normalizePidValue("doi", line[1].substring(0, line[1].indexOf(".refs"))));
relationList.addAll(getRelations(citing, cited));
}
return relationList;
}
private static Collection<Relation> getRelations(String citing, String cited) {
return Arrays
.asList(
getRelation(citing, cited, ModelConstants.CITES),
getRelation(cited, citing, ModelConstants.IS_CITED_BY));
}
public static Relation getRelation(
String source,
String target,
String relclass) {
Relation r = new Relation();
r.setCollectedfrom(getCollectedFrom());
r.setSource(source);
r.setTarget(target);
r.setRelClass(relclass);
r.setRelType(ModelConstants.RESULT_RESULT);
r.setSubRelType(ModelConstants.CITATION);
r
.setDataInfo(
getDataInfo());
return r;
}
public static List<KeyValue> getCollectedFrom() {
KeyValue kv = new KeyValue();
kv.setKey(ModelConstants.OPENOCITATIONS_ID);
kv.setValue(ModelConstants.OPENOCITATIONS_NAME);
return Arrays.asList(kv);
}
public static DataInfo getDataInfo() {
DataInfo di = new DataInfo();
di.setInferred(false);
di.setDeletedbyinference(false);
di.setTrust(TRUST);
di
.setProvenanceaction(
getQualifier(OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS));
return di;
}
public static Qualifier getQualifier(String class_id, String class_name,
String qualifierSchema) {
Qualifier pa = new Qualifier();
pa.setClassid(class_id);
pa.setClassname(class_name);
pa.setSchemeid(qualifierSchema);
pa.setSchemename(qualifierSchema);
return pa;
}
}

View File

@ -0,0 +1,93 @@
package eu.dnetlib.dhp.actionmanager.opencitations;
import java.io.*;
import java.io.Serializable;
import java.util.Objects;
import java.util.zip.GZIPOutputStream;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class GetOpenCitationsRefs implements Serializable {
private static final Logger log = LoggerFactory.getLogger(GetOpenCitationsRefs.class);
public static void main(final String[] args) throws IOException, ParseException {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
Objects
.requireNonNull(
GetOpenCitationsRefs.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json"))));
parser.parseArgument(args);
final String[] inputFile = parser.get("inputFile").split(";");
log.info("inputFile {}", inputFile.toString());
final String workingPath = parser.get("workingPath");
log.info("workingPath {}", workingPath);
final String hdfsNameNode = parser.get("hdfsNameNode");
log.info("hdfsNameNode {}", hdfsNameNode);
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf);
GetOpenCitationsRefs ocr = new GetOpenCitationsRefs();
for (String file : inputFile) {
ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem);
}
}
private void doExtract(String inputFile, String workingPath, FileSystem fileSystem)
throws IOException {
final Path path = new Path(inputFile);
FSDataInputStream oc_zip = fileSystem.open(path);
int count = 1;
try (ZipInputStream zis = new ZipInputStream(oc_zip)) {
ZipEntry entry = null;
while ((entry = zis.getNextEntry()) != null) {
if (!entry.isDirectory()) {
String fileName = entry.getName();
fileName = fileName.substring(0, fileName.indexOf("T")) + "_" + count;
count++;
try (
FSDataOutputStream out = fileSystem
.create(new Path(workingPath + "/COCI/" + fileName + ".gz"));
GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
IOUtils.copy(zis, gzipOs);
}
}
}
}
}
}

View File

@ -0,0 +1,25 @@
[
{
"paramName": "ip",
"paramLongName": "inputPath",
"paramDescription": "the zipped opencitations file",
"paramRequired": true
},
{
"paramName": "op",
"paramLongName": "outputPath",
"paramDescription": "the working path",
"paramRequired": true
},
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "the hdfs name node",
"paramRequired": false
}, {
"paramName": "sdr",
"paramLongName": "shouldDuplicateRels",
"paramDescription": "the hdfs name node",
"paramRequired": false
}
]

