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dnet-hadoop
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pulled from beta

This commit is contained in:
Claudio Atzori 2022-01-11 16:59:41 +01:00
parent 4f212652ca 0163dadb7f
commit dcd282977c
14 changed files with 562 additions and 638 deletions
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5
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
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@ -19,7 +19,7 @@ public class Constants {
public static final String DOI = "doi";
public static final char DEFAULT_DELIMITER = ',';
public static final String DEFAULT_DELIMITER = ",";
public static final String UPDATE_DATA_INFO_TYPE = "update";
public static final String UPDATE_SUBJECT_FOS_CLASS_ID = "subject:fos";
@ -55,7 +55,8 @@ public class Constants {
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
}
public static StructuredProperty getSubject(String sbj, String classid, String classname, String diqualifierclassid) {
public static StructuredProperty getSubject(String sbj, String classid, String classname,
String diqualifierclassid) {
if (sbj.equals(NULL))
return null;
StructuredProperty sp = new StructuredProperty();

91
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFOSSparkJob.java Normal file
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@ -0,0 +1,91 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
import static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_DELIMITER;
import static eu.dnetlib.dhp.actionmanager.Constants.isSparkSessionManaged;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class GetFOSSparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(GetFOSSparkJob.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
GetFOSSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
// the path where the original fos csv file is stored
final String sourcePath = parser.get("sourcePath");
log.info("sourcePath {}", sourcePath);
// the path where to put the file as json
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
final String delimiter = Optional
.ofNullable(parser.get("delimiter"))
.orElse(DEFAULT_DELIMITER);
SparkConf sconf = new SparkConf();
runWithSparkSession(
sconf,
isSparkSessionManaged,
spark -> {
getFOS(
spark,
sourcePath,
outputPath,
delimiter);
});
}
private static void getFOS(SparkSession spark, String sourcePath, String outputPath, String delimiter) {
Dataset<Row> fosData = spark
.read()
.format("csv")
.option("sep", delimiter)
.option("inferSchema", "true")
.option("header", "true")
.option("quotes", "\"")
.load(sourcePath);
fosData.map((MapFunction<Row, FOSDataModel>) r -> {
FOSDataModel fosDataModel = new FOSDataModel();
fosDataModel.setDoi(r.getString(0).toLowerCase());
fosDataModel.setLevel1(r.getString(1));
fosDataModel.setLevel2(r.getString(2));
fosDataModel.setLevel3(r.getString(3));
return fosDataModel;
}, Encoders.bean(FOSDataModel.class))
.write()
.mode(SaveMode.Overwrite)
.json(outputPath);
}
}

80
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetInputData.java
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@ -1,80 +0,0 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.Serializable;
import java.util.Objects;
import java.util.Optional;
import java.util.zip.GZIPInputStream;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
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;
import static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_DELIMITER;
public class GetInputData implements Serializable {
private static final Logger log = LoggerFactory.getLogger(GetInputData.class);
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
Objects
.requireNonNull(
GetInputData.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_input_parameters.json"))));
parser.parseArgument(args);
// the path where the original fos csv file is stored
final String sourcePath = parser.get("sourcePath");
log.info("sourcePath {}", sourcePath);
// the path where to put the file as json
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
final String hdfsNameNode = parser.get("hdfsNameNode");
log.info("hdfsNameNode {}", hdfsNameNode);
final String classForName = parser.get("classForName");
log.info("classForName {}", classForName);
final char delimiter = Optional
.ofNullable(parser.get("delimiter"))
.map(s -> s.charAt(0))
.orElse(DEFAULT_DELIMITER);
log.info("delimiter {}", delimiter);
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf);
new GetInputData().doRewrite(sourcePath, outputPath, classForName, delimiter, fileSystem);
}
public void doRewrite(String inputPath, String outputFile, String classForName, char delimiter, FileSystem fs)
throws IOException, ClassNotFoundException {
// reads the csv and writes it as its json equivalent
try (InputStreamReader reader = new InputStreamReader(new GZIPInputStream(fs.open(new Path(inputPath))))) {
eu.dnetlib.dhp.common.collection.GetCSV.getCsv(fs, reader, outputFile, classForName, delimiter);
}
}
}

91
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetSDGSparkJob.java Normal file
View File

