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Code Issues Pull Requests Projects Releases Wiki Activity

refactoring

This commit is contained in:
Miriam Baglioni 2023-10-09 14:52:17 +02:00
parent 8448b9ebfb
commit a3d01ccb24
21 changed files with 268 additions and 239 deletions
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2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java
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@ -7,7 +7,6 @@ import java.io.IOException;
import java.io.Serializable;
import java.util.*;
import eu.dnetlib.dhp.schema.oaf.utils.*;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
@ -30,6 +29,7 @@ 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.*;
import eu.dnetlib.dhp.schema.oaf.utils.*;
import eu.dnetlib.dhp.utils.DHPUtils;
import scala.Tuple2;

10
dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
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@ -33,15 +33,15 @@ case class mappingAuthor(
case class funderInfo(id: String, uri: String, name: String, synonym: List[String]) {}
case class mappingFunder(name: String, DOI: Option[String], award: Option[List[String]]) {}
case object Crossref2Oaf {
val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
val irishFunder: List[funderInfo] = {
val s = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref/irish_funder.json")).mkString
val s = Source
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/crossref/irish_funder.json"))
.mkString
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: org.json4s.JValue = parse(s)
json.extract[List[funderInfo]]
@ -102,7 +102,9 @@ case object Crossref2Oaf {
def getIrishId(doi: String): Option[String] = {
val id = doi.split("/").last
irishFunder.find(f => id.equalsIgnoreCase(f.id) || (f.synonym.nonEmpty && f.synonym.exists(s => s.equalsIgnoreCase(id)))).map(f => f.id)
irishFunder
.find(f => id.equalsIgnoreCase(f.id) || (f.synonym.nonEmpty && f.synonym.exists(s => s.equalsIgnoreCase(id))))
.map(f => f.id)
}
def mappingResult(result: Result, json: JValue, cobjCategory: String): Result = {

1
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/QueryCommunityAPI.java
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@ -74,5 +74,4 @@ public class QueryCommunityAPI {
return body;
}
}

50
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java
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@ -1,16 +1,6 @@
package eu.dnetlib.dhp.api;
import com.amazonaws.util.StringUtils;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Maps;
import eu.dnetlib.dhp.api.model.*;
import eu.dnetlib.dhp.bulktag.community.Community;
import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration;
import eu.dnetlib.dhp.bulktag.community.Provider;
import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
import eu.dnetlib.dhp.bulktag.criteria.VerbResolverFactory;
import javax.management.Query;
import java.io.IOException;
import java.io.Serializable;
import java.util.ArrayList;
@ -19,6 +9,19 @@ import java.util.Map;
import java.util.Objects;
import java.util.stream.Collectors;
import javax.management.Query;
import com.amazonaws.util.StringUtils;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Maps;
import eu.dnetlib.dhp.api.model.*;
import eu.dnetlib.dhp.bulktag.community.Community;
import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration;
import eu.dnetlib.dhp.bulktag.community.Provider;
import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
import eu.dnetlib.dhp.bulktag.criteria.VerbResolverFactory;
/**
* @author miriam.baglioni
* @Date 09/10/23
@ -33,7 +36,8 @@ public class Utils implements Serializable {
getValidCommunities()
.forEach(community -> {
try {
CommunityModel cm = MAPPER.readValue(QueryCommunityAPI.community(community.getId()), CommunityModel.class);
CommunityModel cm = MAPPER
.readValue(QueryCommunityAPI.community(community.getId()), CommunityModel.class);
validCommunities.add(getCommunity(cm));
} catch (IOException e) {
throw new RuntimeException(e);
@ -41,7 +45,8 @@ public class Utils implements Serializable {
});
validCommunities.forEach(community -> {
try {
DatasourceList dl = MAPPER.readValue(QueryCommunityAPI.communityDatasource(community.getId()), DatasourceList.class);
DatasourceList dl = MAPPER
.readValue(QueryCommunityAPI.communityDatasource(community.getId()), DatasourceList.class);
community.setProviders(dl.stream().map(d -> {
// if(d.getEnabled() == null || Boolean.FALSE.equals(d.getEnabled()))
// return null;
@ -85,19 +90,23 @@ public class Utils implements Serializable {
}
public static List<CommunityModel> getValidCommunities() throws IOException {
return MAPPER.readValue(QueryCommunityAPI.communities(), CommunitySummary.class)
return MAPPER
.readValue(QueryCommunityAPI.communities(), CommunitySummary.class)
.stream()
.filter(community -> !community.getStatus().equals("hidden") &&
.filter(
community -> !community.getStatus().equals("hidden") &&
(community.getType().equals("ri") || community.getType().equals("community")))
.collect(Collectors.toList());
}
public static CommunityEntityMap getCommunityOrganization() throws IOException {
CommunityEntityMap organizationMap = new CommunityEntityMap();
getValidCommunities()
.forEach(community -> {
String id = community.getId();
try {
List<String> associatedOrgs = MAPPER.readValue(QueryCommunityAPI.communityPropagationOrganization(id), OrganizationList.class);
List<String> associatedOrgs = MAPPER
.readValue(QueryCommunityAPI.communityPropagationOrganization(id), OrganizationList.class);
if (associatedOrgs.size() > 0) {
organizationMap.put(id, associatedOrgs);
}
@ -119,11 +128,14 @@ public class Utils implements Serializable {
do {
page++;
try {
cm = MAPPER.readValue( QueryCommunityAPI.communityProjects(community.getId(), String.valueOf(page), String.valueOf(size)), ContentModel.class);
cm = MAPPER
.readValue(
QueryCommunityAPI
.communityProjects(community.getId(), String.valueOf(page), String.valueOf(size)),
ContentModel.class);
if (cm.getContent().size() > 0) {
cm.getContent().forEach(p ->
projectList.add ("40|" + p.getOpenaireId()));
cm.getContent().forEach(p -> projectList.add("40|" + p.getOpenaireId()));
projectMap.put(community.getId(), projectList);
}
} catch (IOException e) {

