forked from D-Net/dnet-hadoop
Indentation fixes
This commit is contained in:
parent
bc1a4611aa
commit
be320ba3c1
|
@ -3,7 +3,6 @@ package eu.dnetlib.dhp.actionmanager;
|
|||
|
||||
import java.util.Optional;
|
||||
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
|
@ -12,6 +11,7 @@ import org.apache.spark.sql.SparkSession;
|
|||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||
import eu.dnetlib.dhp.schema.oaf.Subject;
|
||||
|
@ -94,6 +94,7 @@ public class Constants {
|
|||
return s;
|
||||
|
||||
}
|
||||
|
||||
public static void removeOutputDir(SparkSession spark, String path) {
|
||||
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
|
||||
}
|
||||
|
|
|
@ -8,12 +8,6 @@ import java.util.Arrays;
|
|||
import java.util.List;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import eu.dnetlib.dhp.actionmanager.Constants;
|
||||
import eu.dnetlib.dhp.actionmanager.bipaffiliations.model.*;
|
||||
import eu.dnetlib.dhp.actionmanager.ror.GenerateRorActionSetJob;
|
||||
import eu.dnetlib.dhp.schema.action.AtomicAction;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.io.Text;
|
||||
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
|
||||
|
@ -22,17 +16,23 @@ import org.apache.spark.api.java.JavaRDD;
|
|||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.FlatMapFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.actionmanager.Constants;
|
||||
import eu.dnetlib.dhp.actionmanager.bipaffiliations.model.*;
|
||||
import eu.dnetlib.dhp.actionmanager.ror.GenerateRorActionSetJob;
|
||||
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.oaf.*;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
|
||||
import scala.Tuple2;
|
||||
|
||||
|
@ -41,125 +41,139 @@ import scala.Tuple2;
|
|||
*/
|
||||
public class PrepareAffiliationRelations implements Serializable {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(PrepareAffiliationRelations.class);
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
private static final String ID_PREFIX = "50|doi_________::";
|
||||
public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:bipinference";
|
||||
public static final String BIP_AFFILIATIONS_CLASSNAME = "Affiliation relation inferred by BIP!";
|
||||
public static final String BIP_INFERENCE_PROVENANCE = "bip:affiliation:crossref";
|
||||
private static final Logger log = LoggerFactory.getLogger(PrepareAffiliationRelations.class);
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
private static final String ID_PREFIX = "50|doi_________::";
|
||||
public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:bipinference";
|
||||
public static final String BIP_AFFILIATIONS_CLASSNAME = "Affiliation relation inferred by BIP!";
|
||||
public static final String BIP_INFERENCE_PROVENANCE = "bip:affiliation:crossref";
|
||||
|
||||
public static <I extends Result> void main(String[] args) throws Exception {
|
||||
public static <I extends Result> void main(String[] args) throws Exception {
|
||||
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
PrepareAffiliationRelations.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json"));
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
PrepareAffiliationRelations.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json"));
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||
parser.parseArgument(args);
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||
parser.parseArgument(args);
|
||||
|
||||
Boolean isSparkSessionManaged = Constants.isSparkSessionManaged(parser);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
Boolean isSparkSessionManaged = Constants.isSparkSessionManaged(parser);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
final String inputPath = parser.get("inputPath");
|
||||
log.info("inputPath {}: ", inputPath);
|
||||
final String inputPath = parser.get("inputPath");
|
||||
log.info("inputPath {}: ", inputPath);
|
||||
|
||||
final String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath {}: ", outputPath);
