forked from D-Net/dnet-hadoop
new busuness logic with prepared info before actual job run
This commit is contained in:
parent
8438702b3d
commit
540da4ab61
|
@ -0,0 +1,24 @@
|
|||
package eu.dnetlib.dhp.countrypropagation;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
public class DatasourceCountry implements Serializable {
|
||||
private String dataSourceId;
|
||||
private String country;
|
||||
|
||||
public String getDataSourceId() {
|
||||
return dataSourceId;
|
||||
}
|
||||
|
||||
public void setDataSourceId(String dataSourceId) {
|
||||
this.dataSourceId = dataSourceId;
|
||||
}
|
||||
|
||||
public String getCountry() {
|
||||
return country;
|
||||
}
|
||||
|
||||
public void setCountry(String country) {
|
||||
this.country = country;
|
||||
}
|
||||
}
|
|
@ -0,0 +1,132 @@
|
|||
package eu.dnetlib.dhp.countrypropagation;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
|
||||
import static eu.dnetlib.dhp.PropagationConstant.createOutputDirs;
|
||||
import static eu.dnetlib.dhp.PropagationConstant.getConstraintList;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
/**
|
||||
* For the association of the country to the datasource
|
||||
* The association is computed only for datasource of specific type or having whitelisted ids
|
||||
* The country is registered in the Organization associated to the Datasource, so the
|
||||
* relation provides between Datasource and Organization is exploited to get the country for the datasource
|
||||
*/
|
||||
|
||||
public class PrepareResultCountryAssociation {
|
||||
private static final Logger log = LoggerFactory.getLogger(PrepareResultCountryAssociation.class);
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
String jsonConfiguration = IOUtils.toString(PrepareResultCountryAssociation.class
|
||||
.getResourceAsStream("/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json"));
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
jsonConfiguration);
|
||||
|
||||
parser.parseArgument(args);
|
||||
|
||||
Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
String inputPath = parser.get("sourcePath");
|
||||
log.info("inputPath: {}", inputPath);
|
||||
|
||||
|
||||
String graphTableClassName = parser.get("graphTableClassName");
|
||||
log.info("graphTableClassName: {}", graphTableClassName);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
|
||||
|
||||
runWithSparkSession(conf, isSparkSessionManaged,
|
||||
spark -> {
|
||||
removeOutputDir(spark, outputPath);
|
||||
joinRelationEntity(spark, inputRelationsPath, inputEntityPath, entityClazz, outputPath);
|
||||
});
|
||||
|
||||
|
||||
final SparkSession spark = SparkSession
|
||||
.builder()
|
||||
.appName(PrepareResultCountryAssociation.class.getSimpleName())
|
||||
.master(parser.get("master"))
|
||||
.config(conf)
|
||||
.enableHiveSupport()
|
||||
.getOrCreate();
|
||||
|
||||
//todo add link to working dir
|
||||
final String outputPath = "/tmp/provision/propagation/countrytoresultfrominstitutionalrepositories";
|
||||
|
||||
createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
|
||||
|
||||
List<String> whitelist = Arrays.asList(parser.get("whitelist").split(";"));
|
||||
List<String> allowedtypes = Arrays.asList(parser.get("allowedtypes").split(";"));
|
||||
|
||||
String whitelisted = "";
|
||||
for (String i : whitelist){
|
||||
whitelisted += " OR id = '" + i + "'";
|
||||
}
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
|
||||
Dataset<Datasource> datasource = spark.createDataset(sc.textFile(inputPath + "/datasource")
|
||||
.map(item -> new ObjectMapper().readValue(item, Datasource.class)).rdd(), Encoders.bean(Datasource.class));
|
||||
|
||||
Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
|
||||
.map(item -> new ObjectMapper().readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
|
||||
|
||||
Dataset<Organization> organization = spark.createDataset(sc.textFile(inputPath + "/organization")
|
||||
.map(item -> new ObjectMapper().readValue(item, Organization.class)).rdd(), Encoders.bean(Organization.class));
