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65 Commits

Author SHA1 Message Date
Miriam Baglioni 8981a82011 - 2021-04-23 11:55:20 +02:00
Miriam Baglioni eb0762622c added decision node to upload on zenodo or not 2021-04-23 11:54:54 +02:00
Miriam Baglioni a469d79b84 test for the creation of relationships between context and projects when the funding contains h2020 2021-04-23 11:52:27 +02:00
Miriam Baglioni 251178aca8 the new json schema for the result 2021-04-23 11:51:27 +02:00
Miriam Baglioni 7cf1f49d5e if the funding does not start with H2020 but contains it the nsp should be corda__h2020 2021-04-23 11:50:26 +02:00
Miriam Baglioni 7465fa3f20 dumping only the communities with status "all". We decided those with status manager wil be available on demand 2021-04-23 11:49:45 +02:00
Miriam Baglioni bc501f41f6 added test class for community removal from the set to be dumped 2021-04-13 16:40:24 +02:00
Miriam Baglioni 80a7170794 - 2021-04-13 16:39:55 +02:00
Miriam Baglioni 08e731916b removed parameter communityMap when sending data to Zenodo 2021-04-13 16:38:59 +02:00
Miriam Baglioni 50d13a1d74 changed the workflow for the dump of a single community 2021-04-13 16:33:00 +02:00
Miriam Baglioni 8c4c74a640 changed logic to be able to create a dump for a single community at a time 2021-04-13 16:32:19 +02:00
Miriam Baglioni 6179deb836 removed the part after part-x- in the file name generated by spark. It was too long and created problems while creating the tar entries 2021-04-13 16:30:59 +02:00
Miriam Baglioni 04a0d1ba6e added test method to check the creation of relations between context and projects 2021-04-09 12:49:51 +02:00
Miriam Baglioni 6b51b69cf7 added the creation of the openaireId from funder and grant number if the element is not present in the context profile 2021-04-09 12:49:07 +02:00
Miriam Baglioni bd4b6b053d changed classid with classname in the construction of provenance for the dump 2021-04-09 12:48:09 +02:00
Miriam Baglioni 26b34201ec refactoring 2021-04-09 12:47:03 +02:00
Miriam Baglioni 3d94c12d6e refactoring 2021-04-09 12:45:45 +02:00
Miriam Baglioni 95c5f97259 added the part for the extraction of relations versus projects 2021-04-09 11:31:37 +02:00
Miriam Baglioni eaf86828e6 refactoring 2021-04-09 11:30:30 +02:00
Miriam Baglioni c58206c3ba added test for the creation of relations with funders 2021-04-09 11:30:07 +02:00
Miriam Baglioni 3e3a45d930 refactoring 2021-04-08 10:44:37 +02:00
Miriam Baglioni 46a322b770 changed the name of originalId in acronym 2021-04-08 10:40:06 +02:00
Miriam Baglioni f95ec49a59 changed the substring to be pk for communities of arbitrary name length 2021-04-07 13:22:54 +02:00
Miriam Baglioni c52355b516 refactoring 2021-04-07 12:13:45 +02:00
Miriam Baglioni e1af14833d refactoring 2021-04-07 12:13:00 +02:00
Miriam Baglioni 22f4930479 refactoring 2021-04-07 12:12:04 +02:00
Miriam Baglioni 7f9b7cfcf6 removing from the dump organization that have been deleted by inference 2021-04-07 12:11:36 +02:00
Miriam Baglioni 66d64947af merge branch with master 2021-04-07 10:38:18 +02:00
Miriam Baglioni ad6d0ca9eb added to all the entities the check that deletedbyinference = false 2021-04-07 10:37:49 +02:00
Miriam Baglioni 26cf32c066 changed the test to mirror the change in the logic of the code 2021-04-01 18:22:57 +02:00
Miriam Baglioni 5022f1b50d removing organization deletedbyinference from the dump 2021-04-01 18:16:40 +02:00
Miriam Baglioni 0421f5e1d8 added check to verify not to add void APC 2021-04-01 17:38:30 +02:00
Miriam Baglioni 2c209e1140 added resources for testing selection of valid relations 2021-04-01 16:57:34 +02:00
Miriam Baglioni b3f02083e7 refactoring 2021-04-01 16:56:58 +02:00
Miriam Baglioni 8d28ca9815 added test class for the selection of valid relations 2021-04-01 16:56:32 +02:00
Miriam Baglioni 152ba8e2ef added description 2021-04-01 16:55:57 +02:00
Miriam Baglioni c0c225f3b2 added logic to select only the valid relations: those not deletedbyinference and having both part of the relation as entities in the graph 2021-04-01 16:53:33 +02:00
Miriam Baglioni daabc370c5 changed the workflow to add the step for selecting the valid relations 2021-04-01 16:52:39 +02:00
Miriam Baglioni f93356f690 refactoring 2021-04-01 16:24:08 +02:00
Miriam Baglioni f7714645d2 merge with dump 2021-03-30 16:27:38 +02:00
Miriam Baglioni 4632795f25 merge branch with master 2021-03-30 16:27:23 +02:00
Miriam Baglioni 870ee28dd6 refactoring 2021-03-30 12:55:48 +02:00
Miriam Baglioni 08f8dd9454 refactoring 2021-03-30 12:53:07 +02:00
Miriam Baglioni e5463fea01 added resource for apc dump 2021-03-30 12:47:07 +02:00
Miriam Baglioni 16c1a27852 added test for APC dump 2021-03-30 12:46:42 +02:00
Miriam Baglioni d0c94462e4 refactoring 2021-03-30 12:45:34 +02:00
Miriam Baglioni a896febc02 added APC in the dumped information 2021-03-30 11:13:07 +02:00
Miriam Baglioni 5dea729de3 added article processing charges and modified description 2021-03-30 10:49:39 +02:00
Miriam Baglioni 200e7e9c46 modified description 2021-03-30 10:49:15 +02:00
Miriam Baglioni 931b2a2e15 merge branch with master 2021-03-30 10:27:32 +02:00
Miriam Baglioni 330343937c - 2021-02-24 12:49:27 +01:00
Miriam Baglioni defbb71561 extended resource info to match the new test 2021-02-24 11:52:44 +01:00
Miriam Baglioni 17049f8bde extended the test class - should have done by the start :) 2021-02-24 11:52:07 +01:00
Miriam Baglioni cc11ee1cb9 changed the param value to directly upload on Zenodo 2021-02-24 11:51:40 +01:00
Miriam Baglioni 871e5bea29 should have fixed for real now 2021-02-24 11:51:20 +01:00
Miriam Baglioni 5d92df0627 tried again to fix issue for croatian funder 2021-02-24 10:49:55 +01:00
Miriam Baglioni 9841086ef3 modified code to split the Croazian funders 2021-02-23 18:09:14 +01:00
Miriam Baglioni d4ad740c98 merge branch with master 2021-02-23 11:10:41 +01:00
Miriam Baglioni a684e1065e merge branch with master 2021-02-23 10:45:42 +01:00
Miriam Baglioni f7c35e6311 merge branch with master 2021-02-08 10:39:10 +01:00
Miriam Baglioni 9bdadd4ddb merge branch with master 2021-01-22 11:55:27 +01:00
Miriam Baglioni 0d76e039cf changed to logic to verify in community is contained in the list of context of a result 2020-12-16 10:53:10 +01:00
Miriam Baglioni 7c86e66697 merge branch with master 2020-12-16 10:51:18 +01:00
Miriam Baglioni bc09d37e8c used constants in ModelConstants class 2020-12-10 10:01:23 +01:00
Miriam Baglioni 815c7c11aa merge branch with master 2020-12-03 11:28:01 +01:00
47 changed files with 1054 additions and 93 deletions