|
||||
final String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath {}: ", outputPath);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
SparkConf conf = new SparkConf();
|
||||
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
Constants.removeOutputDir(spark, outputPath);
|
||||
prepareAffiliationRelations(spark, inputPath, outputPath);
|
||||
});
|
||||
}
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
Constants.removeOutputDir(spark, outputPath);
|
||||
prepareAffiliationRelations(spark, inputPath, outputPath);
|
||||
});
|
||||
}
|
||||
|
||||
private static <I extends Result> void prepareAffiliationRelations(SparkSession spark, String inputPath, String outputPath) {
|
||||
private static <I extends Result> void prepareAffiliationRelations(SparkSession spark, String inputPath,
|
||||
String outputPath) {
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
// load and parse affiliation relations from HDFS
|
||||
JavaRDD<AffiliationRelationDeserializer> affiliationRelationsDeserializeRDD = sc
|
||||
.textFile(inputPath)
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, AffiliationRelationDeserializer.class));
|
||||
// load and parse affiliation relations from HDFS
|
||||
JavaRDD<AffiliationRelationDeserializer> affiliationRelationsDeserializeRDD = sc
|
||||
.textFile(inputPath)
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, AffiliationRelationDeserializer.class));
|
||||
|
||||
// convert affiliation to an internal representation
|
||||
Dataset<AffiliationRelationModel> affiliationRelations =
|
||||
spark.createDataset(
|
||||
affiliationRelationsDeserializeRDD.flatMap(entry ->
|
||||
entry.getMatchings().stream().flatMap(matching ->
|
||||
matching.getRorId().stream().map( rorId -> new AffiliationRelationModel(
|
||||
entry.getDoi(),
|
||||
rorId,
|
||||
matching.getConfidence()
|
||||
))).collect(Collectors.toList())
|
||||
.iterator())
|
||||
.rdd(),
|
||||
Encoders.bean(AffiliationRelationModel.class));
|
||||
// convert affiliation to an internal representation
|
||||
Dataset<AffiliationRelationModel> affiliationRelations = spark
|
||||
.createDataset(
|
||||
affiliationRelationsDeserializeRDD
|
||||
.flatMap(
|
||||
entry -> entry
|
||||
.getMatchings()
|
||||
.stream()
|
||||
.flatMap(
|
||||
matching -> matching
|
||||
.getRorId()
|
||||
.stream()
|
||||
.map(
|
||||
rorId -> new AffiliationRelationModel(
|
||||
entry.getDoi(),
|
||||
rorId,
|
||||
matching.getConfidence())))
|
||||
.collect(Collectors.toList())
|
||||
.iterator())
|
||||
.rdd(),
|
||||
Encoders.bean(AffiliationRelationModel.class));
|
||||
|
||||
// prepare action sets for affiliation relations
|
||||
affiliationRelations
|
||||
.flatMap((FlatMapFunction<AffiliationRelationModel, Relation>) affRel -> {
|
||||
// prepare action sets for affiliation relations
|
||||
affiliationRelations
|
||||
.flatMap((FlatMapFunction<AffiliationRelationModel, Relation>) affRel -> {
|
||||
|
||||
// DOI to OpenAIRE id
|
||||
final String paperId = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", affRel.getDoi()));
|
||||
// DOI to OpenAIRE id
|
||||
final String paperId = ID_PREFIX
|
||||
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", affRel.getDoi()));
|
||||
|
||||
// ROR id to OpenAIRE id
|
||||
final String affId = GenerateRorActionSetJob.calculateOpenaireId(affRel.getRorId());
|
||||
// ROR id to OpenAIRE id
|
||||
final String affId = GenerateRorActionSetJob.calculateOpenaireId(affRel.getRorId());
|
||||
|
||||
Qualifier qualifier = OafMapperUtils.qualifier(
|
||||
BIP_AFFILIATIONS_CLASSID,
|
||||
BIP_AFFILIATIONS_CLASSNAME,
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS,
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS);
|
||||
Qualifier qualifier = OafMapperUtils
|
||||
.qualifier(
|
||||
BIP_AFFILIATIONS_CLASSID,
|
||||
BIP_AFFILIATIONS_CLASSNAME,
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS,
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS);