View File

@ -0,0 +1,20 @@
[
{
"paramName": "if",
"paramLongName": "inputFile",
"paramDescription": "the zipped opencitations file",
"paramRequired": true
},
{
"paramName": "wp",
"paramLongName": "workingPath",
"paramDescription": "the working path",
"paramRequired": true
},
{
"paramName": "hnn",
"paramLongName": "hdfsNameNode",
"paramDescription": "the hdfs name node",
"paramRequired": true
}
]

View File

@ -0,0 +1,58 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
<property>
<name>sparkExecutorNumber</name>
<value>4</value>
</property>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/spark2ApplicationHistory</value>
</property>
<property>
<name>sparkDriverMemory</name>
<value>15G</value>
</property>
<property>
<name>sparkExecutorMemory</name>
<value>6G</value>
</property>
<property>
<name>sparkExecutorCores</name>
<value>1</value>
</property>
</configuration>

View File

@ -0,0 +1,2 @@
#!/bin/bash
for file in $(echo $1 | tr ";" "\n"); do curl -L $(echo $file | cut -d '@' -f 1 ) | hdfs dfs -put - $2/$(echo $file | cut -d '@' -f 2) ; done;

View File

@ -0,0 +1,91 @@
<workflow-app name="OpenCitations Integration" xmlns="uri:oozie:workflow:0.5">
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="resume_from"/>
<decision name="resume_from">
<switch>
<case to="download">${wf:conf('resumeFrom') eq 'DownloadDump'}</case>
<case to="extract">${wf:conf('resumeFrom') eq 'ExtractContent'}</case>
<default to="create_actionset"/> <!-- first action to be done when downloadDump is to be performed -->
</switch>
</decision>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="download">
<shell xmlns="uri:oozie:shell-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapred.job.queue.name</name>
<value>${queueName}</value>
</property>
</configuration>
<exec>download.sh</exec>
<argument>${filelist}</argument>
<argument>${workingPath}/Original</argument>
<env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
<file>download.sh</file>
<capture-output/>
</shell>
<ok to="extract"/>
<error to="Kill"/>
</action>
<action name="extract">
<java>
<main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class>
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
<arg>--inputFile</arg><arg>${inputFile}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
</java>
<ok to="create_actionset"/>
<error to="Kill"/>
</action>
<action name="create_actionset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the AS for OC</name>
<class>eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${workingPath}/COCI</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

View File

@ -0,0 +1,8 @@
[
{"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true},
{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true},
{"paramName":"f", "paramLongName":"opencitationFile", "paramDescription": "the name of the file", "paramRequired": true},
{"paramName":"issm", "paramLongName":"isSparkSessionManaged", "paramDescription": "the name of the activities orcid file", "paramRequired": false},
{"paramName":"o", "paramLongName":"outputPath", "paramDescription": "the name of the activities orcid file", "paramRequired": true}
]

