map dmp schematics to zenodo metadata
This commit is contained in:
Aldo Mihasi
parent
61849a5abf
commit
cbcefea3bd
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@ -1,8 +1,11 @@
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package eu.eudat.depositinterface.zenodorepository.mapper;
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import eu.eudat.depositinterface.models.DMPDepositModel;
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import eu.eudat.depositinterface.models.OrganisationDepositModel;
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import eu.eudat.depositinterface.models.UserDMPDepositModel;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.core.type.TypeReference;
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import com.fasterxml.jackson.databind.DeserializationFeature;
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import com.fasterxml.jackson.databind.JsonNode;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.eudat.depositinterface.models.*;
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import eu.eudat.depositinterface.zenodorepository.config.DOIFunder;
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import eu.eudat.depositinterface.zenodorepository.models.*;
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@ -12,10 +15,146 @@ import java.util.stream.Collectors;
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public class DMPToZenodoMapper {
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public static ZenodoDeposit fromDMP(DMPDepositModel dmp, String zenodoCommunity, String zenodoAffiliation, String domain, List<DOIFunder> doiFunders) {
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private static final ObjectMapper objectMapper = new ObjectMapper();
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public static ZenodoDeposit fromDMP(DMPDepositModel dmp, String zenodoCommunity, String zenodoAffiliation, String domain, List<DOIFunder> doiFunders) throws JsonProcessingException {
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Map<String, Object> extraProperties = dmp.getExtraProperties() != null ? new org.json.JSONObject(dmp.getExtraProperties()).toMap() : new HashMap<>();
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ZenodoDeposit deposit = new ZenodoDeposit();
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deposit.setMetadata(new ZenodoDepositMetadata());
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Map<String, Object> schematicsMap = new HashMap<>();
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List<ZenodoRelator> relatedIdentifiers = new ArrayList<>();
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List<ZenodoComunity> communities = new ArrayList<>();
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List<ZenodoContributor> contributors = new ArrayList<>();
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List<ZenodoCreator> creators = new ArrayList<>();
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List<ZenodoGrant> grants = new ArrayList<>();
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List<String> keywords = new ArrayList<>();
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List<String> references = new ArrayList<>();
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//objectMapper.enable(JsonParser.Feature.ALLOW_SINGLE_QUOTES);
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for(DatasetDepositModel dataset: dmp.getDatasets()){
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for(DatasetFieldsDepositModel field: dataset.getFields()){
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for(String schematic: field.getSchematics()){
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if(schematic.contains("zenodo.")){
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if(field.getValue() != null && !field.getValue().isEmpty()){
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if(schematic.contains("related_identifiers")){
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if(schematic.endsWith("relation")){
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Optional<ZenodoRelator> relatorOptional = relatedIdentifiers.stream().filter(r -> r.getRelation() == null).findAny();
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if(relatorOptional.isPresent()){
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relatorOptional.get().setRelation(field.getValue());
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}
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else{
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ZenodoRelator relator = new ZenodoRelator();
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relator.setRelation(field.getValue());
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relatedIdentifiers.add(relator);
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}
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}
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else if(schematic.endsWith("identifier")){
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Optional<ZenodoRelator> relatorOptional = relatedIdentifiers.stream().filter(r -> r.getIdentifier() == null).findAny();
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if(relatorOptional.isPresent()){
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relatorOptional.get().setIdentifier(field.getValue());
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}
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else{
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ZenodoRelator relator = new ZenodoRelator();
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relator.setIdentifier(field.getValue());
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relatedIdentifiers.add(relator);
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}
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}
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else{
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JsonNode relatorNodes = objectMapper.readTree(field.getValue());
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if(relatorNodes.isArray()){
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List<ZenodoRelator> relators = objectMapper.readValue(field.getValue(), new TypeReference<List<ZenodoRelator>>(){});
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relatedIdentifiers.addAll(relators);
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}
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else{
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ZenodoRelator relator = objectMapper.readValue(field.getValue(), ZenodoRelator.class);
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relatedIdentifiers.add(relator);
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}
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}
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}
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else if(schematic.contains("communities")){
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JsonNode communitiesNodes = objectMapper.readTree(field.getValue());
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if(communitiesNodes.isArray()){
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List<ZenodoComunity> communitiesList = objectMapper.readValue(field.getValue(), new TypeReference<List<ZenodoComunity>>(){});
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communities.addAll(communitiesList);
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}
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else{
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ZenodoComunity community = objectMapper.readValue(field.getValue(), ZenodoComunity.class);
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communities.add(community);
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}
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}
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else if(schematic.contains("contributors")){
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JsonNode contributorsNodes = objectMapper.readTree(field.getValue());
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if(contributorsNodes.isArray()){
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List<ZenodoContributor> contributorsList = objectMapper.readValue(field.getValue(), new TypeReference<List<ZenodoContributor>>(){});
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contributors.addAll(contributorsList);
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}
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else{
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ZenodoContributor contributor = objectMapper.readValue(field.getValue(), ZenodoContributor.class);
