Merge pull request '[WebCrawl] adding affiliation relations from web information' (#428) from WebCrowlBeta into beta

Reviewed-on: #428
This commit is contained in:
Claudio Atzori 2024-04-23 09:36:15 +02:00
commit c57cff2d6d
9 changed files with 664 additions and 0 deletions

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package eu.dnetlib.dhp.actionmanager.webcrawl;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.sql.*;
import org.apache.spark.sql.types.StructType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
import scala.Tuple2;
/**
* @author miriam.baglioni
* @Date 18/04/24
*/
public class CreateActionSetFromWebEntries implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CreateActionSetFromWebEntries.class);
private static final String DOI_PREFIX = "50|doi_________::";
private static final String ROR_PREFIX = "20|ror_________::";
private static final String PMID_PREFIX = "50|pmid________::";
private static final String PMCID_PREFIX = "50|pmc_________::";
private static final String WEB_CRAWL_ID = "10|openaire____::fb98a192f6a055ba495ef414c330834b";
private static final String WEB_CRAWL_NAME = "Web Crawl";
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);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
createActionSet(spark, inputPath, outputPath );
});
}
public static void createActionSet(SparkSession spark, String inputPath,
String outputPath) {
final Dataset<Row> dataset = readWebCrawl(spark, inputPath)
.filter("publication_year <= 2020 or country_code=='IE'")
.drop("publication_year");
dataset.flatMap((FlatMapFunction<Row, Relation>) row -> {
List<Relation> ret = new ArrayList<>();
final String ror = ROR_PREFIX
+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror));
ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror));
return ret
.iterator();
}, 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, GzipCodec.class);
}
private static Dataset<Row> readWebCrawl(SparkSession spark, String inputPath) {
StructType webInfo = StructType
.fromDDL(
"`id` STRING , `doi` STRING, `ids` STRUCT<`pmid` :STRING, `pmcid`: STRING >, `publication_year` STRING, "
+
"`authorships` ARRAY<STRUCT <`institutions`: ARRAY <STRUCT <`ror`: STRING, `country_code` :STRING>>>>");
return spark
.read()
.schema(webInfo)
.json(inputPath)
.withColumn(
"authors", functions
.explode(
functions.col("authorships")))
.selectExpr("id", "doi", "ids", "publication_year", "authors.institutions as institutions")
.withColumn(
"institution", functions
.explode(
functions.col("institutions")))
.selectExpr(
"id", "doi", "ids.pmcid as pmcid", "ids.pmid as pmid", "institution.ror as ror",
"institution.country_code as country_code", "publication_year")
.distinct();
}
private static List<Relation> createAffiliationRelationPairPMCID(String pmcid, String ror) {
if (pmcid == null)
return new ArrayList<>();
return createAffiliatioRelationPair(
PMCID_PREFIX
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), removeResolver("PMC" , pmcid))),
ror);
}
private static List<Relation> createAffiliationRelationPairPMID(String pmid, String ror) {
if (pmid == null)
return new ArrayList<>();
return createAffiliatioRelationPair(
PMID_PREFIX
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), removeResolver("PMID", pmid))),
ror);
}
private static String removeResolver(String pidType, String pid) {
switch (pidType){
case "PMID":
return pid.substring(33);
case "PMC":
return "PMC" + pid.substring(43);
case "DOI":
return pid.substring(16);
}
throw new RuntimeException();
}
private static List<Relation> createAffiliationRelationPairDOI(String doi, String ror) {
if (doi == null)
return new ArrayList<>();
return createAffiliatioRelationPair(
DOI_PREFIX
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), removeResolver("DOI" ,doi))),
ror);
}
private static List<Relation> createAffiliatioRelationPair(String resultId, String orgId) {
ArrayList<Relation> newRelations = new ArrayList();
newRelations
.add(
OafMapperUtils
.getRelation(
orgId, resultId, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION,
ModelConstants.IS_AUTHOR_INSTITUTION_OF,
Arrays
.asList(
OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)),
OafMapperUtils
.dataInfo(
false, null, false, false,
OafMapperUtils
.qualifier(
"sysimport:crasswalk:webcrawl", "Imported from Webcrawl",
ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
"0.9"),
null));
newRelations
.add(
OafMapperUtils
.getRelation(
resultId, orgId, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION,
ModelConstants.HAS_AUTHOR_INSTITUTION,
Arrays
.asList(
OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)),
OafMapperUtils
.dataInfo(
false, null, false, false,
OafMapperUtils
.qualifier(
"sysimport:crasswalk:webcrawl", "Imported from Webcrawl",
ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
"0.9"),
null));
return newRelations;
}
}