4
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityContentprovider.java
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@ -1,10 +1,11 @@
package eu.dnetlib.dhp.api.model;
import com.fasterxml.jackson.annotation.JsonAutoDetect;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.google.gson.Gson;
import eu.dnetlib.dhp.bulktag.community.SelectionConstraints;
import eu.dnetlib.dhp.bulktag.community.SelectionConstraints;
@JsonAutoDetect
@JsonIgnoreProperties(ignoreUnknown = true)
@ -30,7 +31,6 @@ public class CommunityContentprovider {
this.openaireId = openaireId;
}
public SelectionConstraints getSelectioncriteria() {
return this.selectioncriteria;

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityModel.java
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@ -5,8 +5,8 @@ import java.io.Serializable;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import eu.dnetlib.dhp.bulktag.community.SelectionConstraints;
import eu.dnetlib.dhp.bulktag.community.SelectionConstraints;
/**
* @author miriam.baglioni

3
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunitySummary.java
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@ -1,3 +1,4 @@
package eu.dnetlib.dhp.api.model;
import java.io.Serializable;
@ -12,5 +13,3 @@ public class CommunitySummary extends ArrayList<CommunityModel> implements Seria
super();
}
}

5
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/ContentModel.java
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@ -1,10 +1,11 @@
package eu.dnetlib.dhp.api.model;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
package eu.dnetlib.dhp.api.model;
import java.io.Serializable;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
/**
* @author miriam.baglioni
* @Date 09/10/23

7
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/DatasourceList.java
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@ -1,10 +1,11 @@
package eu.dnetlib.dhp.api.model;
import eu.dnetlib.dhp.api.model.CommunityContentprovider;
import java.io.Serializable;
import java.util.ArrayList;
import eu.dnetlib.dhp.api.model.CommunityContentprovider;
public class DatasourceList extends ArrayList<CommunityContentprovider> implements Serializable {
public DatasourceList() {
super();

1
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/OrganizationList.java
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@ -1,3 +1,4 @@
package eu.dnetlib.dhp.api.model;
import java.io.Serializable;

5
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/ProjectModel.java
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@ -1,9 +1,10 @@
package eu.dnetlib.dhp.api.model;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import java.io.Serializable;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
/**
* @author miriam.baglioni
* @Date 09/10/23

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java
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@ -6,7 +6,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.*;
import eu.dnetlib.dhp.api.Utils;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
@ -21,6 +20,7 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
import eu.dnetlib.dhp.api.Utils;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.bulktag.community.*;
import eu.dnetlib.dhp.schema.oaf.Datasource;

1
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Community.java
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@ -8,7 +8,6 @@ import java.util.Optional;
import com.google.gson.Gson;
/** Created by miriam on 01/08/2018. */
public class Community implements Serializable {

1
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java
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@ -5,6 +5,7 @@ import java.io.StringReader;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