@ -0,0 +1,91 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
import static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_DELIMITER;
import static eu.dnetlib.dhp.actionmanager.Constants.isSparkSessionManaged;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
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.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class GetSDGSparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(GetSDGSparkJob.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
GetSDGSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
// the path where the original fos csv file is stored
final String sourcePath = parser.get("sourcePath");
log.info("sourcePath {}", sourcePath);
// the path where to put the file as json
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
final String delimiter = Optional
.ofNullable(parser.get("delimiter"))
.orElse(DEFAULT_DELIMITER);
SparkConf sconf = new SparkConf();
runWithSparkSession(
sconf,
isSparkSessionManaged,
spark -> {
getSDG(
spark,
sourcePath,
outputPath,
delimiter);
});
}
private static void getSDG(SparkSession spark, String sourcePath, String outputPath, String delimiter) {
Dataset<Row> sdgData = spark
.read()
.format("csv")
.option("sep", delimiter)
.option("inferSchema", "true")
.option("header", "true")
.option("quotes", "\"")
.load(sourcePath);
sdgData.map((MapFunction<Row, SDGDataModel>) r -> {
SDGDataModel sdgDataModel = new SDGDataModel();
sdgDataModel.setDoi(r.getString(0).toLowerCase());
sdgDataModel.setSbj(r.getString(1));
return sdgDataModel;
}, Encoders.bean(SDGDataModel.class))
.filter((FilterFunction<SDGDataModel>) sdg -> sdg.getSbj() != null)
.write()
.mode(SaveMode.Overwrite)
.json(outputPath);
}
}

35
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java
View File

@ -1,11 +1,13 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.utils.DHPUtils;
import static eu.dnetlib.dhp.actionmanager.Constants.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
@ -16,11 +18,12 @@ import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import static eu.dnetlib.dhp.actionmanager.Constants.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.utils.DHPUtils;
public class PrepareSDGSparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(PrepareSDGSparkJob.class);
@ -62,15 +65,18 @@ public class PrepareSDGSparkJob implements Serializable {
private static void doPrepare(SparkSession spark, String sourcePath, String outputPath) {
Dataset<SDGDataModel> sdgDataset = readPath(spark, sourcePath, SDGDataModel.class);
sdgDataset.groupByKey((MapFunction<SDGDataModel,String>)r -> r.getDoi().toLowerCase(),Encoders.STRING())
sdgDataset
.groupByKey((MapFunction<SDGDataModel, String>) r -> r.getDoi().toLowerCase(), Encoders.STRING())
.mapGroups((MapGroupsFunction<String, SDGDataModel, Result>) (k, it) -> {
Result r = new Result();
r.setId(DHPUtils.generateUnresolvedIdentifier(k, DOI));
SDGDataModel first = it.next();
List<StructuredProperty> sbjs = new ArrayList<>();
sbjs.add(getSubject(first.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID));
it.forEachRemaining(s -> sbjs.add(getSubject(s.getSbj(),SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID)));
it
.forEachRemaining(
s -> sbjs
.add(getSubject(s.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID)));
r.setSubject(sbjs);
return r;
}, Encoders.bean(Result.class))
@ -80,7 +86,4 @@ public class PrepareSDGSparkJob implements Serializable {
.json(outputPath + "/sdg");
}
}

7
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/SDGDataModel.java
View File

@ -1,9 +1,10 @@
package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
import com.opencsv.bean.CsvBindByPosition;
import java.io.Serializable;
import com.opencsv.bean.CsvBindByPosition;
public class SDGDataModel implements Serializable {
@CsvBindByPosition(position = 0)
@ -14,7 +15,6 @@ public class SDGDataModel implements Serializable{
// @CsvBindByName(column = "sdg")
private String sbj;
public SDGDataModel() {
}
@ -37,7 +37,6 @@ public class SDGDataModel implements Serializable{
this.doi = doi;
}
public String getSbj() {
return sbj;
}

14
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_input_parameters.json
View File

@ -19,15 +19,9 @@
"paramRequired": false
},
{
"paramName": "hnn",
"paramLongName": "hdfsNameNode",
"paramDescription": "the path used to store the HostedByMap",
"paramRequired": true
},
{
"paramName": "cfn",
"paramLongName": "classForName",
"paramDescription": "the path used to store the HostedByMap",
"paramRequired": true
"paramName": "d",
"paramLongName": "delimiter",
"paramDescription": "the delimiter if different from the default one (,)",
"paramRequired": false
}
]