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[
{
"paramName": "sp",
"paramLongName": "sourcePath",
"paramDescription": "the zipped opencitations file",
"paramRequired": true
},
{
"paramName": "op",
"paramLongName": "outputPath",
"paramDescription": "the working path",
"paramRequired": true
},
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "the hdfs name node",
"paramRequired": false
}
]

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sourcePath=/user/miriam.baglioni/openalex-snapshot/data/works/
outputPath=/tmp/miriam/webcrawlComplete/

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<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
<property>
<name>sparkExecutorNumber</name>
<value>4</value>
</property>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/spark2ApplicationHistory</value>
</property>
<property>
<name>sparkDriverMemory</name>
<value>15G</value>
</property>
<property>
<name>sparkExecutorMemory</name>
<value>6G</value>
</property>
<property>
<name>sparkExecutorCores</name>
<value>1</value>
</property>
</configuration>

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<workflow-app name="WebCrawl Integration" xmlns="uri:oozie:workflow:0.5">
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="create_actionset"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="create_actionset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the AS for WC</name>
<class>eu.dnetlib.dhp.actionmanager.webcrawl.CreateActionSetFromWebEntries</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>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

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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 CreateASTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory
.getLogger(CreateASTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(CreateASTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(CreateASTest.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(CreateASTest.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/")
.getPath();
CreateActionSetFromWebEntries
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet1"
});
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(64, tmp.count());
}
@Test
void testRelations() throws Exception {
// , "doi":"https://doi.org/10.1126/science.1188021", "pmid":"https://pubmed.ncbi.nlm.nih.gov/20448178", https://www.ncbi.nlm.nih.gov/pmc/articles/5100745
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/webcrawl/")
.getPath();
CreateActionSetFromWebEntries
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet1"
});
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()));
tmp.foreach(r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
Assertions
.assertEquals(
1, tmp
.filter(
r -> r
.getSource()
.equals(
"50|doi_________::" + IdentifierFactory
.md5(
PidCleaner
.normalizePidValue(PidType.doi.toString(), "10.1098/rstl.1684.0023"))))
.count());
Assertions
.assertEquals(
1, tmp
.filter(
r -> r
.getTarget()
.equals(
"50|doi_________::" + IdentifierFactory
.md5(
PidCleaner
.normalizePidValue(PidType.doi.toString(), "10.1098/rstl.1684.0023"))))
.count());
Assertions
.assertEquals(
1, tmp
.filter(
r -> r
.getSource()
.equals(
"20|ror_________::" + IdentifierFactory
.md5(
PidCleaner
.normalizePidValue("ROR", "https://ror.org/03argrj65"))))
.count());
Assertions
.assertEquals(
1, tmp
.filter(
r -> r
.getTarget()
.equals(
"20|ror_________::" + IdentifierFactory
.md5(
PidCleaner
.normalizePidValue("ROR", "https://ror.org/03argrj65"))))
.count());
Assertions
.assertEquals(
5, tmp
.filter(
r -> r
.getSource()
.equals(
"20|ror_________::" + IdentifierFactory
.md5(
PidCleaner
.normalizePidValue("ROR", "https://ror.org/03265fv13"))))
.count());
Assertions
.assertEquals(
5, tmp
.filter(
r -> r
.getTarget()
.equals(
"20|ror_________::" + IdentifierFactory
.md5(
PidCleaner
.normalizePidValue("ROR", "https://ror.org/03265fv13"))))
.count());
Assertions
.assertEquals(
2, tmp
.filter(
r -> r
.getTarget()
.equals(
"20|ror_________::" + IdentifierFactory
.md5(
PidCleaner
.normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13")))
&& r.getSource().startsWith("50|doi"))
.count());
Assertions
.assertEquals(
2, tmp
.filter(
r -> r
.getTarget()
.equals(
"20|ror_________::" + IdentifierFactory
.md5(
PidCleaner
.normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13")))
&& r.getSource().startsWith("50|pmid"))
.count());
Assertions
.assertEquals(
1, tmp
.filter(
r -> r
.getTarget()
.equals(
"20|ror_________::" + IdentifierFactory
.md5(
PidCleaner
.normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13")))
&& r.getSource().startsWith("50|pmc"))
.count());
}
@Test
void testRelationsCollectedFrom() throws Exception {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/webcrawl")
.getPath();
CreateActionSetFromWebEntries
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-sourcePath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet1"
});
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()));
tmp.foreach(r -> {
assertEquals("Web Crawl", r.getCollectedfrom().get(0).getValue());
assertEquals("10|openaire____::fb98a192f6a055ba495ef414c330834b", r.getCollectedfrom().get(0).getKey());
});
}
}

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