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Add rda support for researchers and tags field

This commit is contained in:
George Kalampokis 2020-06-09 16:25:50 +03:00
parent c927e41d83
commit 12587ee865
6 changed files with 73 additions and 21 deletions
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2
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DataManagementPlanManager.java
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@ -1394,7 +1394,7 @@ public class DataManagementPlanManager {
dmp.setStatus((short)0);
dmp.setGroupId(UUID.randomUUID());
if (dmp.getResearchers() != null && !dmp.getResearchers().isEmpty()) {
dmp.getResearchers().forEach(researcher -> {
dmp.getResearchers().stream().filter(Objects::nonNull).forEach(researcher -> {
researcher.setId(UUID.randomUUID());
researcher.setCreated(new Date());
researcher.setModified(new Date());

2
dmp-backend/web/src/main/java/eu/eudat/models/data/dmp/DataManagementPlan.java
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@ -341,7 +341,7 @@ public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
this.id = entity.getId();
this.profile = entity.getProfile() != null ? new Tuple<UUID, String>(entity.getProfile().getId(), entity.getProfile().getLabel()) : null;
this.organisations = entity.getOrganisations() != null ? entity.getOrganisations().stream().map(item -> new Organisation().fromDataModel(item)).collect(Collectors.toList()) : new ArrayList<>();
this.researchers = entity.getResearchers() != null ? entity.getResearchers().stream().map(item -> new Researcher().fromDataModel(item)).collect(Collectors.toList()) : new ArrayList<>();
this.researchers = entity.getResearchers() != null ? entity.getResearchers().stream().filter(Objects::nonNull).map(item -> new Researcher().fromDataModel(item)).collect(Collectors.toList()) : new ArrayList<>();
this.version = entity.getVersion();
this.label = entity.getLabel();
this.grant = new Grant();

2
dmp-backend/web/src/main/java/eu/eudat/models/data/dmp/Researcher.java
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@ -1,5 +1,6 @@
package eu.eudat.models.data.dmp;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import eu.eudat.models.DataModel;
import eu.eudat.logic.utilities.helpers.LabelGenerator;
import org.slf4j.Logger;
@ -8,6 +9,7 @@ import org.slf4j.LoggerFactory;
import java.util.Date;
import java.util.UUID;
@JsonIgnoreProperties(ignoreUnknown = true)
public class Researcher implements DataModel<eu.eudat.data.entities.Researcher, Researcher>, LabelGenerator {
private static final Logger logger = LoggerFactory.getLogger(Researcher.class);
private String label;

45
dmp-backend/web/src/main/java/eu/eudat/models/rda/mapper/ContributorRDAMapper.java
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@ -1,14 +1,18 @@
package eu.eudat.models.rda.mapper;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.data.entities.Researcher;
import eu.eudat.data.entities.UserDMP;
import eu.eudat.models.rda.Contributor;
import eu.eudat.models.rda.ContributorId;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.Arrays;
import java.util.HashSet;
import java.io.IOException;
import java.util.*;
public class ContributorRDAMapper {
private static final Logger logger = LoggerFactory.getLogger(ContributorRDAMapper.class);
public static Contributor toRDA(UserDMP userDMP) {
Contributor rda = new Contributor();
@ -28,23 +32,38 @@ public class ContributorRDAMapper {
return rda;
}
public static Contributor toRDA(String value) {
ObjectMapper mapper = new ObjectMapper();
try {
eu.eudat.models.data.dmp.Researcher researcher = mapper.readValue(value, eu.eudat.models.data.dmp.Researcher.class);
return toRDA(researcher.toDataModel());
} catch (IOException e) {
logger.error(e.getMessage(), e);
}
return null;
}
public static Researcher toEntity(Contributor rda) {
Researcher entity = new Researcher();
String reference;
if (rda.getContributorId().getType() == ContributorId.Type.ORCID) {
String id = rda.getContributorId().getIdentifier().replace("http://orcid.org/", "");
reference = "orcid:" + id;
} else {
String idParts[] = rda.getContributorId().getIdentifier().split(":");
if (idParts.length == 1) {
reference = "dmp:" + rda.getContributorId().getIdentifier();
if (rda.getContributorId() != null) {
if (rda.getContributorId().getType() == ContributorId.Type.ORCID) {
String id = rda.getContributorId().getIdentifier().replace("http://orcid.org/", "");
reference = "orcid:" + id;
} else {
reference = rda.getContributorId().getIdentifier();
String idParts[] = rda.getContributorId().getIdentifier().split(":");
if (idParts.length == 1) {
reference = "dmp:" + rda.getContributorId().getIdentifier();
} else {
reference = rda.getContributorId().getIdentifier();
}
}
entity.setReference(reference);
entity.setLabel(rda.getName());
entity.setPrimaryEmail(rda.getMbox());
} else {
return null;
}
entity.setReference(reference);
entity.setLabel(rda.getName());
entity.setPrimaryEmail(rda.getMbox());
return entity;
}