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contributors.add(contributor);
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}
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}
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else if(schematic.contains("creators")){
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JsonNode creatorsNodes = objectMapper.readTree(field.getValue());
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if(creatorsNodes.isArray()){
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List<ZenodoCreator> creatorsList = objectMapper.readValue(field.getValue(), new TypeReference<List<ZenodoCreator>>(){});
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creators.addAll(creatorsList);
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}
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else{
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ZenodoCreator creator = objectMapper.readValue(field.getValue(), ZenodoCreator.class);
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creators.add(creator);
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}
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}
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else if(schematic.contains("grants")){
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JsonNode grantsNodes = objectMapper.readTree(field.getValue());
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if(grantsNodes.isArray()){
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List<ZenodoGrant> grantsList = objectMapper.readValue(field.getValue(), new TypeReference<List<ZenodoGrant>>(){});
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grants.addAll(grantsList);
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}
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else{
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ZenodoGrant grant = objectMapper.readValue(field.getValue(), ZenodoGrant.class);
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grants.add(grant);
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}
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}
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else if(schematic.contains("keywords")){
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if(field.getValue().startsWith("[")){
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List<String> keywordsList = objectMapper.readValue(field.getValue(), new TypeReference<List<String>>(){});
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keywords.addAll(keywordsList);
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}
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else{
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keywords.add(field.getValue());
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}
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}
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else if(schematic.contains("references")){
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if(field.getValue().startsWith("[")){
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List<String> referencesList = objectMapper.readValue(field.getValue(), new TypeReference<List<String>>(){});
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references.addAll(referencesList);
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}
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else{
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references.add(field.getValue());
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}
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}
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else{
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schematicsMap.put(schematic.replace("zenodo.", ""), field.getValue());
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}
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}
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}
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}
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}
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}
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schematicsMap.put("related_identifiers", relatedIdentifiers);
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schematicsMap.put("communities", communities);
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schematicsMap.put("contributors", contributors);
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schematicsMap.put("creators", creators);
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schematicsMap.put("grants", grants);
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schematicsMap.put("keywords", keywords);
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schematicsMap.put("references", references);
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String schematicsString = objectMapper.writeValueAsString(schematicsMap);
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objectMapper.enable(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY);
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ZenodoDepositMetadata metadata = objectMapper.readValue(schematicsString, new TypeReference<ZenodoDepositMetadata>(){});
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deposit.setMetadata(metadata);
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deposit.getMetadata().setTitle(dmp.getLabel());
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deposit.getMetadata().setUploadType("publication");
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deposit.getMetadata().setPublicationType("datamanagementplan");
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@ -24,7 +163,7 @@ public class DMPToZenodoMapper {
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if(zenodoCommunity != null && !zenodoAffiliation.isEmpty()) {
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ZenodoComunity community = new ZenodoComunity();
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community.setIdentifier(zenodoCommunity);
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deposit.getMetadata().setCommunities(Collections.singletonList(community));
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deposit.getMetadata().getCommunities().add(community);
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}
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if (extraProperties.get("visible") == null) {
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deposit.getMetadata().setAccessRight(ZenodoAccessRight.RESTRICTED);
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@ -51,10 +190,9 @@ public class DMPToZenodoMapper {
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ZenodoRelator relator = new ZenodoRelator();
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relator.setIdentifier(domain + "/external/zenodo/" + dmp.getId().toString());
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relator.setRelation("isIdenticalTo");
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deposit.getMetadata().setRelatedIdentifiers(Collections.singletonList(relator));
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deposit.getMetadata().getRelatedIdentifiers().add(relator);
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}
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deposit.getMetadata().setContributors(new LinkedList<>());
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List<ZenodoContributor> contributors = dmp.getUsers().stream().map(userDMP -> {
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List<ZenodoContributor> contributors1 = dmp.getUsers().stream().map(userDMP -> {
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ZenodoContributor contributor = new ZenodoContributor();
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contributor.setName(userDMP.getUser().getName());
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contributor.setType("ProjectMember");
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@ -82,7 +220,7 @@ public class DMPToZenodoMapper {
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return contributor;
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}).collect(Collectors.toList());
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deposit.getMetadata().getContributors().addAll(contributors);
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deposit.getMetadata().getContributors().addAll(contributors1);
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deposit.getMetadata().getContributors().addAll(researchers);
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if (dmp.getGrant().getReference() == null) {
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@ -98,10 +236,10 @@ public class DMPToZenodoMapper {