|
||||
|
||||
datasource.createOrReplaceTempView("datasource");
|
||||
relation.createOrReplaceTempView("relation");
|
||||
organization.createOrReplaceTempView("organization");
|
||||
|
||||
String query = "SELECT source ds, country.classid country " +
|
||||
"FROM ( SELECT id " +
|
||||
"FROM datasource " +
|
||||
"WHERE (datainfo.deletedbyinference = false " + whitelisted + ") " +
|
||||
getConstraintList("datasourcetype.classid = '", allowedtypes) + ") d " +
|
||||
"JOIN ( SELECT source, target " +
|
||||
"FROM relation " +
|
||||
"WHERE relclass = 'provides' " +
|
||||
"AND datainfo.deletedbyinference = false ) rel " +
|
||||
"ON d.id = rel.source " +
|
||||
"JOIN (SELECT id, country " +
|
||||
"FROM organization " +
|
||||
"WHERE datainfo.deletedbyinference = false " +
|
||||
"AND length(country.classid)>0) o " +
|
||||
"ON o.id = rel.target";
|
||||
|
||||
spark.sql(query)
|
||||
.as(Encoders.bean(DatasourceCountry.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.parquet(outputPath + "/prepared_datasource_country");
|
||||
|
||||
|
||||
}
|
||||
}
|
|
@ -0,0 +1,287 @@
|
|||
package eu.dnetlib.dhp.countrypropagation;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaPairRDD;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.Row;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import scala.Tuple2;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
|
||||
import static eu.dnetlib.dhp.PropagationConstant.*;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
public class SparkCountryPropagationJob2 {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkCountryPropagationJob2.class);
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCountryPropagationJob2.class.getResourceAsStream("/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
|
||||
final SparkSession spark = SparkSession
|
||||
.builder()
|
||||
.appName(SparkCountryPropagationJob2.class.getSimpleName())
|
||||
.master(parser.get("master"))
|
||||
.config(conf)
|
||||
.enableHiveSupport()
|
||||
.getOrCreate();
|
||||
|
||||
|
||||
final String inputPath = parser.get("sourcePath");
|
||||
final String outputPath = "/tmp/provision/propagation/countrytoresultfrominstitutionalrepositories";
|
||||
|
||||
// createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
|
||||
|
||||
boolean writeUpdates = TRUE.equals(parser.get("writeUpdate"));
|
||||
boolean saveGraph = TRUE.equals(parser.get("saveGraph"));
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
|
||||
Dataset<eu.dnetlib.dhp.schema.oaf.Dataset> dataset = spark.createDataset(sc.textFile(inputPath + "/dataset")
|
||||
.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Dataset.class)).rdd(),
|
||||
Encoders.bean(eu.dnetlib.dhp.schema.oaf.Dataset.class));
|
||||
|
||||
Dataset<OtherResearchProduct> other = spark.createDataset(sc.textFile(inputPath + "/otherresearchproduct")
|
||||
.map(item -> new ObjectMapper().readValue(item, OtherResearchProduct.class)).rdd(),
|
||||
Encoders.bean(OtherResearchProduct.class));
|
||||
|
||||
Dataset<Software> software = spark.createDataset(sc.textFile(inputPath + "/software")
|
||||
.map(item -> new ObjectMapper().readValue(item, Software.class)).rdd(),
|
||||
Encoders.bean(Software.class));
|
||||
|
||||
Dataset<Publication> publication = spark.createDataset(sc.textFile(inputPath + "/publication")
|
||||
.map(item -> new ObjectMapper().readValue(item, Publication.class)).rdd(),
|
||||
Encoders.bean(Publication.class));
|
||||
|
||||
|
||||
//todo broadcast
|
||||
|
||||
|
||||
software.createOrReplaceTempView("software");
|
||||
final JavaRDD<Row> toupdateresultsoftware = propagateOnResult(spark, "software");
|
||||
|
||||
dataset.createOrReplaceTempView("dataset");
|
||||
final JavaRDD<Row> toupdateresultdataset = propagateOnResult(spark, "dataset");
|
||||
|
||||
other.createOrReplaceTempView("other");
|
||||
final JavaRDD<Row> toupdateresultother = propagateOnResult(spark, "other");
|
||||
|
||||