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@ -90,6 +90,13 @@ public class MakeTarArchive implements Serializable {
String p_string = p.toString();
if (!p_string.endsWith("_SUCCESS")) {
String name = p_string.substring(p_string.lastIndexOf("/") + 1);
if (name.startsWith("part-") & name.length() > 10) {
String tmp = name.substring(0, 10);
if (name.contains(".")) {
tmp += name.substring(name.indexOf("."));
}
name = tmp;
}
TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name);
entry.setSize(fileStatus.getLen());
current_size += fileStatus.getLen();

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@ -4,7 +4,7 @@ package eu.dnetlib.dhp.schema.dump.oaf;
import java.io.Serializable;
/**
* Used to refer to the Article Processing Charge information. Not dumped in this release. It contains two parameters: -
* Used to refer to the Article Processing Charge information. It contains two parameters: -
* currency of type String to store the currency of the APC - amount of type String to stores the charged amount
*/
public class APC implements Serializable {

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@ -12,9 +12,11 @@ import java.util.List;
* type of type String to store the type of the instance as defined in the corresponding dnet vocabulary
* (dnet:pubication_resource). It corresponds to the instancetype.classname of the instance to be mapped - url of type
* List<String> list of locations where the instance is accessible. It corresponds to url of the instance to be dumped -
* publicationdate of type String to store the publication date of the instance ;// dateofacceptance; - refereed of type
* String to store information abour tthe review status of the instance. Possible values are 'Unknown',
* publicationdate of type String to store the publication date of the instance ;// dateofacceptance;
* - refereed of type
* String to store information abour the review status of the instance. Possible values are 'Unknown',
* 'nonPeerReviewed', 'peerReviewed'. It corresponds to refereed.classname of the instance to be dumped
* - articleprocessingcharge of type APC to store the article processing charges possibly associated to the instance
*/
public class Instance implements Serializable {
@ -28,6 +30,8 @@ public class Instance implements Serializable {
private String publicationdate;// dateofacceptance;
private APC articleprocessingcharge;
private String refereed; // peer-review status
public String getLicense() {
@ -78,4 +82,11 @@ public class Instance implements Serializable {
this.refereed = refereed;
}
public APC getArticleprocessingcharge() {
return articleprocessingcharge;
}
public void setArticleprocessingcharge(APC articleprocessingcharge) {
this.articleprocessingcharge = articleprocessingcharge;
}
}

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@ -19,7 +19,7 @@ import java.io.Serializable;
*/
public class ResearchInitiative implements Serializable {
private String id; // openaireId
private String originalId; // context id
private String acronym; // context id
private String name; // context name
private String type; // context type: research initiative or research community
private String description;
@ -57,12 +57,12 @@ public class ResearchInitiative implements Serializable {
this.name = label;
}
public String getOriginalId() {
return originalId;
public String getAcronym() {
return acronym;
}
public void setOriginalId(String originalId) {
this.originalId = originalId;
public void setAcronym(String acronym) {
this.acronym = acronym;
}
public String getDescription() {

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@ -1,8 +1,6 @@
package eu.dnetlib.dhp.schema.oaf;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import static com.google.common.base.Preconditions.checkArgument;
import java.text.ParseException;
@ -10,6 +8,8 @@ import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import eu.dnetlib.dhp.schema.common.ModelSupport;
/**
* Relation models any edge between two nodes in the OpenAIRE graph. It has a source id and a target id pointing to
* graph node identifiers and it is further characterised by the semantic of the link through the fields relType,
@ -137,7 +137,10 @@ public class Relation extends Oaf {
try {
setValidationDate(ModelSupport.oldest(getValidationDate(), r.getValidationDate()));
} catch (ParseException e) {
throw new IllegalArgumentException(String.format("invalid validation date format in relation [s:%s, t:%s]: %s", getSource(), getTarget(), getValidationDate()));
throw new IllegalArgumentException(String
.format(
"invalid validation date format in relation [s:%s, t:%s]: %s", getSource(), getTarget(),
getValidationDate()));
}
super.mergeFrom(r);

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@ -4,6 +4,11 @@ package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf;
@ -22,11 +27,6 @@ import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.Relation;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
public class PrepareResultInstRepoAssociation {
private static final Logger log = LoggerFactory.getLogger(PrepareResultInstRepoAssociation.class);
@ -56,9 +56,10 @@ public class PrepareResultInstRepoAssociation {
final String alreadyLinkedPath = parser.get("alreadyLinkedPath");
log.info("alreadyLinkedPath {}: ", alreadyLinkedPath);
List<String> blacklist = Optional.ofNullable(parser.get("blacklist"))
.map(v -> Arrays.asList(v.split(";")))
.orElse(new ArrayList<>());
List<String> blacklist = Optional
.ofNullable(parser.get("blacklist"))
.map(v -> Arrays.asList(v.split(";")))
.orElse(new ArrayList<>());
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
@ -91,14 +92,13 @@ public class PrepareResultInstRepoAssociation {
private static void prepareDatasourceOrganization(
SparkSession spark, String datasourceOrganizationPath, List<String> blacklist) {
String blacklisted = "";
if(blacklist.size() > 0 ){
if (blacklist.size() > 0) {
blacklisted = " AND d.id != '" + blacklist.get(0) + "'";
for (int i = 1; i < blacklist.size(); i++) {
blacklisted += " AND d.id != '" + blacklist.get(i) + "'";
}
}
String query = "SELECT source datasourceId, target organizationId "
+ "FROM ( SELECT id "
+ "FROM datasource "