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String finalId = doiFunder.getDOI() + "::" + grantReferenceTail;
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ZenodoGrant grant = new ZenodoGrant();
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grant.setId(finalId);
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deposit.getMetadata().setGrants(Collections.singletonList(grant));
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deposit.getMetadata().getGrants().add(grant);
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}
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}
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ZenodoContributor creator = new ZenodoContributor();
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ZenodoCreator creator = new ZenodoCreator();
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creator.setName(dmp.getUsers().stream().filter(userDMP -> userDMP.getRole().equals(UserDMPDepositModel.UserDMPRoles.OWNER.getValue())).findFirst().get().getUser().getName());
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if (dmp.getOrganisations() != null && !dmp.getOrganisations().isEmpty()) {
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creator.setAffiliation(dmp.getOrganisations()
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@ -111,7 +249,7 @@ public class DMPToZenodoMapper {
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creator.setAffiliation(zenodoAffiliation);
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}
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}
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deposit.getMetadata().setCreators(Collections.singletonList(creator));
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deposit.getMetadata().getCreators().add(creator);
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return deposit;
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}
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@ -0,0 +1,36 @@
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package eu.eudat.depositinterface.zenodorepository.models;
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import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
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import com.fasterxml.jackson.annotation.JsonInclude;
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@JsonIgnoreProperties(ignoreUnknown = true)
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@JsonInclude(JsonInclude.Include.NON_NULL)
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public class ZenodoCreator {
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private String name;
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private String affiliation;
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private String orcid;
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public String getName() {
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return name;
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}
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public void setName(String name) {
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this.name = name;
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}
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public String getAffiliation() {
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return affiliation;
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}
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public void setAffiliation(String affiliation) {
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this.affiliation = affiliation;
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}
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public String getOrcid() {
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return orcid;
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}
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public void setOrcid(String orcid) {
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this.orcid = orcid;
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}
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}
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@ -22,6 +22,15 @@ public class ZenodoDepositMetadata {
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private String version;
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@JsonProperty("publication_date")
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private String publicationDate;
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private List<String> keywords;
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private String notes;
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private List<String> references;
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private List<ZenodoComunity> communities;
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@JsonProperty("access_right")
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@ -42,7 +51,7 @@ public class ZenodoDepositMetadata {
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private List<ZenodoGrant> grants;
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private List<ZenodoContributor> creators;
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private List<ZenodoCreator> creators;
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public String getTitle() {
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return title;
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@ -68,6 +77,38 @@ public class ZenodoDepositMetadata {
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this.publicationType = publicationType;
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}
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public String getPublicationDate() {
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return publicationDate;
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}
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public void setPublicationDate(String publicationDate) {
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this.publicationDate = publicationDate;
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}
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public List<String> getKeywords() {
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return keywords;
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}
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public void setKeywords(List<String> keywords) {
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this.keywords = keywords;
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}
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public String getNotes() {
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return notes;
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}
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public void setNotes(String notes) {
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this.notes = notes;
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}
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public List<String> getReferences() {
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return references;
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}
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public void setReferences(List<String> references) {
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this.references = references;
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}
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public String getDescription() {
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return description;
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}
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@ -148,11 +189,11 @@ public class ZenodoDepositMetadata {
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this.grants = grants;
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}
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public List<ZenodoContributor> getCreators() {
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public List<ZenodoCreator> getCreators() {
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return creators;
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}
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public void setCreators(List<ZenodoContributor> creators) {
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public void setCreators(List<ZenodoCreator> creators) {
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this.creators = creators;
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}
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}
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