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Remove Relation From AS #466

Merged
claudio.atzori merged 5 commits from webCrawlLessBlackList into beta 2024-07-25 15:50:20 +02:00
Conversation 0 Commits 5 Files Changed 7 +330 -15
7 changed files with 330 additions and 15 deletions
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7
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
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@ -8,7 +8,7 @@ import java.util.*;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.io.compress.BZip2Codec;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
@ -112,7 +112,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
.mapToPair(
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
new Text(OBJECT_MAPPER.writeValueAsString(aa))))
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
}
@ -148,8 +148,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
return spark
.read()
.option("header", true)
.csv(inputPath)
.json(inputPath)
.select("OpenAlexId");
}

158
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveRelationFromActionSet.java Normal file
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@ -0,0 +1,158 @@
package eu.dnetlib.dhp.actionmanager.webcrawl;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import static org.apache.spark.sql.functions.*;
import java.io.File;
import java.io.Serializable;
import java.util.Arrays;
import java.util.Optional;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.filefilter.DirectoryFileFilter;
import org.apache.commons.io.filefilter.FileFileFilter;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.BZip2Codec;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
import org.apache.spark.sql.types.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
import scala.Tuple2;
public class RemoveRelationFromActionSet
implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CreateActionSetFromWebEntries.class);
private static final ObjectMapper MAPPER = new ObjectMapper();
private static final StructType KV_SCHEMA = StructType$.MODULE$
.apply(
Arrays
.asList(
StructField$.MODULE$.apply("key", DataTypes.StringType, false, Metadata.empty()),
StructField$.MODULE$.apply("value", DataTypes.StringType, false, Metadata.empty())));
private static final StructType ATOMIC_ACTION_SCHEMA = StructType$.MODULE$
.apply(
Arrays
.asList(
StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()),
StructField$.MODULE$
.apply(
"payload", DataTypes.StringType, false, Metadata.empty())));
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
CreateActionSetFromWebEntries.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/webcrawl/as_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);
// the actionSet path
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String blackListInputPath = parser.get("blackListPath");
log.info("blackListInputPath: {}", blackListInputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
removeFromActionSet(spark, inputPath, outputPath, blackListInputPath);
});
}
private static void removeFromActionSet(SparkSession spark, String inputPath, String outputPath,
String blackListInputPath) {
// read the blacklist
Dataset<String> blackList = readBlackList(spark, blackListInputPath)
.map(
(MapFunction<Row, String>) r -> IdentifierFactory
.idFromPid("50", "doi", ((String) r.getAs("doi")).substring(16), true),
Encoders.STRING());
// read the old actionset and get the relations in the payload
JavaPairRDD<Text, Text> seq = JavaSparkContext
.fromSparkContext(spark.sparkContext())
.sequenceFile(inputPath, Text.class, Text.class);
JavaRDD<Row> rdd = seq
.map(x -> RowFactory.create(x._1().toString(), x._2().toString()));
Dataset<Row> actionSet = spark
.createDataFrame(rdd, KV_SCHEMA)
.withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA))
.select(expr("atomic_action.*"));
Dataset<Relation> relation = actionSet
.map(
(MapFunction<Row, Relation>) r -> MAPPER.readValue((String) r.getAs("payload"), Relation.class),
Encoders.bean(Relation.class));
// select only the relation not matching any pid in the blacklist as source for the relation
Dataset<Relation> relNoSource = relation
.joinWith(blackList, relation.col("source").equalTo(blackList.col("value")), "left")
.filter((FilterFunction<Tuple2<Relation, String>>) t2 -> t2._2() == null)
.map((MapFunction<Tuple2<Relation, String>, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class));
// select only the relation not matching any pid in the blacklist as target of the relation
relNoSource
.joinWith(blackList, relNoSource.col("target").equalTo(blackList.col("value")), "left")
.filter((FilterFunction<Tuple2<Relation, String>>) t2 -> t2._2() == null)
.map((MapFunction<Tuple2<Relation, String>, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class))
.toJavaRDD()
.map(p -> new AtomicAction(p.getClass(), p))
.mapToPair(
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
new Text(OBJECT_MAPPER.writeValueAsString(aa))))
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
;
}
private static Dataset<Row> readBlackList(SparkSession spark, String inputPath) {
return spark
.read()
.json(inputPath)
.select("doi");
}
}

