new busuness logic with prepared info before actual job run

This commit is contained in:
Miriam Baglioni 2020-04-08 13:04:04 +02:00
parent 8438702b3d
commit 540da4ab61
3 changed files with 443 additions and 0 deletions

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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;
}
}

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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");
}
}

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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);
}
}