46
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/workflow.xml
View File

@ -107,17 +107,30 @@
</action>
<action name="getFOS">
<java>
<main-class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetInputData</main-class>
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Gets Data from FOS csv file</name>
<class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetFOSSparkJob</class>
<jar>dhp-aggregation-${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=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${fosPath}</arg>
<arg>--outputPath</arg><arg>${workingDir}/input/fos</arg>
<arg>--classForName</arg><arg>eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel</arg>
</java>
</spark>
<ok to="prepareFos"/>
<error to="Kill"/>
</action>
<action name="prepareFos">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
@ -144,17 +157,30 @@
</action>
<action name="getSDG">
<java>
<main-class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetInputData</main-class>
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Gets Data from SDG csv file</name>
<class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetSDGSparkJob</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>--sourcePath</arg><arg>${sdgPath}</arg>
<arg>--outputPath</arg><arg>${workingDir}/input/sdg</arg>
<arg>--classForName</arg><arg>eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel</arg>
</java>
</spark>
<ok to="prepareSDG"/>
<error to="Kill"/>
</action>
<action name="prepareSDG">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>

122
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java
View File

@ -10,7 +10,6 @@ import java.nio.file.Files;
import java.nio.file.Path;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel;
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
@ -26,6 +25,7 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel;
import eu.dnetlib.dhp.schema.oaf.Result;
public class PrepareTest {
@ -148,37 +148,6 @@ public class PrepareTest {
}
@Test
void getFOSFileTest() throws IOException, ClassNotFoundException {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs.csv")
.getPath();
final String outputPath = workingDir.toString() + "/fos.json";
new GetInputData()
.doRewrite(
sourcePath, outputPath, "eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel",
',', fs);
BufferedReader in = new BufferedReader(
new InputStreamReader(fs.open(new org.apache.hadoop.fs.Path(outputPath))));
String line;
int count = 0;
while ((line = in.readLine()) != null) {
FOSDataModel fos = new ObjectMapper().readValue(line, FOSDataModel.class);
System.out.println(new ObjectMapper().writeValueAsString(fos));
count += 1;
}
assertEquals(39, count);
}
@Test
void fosPrepareTest() throws Exception {
final String sourcePath = getClass()
@ -206,7 +175,6 @@ public class PrepareTest {
assertEquals(20, tmp.count());
assertEquals(1, tmp.filter(row -> row.getId().equals(doi1)).count());
assertTrue(
tmp
.filter(r -> r.getId().equals(doi1))
@ -249,35 +217,6 @@ public class PrepareTest {
}
@Test
void getSDGFileTest() throws IOException, ClassNotFoundException {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/sdg/sdg_sbs.csv")
.getPath();
final String outputPath = workingDir.toString() + "/sdg.json";
new GetInputData()
.doRewrite(
sourcePath, outputPath, "eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel",
',', fs);
BufferedReader in = new BufferedReader(
new InputStreamReader(fs.open(new org.apache.hadoop.fs.Path(outputPath))));
String line;
int count = 0;
while ((line = in.readLine()) != null) {
SDGDataModel sdg = new ObjectMapper().readValue(line, SDGDataModel.class);
System.out.println(new ObjectMapper().writeValueAsString(sdg));
count += 1;
}
assertEquals(37, count);
}
@Test
void sdgPrepareTest() throws Exception {
final String sourcePath = getClass()
@ -305,7 +244,6 @@ public class PrepareTest {
assertEquals(32, tmp.count());
assertEquals(1, tmp.filter(row -> row.getId().equals(doi1)).count());
assertTrue(
tmp
.filter(r -> r.getId().equals(doi1))
@ -321,33 +259,59 @@ public class PrepareTest {
.collect()
.contains("8. Economic growth"));
}
@Test
void test3() throws Exception {
final String sourcePath = "/Users/miriam.baglioni/Downloads/doi_fos_results_20_12_2021.csv.gz";
final String outputPath = workingDir.toString() + "/fos.json";
GetFOSSparkJob
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", sourcePath,
"-outputPath", outputPath
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<FOSDataModel> tmp = sc
.textFile(outputPath)
.map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class));
tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null));
tmp.foreach(t -> Assertions.assertTrue(t.getLevel1() != null));
tmp.foreach(t -> Assertions.assertTrue(t.getLevel2() != null));
tmp.foreach(t -> Assertions.assertTrue(t.getLevel3() != null));
}
@Disabled
@Test
void test2() throws Exception {
void test4() throws Exception {
final String sourcePath = "/Users/miriam.baglioni/Downloads/doi_sdg_results_20_12_21.csv.gz";
final String outputPath = workingDir.toString() + "/sdg.json";
GetSDGSparkJob
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", sourcePath,
new GetInputData()
.doRewrite(
sourcePath, outputPath, "eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel",
',', fs);
"-outputPath", outputPath
BufferedReader in = new BufferedReader(
new InputStreamReader(fs.open(new org.apache.hadoop.fs.Path(outputPath))));
});
String line;
int count = 0;
while ((line = in.readLine()) != null) {
SDGDataModel sdg = new ObjectMapper().readValue(line, SDGDataModel.class);
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
System.out.println(new ObjectMapper().writeValueAsString(sdg));
count += 1;
}
JavaRDD<SDGDataModel> tmp = sc
.textFile(outputPath)
.map(item -> OBJECT_MAPPER.readValue(item, SDGDataModel.class));
tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null));
tmp.foreach(t -> Assertions.assertTrue(t.getSbj() != null));
}
}

