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https://github.com/metadatacenter/cedar-project/issues/1198
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Attila L. Egyedi committed Nov 8, 2023
1 parent 86a9542 commit 9687849
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Showing 31 changed files with 87 additions and 109 deletions.
66 changes: 33 additions & 33 deletions ...application/src/main/java/org/metadatacenter/cedar/bridge/resources/DataCiteResource.java
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Original file line number Diff line number Diff line change
Expand Up @@ -13,10 +13,10 @@
import org.apache.http.HttpEntity;
import org.apache.http.util.EntityUtils;
import org.metadatacenter.bridge.CedarDataServices;
import org.metadatacenter.cedar.bridge.resource.*;
import org.metadatacenter.cedar.bridge.resource.Cedar.MetadataInstance;
import org.metadatacenter.cedar.bridge.resource.DataCiteProperties.Attributes;
import org.metadatacenter.cedar.bridge.resource.DataCiteProperties.DataCiteSchema;
import org.metadatacenter.cedar.bridge.resource.*;
import org.metadatacenter.cedar.bridge.resource.datacite.Attributes;
import org.metadatacenter.cedar.bridge.resource.datacite.DataCiteSchema;
import org.metadatacenter.cedar.util.dw.CedarMicroserviceResource;
import org.metadatacenter.config.CedarConfig;
import org.metadatacenter.constant.HttpConstants;
Expand Down Expand Up @@ -178,16 +178,16 @@ public Response createDOIStart(@QueryParam(QP_SOURCE_ARTIFACT_ID) String sourceA
.errorMessage("The source artifact is not found")
.id(sourceArtifactIdTyped)
.build();
} else if (!(folderServerResource.isOpen() || folderSession.isArtifactOpenImplicitly(sourceArtifactIdTyped))){
return CedarResponse
.badRequest()
.errorMessage("Please make the " + sourceArtifactResourceId.getType().getValue().toLowerCase() + " open to create a DOI")
.build();
}
} else if (!(folderServerResource.isOpen() || folderSession.isArtifactOpenImplicitly(sourceArtifactIdTyped))) {
return CedarResponse
.badRequest()
.errorMessage("Please make the " + sourceArtifactResourceId.getType().getValue().toLowerCase() + " open to create a DOI")
.build();
}

// check if the source artifact is published (version) - if it is a template
if (sourceArtifactResourceId.getType() == CedarResourceType.TEMPLATE){
if (!Objects.equals(sourceArtifactProxyJson.get("bibo:status").asText(), BiboStatus.PUBLISHED.getValue())){
if (sourceArtifactResourceId.getType() == CedarResourceType.TEMPLATE) {
if (!Objects.equals(sourceArtifactProxyJson.get("bibo:status").asText(), BiboStatus.PUBLISHED.getValue())) {
return CedarResponse
.badRequest()
.errorMessage("Please make the template publish to create a DOI")
Expand All @@ -205,7 +205,7 @@ public Response createDOIStart(@QueryParam(QP_SOURCE_ARTIFACT_ID) String sourceA
boolean hasDraftDoi = (boolean) entity.get("hasDraftDoi");
JsonNode dataNode = (JsonNode) entity.get("draftMetadata");

if (hasDraftDoi){
if (hasDraftDoi) {
// if draft DOI is returned, convert the data from dataCite JSON to Cedar Instance JSON-LD, and put it into response
JsonNode attributesNode = dataNode.get(0).get("attributes");
JsonNode draftDoi = attributesNode.get("doi");
Expand All @@ -224,14 +224,13 @@ public Response createDOIStart(@QueryParam(QP_SOURCE_ARTIFACT_ID) String sourceA