publication.createOrReplaceTempView("publication");
|
||||
final JavaRDD<Row> toupdateresultpublication = propagateOnResult(spark, "publication");
|
||||
|
||||
if(writeUpdates){
|
||||
writeUpdates(toupdateresultsoftware, toupdateresultdataset, toupdateresultother, toupdateresultpublication, outputPath);
|
||||
}
|
||||
|
||||
if(saveGraph){
|
||||
createUpdateForSoftwareDataset(toupdateresultsoftware, inputPath, spark)
|
||||
.map(s -> new ObjectMapper().writeValueAsString(s))
|
||||
.saveAsTextFile(outputPath + "/software");
|
||||
|
||||
createUpdateForDatasetDataset(toupdateresultdataset,inputPath,spark)
|
||||
.map(d -> new ObjectMapper().writeValueAsString(d))
|
||||
.saveAsTextFile(outputPath + "/dataset");
|
||||
|
||||
createUpdateForOtherDataset(toupdateresultother, inputPath, spark)
|
||||
.map(o -> new ObjectMapper().writeValueAsString(o))
|
||||
.saveAsTextFile(outputPath + "/otherresearchproduct");
|
||||
|
||||
createUpdateForPublicationDataset(toupdateresultpublication, inputPath, spark)
|
||||
.map(p -> new ObjectMapper().writeValueAsString(p))
|
||||
.saveAsTextFile(outputPath + "/publication");
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private static void writeUpdates(JavaRDD<Row> software, JavaRDD<Row> dataset, JavaRDD<Row> other , JavaRDD<Row> publication, String outputPath){
|
||||
createUpdateForResultDatasetWrite(software, outputPath, "update_software");
|
||||
createUpdateForResultDatasetWrite(dataset, outputPath, "update_dataset");
|
||||
createUpdateForResultDatasetWrite(other, outputPath, "update_other");
|
||||
createUpdateForResultDatasetWrite(publication, outputPath, "update_publication");
|
||||
}
|
||||
|
||||
private static JavaRDD<OtherResearchProduct> createUpdateForOtherDataset(JavaRDD<Row> toupdateresult, String inputPath, SparkSession spark) {
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
return sc.textFile(inputPath + "/otherresearchproduct")
|
||||
.map(item -> new ObjectMapper().readValue(item, OtherResearchProduct.class))
|
||||
.mapToPair(s -> new Tuple2<>(s.getId(), s)).leftOuterJoin(getStringResultJavaPairRDD(toupdateresult))
|
||||
.map(c -> {
|
||||
OtherResearchProduct oaf = c._2()._1();
|
||||
List<Country> countryList = oaf.getCountry();
|
||||
if (c._2()._2().isPresent()) {
|
||||
HashSet<String> countries = new HashSet<>();
|
||||
for (Qualifier country : countryList) {
|
||||
countries.add(country.getClassid());
|
||||
}
|
||||
Result r = c._2()._2().get();
|
||||
for (Country country : r.getCountry()) {
|
||||
if (!countries.contains(country.getClassid())) {
|
||||
countryList.add(country);
|
||||
}
|
||||
}
|
||||
oaf.setCountry(countryList);
|
||||
}
|
||||
return oaf;
|
||||
});
|
||||
}
|
||||
|
||||
private static JavaRDD<Publication> createUpdateForPublicationDataset(JavaRDD<Row> toupdateresult, String inputPath, SparkSession spark) {
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
return sc.textFile(inputPath + "/publication")
|
||||
.map(item -> new ObjectMapper().readValue(item, Publication.class))
|
||||
.mapToPair(s -> new Tuple2<>(s.getId(), s)).leftOuterJoin(getStringResultJavaPairRDD(toupdateresult))
|
||||
.map(c -> {
|
||||
Publication oaf = c._2()._1();
|
||||
List<Country> countryList = oaf.getCountry();
|
||||
if (c._2()._2().isPresent()) {
|
||||
HashSet<String> countries = new HashSet<>();
|
||||
for (Qualifier country : countryList) {
|
||||
countries.add(country.getClassid());
|
||||
}
|
||||
Result r = c._2()._2().get();
|
||||
for (Country country : r.getCountry()) {
|
||||
if (!countries.contains(country.getClassid())) {
|
||||
countryList.add(country);
|
||||
}
|
||||
}
|
||||
oaf.setCountry(countryList);
|
||||
}
|
||||
return oaf;
|
||||
});
|
||||
}
|
||||
|
||||
private static JavaRDD<Software> createUpdateForSoftwareDataset(JavaRDD<Row> toupdateresult, String inputPath, SparkSession spark) {
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
return sc.textFile(inputPath + "/software")
|
||||