41
dmp-backend/web/src/main/java/eu/eudat/models/rda/mapper/DatasetRDAMapper.java
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@ -8,6 +8,7 @@ import eu.eudat.logic.managers.DatasetManager;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.utilities.json.JsonSearcher;
import eu.eudat.models.data.datasetwizard.DatasetWizardModel;
import eu.eudat.models.rda.Contributor;
import eu.eudat.models.rda.Dataset;
import eu.eudat.models.rda.Language;
import org.json.JSONObject;
@ -36,7 +37,7 @@ public class DatasetRDAMapper {
}
@Transactional
public Dataset toRDA(eu.eudat.data.entities.Dataset dataset) {
public Dataset toRDA(eu.eudat.data.entities.Dataset dataset, List<Contributor> contributors) {
Dataset rda = new Dataset();
// rda.setDatasetId(DatasetIdRDAMapper.toRDA(dataset.getId()));
rda.setTitle(dataset.getLabel());
@ -91,11 +92,11 @@ public class DatasetRDAMapper {
rda.setKeyword(keywordNodes.stream().map(keywordNode -> {
JsonNode value = keywordNode.get("value");
if (value.isArray()) {
return StreamSupport.stream(value.spliterator(), false).map(node -> KeywordRDAMapper.toRDA(node.asText())).collect(Collectors.joining("\", \"")).replaceAll("\"", "\"");
return StreamSupport.stream(value.spliterator(), false).map(node -> KeywordRDAMapper.toRDA(node.asText())).collect(Collectors.toList());
} else {
return KeywordRDAMapper.toRDA(keywordNode.get("value").asText());
return Collections.singletonList(KeywordRDAMapper.toRDA(keywordNode.get("value").asText()));
}
}).collect(Collectors.toList()));
}).flatMap(Collection::stream).collect(Collectors.toList()));
for (int i = 0; i < keywordNodes.size(); i++) {
rda.setAdditionalProperty("keyword" + (i + 1), keywordNodes.get(i).get("id").asText());
}
@ -125,6 +126,17 @@ public class DatasetRDAMapper {
if (!issuedNodes.isEmpty()) {
rda.setIssued(issuedNodes.get(0).get("value").asText());
}
List<JsonNode> contributorNodes = JsonSearcher.findNodes(datasetDescriptionObj, "rdaProperty", "dmp.contributor");
if (!contributorNodes.isEmpty()) {
contributors.addAll(contributorNodes.stream().map(contributorNode -> {
JsonNode value = contributorNode.get("value");
if (value.isArray()) {
return StreamSupport.stream(value.spliterator(), false).map(node -> ContributorRDAMapper.toRDA(node.asText())).collect(Collectors.toList());
} else {
return Collections.singletonList(new Contributor());
}
}).flatMap(Collection::stream).collect(Collectors.toList()));
}
List<JsonNode> foundNodes = Stream.of(typeNodes, languageNodes, metadataNodes, qaNodes, preservationNodes, distributionNodes,
keywordNodes, personalDataNodes, securityAndPrivacyNodes, sensitiveDataNodes, technicalResourceNodes).flatMap(Collection::stream).collect(Collectors.toList());
templateIdsToValues.entrySet().forEach(entry -> {
@ -206,8 +218,20 @@ public class DatasetRDAMapper {
}
List <String> keywordIds = rda.getAdditionalProperties().entrySet().stream().filter(entry -> entry.getKey().startsWith("keyword")).map(entry -> entry.getValue().toString()).collect(Collectors.toList());
boolean takeAll = false;
if (keywordIds.size() < rda.getKeyword().size()) {
takeAll = true;
}
for (int i = 0; i < keywordIds.size(); i++) {
properties.put(keywordIds.get(i), rda.getKeyword().get(i));
if (takeAll) {
List<String> tags = new ArrayList<>();
for (String keyword: rda.getKeyword()) {
tags.add(mapper.writeValueAsString(toTagEntity(keyword)));
}
properties.put(keywordIds.get(i), tags);
} else {
properties.put(keywordIds.get(i), mapper.writeValueAsString(toTagEntity(rda.getKeyword().get(i))));
}
}
List<JsonNode> personalDataNodes = JsonSearcher.findNodes(datasetDescriptionObj, "rdaProperty", "dataset.personal_data");
@ -239,4 +263,11 @@ public class DatasetRDAMapper {
return entity;
}
private static Tag toTagEntity(String name) {
Tag tag = new Tag();
tag.setId("");
tag.setName(name);
return tag;
}
}

2
dmp-backend/web/src/main/java/eu/eudat/models/rda/mapper/DmpRDAMapper.java
View File

@ -55,7 +55,7 @@ public class DmpRDAMapper {
rda.getContributor().addAll(dmp.getResearchers().stream().map(ContributorRDAMapper::toRDA).collect(Collectors.toList()));
}
// rda.getContributor().addAll(dmp.getUsers().stream().map(ContributorRDAMapper::toRDA).collect(Collectors.toList()));
rda.setDataset(dmp.getDataset().stream().map(dataset -> datasetRDAMapper.toRDA(dataset)).collect(Collectors.toList()));
rda.setDataset(dmp.getDataset().stream().map(dataset -> datasetRDAMapper.toRDA(dataset, rda.getContributor())).collect(Collectors.toList()));
rda.setProject(Collections.singletonList(ProjectRDAMapper.toRDA(dmp.getProject(), dmp.getGrant())));
rda.setAdditionalProperty("templates", dmp.getAssociatedDmps().stream().map(datasetProfile -> datasetProfile.getId().toString()).toArray());
return rda;