String cedarDataCiteInstanceString = mapper.writeValueAsString(cedarExistingDoiMetadata);
System.out.println("Converted Cedar DataCite Instance JSON-LD: " + cedarDataCiteInstanceString);
}
else{
} else {
// if draft DOI is not available, set the url and resourceType fields
MetadataInstance defaultInstance = GenerateInstance.getDefaultInstance(sourceArtifactId);
response.put("existingDataCiteMetadata", defaultInstance);
response.put("draftDoi", null);
}
} catch(IOException | InterruptedException e){
} catch (IOException | InterruptedException e) {
throw new RuntimeException(e);
}
response.put("sourceArtifactType", sourceArtifactResourceId.getType().getValue());
Expand All @@ -246,7 +245,8 @@ public Response createDOIStart(@QueryParam(QP_SOURCE_ARTIFACT_ID) String sourceA
@Produces(MediaType.APPLICATION_JSON)
@Timed
@Path("/create-doi")
public Response createDOI(@QueryParam(QP_SOURCE_ARTIFACT_ID) String sourceArtifactId, @QueryParam("state") String state, JsonNode dataCiteInstance) throws CedarException, IOException, InterruptedException {
public Response createDOI(@QueryParam(QP_SOURCE_ARTIFACT_ID) String sourceArtifactId, @QueryParam("state") String state, JsonNode dataCiteInstance) throws CedarException, IOException,
InterruptedException {
CedarRequestContext c = buildRequestContext();

// c.must(c.user()).be(LoggedIn);
Expand Down Expand Up @@ -301,7 +301,7 @@ public Response createDOI(@QueryParam(QP_SOURCE_ARTIFACT_ID) String sourceArtifa
int statusCode = putOrPostResponse.statusCode();
//If the Put or Post response status code is 200 or 201
String jsonResponse = putOrPostResponse.body();
try{
try {
if (statusCode == HttpConstants.CREATED | statusCode == HttpConstants.OK) {
// Deserialize DataCite response json file to DataCiteRequest Class
ObjectMapper mapper = new ObjectMapper();
Expand All @@ -323,7 +323,7 @@ else if (statusCode == CedarResponseStatus.UNPROCESSABLE_ENTITY.getStatusCode())
JsonNode jsonResource = JsonMapper.MAPPER.readTree(jsonResponse);
JsonNode errorsNode = jsonResource.get("errors");
StringBuilder errorMessageBuilder = new StringBuilder();
for(JsonNode errorNode: errorsNode){
for (JsonNode errorNode : errorsNode) {
JsonNode sourceNode = errorNode.get("source");
if (sourceNode != null && sourceNode.isTextual()) {
String source = sourceNode.asText();
Expand All @@ -336,7 +336,7 @@ else if (statusCode == CedarResponseStatus.UNPROCESSABLE_ENTITY.getStatusCode())
if (titleParts.length > 1) {
String titleMessage = String.join(":", Arrays.copyOfRange(titleParts, 1, titleParts.length)).trim();
errorMessageBuilder.append(titleMessage).append("\n");
} else{
} else {
errorMessageBuilder.append(title).append("\n");
}
}
Expand All @@ -354,7 +354,7 @@ else if (statusCode == CedarResponseStatus.UNPROCESSABLE_ENTITY.getStatusCode())
.entity(jsonResource)
.build();
}
} catch (Exception e){
} catch (Exception e) {
return CedarResponse
.internalServerError()
.errorMessage(e.getMessage())
Expand Down Expand Up @@ -464,7 +464,7 @@ private String getRequestJson(JsonNode metadata, String sourceArtifactId, String
// Pass the value from dataCiteInstance to dataCiteRequest
try {
CedarInstanceParser.parseCedarInstance(cedarInstance, dataCiteSchema, sourceArtifactId, state);
} catch (DataCiteInstanceValidationException e){
} catch (DataCiteInstanceValidationException e) {
e.printStackTrace();
throw new DataCiteInstanceValidationException(e.getMessage());
}
Expand All @@ -486,9 +486,9 @@ private String getRequestJson(JsonNode metadata, String sourceArtifactId, String
* @param endPointUrl URL of API call
* @param basicAuth Authentication at heater
* @param jsonData DataCite metadata instance JSON
* @return Http POST Response from DataCite
* @return Http POST Response from DataCite
*/
private HttpResponse<String> httpDataCitePostCall(String endPointUrl, String basicAuth, String jsonData){
private HttpResponse<String> httpDataCitePostCall(String endPointUrl, String basicAuth, String jsonData) {
try {
URI uri = URI.create(endPointUrl);
HttpClient client = HttpClient.newHttpClient();
Expand All @@ -509,13 +509,14 @@ private HttpResponse<String> httpDataCitePostCall(String endPointUrl, String bas
/**
* This function send HTTP Put request to DataCite to update DOI's metadata
*
* @param draftDoi String of draft DOI
* @param basicAuth Authentication at heater
* @param jsonData DataCite metadata instance JSON
* @return Http Put Response from DataCite
* @param draftDoi String of draft DOI
* @param basicAuth Authentication at heater
* @param jsonData DataCite metadata instance JSON
* @return Http Put Response from DataCite
*/
private HttpResponse<String> httpDataCitePutCall(String draftDoi, String basicAuth, String jsonData)throws IOException, InterruptedException{
String url = endpointUrl + "/" + draftDoi.replace("\"", "");;
private HttpResponse<String> httpDataCitePutCall(String draftDoi, String basicAuth, String jsonData) throws IOException, InterruptedException {
String url = endpointUrl + "/" + draftDoi.replace("\"", "");
;
URI uri = URI.create(url);
HttpClient client = HttpClient.newHttpClient();
HttpRequest request = HttpRequest.newBuilder(uri)
Expand All @@ -532,8 +533,8 @@ private HttpResponse<String> httpDataCitePutCall(String draftDoi, String basicAu
/**
* This function send HTTP Get request to DataCite to query the draft DOI
*
* @param sourceArtifactId ID of source template or instance for which you want to create the DOI
* @return CedarResponse which contains draft DOI's metadata and boolean value of if draft DOI exists
* @param sourceArtifactId ID of source template or instance for which you want to create the DOI
* @return CedarResponse which contains draft DOI's metadata and boolean value of if draft DOI exists
*/
private Response getDraftDoiMetadata(String sourceArtifactId) throws IOException, InterruptedException {
Map<String, Object> response = new HashMap<>();
Expand Down Expand Up @@ -571,8 +572,7 @@ private Boolean hasDraftDoi(JsonNode dataNode) {
private JsonNode getCEDARTemplate(CedarRequestContext c, String templateId) {
try {
CedarTemplateId cedarTemplateId = CedarTemplateId.build(templateId);
String artifactServerUrl = microserviceUrlUtil.getArtifact().getArtifactTypeWithId(CedarResourceType.TEMPLATE,
(CedarArtifactId) cedarTemplateId);
String artifactServerUrl = microserviceUrlUtil.getArtifact().getArtifactTypeWithId(CedarResourceType.TEMPLATE, cedarTemplateId);