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@ -24,8 +24,6 @@ public class Constants {
public static String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative";
public static String ORCID = "orcid";
static {
accessRightsCoarMap.put("OPEN", "c_abf2");
accessRightsCoarMap.put("RESTRICTED", "c_16ec");

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@ -37,7 +37,8 @@ public class DumpProducts implements Serializable {
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
execDump(spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType);
execDump(
spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType);
});
}
@ -89,7 +90,7 @@ public class DumpProducts implements Serializable {
return c.getId();
}
if (c.getId().contains("::") && communities.contains(c.getId().substring(0, c.getId().indexOf("::")))) {
return c.getId().substring(0, 3);
return c.getId().substring(0, c.getId().indexOf("::"));
}
return null;
}).filter(Objects::nonNull).collect(Collectors.toList());

View File

@ -20,7 +20,7 @@ public class QueryInformationSystem {
private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "
+
" where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " +
" and ($x//context/param[./@name = 'status']/text() = 'manager' or $x//context/param[./@name = 'status']/text() = 'all') "
" and ($x//context/param[./@name = 'status']/text() = 'all') "
+
" return " +
"<community> " +

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@ -424,6 +424,19 @@ public class ResultMapper implements Serializable {
.ifPresent(value -> instance.setType(value.getClassname()));
Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value));
Optional<Field<String>> oPca = Optional.ofNullable(i.getProcessingchargeamount());
Optional<Field<String>> oPcc = Optional.ofNullable(i.getProcessingchargecurrency());
if (oPca.isPresent() && oPcc.isPresent()) {
Field<String> pca = oPca.get();
Field<String> pcc = oPcc.get();
if (!pca.getValue().trim().equals("") && !pcc.getValue().trim().equals("")) {
APC apc = new APC();
apc.setCurrency(oPcc.get().getValue());
apc.setAmount(oPca.get().getValue());
instance.setArticleprocessingcharge(apc);
}
}
}
private static List<Provenance> getUniqueProvenance(List<Provenance> provenance) {
@ -503,7 +516,7 @@ public class ResultMapper implements Serializable {
private static Pid getOrcid(List<StructuredProperty> p) {
for (StructuredProperty pid : p) {
if (pid.getQualifier().getClassid().equals(Constants.ORCID)) {
if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID)) {
Optional<DataInfo> di = Optional.ofNullable(pid.getDataInfo());
if (di.isPresent()) {
return Pid

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@ -1,6 +1,7 @@
package eu.dnetlib.dhp.oa.graph.dump;
import java.io.IOException;
import java.io.Serializable;
import java.util.Optional;
@ -9,6 +10,7 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.*;
import org.jetbrains.annotations.NotNull;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.api.MissingConceptDoiException;
@ -48,15 +50,12 @@ public class SendToZenodoHDFS implements Serializable {
.orElse(false);
final String depositionId = Optional.ofNullable(parser.get("depositionId")).orElse(null);
final String communityMapPath = parser.get("communityMapPath");
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf);
CommunityMap communityMap = Utils.readCommunityMap(fileSystem, communityMapPath);
RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
.listFiles(
new Path(hdfsPath), true);
@ -87,11 +86,6 @@ public class SendToZenodoHDFS implements Serializable {
if (!p_string.endsWith("_SUCCESS")) {
// String tmp = p_string.substring(0, p_string.lastIndexOf("/"));
String name = p_string.substring(p_string.lastIndexOf("/") + 1);
log.info("Sending information for community: " + name);
if (communityMap.containsKey(name.substring(0, name.lastIndexOf(".")))) {
name = communityMap.get(name.substring(0, name.lastIndexOf("."))).replace(" ", "_") + ".tar";
}
FSDataInputStream inputStream = fileSystem.open(p);
zenodoApiClient.uploadIS(inputStream, name, fileStatus.getLen());

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@ -34,12 +34,14 @@ public class CommunitySplit implements Serializable {
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
execSplit(spark, inputPath, outputPath, Utils.getCommunityMap(spark, communityMapPath).keySet());
CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath);
execSplit(spark, inputPath, outputPath, communityMap);
});
}
private static void execSplit(SparkSession spark, String inputPath, String outputPath,
Set<String> communities) {
CommunityMap communities) {
Dataset<CommunityResult> result = Utils
.readPath(spark, inputPath + "/publication", CommunityResult.class)
@ -48,8 +50,9 @@ public class CommunitySplit implements Serializable {
.union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class));
communities
.keySet()
.stream()
.forEach(c -> printResult(c, result, outputPath));
.forEach(c -> printResult(c, result, outputPath + "/" + communities.get(c).replace(" ", "_")));
}
@ -57,16 +60,11 @@ public class CommunitySplit implements Serializable {
Dataset<CommunityResult> community_products = result
.filter((FilterFunction<CommunityResult>) r -> containsCommunity(r, c));
try {
community_products.first();
community_products
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputPath + "/" + c);
} catch (Exception e) {
}
community_products
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputPath);
}
@ -75,9 +73,9 @@ public class CommunitySplit implements Serializable {
return r
.getContext()
.stream()
.filter(con -> con.getCode().equals(c))
.map(con -> con.getCode())
.collect(Collectors.toList())
.size() > 0;
.contains(c);
}
return false;
}

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@ -0,0 +1,85 @@
package eu.dnetlib.dhp.oa.graph.dump.community;
import java.io.*;
import java.nio.charset.StandardCharsets;
import java.util.Objects;
import java.util.Set;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class RemoveCommunities implements Serializable {
private static final Logger log = LoggerFactory.getLogger(RemoveCommunities.class);
private final static ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private final Configuration conf;
private final BufferedWriter writer;
private final CommunityMap communityMap;
public RemoveCommunities(String path, String hdfsNameNode) throws IOException {
conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf);
Path hdfsPath = new Path(path);
// FSDataInputStream p = fileSystem.open(hdfsPath);
// ObjectMapper mapper = new ObjectMapper();
communityMap = OBJECT_MAPPER.readValue((InputStream) fileSystem.open(hdfsPath), CommunityMap.class);
FSDataOutputStream fsDataOutputStream = null;
if (fileSystem.exists(hdfsPath)) {
fileSystem.delete(hdfsPath);
}
fsDataOutputStream = fileSystem.create(hdfsPath);
writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
}
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
RemoveCommunities.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_rc_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
final String nameNode = parser.get("nameNode");
log.info("nameNode: {}", nameNode);
final String outputPath = parser.get("path");
log.info("outputPath: {}", outputPath);
final String communityId = parser.get("communityId");
final RemoveCommunities scm = new RemoveCommunities(outputPath, nameNode);
scm.removeCommunities(communityId);
}
private void removeCommunities(String communityId) throws IOException {
Set<String> toRemove = communityMap.keySet().stream().map(key -> {
if (key.equals(communityId))
return null;
return key;
}).filter(Objects::nonNull).collect(Collectors.toSet());
toRemove.forEach(key -> communityMap.remove(key));
writer.write(OBJECT_MAPPER.writeValueAsString(communityMap));
writer.close();
}
}