4
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java
View File

@ -7,7 +7,6 @@ import java.nio.file.Path;
import java.util.List;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.actionmanager.Constants;
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
@ -25,6 +24,7 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.Constants;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
@ -349,7 +349,6 @@ public class ProduceTest {
}
private JavaRDD<Result> getResultJavaRDDPlusSDG() throws Exception {
final String bipPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json")
@ -402,7 +401,6 @@ public class ProduceTest {
.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
}
@Test
void produceTestSomeNumbersWithSDG() throws Exception {

259
dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/SparkImportMagIntoDataset.scala
View File

@ -8,7 +8,6 @@ import org.apache.spark.sql.{SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
object SparkImportMagIntoDataset {
val datatypedict = Map(
"bool" -> BooleanType,
"int" -> IntegerType,
@ -20,232 +19,33 @@ object SparkImportMagIntoDataset {
"DateTime" -> DateType
)
val stream = Map(
"Affiliations" -> Tuple2(
"mag/Affiliations.txt",
Seq(
"AffiliationId:long",
"Rank:uint",
"NormalizedName:string",
"DisplayName:string",
"GridId:string",
"OfficialPage:string",
"WikiPage:string",
"PaperCount:long",
"PaperFamilyCount:long",
"CitationCount:long",
"Iso3166Code:string",
"Latitude:float?",
"Longitude:float?",
"CreatedDate:DateTime"
)
),
"AuthorExtendedAttributes" -> Tuple2(
"mag/AuthorExtendedAttributes.txt",
Seq("AuthorId:long", "AttributeType:int", "AttributeValue:string")
),
"Authors" -> Tuple2(
"mag/Authors.txt",
Seq(
"AuthorId:long",
"Rank:uint",
"NormalizedName:string",
"DisplayName:string",
"LastKnownAffiliationId:long?",
"PaperCount:long",
"PaperFamilyCount:long",
"CitationCount:long",
"CreatedDate:DateTime"
)
),
"ConferenceInstances" -> Tuple2(
"mag/ConferenceInstances.txt",
Seq(
"ConferenceInstanceId:long",
"NormalizedName:string",
"DisplayName:string",
"ConferenceSeriesId:long",
"Location:string",
"OfficialUrl:string",
"StartDate:DateTime?",
"EndDate:DateTime?",
"AbstractRegistrationDate:DateTime?",
"SubmissionDeadlineDate:DateTime?",
"NotificationDueDate:DateTime?",
"FinalVersionDueDate:DateTime?",
"PaperCount:long",
"PaperFamilyCount:long",
"CitationCount:long",
"Latitude:float?",
"Longitude:float?",
"CreatedDate:DateTime"
)
),
"ConferenceSeries" -> Tuple2(
"mag/ConferenceSeries.txt",
Seq(
"ConferenceSeriesId:long",
"Rank:uint",
"NormalizedName:string",
"DisplayName:string",
"PaperCount:long",
"PaperFamilyCount:long",
"CitationCount:long",
"CreatedDate:DateTime"
)
),
"EntityRelatedEntities" -> Tuple2(
"advanced/EntityRelatedEntities.txt",
Seq(
"EntityId:long",
"EntityType:string",
"RelatedEntityId:long",
"RelatedEntityType:string",
"RelatedType:int",
"Score:float"
)
),
"FieldOfStudyChildren" -> Tuple2(
"advanced/FieldOfStudyChildren.txt",
Seq("FieldOfStudyId:long", "ChildFieldOfStudyId:long")
),
"FieldOfStudyExtendedAttributes" -> Tuple2(
"advanced/FieldOfStudyExtendedAttributes.txt",
Seq("FieldOfStudyId:long", "AttributeType:int", "AttributeValue:string")
),
"FieldsOfStudy" -> Tuple2(
"advanced/FieldsOfStudy.txt",
Seq(
"FieldOfStudyId:long",
"Rank:uint",
"NormalizedName:string",
"DisplayName:string",
"MainType:string",
"Level:int",
"PaperCount:long",
"PaperFamilyCount:long",
"CitationCount:long",
"CreatedDate:DateTime"
)
),
"Journals" -> Tuple2(
"mag/Journals.txt",
Seq(
"JournalId:long",
"Rank:uint",
"NormalizedName:string",
"DisplayName:string",
"Issn:string",
"Publisher:string",
"Webpage:string",
"PaperCount:long",