HttpEntity currentTemplateEntity = ProxyUtil.proxyGet(artifactServerUrl, c).getEntity();
String currentTemplateEntityContent = EntityUtils.toString(currentTemplateEntity, CharEncoding.UTF_8);
Expand Down
2 changes: 1 addition & 1 deletion ...ication/src/test/java/org/metadatacenter/cedar/bridge/resources/DataCiteResourceTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
import org.metadatacenter.cedar.bridge.resource.*;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.metadatacenter.cedar.bridge.resource.DataCiteProperties.DataCiteSchema;
import org.metadatacenter.cedar.bridge.resource.datacite.DataCiteSchema;
import org.metadatacenter.http.CedarResponseStatus;

import javax.ws.rs.client.Entity;
Expand Down
3 changes: 0 additions & 3 deletions cedar-bridge-server-core/src/main/java/org/metadatacenter/cedar/bridge/resource/Cedar.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,9 +6,6 @@
import com.fasterxml.jackson.annotation.JsonView;
import com.fasterxml.jackson.annotation.JsonCreator;
import com.fasterxml.jackson.annotation.JsonValue;
import com.fasterxml.jackson.annotation.JsonAnySetter;
import com.fasterxml.jackson.annotation.JsonAnyGetter;
import com.fasterxml.jackson.annotation.JsonUnwrapped;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.fasterxml.jackson.annotation.JsonPropertyOrder;
Expand Down
26 changes: 13 additions & 13 deletions ...rver-core/src/main/java/org/metadatacenter/cedar/bridge/resource/CedarInstanceParser.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
package org.metadatacenter.cedar.bridge.resource;

import org.metadatacenter.cedar.bridge.resource.DataCiteProperties.*;
import org.metadatacenter.cedar.bridge.resource.datacite.*;
import org.metadatacenter.id.CedarFQResourceId;
import org.metadatacenter.model.CedarResourceType;