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@ -70,10 +70,10 @@ public class CreateContextRelation implements Serializable {
cce.execute(Process::getRelation, CONTEX_RELATION_DATASOURCE, ModelSupport.getIdPrefix(Datasource.class));
log.info("Creating relations for projects... ");
// cce
// .execute(
// Process::getRelation, CONTEX_RELATION_PROJECT,
// ModelSupport.getIdPrefix(eu.dnetlib.dhp.schema.oaf.Project.class));
cce
.execute(
Process::getRelation, CONTEX_RELATION_PROJECT,
ModelSupport.getIdPrefix(eu.dnetlib.dhp.schema.oaf.Project.class));
cce.close();

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@ -9,6 +9,7 @@ import java.util.*;
import java.util.stream.Collectors;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
@ -453,6 +454,7 @@ public class DumpGraphEntities implements Serializable {
.map(
(MapFunction<E, Organization>) o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o),
Encoders.bean(Organization.class))
.filter((FilterFunction<Organization>) o -> o != null)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
@ -461,6 +463,8 @@ public class DumpGraphEntities implements Serializable {
private static Organization mapOrganization(eu.dnetlib.dhp.schema.oaf.Organization org) {
Organization organization = new Organization();
if (org.getDataInfo().getDeletedbyinference())
return null;
Optional
.ofNullable(org.getLegalshortname())

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@ -147,7 +147,7 @@ public class Extractor implements Serializable {
.map(
paction -> Provenance
.newInstance(
paction.getClassid(),
paction.getClassname(),
dinfo.getTrust()))
.orElse(
Provenance

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@ -35,7 +35,7 @@ public class Process implements Serializable {
ri.setType(Constants.RESEARCH_INFRASTRUCTURE);
}
ri.setId(Utils.getContextId(ci.getId()));
ri.setOriginalId(ci.getId());
ri.setAcronym(ci.getId());
ri.setDescription(ci.getDescription());
ri.setName(ci.getName());

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@ -12,6 +12,7 @@ import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import org.jetbrains.annotations.NotNull;
import eu.dnetlib.dhp.utils.DHPUtils;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ -113,14 +114,72 @@ public class QueryInformationSystem {
@NotNull
private List<String> getCategoryList(Element el, String prefix) {
List<String> datasourceList = new ArrayList<>();
for (Object node : el.selectNodes(".//param")) {
Node n = (Node) node;
if (n.valueOf("./@name").equals("openaireId")) {
datasourceList.add(prefix + "|" + n.getText());
}
for (Object node : el.selectNodes(".//concept")) {
String oid = getOpenaireId((Node) node, prefix);
if (oid != null)
datasourceList.add(oid);
}
return datasourceList;
}
private String getOpenaireId(Node el, String prefix) {
for (Object node : el.selectNodes(".//param")) {
Node n = (Node) node;
if (n.valueOf("./@name").equals("openaireId")) {
return prefix + "|" + n.getText();
}
}
return makeOpenaireId(el, prefix);
}
private String makeOpenaireId(Node el, String prefix) {
String funder = null;
String grantId = null;
String funding = null;
for (Object node : el.selectNodes(".//param")) {
Node n = (Node) node;
switch (n.valueOf("./@name")) {
case "funding":
funding = n.getText();
break;
case "funder":
funder = n.getText();
break;
case "CD_PROJECT_NUMBER":
grantId = n.getText();
break;
}
}
String nsp = null;
switch (funder.toLowerCase()) {
case "ec":
if (funding == null) {
return null;
}
if (funding.toLowerCase().contains("h2020")) {
nsp = "corda__h2020::";
} else {
nsp = "corda_______::";
}
break;
case "tubitak":
nsp = "tubitakf____::";
break;
case "dfg":
nsp = "dfgf________::";
break;
default:
nsp = funder.toLowerCase();
for (int i = funder.length(); i < 12; i++)
nsp += "_";
nsp += "::";
}
return prefix + "|" + nsp + DHPUtils.md5(grantId);
}
}

View File

@ -0,0 +1,137 @@
package eu.dnetlib.dhp.oa.graph.dump.complete;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.oaf.*;
/**
* It selects the valid relations among those present in the graph. One relation is valid if it is not deletedbyinference
* and if both the source and the target node are present in the graph and are not deleted by inference nor invisible.
* To check this I made a view of the ids of all the entities in the graph, and select the relations for which a join exists
* with this view for both the source and the target
*/
public class SparkSelectValidRelationsJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkSelectValidRelationsJob.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkSelectValidRelationsJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/complete/input_relationdump_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 -> {
Utils.removeOutputDir(spark, outputPath);
selectValidRelation(spark, inputPath, outputPath);
});
}
private static void selectValidRelation(SparkSession spark, String inputPath, String outputPath) {
Dataset<Relation> relation = Utils.readPath(spark, inputPath + "/relation", Relation.class);
Dataset<Publication> publication = Utils.readPath(spark, inputPath + "/publication", Publication.class);
Dataset<eu.dnetlib.dhp.schema.oaf.Dataset> dataset = Utils
.readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class);
Dataset<Software> software = Utils.readPath(spark, inputPath + "/software", Software.class);
Dataset<OtherResearchProduct> other = Utils
.readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class);
Dataset<Organization> organization = Utils.readPath(spark, inputPath + "/organization", Organization.class);
Dataset<Project> project = Utils.readPath(spark, inputPath + "/project", Project.class);
Dataset<Datasource> datasource = Utils.readPath(spark, inputPath + "/datasource", Datasource.class);
relation.createOrReplaceTempView("relation");
publication.createOrReplaceTempView("publication");
dataset.createOrReplaceTempView("dataset");
other.createOrReplaceTempView("other");
software.createOrReplaceTempView("software");
organization.createOrReplaceTempView("organization");
project.createOrReplaceTempView("project");
datasource.createOrReplaceTempView("datasource");
spark
.sql(
"SELECT id " +
"FROM publication " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
"UNION ALL " +
"SELECT id " +
"FROM dataset " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
"UNION ALL " +
"SELECT id " +
"FROM other " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
"UNION ALL " +
"SELECT id " +
"FROM software " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
"UNION ALL " +
"SELECT id " +
"FROM organization " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
"UNION ALL " +
"SELECT id " +
"FROM project " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
"UNION ALL " +
"SELECT id " +
"FROM datasource " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false ")
.createOrReplaceTempView("identifiers");
spark
.sql(
"SELECT relation.* " +
"FROM relation " +
"JOIN identifiers i1 " +
"ON source = i1.id " +
"JOIN identifiers i2 " +
"ON target = i2.id " +
"WHERE datainfo.deletedbyinference = false")
.as(Encoders.bean(Relation.class))
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputPath);
;
}
}

