[Clean Context] changed a bit the logic. Added the check not to have result hosted by a datasource of type institutional repository from NL. Added also the check that the country should have been included in the result via propagation for it to be removed

This commit is contained in:
Miriam Baglioni 2022-08-08 14:10:47 +02:00
parent 390013a4b2
commit 62d2138806
5 changed files with 315 additions and 270 deletions

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@ -1,15 +1,15 @@
package eu.dnetlib.dhp.oa.graph.clean.country;
/**
* @author miriam.baglioni
* @Date 20/07/22
*/
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import javax.swing.text.html.Option;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
@ -21,128 +21,147 @@ import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.Serializable;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
/**
* @author miriam.baglioni
* @Date 20/07/22
*/
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob;
import eu.dnetlib.dhp.schema.oaf.Country;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class CleanCountrySparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.class);
private static final Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
CleanContextSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
String jsonConfiguration = IOUtils
.toString(
CleanContextSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/input_clean_country_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);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("inputPath");
log.info("inputPath: {}", inputPath);
String inputPath = parser.get("inputPath");
log.info("inputPath: {}", inputPath);
String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
String datasourcePath = parser.get("datasourcePath");
log.info("datasourcePath: {}", datasourcePath);
String datasourcePath = parser.get("hostedBy");
log.info("datasourcePath: {}", datasourcePath);
String country = parser.get("country");
log.info("country: {}", country);
String country = parser.get("country");
log.info("country: {}", country);
String[] verifyParam = parser.get("verifyParam").split(";");
log.info("verifyParam: {}", verifyParam);
String[] verifyParam = parser.get("verifyParam").split(";");
log.info("verifyParam: {}", verifyParam);
String collectedfrom = parser.get("collectedfrom");
log.info("collectedfrom: {}", collectedfrom);
String collectedfrom = parser.get("collectedfrom");
log.info("collectedfrom: {}", collectedfrom);
String graphTableClassName = parser.get("graphTableClassName");
log.info("graphTableClassName: {}", graphTableClassName);
String graphTableClassName = parser.get("graphTableClassName");
log.info("graphTableClassName: {}", graphTableClassName);
Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName);
Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
cleanCountry(spark, country, verifyParam, inputPath, entityClazz, workingPath,collectedfrom, datasourcePath);
});
}
cleanCountry(
spark, country, verifyParam, inputPath, entityClazz, workingPath, collectedfrom, datasourcePath);
});
}
private static <T extends Result> void cleanCountry(SparkSession spark, String country, String[] verifyParam,
String inputPath, Class<T> entityClazz, String workingPath, String collectedfrom, String datasourcePath) {
private static <T extends Result> void cleanCountry(SparkSession spark, String country, String[] verifyParam,
String inputPath, Class<T> entityClazz, String workingPath, String collectedfrom, String datasourcePath) {
List<String> hostedBy = spark.read().textFile(datasourcePath)
// .filter((FilterFunction<String>) ds -> !ds.equals(collectedfrom))
.collectAsList();
List<String> hostedBy = spark
.read()
.textFile(datasourcePath)
// .filter((FilterFunction<String>) ds -> !ds.equals(collectedfrom))
.collectAsList();
Dataset<T> res = spark
.read()
.textFile(inputPath)
.map(
(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
Encoders.bean(entityClazz))
;
Dataset<T> res = spark
.read()
.textFile(inputPath)
.map(
(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
Encoders.bean(entityClazz));
res.map((MapFunction<T, T>) r -> {
if(r.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) ||
!r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))){
return r;
}
res.map((MapFunction<T, T>) r -> {
if (r.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) ||
!r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))) {
return r;
}
if(r.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals("doi") && pidInParam(p.getValue(), verifyParam))
&& r.getCountry().stream().anyMatch(c -> c.getClassid().equals(country) && c.getDataInfo().getInferenceprovenance().equals("propagation")))
{ r
.setCountry(
r
.getCountry()
.stream()
.filter(
c -> !c.getClassid()
.equalsIgnoreCase(country))
.collect(Collectors.toList()));
if (r
.getPid()
.stream()
.anyMatch(p -> p.getQualifier().getClassid().equals("doi") && pidInParam(p.getValue(), verifyParam))) {
r
.setCountry(
r
.getCountry()
.stream()
.filter(
c -> toTakeCountry(c, country))