|
||||
|
||||
// format data info; setting `confidence` into relation's `trust`
|
||||
DataInfo dataInfo = OafMapperUtils.dataInfo(
|
||||
false,
|
||||
BIP_INFERENCE_PROVENANCE,
|
||||
true,
|
||||
false,
|
||||
qualifier,
|
||||
Double.toString(affRel.getConfidence()));
|
||||
// format data info; setting `confidence` into relation's `trust`
|
||||
DataInfo dataInfo = OafMapperUtils
|
||||
.dataInfo(
|
||||
false,
|
||||
BIP_INFERENCE_PROVENANCE,
|
||||
true,
|
||||
false,
|
||||
qualifier,
|
||||
Double.toString(affRel.getConfidence()));
|
||||
|
||||
// return bi-directional relations
|
||||
return getAffiliationRelationPair(paperId, affId, dataInfo).iterator();
|
||||
// return bi-directional relations
|
||||
return getAffiliationRelationPair(paperId, affId, dataInfo).iterator();
|
||||
|
||||
}, Encoders.bean(Relation.class))
|
||||
.toJavaRDD()
|
||||
.map(p -> new AtomicAction(Relation.class, p))
|
||||
.mapToPair(
|
||||
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
|
||||
new Text(OBJECT_MAPPER.writeValueAsString(aa))))
|
||||
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
|
||||
}, Encoders.bean(Relation.class))
|
||||
.toJavaRDD()
|
||||
.map(p -> new AtomicAction(Relation.class, 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> getAffiliationRelationPair(String paperId, String affId, DataInfo dataInfo) {
|
||||
return Arrays.asList(
|
||||
OafMapperUtils.getRelation(
|
||||
paperId,
|
||||
affId,
|
||||
ModelConstants.RESULT_ORGANIZATION,
|
||||
ModelConstants.AFFILIATION,
|
||||
ModelConstants.HAS_AUTHOR_INSTITUTION,
|
||||
null,
|
||||
dataInfo,
|
||||
null),
|
||||
OafMapperUtils.getRelation(
|
||||
affId,
|
||||
paperId,
|
||||
ModelConstants.RESULT_ORGANIZATION,
|
||||
ModelConstants.AFFILIATION,
|
||||
ModelConstants.IS_AUTHOR_INSTITUTION_OF,
|
||||
null,
|
||||
dataInfo,
|
||||
null)
|
||||
);
|
||||
}
|
||||
private static List<Relation> getAffiliationRelationPair(String paperId, String affId, DataInfo dataInfo) {
|
||||
return Arrays
|
||||
.asList(
|
||||
OafMapperUtils
|
||||
.getRelation(
|
||||
paperId,
|
||||
affId,
|
||||
ModelConstants.RESULT_ORGANIZATION,
|
||||
ModelConstants.AFFILIATION,
|
||||
ModelConstants.HAS_AUTHOR_INSTITUTION,
|
||||
null,
|
||||
dataInfo,
|
||||
null),
|
||||
OafMapperUtils
|
||||
.getRelation(
|
||||
affId,
|
||||
paperId,
|
||||
ModelConstants.RESULT_ORGANIZATION,
|
||||
ModelConstants.AFFILIATION,
|
||||
ModelConstants.IS_AUTHOR_INSTITUTION_OF,
|
||||
null,
|
||||
dataInfo,
|
||||
null));
|
||||
}
|
||||
}
|
||||
|
|
|
@ -1,26 +1,27 @@
|
|||
package eu.dnetlib.dhp.actionmanager.bipaffiliations.model;
|
||||
|
||||
import com.fasterxml.jackson.annotation.JsonProperty;
|
||||
import lombok.Data;
|
||||
package eu.dnetlib.dhp.actionmanager.bipaffiliations.model;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.List;
|
||||
|
||||
import com.fasterxml.jackson.annotation.JsonProperty;
|
||||
|
||||
import lombok.Data;
|
||||
|
||||
@Data
|
||||
public class AffiliationRelationDeserializer implements Serializable {
|
||||
@JsonProperty("DOI")
|
||||
private String doi;
|
||||
@JsonProperty("Matchings")
|
||||
private List<Matching> matchings;
|
||||
@JsonProperty("DOI")
|
||||
private String doi;
|
||||
@JsonProperty("Matchings")
|
||||
private List<Matching> matchings;
|
||||
|
||||
@Data
|
||||
public static class Matching implements Serializable {
|
||||
@JsonProperty("RORid")
|
||||
private List<String> rorId;
|
||||
@JsonProperty("Confidence")
|
||||
private double confidence;
|
||||
@Data
|
||||
public static class Matching implements Serializable {
|
||||
@JsonProperty("RORid")
|
||||
private List<String> rorId;
|
||||
@JsonProperty("Confidence")
|
||||
private double confidence;
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
|
|
@ -1,15 +1,16 @@
|
|||
|
||||
package eu.dnetlib.dhp.actionmanager.bipaffiliations.model;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
import lombok.AllArgsConstructor;