14
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/job.properties
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@ -1,3 +1,11 @@
sourcePath=/user/miriam.baglioni/openalex-snapshot/data/works/
outputPath=/tmp/miriam/webcrawlComplete/
blackListPath=/user/miriam.baglioni/openalex-blackList
#PROPERTIES TO CREATE THE ACTION SET
#sourcePath=/user/miriam.baglioni/openalex-snapshot/data/works/
#outputPath=/tmp/miriam/webcrawlComplete/
#blackListPath=/user/miriam.baglioni/openalex-blackList
#resumeFrom=create
#PROPERTIES TO REMOVE FROM THE ACTION SET
sourcePath=/var/lib/dnet/actionManager_PROD/webcrawl/rawset_28247629-468b-478e-9a42-bc540877125d_1718121542061/
outputPath=/tmp/miriam/webcrawlRemoved/
blackListPath=/user/miriam.baglioni/oalexBlackListNormalized
resumeFrom=remove

34
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/workflow.xml
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@ -20,12 +20,19 @@
</configuration>
</global>
<start to="create_actionset"/>
<start to="resumeFrom"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<decision name="resumeFrom">
<switch>
<case to="create_actionset">${wf:conf('resumeFrom') eq 'create'}</case>
<default to="remove_from_actionset"/>
</switch>
</decision>
<action name="create_actionset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
@ -50,5 +57,30 @@
<ok to="End"/>
<error to="Kill"/>
</action>
<action name="remove_from_actionset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Removes some relations found to be wrong from the AS</name>
<class>eu.dnetlib.dhp.actionmanager.webcrawl.RemoveRelationFromActionSet</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>${sourcePath}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
<arg>--blackListPath</arg><arg>${blackListPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

23
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java
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@ -2,6 +2,7 @@
package eu.dnetlib.dhp.actionmanager.webcrawl;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.IOException;
import java.nio.file.Files;
@ -101,7 +102,10 @@ public class CreateASTest {
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
Assertions.assertEquals(58, tmp.count());
tmp.foreach(r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
tmp.foreach(r -> assertTrue(r.getSource().startsWith("20|ror") || r.getSource().startsWith("50|doi")));
tmp.foreach(r -> assertTrue(r.getTarget().startsWith("20|ror") || r.getTarget().startsWith("50|doi")));
Assertions.assertEquals(24, tmp.count());
}
@ -112,7 +116,7 @@ public class CreateASTest {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/webcrawl/")
"/eu/dnetlib/dhp/actionmanager/webcrawl/input/")
.getPath();
String blackListPath = getClass()
.getResource(
@ -194,7 +198,7 @@ public class CreateASTest {
Assertions
.assertEquals(
2, tmp
1, tmp
.filter(
r -> r
.getSource()
@ -207,7 +211,7 @@ public class CreateASTest {
Assertions
.assertEquals(
2, tmp
1, tmp
.filter(
r -> r
.getTarget()
@ -228,13 +232,13 @@ public class CreateASTest {
"20|ror_________::" + IdentifierFactory
.md5(
PidCleaner
.normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13")))
.normalizePidValue("ROR", "https://ror.org/03265fv13")))
&& r.getSource().startsWith("50|doi"))
.count());
Assertions
.assertEquals(
1, tmp
0, tmp
.filter(
r -> r
.getTarget()
@ -268,6 +272,10 @@ public class CreateASTest {
.getResource(
"/eu/dnetlib/dhp/actionmanager/webcrawl")
.getPath();
String blackListPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/webcrawl/blackList/")
.getPath();
CreateActionSetFromWebEntries
.main(
@ -277,7 +285,8 @@ public class CreateASTest {
"-sourcePath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet1"
workingDir.toString() + "/actionSet1",
"-blackListPath", blackListPath
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());

108
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveFromASTest.java Normal file
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@ -0,0 +1,108 @@
package eu.dnetlib.dhp.actionmanager.webcrawl;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.io.Text;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
/**
* @author miriam.baglioni
* @Date 22/04/24
*/
public class RemoveFromASTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory
.getLogger(RemoveFromASTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(RemoveFromASTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(RemoveFromASTest.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());
spark = SparkSession
.builder()
.appName(RemoveFromASTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void testNumberofRelations() throws Exception {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/webcrawl/actionSet/")
.getPath();
String blackListPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/webcrawl/blackListRemove/")
.getPath();
RemoveRelationFromActionSet
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet1",
"-blackListPath", blackListPath
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
Assertions.assertEquals(22, tmp.count());
}
}

1
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/blackListRemove/not_irish.json Normal file
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@ -0,0 +1 @@
{"doi":"https://doi.org/10.1098/rstl.1684.0023","OpenAlexId":"https://openalex.org/W2124362779"}