.collect(Collectors.toList()));
}
}
return r;
}, Encoders.bean(entityClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingPath);
return r;
}, Encoders.bean(entityClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingPath);
spark
.read()
.textFile(workingPath)
.map(
(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
Encoders.bean(entityClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(inputPath);
}
spark
.read()
.textFile(workingPath)
.map(
(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
Encoders.bean(entityClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(inputPath);
}
private static boolean pidInParam(String value, String[] verifyParam) {
for (String s : verifyParam )
if (value.startsWith(s))
return true;
return false;
}
private static boolean pidInParam(String value, String[] verifyParam) {
for (String s : verifyParam)
if (value.startsWith(s))
return true;
return false;
}
private static boolean toTakeCountry(Country c, String country) {
// If dataInfo is not set, or dataInfo.inferenceprovenance is not set or not present then it cannot be
// inserted via propagation
if (!Optional.ofNullable(c.getDataInfo()).isPresent())
return true;
if (!Optional.ofNullable(c.getDataInfo().getInferenceprovenance()).isPresent())
return true;
return !(c
.getClassid()
.equalsIgnoreCase(country) &&
c.getDataInfo().getInferenceprovenance().equals("propagation"));
}
}

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@ -1,10 +1,12 @@
package eu.dnetlib.dhp.oa.graph.clean.country;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.List;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
@ -15,85 +17,92 @@ import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import scala.Tuple2;
import java.io.Serializable;
import java.util.List;
import java.util.Optional;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
/**
* @author miriam.baglioni
* @Date 22/07/22
*/
public class GetDatasourceFromCountry implements Serializable {
private static final Logger log = LoggerFactory.getLogger(GetDatasourceFromCountry.class);
private static final Logger log = LoggerFactory.getLogger(GetDatasourceFromCountry.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
GetDatasourceFromCountry.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/input_datasource_country_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
String jsonConfiguration = IOUtils
.toString(
GetDatasourceFromCountry.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/input_datasource_country_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);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
String inputPath = parser.get("inputPath");
log.info("inputPath: {}", inputPath);
String inputPath = parser.get("inputPath");
log.info("inputPath: {}", inputPath);
String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
String country = parser.get("country");
log.info("country: {}", country);
String country = parser.get("country");
log.info("country: {}", country);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
getDatasourceFromCountry(spark, country, inputPath, workingPath);
});
}
getDatasourceFromCountry(spark, country, inputPath, workingPath);
});
}
private static void getDatasourceFromCountry(SparkSession spark, String country, String inputPath, String workingPath) {
private static void getDatasourceFromCountry(SparkSession spark, String country, String inputPath,
String workingPath) {
Dataset<Organization> organization = spark.read().textFile(inputPath + "/organization")
.map(
(MapFunction<String, Organization>) value -> OBJECT_MAPPER.readValue(value, Organization.class),
Encoders.bean(Organization.class))
.filter(
(FilterFunction<Organization>) o -> !o.getDataInfo().getDeletedbyinference() &&
o.getCountry().getClassid().length() > 0 &&
o.getCountry().getClassid().equals(country));;
Dataset<Organization> organization = spark
.read()
.textFile(inputPath + "/organization")
.map(
(MapFunction<String, Organization>) value -> OBJECT_MAPPER.readValue(value, Organization.class),
Encoders.bean(Organization.class))
.filter(
(FilterFunction<Organization>) o -> !o.getDataInfo().getDeletedbyinference() &&
o.getCountry().getClassid().length() > 0 &&
o.getCountry().getClassid().equals(country));
;
// filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass
Dataset<Relation> relation = spark
.read()
.textFile(inputPath + "/relation")
.map(
(MapFunction<String, Relation>) value -> OBJECT_MAPPER.readValue(value, Relation.class),
Encoders.bean(Relation.class))
.filter(
(FilterFunction<Relation>) rel -> rel.getRelClass().equalsIgnoreCase(ModelConstants.IS_PROVIDED_BY) &&
!rel.getDataInfo().getDeletedbyinference());
// filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass
Dataset<Relation> relation = spark.read().textFile( inputPath + "/relation")
.map(
(MapFunction<String, Relation>) value -> OBJECT_MAPPER.readValue(value, Relation.class),
Encoders.bean(Relation.class))
.filter(
(FilterFunction<Relation>) rel -> rel.getRelClass().equalsIgnoreCase(ModelConstants.IS_PROVIDED_BY) &&