|
||||
import lombok.Data;
|
||||
import lombok.NoArgsConstructor;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
@Data
|
||||
@AllArgsConstructor
|
||||
public class AffiliationRelationModel implements Serializable {
|
||||
private String doi;
|
||||
private String rorId;
|
||||
private double confidence;
|
||||
private String doi;
|
||||
private String rorId;
|
||||
private double confidence;
|
||||
}
|
||||
|
|
|
@ -28,15 +28,8 @@ oozie.use.system.libpath=true
|
|||
spark2ExtraListeners=com.cloudera.spark.lineage.NavigatorAppListener
|
||||
spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListener
|
||||
|
||||
# I think this should be the oozie workflow directory
|
||||
# oozieWorkflowPath=/user/ilias.kanellos/workflow_example/
|
||||
|
||||
|
||||
# The workflow application path
|
||||
wfAppPath=${oozieTopWfApplicationPath}
|
||||
|
||||
# The following is needed as a property of a workflow
|
||||
oozie.wf.application.path=${oozieTopWfApplicationPath}
|
||||
|
||||
inputPath=/user/schatz/affiliations/data-v3.json
|
||||
outputPath=/tmp/crossref-affiliations-output-v3
|
||||
inputPath=/user/schatz/affiliations/data-v3.1.json
|
||||
outputPath=/tmp/crossref-affiliations-output-v3.1
|
||||
|
|
|
@ -1,4 +1,4 @@
|
|||
<workflow-app name="BipFinderScore" xmlns="uri:oozie:workflow:0.5">
|
||||
<workflow-app name="BipAffiliations" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
|
||||
<property>
|
||||
|
@ -84,7 +84,7 @@
|
|||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Produces the atomic action with the inferred by BIP! affiliation relations from Crossref</name>
|
||||
<class>eu.dnetlib.dhp.actionmanager.bipaffiliations.PrepareAffiliationRelations/class>
|
||||
<class>eu.dnetlib.dhp.actionmanager.bipaffiliations.PrepareAffiliationRelations</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
|
|
|
@ -1,3 +1,4 @@
|
|||
|
||||
package eu.dnetlib.dhp.actionmanager.bipaffiliations;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.*;
|
||||
|
@ -6,10 +7,6 @@ import java.io.IOException;
|
|||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.hadoop.io.Text;
|
||||
import org.apache.spark.SparkConf;
|
||||
|
@ -29,107 +26,120 @@ 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.Relation;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
|
||||
|
||||
public class PrepareAffiliationRelationsTest {
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
private static SparkSession spark;
|
||||
private static SparkSession spark;
|
||||
|
||||
private static Path workingDir;
|
||||
private static final String ID_PREFIX = "50|doi_________::";
|
||||
private static final Logger log = LoggerFactory
|
||||
.getLogger(PrepareAffiliationRelationsTest.class);
|
||||
private static Path workingDir;
|
||||
private static final String ID_PREFIX = "50|doi_________::";
|
||||
private static final Logger log = LoggerFactory
|
||||
.getLogger(PrepareAffiliationRelationsTest.class);
|
||||
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files.createTempDirectory(PrepareAffiliationRelationsTest.class.getSimpleName());
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files.createTempDirectory(PrepareAffiliationRelationsTest.class.getSimpleName());
|
||||
|
||||
log.info("Using work dir {}", workingDir);
|
||||
log.info("Using work dir {}", workingDir);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.setAppName(PrepareAffiliationRelationsTest.class.getSimpleName());
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.setAppName(PrepareAffiliationRelationsTest.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());
|
||||
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(PrepareAffiliationRelationsTest.class.getSimpleName())
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
}
|
||||
spark = SparkSession
|
||||
.builder()
|
||||
.appName(PrepareAffiliationRelationsTest.class.getSimpleName())
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
spark.stop();
|
||||
}