View File

@ -102,19 +102,26 @@ public class SparkDumpFunderResults implements Serializable {
} else {
funderdump = fundernsp.substring(0, fundernsp.indexOf("_")).toUpperCase();
}
writeFunderResult(funder, result, outputPath + "/" + funderdump);
writeFunderResult(funder, result, outputPath, funderdump);
});
}
private static void writeFunderResult(String funder, Dataset<CommunityResult> results, String outputPath) {
private static void dumpResults(String nsp, Dataset<CommunityResult> results, String outputPath,
String funderName) {
results.map((MapFunction<CommunityResult, CommunityResult>) r -> {
if (!Optional.ofNullable(r.getProjects()).isPresent()) {
return null;
}
for (Project p : r.getProjects()) {
if (p.getId().startsWith(funder)) {
if (p.getId().startsWith(nsp)) {
if (nsp.startsWith("40|irb")) {
if (p.getFunder().getShortName().equals(funderName))
return r;
else
return null;
}
return r;
}
}
@ -124,7 +131,18 @@ public class SparkDumpFunderResults implements Serializable {
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
.json(outputPath + "/" + funderName);
}
private static void writeFunderResult(String funder, Dataset<CommunityResult> results, String outputPath,
String funderDump) {
if (funder.startsWith("40|irb")) {
dumpResults(funder, results, outputPath, "HRZZ");
dumpResults(funder, results, outputPath, "MZOS");
} else
dumpResults(funder, results, outputPath, funderDump);
}
}

View File

@ -1,6 +1,18 @@
<workflow-app name="dump_community_products" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>singleDeposition</name>
<description>Indicates if each file in the directory should be uploaded in a own deposition</description>
</property>
<property>
<name>upload</name>
<description>true if the dump should be upload in zenodo</description>
</property>
<property>
<name>communityId</name>
<description>the id of the community to be dumped if a dump for a single community should be done</description>
</property>
<property>
<name>sourcePath</name>
<description>the source path</description>
@ -123,6 +135,24 @@
<arg>--nameNode</arg><arg>${nameNode}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</java>
<ok to="single_deposition"/>
<error to="Kill"/>
</action>
<decision name="single_deposition">
<switch>
<case to="remove_communities">${wf:conf('singleDeposition') eq true}</case>
<default to="fork_dump"/>
</switch>
</decision>
<action name="remove_communities">
<java>
<main-class>eu.dnetlib.dhp.oa.graph.dump.community.RemoveCommunities</main-class>
<arg>--path</arg><arg>${workingDir}/communityMap</arg>
<arg>--nameNode</arg><arg>${nameNode}</arg>
<arg>--communityId</arg><arg>${communityId}</arg>
</java>
<ok to="fork_dump"/>
<error to="Kill"/>
</action>
@ -405,10 +435,16 @@
<arg>--nameNode</arg><arg>${nameNode}</arg>
<arg>--sourcePath</arg><arg>${workingDir}/split</arg>
</java>
<ok to="send_zenodo"/>
<ok to="should_upload"/>
<error to="Kill"/>
</action>
<decision name="should_upload">
<switch>
<case to="send_zenodo">${wf:conf('upload') eq true}</case>
<default to="End"/>
</switch>
</decision>
<action name="send_zenodo">
<java>
<main-class>eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS</main-class>
@ -417,7 +453,6 @@
<arg>--accessToken</arg><arg>${accessToken}</arg>
<arg>--connectionUrl</arg><arg>${connectionUrl}</arg>
<arg>--metadata</arg><arg>${metadata}</arg>
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
<arg>--conceptRecordId</arg><arg>${conceptRecordId}</arg>
<arg>--depositionId</arg><arg>${depositionId}</arg>
<arg>--depositionType</arg><arg>${depositionType}</arg>

View File

@ -148,7 +148,7 @@
<path start="dump_organization"/>
<path start="dump_project"/>
<path start="dump_datasource"/>
<path start="dump_relation"/>
<path start="select_relation"/>
</fork>
<action name="dump_publication">
@ -333,6 +333,30 @@
<error to="Kill"/>
</action>
<action name="select_relation">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Select valid table relation </name>
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkSelectValidRelationsJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${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>${sourcePath}</arg>
<arg>--outputPath</arg><arg>${workingDir}/validrelation</arg>
</spark>
<ok to="dump_relation"/>
<error to="Kill"/>
</action>
<action name="dump_relation">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
@ -350,7 +374,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
<arg>--sourcePath</arg><arg>${workingDir}/validrelation</arg>
<arg>--outputPath</arg><arg>${workingDir}/relation/relation</arg>
</spark>
<ok to="join_dump"/>
@ -572,7 +596,6 @@
<arg>--accessToken</arg><arg>${accessToken}</arg>
<arg>--connectionUrl</arg><arg>${connectionUrl}</arg>
<arg>--metadata</arg><arg>${metadata}</arg>
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
<arg>--conceptRecordId</arg><arg>${conceptRecordId}</arg>
<arg>--depositionType</arg><arg>${depositionType}</arg>
<arg>--depositionId</arg><arg>${depositionId}</arg>