"PaperFamilyCount:long",
"CitationCount:long",
"CreatedDate:DateTime"
)
),
"PaperAbstractsInvertedIndex" -> Tuple2(
"nlp/PaperAbstractsInvertedIndex.txt.*",
Seq("PaperId:long", "IndexedAbstract:string")
),
"PaperAuthorAffiliations" -> Tuple2(
"mag/PaperAuthorAffiliations.txt",
Seq(
"PaperId:long",
"AuthorId:long",
"AffiliationId:long?",
"AuthorSequenceNumber:uint",
"OriginalAuthor:string",
"OriginalAffiliation:string"
)
),
"PaperCitationContexts" -> Tuple2(
"nlp/PaperCitationContexts.txt",
Seq("PaperId:long", "PaperReferenceId:long", "CitationContext:string")
),
"PaperExtendedAttributes" -> Tuple2(
"mag/PaperExtendedAttributes.txt",
Seq("PaperId:long", "AttributeType:int", "AttributeValue:string")
),
"PaperFieldsOfStudy" -> Tuple2(
"advanced/PaperFieldsOfStudy.txt",
Seq("PaperId:long", "FieldOfStudyId:long", "Score:float")
),
"PaperMeSH" -> Tuple2(
"advanced/PaperMeSH.txt",
Seq(
"PaperId:long",
"DescriptorUI:string",
"DescriptorName:string",
"QualifierUI:string",
"QualifierName:string",
"IsMajorTopic:bool"
)
),
"PaperRecommendations" -> Tuple2(
"advanced/PaperRecommendations.txt",
Seq("PaperId:long", "RecommendedPaperId:long", "Score:float")
),
"PaperReferences" -> Tuple2(
"mag/PaperReferences.txt",
Seq("PaperId:long", "PaperReferenceId:long")
),
"PaperResources" -> Tuple2(
"mag/PaperResources.txt",
Seq(
"PaperId:long",
"ResourceType:int",
"ResourceUrl:string",
"SourceUrl:string",
"RelationshipType:int"
)
),
"PaperUrls" -> Tuple2(
"mag/PaperUrls.txt",
Seq("PaperId:long", "SourceType:int?", "SourceUrl:string", "LanguageCode:string")
),
"Papers" -> Tuple2(
"mag/Papers.txt",
Seq(
"PaperId:long",
"Rank:uint",
"Doi:string",
"DocType:string",
"PaperTitle:string",
"OriginalTitle:string",
"BookTitle:string",
"Year:int?",
"Date:DateTime?",
"OnlineDate:DateTime?",
"Publisher:string",
"JournalId:long?",
"ConferenceSeriesId:long?",
"ConferenceInstanceId:long?",
"Volume:string",
"Issue:string",
"FirstPage:string",
"LastPage:string",
"ReferenceCount:long",
"CitationCount:long",
"EstimatedCitation:long",
"OriginalVenue:string",
"FamilyId:long?",
"FamilyRank:uint?",
"CreatedDate:DateTime"
)
),
"RelatedFieldOfStudy" -> Tuple2(
"advanced/RelatedFieldOfStudy.txt",
Seq(
"FieldOfStudyId1:long",
"Type1:string",
"FieldOfStudyId2:long",
"Type2:string",
"Rank:float"
)
)
"Affiliations" -> Tuple2("mag/Affiliations.txt", Seq("AffiliationId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "GridId:string", "OfficialPage:string", "WikiPage:string", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "Iso3166Code:string", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")),
"AuthorExtendedAttributes" -> Tuple2("mag/AuthorExtendedAttributes.txt", Seq("AuthorId:long", "AttributeType:int", "AttributeValue:string")),
"Authors" -> Tuple2("mag/Authors.txt", Seq("AuthorId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "LastKnownAffiliationId:long?", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")),
"ConferenceInstances" -> Tuple2("mag/ConferenceInstances.txt", Seq("ConferenceInstanceId:long", "NormalizedName:string", "DisplayName:string", "ConferenceSeriesId:long", "Location:string", "OfficialUrl:string", "StartDate:DateTime?", "EndDate:DateTime?", "AbstractRegistrationDate:DateTime?", "SubmissionDeadlineDate:DateTime?", "NotificationDueDate:DateTime?", "FinalVersionDueDate:DateTime?", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")),
"ConferenceSeries" -> Tuple2("mag/ConferenceSeries.txt", Seq("ConferenceSeriesId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")),
"EntityRelatedEntities" -> Tuple2("advanced/EntityRelatedEntities.txt", Seq("EntityId:long", "EntityType:string", "RelatedEntityId:long", "RelatedEntityType:string", "RelatedType:int", "Score:float")),