5
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java
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@ -4,9 +4,10 @@ package eu.dnetlib.dhp.bulktag.community;
import java.io.Serializable;
import java.lang.reflect.InvocationTargetException;
import org.apache.htrace.fasterxml.jackson.annotation.JsonIgnore;
import eu.dnetlib.dhp.bulktag.criteria.Selection;
import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
import org.apache.htrace.fasterxml.jackson.annotation.JsonIgnore;
public class Constraint implements Serializable {
private String verb;
@ -39,6 +40,7 @@ public class Constraint implements Serializable {
public void setValue(String value) {
this.value = value;
}
//@JsonIgnore
// public void setSelection(Selection sel) {
// selection = sel;
@ -54,5 +56,4 @@ public class Constraint implements Serializable {
return selection.apply(metadata);
}
}

1
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/SelectionConstraints.java
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@ -12,6 +12,7 @@ import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken;
import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
@JsonAutoDetect
public class SelectionConstraints implements Serializable {
private List<Constraints> criteria;

4
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java
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@ -6,8 +6,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.util.*;
import eu.dnetlib.dhp.api.Utils;
import eu.dnetlib.dhp.api.model.CommunityEntityMap;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
@ -20,6 +18,8 @@ import org.slf4j.LoggerFactory;
import com.google.gson.Gson;
import eu.dnetlib.dhp.api.Utils;
import eu.dnetlib.dhp.api.model.CommunityEntityMap;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Relation;

45
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/QueryCommunityAPITest.java
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@ -1,14 +1,8 @@
package eu.dnetlib.dhp.bulktag;
import eu.dnetlib.dhp.api.Utils;
import eu.dnetlib.dhp.api.model.CommunityEntityMap;
import eu.dnetlib.dhp.bulktag.community.Community;
import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration;
import java.util.List;
import eu.dnetlib.dhp.api.model.CommunityModel;
import eu.dnetlib.dhp.api.model.CommunitySummary;
import eu.dnetlib.dhp.api.model.DatasourceList;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
@ -16,8 +10,13 @@ import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.api.QueryCommunityAPI;
import java.util.List;
import eu.dnetlib.dhp.api.Utils;
import eu.dnetlib.dhp.api.model.CommunityEntityMap;
import eu.dnetlib.dhp.api.model.CommunityModel;
import eu.dnetlib.dhp.api.model.CommunitySummary;
import eu.dnetlib.dhp.api.model.DatasourceList;
import eu.dnetlib.dhp.bulktag.community.Community;
import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration;
/**
* @author miriam.baglioni
@ -43,9 +42,12 @@ public class QueryCommunityAPITest {
void community() throws Exception {
String id = "dh-ch";
String body = QueryCommunityAPI.community(id);
System.out.println(new ObjectMapper().writeValueAsString(new ObjectMapper()
.readValue(body, CommunityModel.class)))
;
System.out
.println(
new ObjectMapper()
.writeValueAsString(
new ObjectMapper()
.readValue(body, CommunityModel.class)));
}
@Test
@ -73,10 +75,15 @@ public class QueryCommunityAPITest {
Assertions.assertEquals(null, community.getConstraints());
Assertions.assertEquals(null, community.getRemoveConstraints());
Assertions.assertEquals(2, community.getZenodoCommunities().size());
Assertions.assertTrue(community.getZenodoCommunities().stream().anyMatch(c -> c.equals("aurora-universities-network")));
Assertions.assertTrue(community.getZenodoCommunities().stream().anyMatch(c -> c.equals("university-of-innsbruck")));
Assertions
.assertTrue(
community.getZenodoCommunities().stream().anyMatch(c -> c.equals("aurora-universities-network")));
Assertions
.assertTrue(community.getZenodoCommunities().stream().anyMatch(c -> c.equals("university-of-innsbruck")));
Assertions.assertEquals(35, community.getProviders().size());
Assertions.assertEquals(35, community.getProviders().stream().filter(p->p.getSelectionConstraints()==null).count());
Assertions
.assertEquals(
35, community.getProviders().stream().filter(p -> p.getSelectionConstraints() == null).count());
}
@Test
@ -84,8 +91,12 @@ public class QueryCommunityAPITest {
CommunityEntityMap projectMap = Utils.getCommunityProjects();
Assertions.assertFalse(projectMap.containsKey("mes"));
Assertions.assertEquals(33, projectMap.size());
Assertions.assertTrue(projectMap.keySet().stream().allMatch(k -> projectMap.get(k).stream().allMatch(p -> p.startsWith("40|"))));
Assertions
.assertTrue(
projectMap
.keySet()
.stream()
.allMatch(k -> projectMap.get(k).stream().allMatch(p -> p.startsWith("40|"))));
}
}