View File

@ -1,6 +1,23 @@
{
"$schema": "http://json-schema.org/draft-07/schema#",
"definitions": {
"AccessRight":{
"type":"object",
"properties":{
"code": {
"type": "string",
"description": "COAR access mode code: http://vocabularies.coar-repositories.org/documentation/access_rights/"
},
"label": {
"type": "string",
"description": "Label for the access mode"
},
"scheme": {
"type": "string",
"description": "Scheme of reference for access right code. Always set to COAR access rights vocabulary: http://vocabularies.coar-repositories.org/documentation/access_rights/"
}
}
},
"ControlledField": {
"type": "object",
"properties": {
@ -266,6 +283,57 @@
]
}
},
"instance":{
"type":"array",
"items":{
"type":"object",
"properties":{
"accessright":{
"allOf":[
{
"$ref":"#/definitions/AccessRight"
},
{
"description":"The accessright of this materialization of the result"
}
]
},
"articleprocessingcharge":{
"type":"object",
"properties":{
"amount":{
"type":"string"
},
"currency":{
"type":"string"
}
}
},
"license":{
"type":"string"
},
"publicationdate":{
"type":"string"
},
"refereed":{
"type":"string"
},
"type":{
"type":"string",
"description":"The specific sub-type of this materialization of the result (see https://api.openaire.eu/vocabularies/dnet:result_typologies following the links)"
},
"url":{
"description":"Description of url",
"type":"array",
"items":{
"type":"string",
"description":"urls where it is possible to access the materialization of the result"
}
}
},
"description":"One of the materialization for this result"
}
},
"programmingLanguage": {
"type": "string",
"description": "Only for results with type 'software': the programming language"
@ -302,7 +370,7 @@
"subject": {
"allOf": [
{"$ref": "#/definitions/ControlledField"},
{"description": "OpenAIRE subject classification scheme (https://api.openaire.eu/vocabularies/dnet:subject_classification_typologies) and value. When the scheme is 'keyword', it means that the subject is free-text (i.e. not a term from a controlled vocabulary)."},
{"description": "OpenAIRE subject classification scheme (https://api.openaire.eu/vocabularies/dnet:subject_classification_typologies) and value. When the scheme is 'keyword', it means that the subject is free-text (i.e. not a term from a controlled vocabulary)."}
]
}
}

View File

@ -1,9 +1,8 @@
<workflow-app name="dump_funder_results" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>upload</name>
<value>false</value>
<value>true</value>
<description>true to upload the dump for the funders in Zenodo</description>
</property>
<property>
@ -549,7 +548,6 @@
<arg>--accessToken</arg><arg>${accessToken}</arg>
<arg>--connectionUrl</arg><arg>${connectionUrl}</arg>
<arg>--metadata</arg><arg>${metadata}</arg>
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
<arg>--conceptRecordId</arg><arg>${conceptRecordId}</arg>
<arg>--depositionType</arg><arg>${depositionType}</arg>
<arg>--depositionId</arg><arg>${depositionId}</arg>

View File

@ -35,7 +35,12 @@
"paramLongName":"dumpType",
"paramDescription": "the type of the dump (complete for the whole graph, community for the products related to communities, funder for the results with at least a link to project",
"paramRequired": false
}
}, {
"paramName":"cid",
"paramLongName":"communityId",
"paramDescription": "the id of the community to be dumped",
"paramRequired": false
}
]

View File

@ -0,0 +1,25 @@
[
{
"paramName":"ci",
"paramLongName":"communityId",
"paramDescription": "URL of the isLookUp Service",
"paramRequired": true
},
{
"paramName":"nn",
"paramLongName":"nameNode",
"paramDescription": "the name node",
"paramRequired": true
},
{
"paramName": "p",
"paramLongName": "path",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
}
]

View File

@ -25,6 +25,12 @@
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
},
{
"paramName": "cid",
"paramLongName": "communityId",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
}
]

View File

@ -12,12 +12,6 @@
"paramDescription": "The id of the concept record for a new version",
"paramRequired": false
},
{
"paramName":"cmp",
"paramLongName":"communityMapPath",
"paramDescription": "the path to the serialization of the community map",
"paramRequired": false
},
{
"paramName":"di",
"paramLongName":"depositionId",

View File

@ -13,6 +13,7 @@ import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.*;
import org.slf4j.Logger;
@ -408,4 +409,53 @@ public class DumpJobTest {
}
@Test
public void testArticlePCA() {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_pca")
.getPath();
final String communityMapPath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
.getPath();
DumpProducts dump = new DumpProducts();
dump
.run(
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType());
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<GraphResult> tmp = sc
.textFile(workingDir.toString() + "/result")
.map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class));
org.apache.spark.sql.Dataset<GraphResult> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(GraphResult.class));
Assertions.assertEquals(23, verificationDataset.count());
// verificationDataset.show(false);
Assertions.assertEquals(23, verificationDataset.filter("type = 'publication'").count());
verificationDataset.createOrReplaceTempView("check");
org.apache.spark.sql.Dataset<Row> temp = spark
.sql(
"select id " +
"from check " +
"lateral view explode (instance) i as inst " +
"where inst.articleprocessingcharge is not null");
Assertions.assertTrue(temp.count() == 2);
Assertions.assertTrue(temp.filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'").count() == 1);
Assertions.assertTrue(temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1);
//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright)
}
}

View File

@ -9,7 +9,7 @@ import com.github.victools.jsonschema.generator.*;
import eu.dnetlib.dhp.schema.dump.oaf.graph.*;
@Disabled
//@Disabled
public class GenerateJsonSchema {
@Test
@ -21,7 +21,7 @@ public class GenerateJsonSchema {
configBuilder.forFields().withDescriptionResolver(field -> "Description of " + field.getDeclaredName());
SchemaGeneratorConfig config = configBuilder.build();
SchemaGenerator generator = new SchemaGenerator(config);
JsonNode jsonSchema = generator.generateSchema(Relation.class);
JsonNode jsonSchema = generator.generateSchema(GraphResult.class);
System.out.println(jsonSchema.toString());
}

View File

@ -0,0 +1,60 @@
package eu.dnetlib.dhp.oa.graph.dump.community;
import java.io.FileInputStream;
import java.io.IOException;
import java.nio.file.Files;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.LocalFileSystem;
import org.apache.hadoop.fs.Path;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.dump.MakeTar;
import eu.dnetlib.dhp.oa.graph.dump.MakeTarTest;
public class RemoveCommunityTest {
private static String workingDir;
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(MakeTarTest.class.getSimpleName())
.toString();
}
@Test
public void testRemove() throws Exception {
LocalFileSystem fs = FileSystem.getLocal(new Configuration());
fs
.copyFromLocalFile(
false, new Path(getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
.getPath()),
new Path(workingDir + "/communityMap"));
String path = workingDir + "/communityMap";
RemoveCommunities.main(new String[] {
"-nameNode", "local",
"-path", path,
"-communityId", "beopen"
}
);
CommunityMap cm = new ObjectMapper()
.readValue(new FileInputStream(workingDir + "/communityMap"), CommunityMap.class);
Assertions.assertEquals(1, cm.size());
Assertions.assertTrue(cm.containsKey("beopen"));
}
}