"FieldOfStudyChildren" -> Tuple2("advanced/FieldOfStudyChildren.txt", Seq("FieldOfStudyId:long", "ChildFieldOfStudyId:long")),
"FieldOfStudyExtendedAttributes" -> Tuple2("advanced/FieldOfStudyExtendedAttributes.txt", Seq("FieldOfStudyId:long", "AttributeType:int", "AttributeValue:string")),
"FieldsOfStudy" -> Tuple2("advanced/FieldsOfStudy.txt", Seq("FieldOfStudyId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "MainType:string", "Level:int", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")),
"Journals" -> Tuple2("mag/Journals.txt", Seq("JournalId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "Issn:string", "Publisher:string", "Webpage:string", "PaperCount:long", "PaperFamilyCount:long", "CitationCount:long", "CreatedDate:DateTime")),
"PaperAbstractsInvertedIndex" -> Tuple2("nlp/PaperAbstractsInvertedIndex.txt.*", Seq("PaperId:long", "IndexedAbstract:string")),
"PaperAuthorAffiliations" -> Tuple2("mag/PaperAuthorAffiliations.txt", Seq("PaperId:long", "AuthorId:long", "AffiliationId:long?", "AuthorSequenceNumber:uint", "OriginalAuthor:string", "OriginalAffiliation:string")),
"PaperCitationContexts" -> Tuple2("nlp/PaperCitationContexts.txt", Seq("PaperId:long", "PaperReferenceId:long", "CitationContext:string")),
"PaperExtendedAttributes" -> Tuple2("mag/PaperExtendedAttributes.txt", Seq("PaperId:long", "AttributeType:int", "AttributeValue:string")),
"PaperFieldsOfStudy" -> Tuple2("advanced/PaperFieldsOfStudy.txt", Seq("PaperId:long", "FieldOfStudyId:long", "Score:float")),
"PaperMeSH" -> Tuple2("advanced/PaperMeSH.txt", Seq("PaperId:long", "DescriptorUI:string", "DescriptorName:string", "QualifierUI:string", "QualifierName:string", "IsMajorTopic:bool")),
"PaperRecommendations" -> Tuple2("advanced/PaperRecommendations.txt", Seq("PaperId:long", "RecommendedPaperId:long", "Score:float")),
"PaperReferences" -> Tuple2("mag/PaperReferences.txt", Seq("PaperId:long", "PaperReferenceId:long")),
"PaperResources" -> Tuple2("mag/PaperResources.txt", Seq("PaperId:long", "ResourceType:int", "ResourceUrl:string", "SourceUrl:string", "RelationshipType:int")),
"PaperUrls" -> Tuple2("mag/PaperUrls.txt", Seq("PaperId:long", "SourceType:int?", "SourceUrl:string", "LanguageCode:string")),
"Papers" -> Tuple2("mag/Papers.txt", Seq("PaperId:long", "Rank:uint", "Doi:string", "DocType:string", "PaperTitle:string", "OriginalTitle:string", "BookTitle:string", "Year:int?", "Date:DateTime?", "OnlineDate:DateTime?", "Publisher:string", "JournalId:long?", "ConferenceSeriesId:long?", "ConferenceInstanceId:long?", "Volume:string", "Issue:string", "FirstPage:string", "LastPage:string", "ReferenceCount:long", "CitationCount:long", "EstimatedCitation:long", "OriginalVenue:string", "FamilyId:long?", "FamilyRank:uint?", "DocSubTypes:string", "CreatedDate:DateTime")),
"RelatedFieldOfStudy" -> Tuple2("advanced/RelatedFieldOfStudy.txt", Seq("FieldOfStudyId1:long", "Type1:string", "FieldOfStudyId2:long", "Type2:string", "Rank:float"))
)
def getSchema(streamName: String): StructType = {
var schema = new StructType()
val d: Seq[String] = stream(streamName)._2
@ -261,22 +61,19 @@ object SparkImportMagIntoDataset {
schema
}
def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(
IOUtils.toString(
getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/mag/convert_mag_to_oaf_params.json")
)
)
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/mag/convert_mag_to_oaf_params.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master"))
.getOrCreate()
.master(parser.get("master")).getOrCreate()
stream.foreach { case (k, v) =>
val s: StructType = getSchema(k)