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
spark.stop();
|
||||
}
|
||||
|
||||
@Test
|
||||
void testMatch() throws Exception {
|
||||
@Test
|
||||
void testMatch() throws Exception {
|
||||
|
||||
String affiliationRelationsPath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
|
||||
.getPath();
|
||||
String affiliationRelationsPath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
|
||||
.getPath();
|
||||
|
||||
String outputPath = workingDir.toString() + "/actionSet";
|
||||
String outputPath = workingDir.toString() + "/actionSet";
|
||||
|
||||
PrepareAffiliationRelations
|
||||
.main(
|
||||
new String[] {
|
||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"-inputPath", affiliationRelationsPath,
|
||||
"-outputPath", outputPath
|
||||
});
|
||||
PrepareAffiliationRelations
|
||||
.main(
|
||||
new String[] {
|
||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"-inputPath", affiliationRelationsPath,
|
||||
"-outputPath", outputPath
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(outputPath, Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(outputPath, Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
|
||||
// for (Relation r : tmp.collect()) {
|
||||
// System.out.println(
|
||||
// r.getSource() + "\t" + r.getTarget() + "\t" + r.getRelType() + "\t" + r.getRelClass() + "\t" + r.getSubRelType() + "\t" + r.getValidationDate() + "\t" + r.getDataInfo().getTrust() + "\t" + r.getDataInfo().getInferred()
|
||||
// );
|
||||
// }
|
||||
// count the number of relations
|
||||
assertEquals(16, tmp.count());
|
||||
// count the number of relations
|
||||
assertEquals(16, tmp.count());
|
||||
|
||||
Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
|
||||
dataset.createOrReplaceTempView("result");
|
||||
Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
|
||||
dataset.createOrReplaceTempView("result");
|
||||
|
||||
Dataset<Row> execVerification = spark.sql("select r.relType, r.relClass, r.source, r.target, r.dataInfo.trust from result r");
|
||||
Dataset<Row> execVerification = spark
|
||||
.sql("select r.relType, r.relClass, r.source, r.target, r.dataInfo.trust from result r");
|
||||
|
||||
// verify that we have equal number of bi-directional relations
|
||||
Assertions.assertEquals(8, execVerification
|
||||
.filter(
|
||||
"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION +"'")
|
||||
.collectAsList()
|
||||
.size());
|
||||
// verify that we have equal number of bi-directional relations
|
||||
Assertions
|
||||
.assertEquals(
|
||||
8, execVerification
|
||||
.filter(
|
||||
"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
|
||||
.collectAsList()
|
||||
.size());
|
||||
|
||||
Assertions.assertEquals(8, execVerification
|
||||
.filter(
|
||||
"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF +"'")
|
||||
.collectAsList()
|
||||
.size());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
8, execVerification
|
||||
.filter(
|
||||
"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
|
||||
.collectAsList()
|
||||
.size());
|
||||
|
||||
// check confidence value of a specific relation
|
||||
String sourceDOI = "10.1105/tpc.8.3.343";
|
||||
// check confidence value of a specific relation
|
||||
String sourceDOI = "10.1105/tpc.8.3.343";
|
||||
|
||||
final String sourceOpenaireId = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", sourceDOI));
|
||||
final String sourceOpenaireId = ID_PREFIX
|
||||
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", sourceDOI));
|
||||
|
||||
Assertions.assertEquals("0.7071067812", execVerification
|
||||
.filter(
|
||||
"source='" + sourceOpenaireId +"'")
|
||||
.collectAsList().get(0).getString(4));
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"0.7071067812", execVerification
|
||||
.filter(
|
||||
"source='" + sourceOpenaireId + "'")
|
||||
.collectAsList()
|
||||
.get(0)
|
||||
.getString(4));
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
Loading…
Reference in New Issue