View File

@ -97,7 +97,7 @@ public class CreateEntityTest {
Assertions.assertEquals(12, riList.size());
riList.stream().forEach(c -> {
switch (c.getOriginalId()) {
switch (c.getAcronym()) {
case "mes":
Assertions
.assertTrue(c.getType().equals(eu.dnetlib.dhp.oa.graph.dump.Constants.RESEARCH_COMMUNITY));
@ -115,9 +115,9 @@ public class CreateEntityTest {
String
.format(
"%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX,
DHPUtils.md5(c.getOriginalId()))));
DHPUtils.md5(c.getAcronym()))));
Assertions.assertTrue(c.getZenodo_community().equals("https://zenodo.org/communities/oac_mes"));
Assertions.assertTrue("mes".equals(c.getOriginalId()));
Assertions.assertTrue("mes".equals(c.getAcronym()));
break;
case "clarin":
Assertions
@ -130,9 +130,9 @@ public class CreateEntityTest {
String
.format(
"%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX,
DHPUtils.md5(c.getOriginalId()))));
DHPUtils.md5(c.getAcronym()))));
Assertions.assertTrue(c.getZenodo_community().equals("https://zenodo.org/communities/oac_clarin"));
Assertions.assertTrue("clarin".equals(c.getOriginalId()));
Assertions.assertTrue("clarin".equals(c.getAcronym()));
break;
}
// TODO add check for all the others Entities

View File

@ -9,11 +9,14 @@ import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.utils.DHPUtils;
public class CreateRelationTest {
@ -203,6 +206,7 @@ public class CreateRelationTest {
" <param name=\"suggestedAcknowledgement\"/>\n" +
" <param name=\"zenodoCommunity\">oac_ni</param>\n" +
" <param name=\"creationdate\">2018-03-01T12:00:00</param>\n" +
" <category claim=\"false\" id=\"ni::projects\" label=\"NI Content providers\"/>\n" +
" <category claim=\"false\" id=\"ni::contentproviders\" label=\"NI Content providers\">\n" +
" <concept claim=\"false\" id=\"ni::contentproviders::1\" label=\"OpenNeuro\">\n" +
" <param name=\"openaireId\">re3data_____::5b9bf9171d92df854cf3c520692e9122</param>\n" +
@ -376,7 +380,7 @@ public class CreateRelationTest {
" <param name=\"rule\"/>\n" +
" <param name=\"CD_PROJECT_NUMBER\">675858</param>\n" +
" <param name=\"url\"/>\n" +
" <param name=\"funding\">H2020-EINFRA-2015-1</param>\n" +
" <param name=\"funding\">EC | H2020 | RIA</param>\n" +
" <param name=\"funder\">EC</param>\n" +
" <param name=\"acronym\">West-Life</param>\n" +
" </concept>\n" +
@ -437,7 +441,65 @@ public class CreateRelationTest {
" <param name=\"suggestedAcknowledgement\"/>\n" +
" <param name=\"zenodoCommunity\">oaa_elixir-gr</param>\n" +
" <param name=\"creationdate\">2018-03-01T12:00:00</param>\n" +
" <category claim=\"false\" id=\"elixir-gr::projects\" label=\"ELIXIR GR Projects\"/>\n" +
" <category claim=\"false\" id=\"elixir-gr::projects\" label=\"ELIXIR GR Projects\">\n" +
" <concept claim=\"false\" id=\"ni::projects::12\" label=\"\">\n" +
" <param name=\"projectfullname\">BIO-INFORMATICS RESEARCH NETWORK COORDINATING CENTER (BIRN-CC)</param>\n"
+
" <param name=\"acronym\"/>\n" +
" <param name=\"CD_PROJECT_NUMBER\">1U24RR025736-01</param>\n" +
" <param name=\"funder\">NIH</param>\n" +
" </concept>\n" +
" <concept claim=\"false\" id=\"ni::projects::13\" label=\"\">\n" +
" <param name=\"projectfullname\">COLLABORATIVE RESEARCH: The Cognitive Neuroscience of Category Learning</param>\n"
+
" <param name=\"acronym\"/>\n" +
" <param name=\"CD_PROJECT_NUMBER\">0223843</param>\n" +
" <param name=\"funder\">NSF</param>\n" +
" </concept>\n" +
" <concept claim=\"false\" id=\"ni::projects::14\" label=\"\">\n" +
" <param name=\"projectfullname\">The Cognitive Atlas: Developing an Interdisciplinary Knowledge Base Through Socia</param>\n"
+
" <param name=\"acronym\"/>\n" +
" <param name=\"CD_PROJECT_NUMBER\">5R01MH082795-05</param>\n" +
" <param name=\"funder\">NIH</param>\n" +
" </concept>\n" +
" <concept claim=\"false\" id=\"ni::projects::15\" label=\"\">\n" +
" <param name=\"projectfullname\">Fragmented early life environmental and emotional / cognitive vulnerabilities</param>\n"
+
" <param name=\"acronym\"/>\n" +
" <param name=\"CD_PROJECT_NUMBER\">1P50MH096889-01A1</param>\n" +
" <param name=\"funder\">NIH</param>\n" +
" </concept>\n" +
" <concept claim=\"false\" id=\"ni::projects::16\" label=\"\">\n" +
" <param name=\"projectfullname\">Enhancement of the 1000 Functional Connectome Project</param>\n"
+
" <param name=\"acronym\"/>\n" +
" <param name=\"CD_PROJECT_NUMBER\">1R03MH096321-01A1</param>\n" +
" <param name=\"funder\">TUBITAK</param>\n" +
" </concept>\n" +
" <concept claim=\"false\" id=\"ni::projects::17\" label=\"\">\n" +
" <param name=\"projectfullname\">CRCNS Data Sharing: An open data repository for cognitive neuroscience: The OpenfMRI Project</param>\n"
+
" <param name=\"acronym\"/>\n" +
" <param name=\"CD_PROJECT_NUMBER\">1131441</param>\n" +
" <param name=\"funder\">NSF</param>\n" +
" </concept>\n" +
" <concept claim=\"false\" id=\"ni::projects::18\" label=\"\">\n" +
" <param name=\"projectfullname\">Enhancing Human Cortical Plasticity: Visual Psychophysics and fMRI</param>\n"
+
" <param name=\"acronym\"/>\n" +
" <param name=\"CD_PROJECT_NUMBER\">0121950</param>\n" +
" <param name=\"funder\">NSF</param>\n" +
" </concept>\n" +
" <concept claim=\"false\" id=\"ni::projects::18\" label=\"\">\n" +
" <param name=\"projectfullname\">Transforming statistical methodology for neuroimaging meta-analysis.</param>\n"
+
" <param name=\"acronym\"/>\n" +
" <param name=\"CD_PROJECT_NUMBER\">100309</param>\n" +
" <param name=\"funder\">WT</param>\n" +
" </concept>\n" +
" </category>" +
" <category claim=\"false\" id=\"elixir-gr::contentproviders\" label=\"Elixir-GR Content providers\">\n"
+
" <concept claim=\"false\" id=\"elixir-gr::contentproviders::1\" label=\"bio.tools\">\n" +
@ -566,4 +628,98 @@ public class CreateRelationTest {
tmp.contains("10|doajarticles::2899208a99aa7d142646e0a80bfeef05"));
}
@Test
public void test2() {
List<ContextInfo> cInfoList = new ArrayList<>();
final Consumer<ContextInfo> consumer = ci -> cInfoList.add(ci);
queryInformationSystem
.getContextRelation(consumer, "projects", ModelSupport.getIdPrefix(Project.class));
cInfoList.forEach(c -> System.out.println(new Gson().toJson(c)));
List<Relation> rList = new ArrayList<>();
cInfoList.forEach(cInfo -> Process.getRelation(cInfo).forEach(rList::add));
Assertions.assertEquals(44, rList.size());
Assertions
.assertFalse(
rList
.stream()
.map(r -> r.getSource().getId())
.collect(Collectors.toSet())
.contains(
String
.format(
"%s|%s::%s", Constants.CONTEXT_ID,
Constants.CONTEXT_NS_PREFIX,
DHPUtils.md5("dh-ch"))));
Assertions
.assertEquals(
2,
rList
.stream()
.filter(
r -> r
.getSource()
.getId()
.equals(
String
.format(
"%s|%s::%s", Constants.CONTEXT_ID,
Constants.CONTEXT_NS_PREFIX,
DHPUtils.md5("clarin"))))
.collect(Collectors.toList())
.size());
Assertions
.assertEquals(
2,
rList
.stream()
.filter(
r -> r
.getTarget()
.getId()
.equals(
String
.format(
"%s|%s::%s", Constants.CONTEXT_ID,
Constants.CONTEXT_NS_PREFIX,
DHPUtils.md5("clarin"))))
.collect(Collectors.toList())
.size());
Set<String> tmp = rList
.stream()
.filter(
r -> r
.getSource()
.getId()
.equals(
String
.format(
"%s|%s::%s", Constants.CONTEXT_ID,
Constants.CONTEXT_NS_PREFIX,
DHPUtils.md5("clarin"))))
.map(r -> r.getTarget().getId())
.collect(Collectors.toSet());
Assertions
.assertTrue(
tmp.contains("40|corda__h2020::b5a4eb56bf84bef2ebc193306b4d423f") &&
tmp.contains("40|corda_______::ef782b2d85676aa3e5a907427feb18c4"));
rList.forEach(rel -> {
if (rel.getSource().getId().startsWith("40|")) {
String proj = rel.getSource().getId().substring(3);
Assertions.assertTrue(proj.substring(0, proj.indexOf("::")).length() == 12);
}
});
}
}