!rel.getDataInfo().getDeletedbyinference());
organization
.joinWith(relation, organization.col("id").equalTo(relation.col("target")), "left")
.map((MapFunction<Tuple2<Organization, Relation>, String>) t2 -> t2._2().getSource(), Encoders.STRING())
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingPath);
organization.joinWith(relation, organization.col("id").equalTo(relation.col("target")), "left")
.map((MapFunction<Tuple2<Organization, Relation>, String>) t2 -> t2._2().getSource(), Encoders.STRING() )
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.json(workingPath);
}
}
}

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@ -1,13 +1,10 @@
package eu.dnetlib.dhp.oa.graph.clean;
/**
* @author miriam.baglioni
* @Date 20/07/22
*/
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob;
import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest;
import eu.dnetlib.dhp.schema.oaf.Publication;
package eu.dnetlib.dhp.oa.graph.clean;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
@ -22,113 +19,132 @@ import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
/**
* @author miriam.baglioni
* @Date 20/07/22
*/
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob;
import eu.dnetlib.dhp.schema.oaf.Publication;
public class CleanCountryTest {
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 Path workingDir;
private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class);
private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(CleanCountryTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(DumpJobTest.class.getSimpleName());
SparkConf conf = new SparkConf();
conf.setAppName(CleanCountryTest.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(DumpJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
spark = SparkSession
.builder()
.appName(CleanCountryTest.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
public void testResultClean() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json")
.getPath();
final String prefix = "gcube ";
@Test
public void testResultClean() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json")
.getPath();
spark
.read()
.textFile(sourcePath)
.map(
(MapFunction<String, Publication>) r -> OBJECT_MAPPER.readValue(r, Publication.class),
Encoders.bean(Publication.class))
.write()
.json(workingDir.toString() + "/publication");
spark
.read()
.textFile(sourcePath)
.map(
(MapFunction<String, Publication>) r -> OBJECT_MAPPER.readValue(r, Publication.class),
Encoders.bean(Publication.class))
.write()
.json(workingDir.toString() + "/publication");
CleanCountrySparkJob.main(new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--inputPath", workingDir.toString() + "/publication",
"-graphTableClassName", Publication.class.getCanonicalName(),
"-workingPath", workingDir.toString() + "/working",
"-country", "NL",
"-verifyParam", "10.17632",
"-collectedfrom", "NARCIS"
});
CleanCountrySparkJob.main(new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--inputPath", workingDir.toString() + "/publication",
"-graphTableClassName", Publication.class.getCanonicalName(),
"-workingPath", workingDir.toString() + "/working",
"-country", "NL",
"-verifyParam", "10.17632",
"-collectedfrom", "NARCIS",
"-hostedBy", getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy")
.getPath()
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.textFile(workingDir.toString() + "/publication")
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.textFile(workingDir.toString() + "/publication")
.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
Assertions.assertEquals(7, tmp.count());
Assertions.assertEquals(8, tmp.count());
// original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS
Assertions
.assertEquals(
1,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))
.collect()
.get(0)
.getCountry()
.size());
// original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS
Assertions
.assertEquals(
1,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))
.collect()
.get(0)
.getCountry()
.size());
// original result with NL country and pid not starting with Mendely prefix
Assertions
.assertEquals(
1,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
.collect()
.get(0)
.getCountry()
.size());
// original result with NL country and pid not starting with Mendely prefix
Assertions
.assertEquals(
1,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
.collect()
.get(0)
.getCountry()
.size());
// original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS
Assertions
.assertEquals(
0,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
.collect()
.get(0)
.getCountry()
.size());
}
// original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS but not
// inserted with propagation
Assertions
.assertEquals(
1,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
.collect()
.get(0)
.getCountry()
.size());
// original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS inserted with
// propagation
Assertions
.assertEquals(
0,
tmp
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6ag"))
.collect()
.get(0)
.getCountry()
.size());
}
}