View File

@ -0,0 +1,335 @@
package eu.dnetlib.dhp.actionmanager.opencitations;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.io.Text;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
public class CreateOpenCitationsASTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory
.getLogger(CreateOpenCitationsASTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(CreateOpenCitationsASTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(CreateOpenCitationsASTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(CreateOpenCitationsASTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void testNumberofRelations() throws Exception {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
.getPath();
CreateActionSetSparkJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-shouldDuplicateRels",
Boolean.TRUE.toString(),
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
assertEquals(60, tmp.count());
// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
}
@Test
void testNumberofRelations2() throws Exception {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
.getPath();
CreateActionSetSparkJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
assertEquals(44, tmp.count());
// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
}
@Test
void testRelationsCollectedFrom() throws Exception {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
.getPath();
CreateActionSetSparkJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
tmp.foreach(r -> {
assertEquals(ModelConstants.OPENOCITATIONS_NAME, r.getCollectedfrom().get(0).getValue());
assertEquals(ModelConstants.OPENOCITATIONS_ID, r.getCollectedfrom().get(0).getKey());
});
}
@Test
void testRelationsDataInfo() throws Exception {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
.getPath();
CreateActionSetSparkJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
tmp.foreach(r -> {
assertEquals(false, r.getDataInfo().getInferred());
assertEquals(false, r.getDataInfo().getDeletedbyinference());
assertEquals("0.91", r.getDataInfo().getTrust());
assertEquals(
CreateActionSetSparkJob.OPENCITATIONS_CLASSID, r.getDataInfo().getProvenanceaction().getClassid());
assertEquals(
CreateActionSetSparkJob.OPENCITATIONS_CLASSNAME, r.getDataInfo().getProvenanceaction().getClassname());
assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemeid());
assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemename());
});
}
@Test
void testRelationsSemantics() throws Exception {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
.getPath();
CreateActionSetSparkJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
tmp.foreach(r -> {
assertEquals("citation", r.getSubRelType());
assertEquals("resultResult", r.getRelType());
});
assertEquals(22, tmp.filter(r -> r.getRelClass().equals("Cites")).count());
assertEquals(22, tmp.filter(r -> r.getRelClass().equals("IsCitedBy")).count());
}
@Test
void testRelationsSourceTargetPrefix() throws Exception {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
.getPath();
CreateActionSetSparkJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
tmp.foreach(r -> {
assertEquals("50|doi_________::", r.getSource().substring(0, 17));
assertEquals("50|doi_________::", r.getTarget().substring(0, 17));
});
}
@Test
void testRelationsSourceTargetCouple() throws Exception {
final String doi1 = "50|doi_________::"
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-015-3684-x"));
final String doi2 = "50|doi_________::"
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1111/j.1551-2916.2008.02408.x"));
final String doi3 = "50|doi_________::"
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-014-2114-9"));
final String doi4 = "50|doi_________::"
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/j.ceramint.2013.09.069"));
final String doi5 = "50|doi_________::"
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-009-9913-4"));
final String doi6 = "50|doi_________::"
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/0038-1098(72)90370-5"));
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
.getPath();
CreateActionSetSparkJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
JavaRDD<Relation> check = tmp.filter(r -> r.getSource().equals(doi1) || r.getTarget().equals(doi1));
assertEquals(10, check.count());
check.foreach(r -> {
if (r.getSource().equals(doi2) || r.getSource().equals(doi3) || r.getSource().equals(doi4) ||
r.getSource().equals(doi5) || r.getSource().equals(doi6)) {
assertEquals(ModelConstants.IS_CITED_BY, r.getRelClass());
assertEquals(doi1, r.getTarget());
}
});
assertEquals(5, check.filter(r -> r.getSource().equals(doi1)).count());
check.filter(r -> r.getSource().equals(doi1)).foreach(r -> assertEquals(ModelConstants.CITES, r.getRelClass()));
}
}

View File

@ -0,0 +1,8 @@
oci,citing,cited,creation,timespan,journal_sc,author_sc
02001000007362801000805046300010563030608046333-0200101010136193701050501630209010637020000083700020400083733,10.1007/s10854-015-3684-x,10.1111/j.1551-2916.2008.02408.x,2015-09-01,P7Y2M,no,no
02001000007362801000805046300010563030608046333-02001000007362801000805046300010463020101046309,10.1007/s10854-015-3684-x,10.1007/s10854-014-2114-9,2015-09-01,P1Y2M4D,yes,no
02001000007362801000805046300010563030608046333-020010001063619371214271022182329370200010337000937000609,10.1007/s10854-015-3684-x,10.1016/j.ceramint.2013.09.069,2015-09-01,P1Y6M,no,no
02001000007362801000805046300010563030608046333-02001000007362801000805046300000963090901036304,10.1007/s10854-015-3684-x,10.1007/s10854-009-9913-4,2015-09-01,P6Y3M10D,yes,no
02001000007362801000805046300010563030608046333-02001000106360000030863010009085807025909000307006305,10.1007/s10854-015-3684-x,10.1016/0038-1098(72)90370-5,2015-09-01,P43Y8M,no,no
02001000007362801000805046300010563030608056309-02001000106361937281010370200010437000937000308,10.1007/s10854-015-3685-9,10.1016/j.saa.2014.09.038,2015-09-03,P0Y7M,no,no
02001000007362801000805046300010563030608056309-0200100010636193722102912171027370200010537000437000106,10.1007/s10854-015-3685-9,10.1016/j.matchar.2015.04.016,2015-09-03,P0Y2M,no,no