Expand Down Expand Up @@ -235,7 +235,7 @@ private static List<DataCiteAffiliation> parseAffiliationValue(List<?> affiliati
name = a.name() != null ? a.name().value() : null;
affiliationIdentifier = a.affiliationIdentifier() != null ? a.affiliationIdentifier().value():null;
affiliationIdentifierScheme = a.affiliationIdentifierScheme() != null ? a.affiliationIdentifierScheme().value() : null;
if (affiliationIdentifierScheme == null || affiliationIdentifierScheme.equals("")){
if (affiliationIdentifierScheme == null || affiliationIdentifierScheme.isEmpty()){
missedProperties.add("Affiliation Identifier Scheme under Creators");
}
affiliationSchemeURI = a.schemeUri() != null ? a.schemeUri().id() : null;
Expand All @@ -244,7 +244,7 @@ private static List<DataCiteAffiliation> parseAffiliationValue(List<?> affiliati
name = a.name() != null ? a.name().value() : null;
affiliationIdentifier = a.affiliationIdentifier() != null ? a.affiliationIdentifier().value():null;
affiliationIdentifierScheme = a.affiliationIdentifierScheme() != null ? a.affiliationIdentifierScheme().value() : null;
if (affiliationIdentifierScheme == null || affiliationIdentifierScheme.equals("")){
if (affiliationIdentifierScheme == null || affiliationIdentifierScheme.isEmpty()){
missedProperties.add("Affiliation Identifier Scheme under Contributors");
}
affiliationSchemeURI = a.schemeUri() != null ? a.schemeUri().id() : null;
Expand Down Expand Up @@ -275,15 +275,15 @@ private static List<DataCiteNameIdentifier> parseNameIdentifierValue(List<?> nam
CreatorElement.NameIdentifierElement n = (CreatorElement.NameIdentifierElement) obj;
nameIdentifierName = n.name() != null ? n.name().value() : null;
nameIdentifierScheme = n.nameIdentifierScheme() != null ? n.nameIdentifierScheme().value() : null;
if (nameIdentifierScheme == null || nameIdentifierScheme.equals("")){
if (nameIdentifierScheme == null || nameIdentifierScheme.isEmpty()){
missedProperties.add("Name Identifier Scheme under Creators");
}
nameIdentifierSchemeUri = n.schemeUri() != null ? n.schemeUri().id() : null;
} else if(obj instanceof ContributorElement.NameIdentifierElement){
ContributorElement.NameIdentifierElement n = (ContributorElement.NameIdentifierElement) obj;
nameIdentifierName = n.name() != null ? n.name().value() : null;
nameIdentifierScheme = n.nameIdentifierScheme() != null ? n.nameIdentifierScheme().value() : null;
if (nameIdentifierScheme == null || nameIdentifierScheme.equals("")){
if (nameIdentifierScheme == null || nameIdentifierScheme.isEmpty()){
missedProperties.add("Name Identifier Scheme under Contributors");
}
nameIdentifierSchemeUri = n.schemeUri() != null ? n.schemeUri().id() : null;
Expand All @@ -309,7 +309,7 @@ private static List<DataCiteCreator> parseCreatorValue(List<CreatorElement> crea
DataCiteCreator dataCiteCreator = new DataCiteCreator();
// Retrieve values from CEDAR class
String creatorName = c.creatorName().value();
if (creatorName == null || creatorName.equals("")){
if (creatorName == null || creatorName.isEmpty()){
missedProperties.add("Creator Name under Creators");
}