.map(item -> new ObjectMapper().readValue(item, Software.class))
|
||||
.mapToPair(s -> new Tuple2<>(s.getId(), s)).leftOuterJoin(getStringResultJavaPairRDD(toupdateresult))
|
||||
.map(c -> {
|
||||
Software oaf = c._2()._1();
|
||||
List<Country> countryList = oaf.getCountry();
|
||||
if (c._2()._2().isPresent()) {
|
||||
HashSet<String> countries = new HashSet<>();
|
||||
for (Qualifier country : countryList) {
|
||||
countries.add(country.getClassid());
|
||||
}
|
||||
Result r = c._2()._2().get();
|
||||
for (Country country : r.getCountry()) {
|
||||
if (!countries.contains(country.getClassid())) {
|
||||
countryList.add(country);
|
||||
}
|
||||
}
|
||||
oaf.setCountry(countryList);
|
||||
}
|
||||
return oaf;
|
||||
});
|
||||
}
|
||||
|
||||
private static JavaRDD<eu.dnetlib.dhp.schema.oaf.Dataset> createUpdateForDatasetDataset(JavaRDD<Row> toupdateresult, String inputPath, SparkSession spark) {
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
return sc.textFile(inputPath + "/dataset")
|
||||
.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Dataset.class))
|
||||
.mapToPair(d -> new Tuple2<>(d.getId(), d)).leftOuterJoin(getStringResultJavaPairRDD(toupdateresult))
|
||||
.map(c -> {
|
||||
eu.dnetlib.dhp.schema.oaf.Dataset oaf = c._2()._1();
|
||||
List<Country> countryList = oaf.getCountry();
|
||||
if (c._2()._2().isPresent()) {
|
||||
HashSet<String> countries = new HashSet<>();
|
||||
for (Qualifier country : countryList) {
|
||||
countries.add(country.getClassid());
|
||||
}
|
||||
Result r = c._2()._2().get();
|
||||
for (Country country : r.getCountry()) {
|
||||
if (!countries.contains(country.getClassid())) {
|
||||
countryList.add(country);
|
||||
}
|
||||
}
|
||||
oaf.setCountry(countryList);
|
||||
}
|
||||
return oaf;
|
||||
});
|
||||
}
|
||||
|
||||
private static JavaRDD<Row> propagateOnResult(SparkSession spark, String result_type) {
|
||||
String query;
|
||||
query = "SELECT id, inst.collectedfrom.key cf , inst.hostedby.key hb " +
|
||||
"FROM ( SELECT id, instance " +
|
||||
"FROM " + result_type +
|
||||
" WHERE datainfo.deletedbyinference = false) ds " +
|
||||
"LATERAL VIEW EXPLODE(instance) i AS inst";
|
||||
Dataset<Row> cfhb = spark.sql(query);
|
||||
cfhb.createOrReplaceTempView("cfhb");
|
||||
|
||||
return countryPropagationAssoc(spark, "cfhb").toJavaRDD();
|
||||
|
||||
}
|
||||
|
||||
private static Dataset<Row> countryPropagationAssoc(SparkSession spark, String cfhbTable){
|
||||
String query = "SELECT id, collect_set(country) country "+
|
||||
"FROM ( SELECT id, country " +
|
||||
"FROM rels " +
|
||||
"JOIN " + cfhbTable +
|
||||
" ON cf = ds " +
|
||||
"UNION ALL " +
|
||||
"SELECT id , country " +
|
||||
"FROM rels " +
|
||||
"JOIN " + cfhbTable +
|
||||
" ON hb = ds ) tmp " +
|
||||
"GROUP BY id";
|
||||
return spark.sql(query);
|
||||
}
|
||||
|
||||
private static JavaPairRDD<String, Result> getStringResultJavaPairRDD(JavaRDD<Row> toupdateresult) {
|
||||
return toupdateresult.map(c -> {
|
||||
List<Country> countryList = new ArrayList<>();
|
||||
List<String> tmp = c.getList(1);
|
||||
for (String country : tmp) {
|
||||
countryList.add(getCountry(country));
|
||||
}
|
||||
Result r = new Result();
|
||||
r.setId(c.getString(0));
|
||||
r.setCountry(countryList);
|
||||
return r;
|
||||
}).mapToPair(r -> new Tuple2<>(r.getId(), r));
|
||||
}
|
||||
|
||||
private static void createUpdateForResultDatasetWrite(JavaRDD<Row> toupdateresult, String outputPath, String type){
|
||||
toupdateresult.map(c -> {
|
||||
List<Country> countryList = new ArrayList<>();
|
||||
List<String> tmp = c.getList(1);
|
||||
for (String country : tmp) {
|
||||
countryList.add(getCountry(country));
|
||||
}
|
||||
Result r = new Result();
|
||||
r.setId(c.getString(0));
|
||||
r.setCountry(countryList);
|
||||
return r;
|
||||
|
||||
}).map(r ->new ObjectMapper().writeValueAsString(r))
|
||||
.saveAsTextFile(outputPath+"/"+type);
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
Loading…
Reference in New Issue