View File

@ -0,0 +1,8 @@
oci,citing,cited,creation,timespan,journal_sc,author_sc
02001000308362804010509076300010963000003086301-0200100020936020001003227000009010004,10.1038/s41597-019-0038-1,10.1029/2010wr009104,2019-04-15,P8Y1M,no,no
02001000308362804010509076300010963000003086301-0200100010636280103060463080105025800015900000006006303,10.1038/s41597-019-0038-1,10.1016/s1364-8152(01)00060-3,2019-04-15,P17Y3M,no,no
02001000308362804010509076300010963000003086301-02001000007362800000407076300010063000401066333,10.1038/s41597-019-0038-1,10.1007/s00477-010-0416-x,2019-04-15,P8Y9M6D,no,no
02001000308362804010509076300010963000003086301-02001000007362800000700046300010363000905016308,10.1038/s41597-019-0038-1,10.1007/s00704-013-0951-8,2019-04-15,P5Y9M23D,no,no
02001000308362804010509076300010963000003086301-02001000002361924123705070707,10.1038/s41597-019-0038-1,10.1002/joc.5777,2019-04-15,P0Y8M1D,no,no
02001000308362804010509076300010963000003086301-02005010904361714282863020263040504076302000108,10.1038/s41597-019-0038-1,10.5194/hess-22-4547-2018,2019-04-15,P0Y7M18D,no,no
02001000308362804010509076300010963000003086301-02001000002361924123703050404,10.1038/s41597-019-0038-1,10.1002/joc.3544,2019-04-15,P6Y9M6D,no,no

View File

@ -0,0 +1,9 @@
oci,citing,cited,creation,timespan,journal_sc,author_sc
0200100000236090708010101090307000202023727141528-020050302063600040000010307,10.1002/9781119370222.refs,10.5326/0400137,2020-06-22,P16Y3M,no,no
0200100000236090708010101090307000202023727141528-0200101010136193701050302630905003337020000073700000301093733,10.1002/9781119370222.refs,10.1111/j.1532-950x.2007.00319.x,2020-06-22,P12Y8M,no,no
0200100000236090708010101090307000202023727141528-0200101010136312830370102030509,10.1002/9781119370222.refs,10.1111/vsu.12359,2020-06-22,P4Y10M29D,no,no
0200100000236090708010101090307000202023727141528-020050302063600030900020904,10.1002/9781119370222.refs,10.5326/0390294,2020-06-22,P17Y1M,no,no
0200100000236090708010101090307000202023727141528-020050302063600040200030701,10.1002/9781119370222.refs,10.5326/0420371,2020-06-22,P13Y9M,no,no
0200100000236090708010101090307000202023727141528-0200101010136193701050302630905003337020001033701020000003733,10.1002/9781119370222.refs,10.1111/j.1532-950x.2013.12000.x,2020-06-22,P7Y2M,no,no
0200100000236090708010101090307000202023727141528-020010008003600000408000106093702000006370306070200,10.1002/9781119370222.refs,10.1080/00480169.2006.36720,2020-06-22,P13Y6M,no,no
0200100000236090708010101090307000202023727141528-0200101010136193701070501630008010337020000063700000003033733,10.1002/9781119370222.refs,10.1111/j.1751-0813.2006.00033.x,2020-06-22,P13Y8M,no,no