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[AffiliationIngestion]Extended the ingestion of affiliation from open aire to include also links derived from Web Crawl. Extended the test. Inserted in Constatns the id and name of the webcrawl datasource to be used here and also in the ingestion of links from web crawl

This commit is contained in:
Miriam Baglioni 2024-06-29 18:29:20 +02:00
parent 14539f9c8b
commit 236b64d830
7 changed files with 40 additions and 13 deletions
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3
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
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@ -42,6 +42,9 @@ public class Constants {
public static final String NULL = "NULL";
public static final String NA = "N/A";
public static final String WEB_CRAWL_ID = "10|openaire____::fb98a192f6a055ba495ef414c330834b";
public static final String WEB_CRAWL_NAME = "Web Crawl";
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private Constants() {

15
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
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@ -41,9 +41,9 @@ public class PrepareAffiliationRelations implements Serializable {
private static final Logger log = LoggerFactory.getLogger(PrepareAffiliationRelations.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final String ID_PREFIX = "50|doi_________::";
public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:bipinference";
public static final String BIP_AFFILIATIONS_CLASSNAME = "Affiliation relation inferred by BIP!";
public static final String BIP_INFERENCE_PROVENANCE = "bip:affiliation:crossref";
public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:openaireinference";
public static final String BIP_AFFILIATIONS_CLASSNAME = "Affiliation relation inferred by OpenAIRE";
public static final String BIP_INFERENCE_PROVENANCE = "openaire:affiliation";
public static <I extends Result> void main(String[] args) throws Exception {
@ -71,6 +71,9 @@ public class PrepareAffiliationRelations implements Serializable {
final String dataciteInputPath = parser.get("dataciteInputPath");
log.info("dataciteInputPath: {}", dataciteInputPath);
final String webcrawlInputPath = parser.get("webCrawlInputPath");
log.info("webcrawlInputPath: {}", webcrawlInputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
@ -102,10 +105,16 @@ public class PrepareAffiliationRelations implements Serializable {
JavaPairRDD<Text, Text> dataciteRelations = prepareAffiliationRelations(
spark, dataciteInputPath, collectedFromDatacite);
List<KeyValue> collectedFromWebCrawl = OafMapperUtils
.listKeyValues(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME);
JavaPairRDD<Text, Text> webCrawlRelations = prepareAffiliationRelations(
spark, webcrawlInputPath, collectedFromWebCrawl);
crossrefRelations
.union(pubmedRelations)
.union(openAPCRelations)
.union(dataciteRelations)
.union(webCrawlRelations)
.saveAsHadoopFile(
outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);

10
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
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@ -1,12 +1,15 @@
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 eu.dnetlib.dhp.actionmanager.Constants;
import io.netty.util.Constant;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
@ -44,8 +47,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
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 {
@ -214,7 +216,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
ModelConstants.IS_AUTHOR_INSTITUTION_OF,
Arrays
.asList(
OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)),
OafMapperUtils.keyValue(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME)),
OafMapperUtils
.dataInfo(
false, null, false, false,
@ -233,7 +235,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
ModelConstants.HAS_AUTHOR_INSTITUTION,
Arrays
.asList(
OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)),
OafMapperUtils.keyValue(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME)),
OafMapperUtils
.dataInfo(
false, null, false, false,

8
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json
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@ -28,7 +28,13 @@
"paramLongName": "dataciteInputPath",
"paramDescription": "the path to get the input data from Datacite",
"paramRequired": true
},
},{
"paramName": "wip",
"paramLongName": "webCrawlInputPath",
"paramDescription": "the path to get the input data from Web Crawl",
"paramRequired": true
}
,
{
"paramName": "o",
"paramLongName": "outputPath",

6
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml
View File

@ -17,6 +17,10 @@
<name>dataciteInputPath</name>
<description>the path where to find the inferred affiliation relations from Datacite</description>
</property>
<property>
<name>webCrawlInputPath</name>
<description>the path where to find the inferred affiliation relations from webCrawl</description>
</property>
<property>
<name>outputPath</name>
<description>the path where to store the actionset</description>
@ -112,7 +116,7 @@
<arg>--pubmedInputPath</arg><arg>${pubmedInputPath}</arg>
<arg>--openapcInputPath</arg><arg>${openapcInputPath}</arg>
<arg>--dataciteInputPath</arg><arg>${dataciteInputPath}</arg>
<arg>--webCrawlInputPath</arg><arg>${webCrawlInputPath}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
</spark>
<ok to="End"/>

7
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
View File

@ -88,6 +88,7 @@ public class PrepareAffiliationRelationsTest {
"-pubmedInputPath", crossrefAffiliationRelationPath,
"-openapcInputPath", crossrefAffiliationRelationPath,
"-dataciteInputPath", crossrefAffiliationRelationPath,
"-webCrawlInputPath", crossrefAffiliationRelationPath,
"-outputPath", outputPath
});
@ -104,7 +105,7 @@ public class PrepareAffiliationRelationsTest {
// );
// }
// count the number of relations
assertEquals(80, tmp.count());
assertEquals(120, tmp.count());
Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
dataset.createOrReplaceTempView("result");
@ -115,7 +116,7 @@ public class PrepareAffiliationRelationsTest {
// verify that we have equal number of bi-directional relations
Assertions
.assertEquals(
40, execVerification
60, execVerification
.filter(
"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
.collectAsList()
@ -123,7 +124,7 @@ public class PrepareAffiliationRelationsTest {
Assertions
.assertEquals(
40, execVerification
60, execVerification
.filter(
"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
.collectAsList()

4
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json
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@ -4,4 +4,6 @@
{"DOI":"10.1142\/s021821650200186x","Matchings":[{"RORid":"https:\/\/ror.org\/035xkbk20","Confidence":1},{"RORid":"https:\/\/ror.org\/05apxxy63","Confidence":1}]}
{"DOI":"10.1061\/(asce)0733-9372(2002)128:7(575)","Matchings":[{"RORid":"https:\/\/ror.org\/04j198w64","Confidence":0.82}]}
{"DOI":"10.1061\/(asce)0733-9372(2002)128:7(588)","Matchings":[{"RORid":"https:\/\/ror.org\/03m8km719","Confidence":0.8660254038},{"RORid":"https:\/\/ror.org\/02aze4h65","Confidence":0.87}]}
{"DOI":"10.1161\/hy0202.103001","Matchings":[{"RORid":"https:\/\/ror.org\/057xtrt18","Confidence":0.7071067812}]}
{"DOI":"10.1161\/hy0202.103001","Matchings":[{"RORid":"https:\/\/ror.org\/057xtrt18","Confidence":0.7071067812}]}
{"DOI": "10.1080/13669877.2015.1042504", "Matchings": [{"Confidence": 1.0, "RORid": "https://ror.org/03265fv13"}]}
{"DOI": "10.1007/3-540-47984-8_14", "Matchings": [{"Confidence": 1.0, "RORid": "https://ror.org/00a0n9e72"}]}