View File

@ -88,7 +88,7 @@ public class DumpOrganizationProjectDatasourceTest {
org.apache.spark.sql.Dataset<eu.dnetlib.dhp.schema.dump.oaf.graph.Organization> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Organization.class));
Assertions.assertEquals(34, verificationDataset.count());
Assertions.assertEquals(15, verificationDataset.count());
verificationDataset
.foreach(

View File

@ -0,0 +1,100 @@
package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.HashMap;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
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.oaf.Relation;
import net.sf.saxon.expr.instruct.ForEach;
public class SelectRelationTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory
.getLogger(SelectRelationTest.class);
private static HashMap<String, String> map = new HashMap<>();
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(SelectRelationTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(SelectRelationTest.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(SelectRelationTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
public void test1() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/selectrelations")
.getPath();
SparkSelectValidRelationsJob.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/relation",
"-sourcePath", sourcePath
});
// dumpCommunityProducts.exec(MOCK_IS_LOOK_UP_URL,Boolean.FALSE, workingDir.toString()+"/dataset",sourcePath,"eu.dnetlib.dhp.schema.oaf.Dataset","eu.dnetlib.dhp.schema.dump.oaf.Dataset");
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<eu.dnetlib.dhp.schema.oaf.Relation> tmp = sc
.textFile(workingDir.toString() + "/relation")
.map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.oaf.Relation.class));
org.apache.spark.sql.Dataset<Relation> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.oaf.Relation.class));
Assertions.assertTrue(verificationDataset.count() == 7);
}
}

View File

@ -137,5 +137,10 @@ public class SplitPerFunderTest {
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
Assertions.assertEquals(3, tmp.count());
// H2020 3
tmp = sc
.textFile(workingDir.toString() + "/split/MZOS")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
Assertions.assertEquals(1, tmp.count());
}
}

View File

@ -5,4 +5,5 @@
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{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::9f3ff882f023209d9ffb4dc32b77d376","subRelType":"provision","target":"40|corda_______::ffc1811633b3222e4764c7b0517f83e8"}
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::b566fa319c3923454e1e8eb886ab62d2","subRelType":"provision","target":"40|nhmrc_______::4e6c928fef9851b37ec73f4f6daca35b"}
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::e0554fb004a155bc23cfb43ee9fc8eae","subRelType":"provision","target":"40|corda__h2020::846b777af165fef7c904a81712a83b66"}
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::e0554fb004a155bc23cfb43ee9fc8eae","subRelType":"provision","target":"40|corda__h2020::846b777af165fef7c904a81712a83b66"}
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1603715146539,"properties":[],"relClass":"isProducedBy","relType":"datasourceOrganization","source":"10|doajarticles::2baa9032dc058d3c8ff780c426b0c19f","subRelType":"provision","target":"40|irb_hr______::1e5e62235d094afd01cd56e65112fc63"}

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@ -0,0 +1,15 @@
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1592688952862,"properties":[],"relClass":"isProvidedBy","relType":"datasourceOrganization","source":"10|doajarticles::2baa9032dc058d3c8ff780c426b0c19f","subRelType":"provision","target":"20|dedup_wf_001::2899e571609779168222fdeb59cb916d"}
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1592688952862,"properties":[],"relClass":"isProvidedBy","relType":"datasourceOrganization","source":"10|doajarticles::5ac587eb28411c351c2e357eb097fd3d","subRelType":"provision","target":"20|grid________::b91f67a34df55a0aa1aabdcb3700f413"}
{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":true,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1592688952862,"properties":[],"relClass":"isProvidedBy","relType":"datasourceOrganization","source":"10|doajarticles::690b3aaf177a4c70b81bacd8d023cbdc","subRelType":"provision","target":"20|doajarticles::396262ee936f3d3e26ff0e60bea6cae0"}
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