Expand Down Expand Up @@ -421,7 +421,7 @@ private static List<DataCiteContributor> parseContributorValue(List<ContributorE
DataCiteContributor dataCiteContributor = new DataCiteContributor();
// Retrieve values from CEDAR class
String name = c.contributorName()!=null ? c.contributorName().value() : null;
if (name == null || name.equals("")){
if (name == null || name.isEmpty()){
missedProperties.add("Contributor Name under Contributors");
}
String nameType = c.nameType() != null ? c.nameType().label() : null;
Expand Down Expand Up @@ -469,7 +469,7 @@ private static List<DataCiteDate> parseDateValue(List<DateElement> dateList, Has
DataCiteDate dataCiteDate = new DataCiteDate();
String date = d.date() != null ? d.date().value() : null;
String dateType = d.dateType() != null ? d.dateType().label() : null;
if (dateType == null || dateType.equals("")){
if (dateType == null || dateType.isEmpty()){
missedProperties.add("Date Type under Date");
}
String dateInformation = d.dateInformation()!=null ? d.dateInformation().value():null;
Expand All @@ -490,7 +490,7 @@ private static List<DataCiteAlternateIdentifier> parseAlternateIdentifier(List<A
DataCiteAlternateIdentifier dataCiteAlternateIdentifier = new DataCiteAlternateIdentifier();
String alternateIdentifier = a.alternateIdentifier() != null ? a.alternateIdentifier().value() : null;
String alternateIdentifierType = a.alternateIdentifierType() != null ? a.alternateIdentifierType().value() : null;
if (alternateIdentifierType == null || alternateIdentifierType.equals("")){
if (alternateIdentifierType == null || alternateIdentifierType.isEmpty()){
missedProperties.add("Alternate Identifier Type under Alternate Identifiers");
}

Expand Down Expand Up @@ -749,7 +749,7 @@ private static List<DataCiteFundingReference> parseFundingReference(List<Funding
for(FundingReferenceElement f : fundingReferenceList) {
DataCiteFundingReference dataCiteFundingReference = new DataCiteFundingReference();
String funderName = f.funderName() != null ? f.funderName().value() : null;
if (funderName == null || funderName.equals("")){
if (funderName == null || funderName.isEmpty()){
missedProperties.add("Funder Name under Funding Reference");
}
String funderIdentifier = f.funderIdentifier() != null ? f.funderIdentifier().value() : null;
Expand Down Expand Up @@ -862,7 +862,7 @@ private static List<DataCiteCreator> parseRelatedItemCreators(List<RelatedItemCr
DataCiteCreator dataCiteCreator = new DataCiteCreator();
// Retrieve values from CEDAR class
String creatorName = c.creatorName().value();
if (creatorName == null || creatorName.equals("")){
if (creatorName == null || creatorName.isEmpty()){
missedProperties.add("Creator Name under Related Items");
}

Expand All @@ -887,14 +887,14 @@ private static List<DataCiteRelatedItemContributor> parseRelatedItemContributors
DataCiteRelatedItemContributor dataCiteRelatedItemContributor = new DataCiteRelatedItemContributor();
// Retrieve values from CEDAR class
String name = c.contributorName() != null ? c.contributorName().value() : null;
if (name == null || name.equals("")) {
if (name == null || name.isEmpty()) {
missedProperties.add("Contributor Name under Related Items");
}
String nameType = c.nameType() != null ? c.nameType().label() : null;
String givenName = c.givenName() != null ? c.givenName().value() : null;
String familyName = c.familyName() != null ? c.familyName().value() : null;
String contributorType = c.contributorType() != null ? c.contributorType().label() : null;
if (contributorType == null || contributorType.equals("")) {
if (contributorType == null || contributorType.isEmpty()) {
missedProperties.add("Contributor Type under Related Items");
}

Expand Down
2 changes: 1 addition & 1 deletion ...dge-server-core/src/main/java/org/metadatacenter/cedar/bridge/resource/CompareValues.java
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
import org.metadatacenter.cedar.bridge.resource.DataCiteProperties.*;
import org.metadatacenter.cedar.bridge.resource.datacite.*;


import java.util.*;
Expand Down
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