37
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/SparkResultToOrganizationFromSemRel.java
View File

@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.io.Serializable;
import java.util.Arrays;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
@ -64,6 +65,18 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
final String workingPath = parser.get("workingDir");
log.info("workingPath: {}", workingPath);
final int iterations = Optional
.ofNullable(parser.get("iterations"))
.map(v -> {
if (Integer.valueOf(v) < MAX_ITERATION) {
return Integer.valueOf(v);
} else
return MAX_ITERATION;
})
.orElse(MAX_ITERATION);
log.info("iterations: {}", iterations);
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
@ -77,7 +90,8 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
resultOrganizationPath,
relationPath,
workingPath,
outputPath));
outputPath,
iterations));
}
public static void execPropagation(SparkSession spark,
@ -86,7 +100,13 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
String resultOrganizationPath,
String graphPath,
String workingPath,
String outputPath) {
String outputPath,
int iterations) {
if (iterations == 1) {
doPropagateOnce(
spark, leavesPath, childParentPath, resultOrganizationPath, graphPath,
workingPath, outputPath);
} else {
final LongAccumulator iterationOne = spark.sparkContext().longAccumulator(ITERATION_ONE);
final LongAccumulator iterationTwo = spark.sparkContext().longAccumulator(ITERATION_TWO);
@ -105,9 +125,22 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
doPropagate(
spark, leavesPath, childParentPath, resultOrganizationPath, graphPath,
workingPath, outputPath, propagationCounter);
}
}
private static void doPropagateOnce(SparkSession spark, String leavesPath, String childParentPath,
String resultOrganizationPath, String graphPath, String workingPath,
String outputPath) {
StepActions
.execStep(
spark, graphPath, workingPath + NEW_RELATION_PATH,
leavesPath, childParentPath, resultOrganizationPath);
addNewRelations(spark, workingPath + NEW_RELATION_PATH, outputPath);
}
private static void doPropagate(SparkSession spark, String leavesPath, String childParentPath,
String resultOrganizationPath, String graphPath, String workingPath, String outputPath,
PropagationCounter propagationCounter) {

6
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/input_propagation_parameter.json
View File

@ -46,5 +46,11 @@
"paramLongName": "outputPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
{
"paramName": "it",
"paramLongName": "iterations",
"paramDescription": "the number of iterations to be computed",
"paramRequired": false
}
]

3
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfromsemrel/oozie_app/workflow.xml
View File

@ -1,4 +1,4 @@
<workflow-app name="affiliation_from_instrepo_propagation" xmlns="uri:oozie:workflow:0.5">
<workflow-app name="affiliation_from_semrel_propagation" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
@ -181,6 +181,7 @@
<arg>--resultOrgPath</arg><arg>${workingDir}/preparedInfo/resultOrgPath</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--workingDir</arg><arg>${workingDir}/working</arg>
<arg>--iterations</arg><arg>${iterations}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>