Merge pull request #6 from DiSSCo/feature/tombstoning

add tombstoning event

pom.xml

@@ -6,7 +6,7 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>3.2.5</version>
+    <version>3.3.2</version>
     <relativePath/> <!-- lookup parent from repository -->
   </parent>
   <groupId>eu.dissco.core</groupId>

src/main/java/eu/dissco/core/datacitepublisher/Profiles.java

@@ -8,6 +8,7 @@ public class Profiles {
   private Profiles() {
   }
 
-  public static final String TEST = "test";
+  public static final String SANDBOX = "sandbox";
+  public static final String PRODUCTION = "production";
 
 }

src/main/java/eu/dissco/core/datacitepublisher/component/XmlLocReader.java

@@ -4,7 +4,7 @@
 import com.fasterxml.jackson.dataformat.xml.XmlMapper;
 import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlCData;
 import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlElementWrapper;
-import eu.dissco.core.datacitepublisher.exceptions.InvalidFdoProfileRecievedException;
+import eu.dissco.core.datacitepublisher.exceptions.InvalidFdoProfileReceivedException;
 import java.util.Collections;
 import java.util.List;
 import lombok.Getter;
@@ -22,7 +22,7 @@ public class XmlLocReader {
   @Qualifier("xmlMapper")
   private final XmlMapper xmlMapper;
 
-  public List<String> getLocationsFromXml(String xmlDoc) throws InvalidFdoProfileRecievedException {
+  public List<String> getLocationsFromXml(String xmlDoc) throws InvalidFdoProfileReceivedException {
     if (xmlDoc == null) {
       log.warn("No url provided");
       return Collections.emptyList();
@@ -32,7 +32,7 @@ public List<String> getLocationsFromXml(String xmlDoc) throws InvalidFdoProfileR
       return locations.getLocation().stream().map(LocationXml::getHref).toList();
     } catch (JsonProcessingException e){
       log.error("Unable to parse 10320/loc field for fdo", e);
-      throw new InvalidFdoProfileRecievedException();
+      throw new InvalidFdoProfileReceivedException();
     }
   }
 

src/main/java/eu/dissco/core/datacitepublisher/configuration/ApplicationConfig.java

@@ -5,6 +5,7 @@
 import com.fasterxml.jackson.databind.module.SimpleModule;
 import com.fasterxml.jackson.dataformat.xml.XmlMapper;
 import java.time.Instant;
+import java.time.ZoneId;
 import java.time.ZoneOffset;
 import java.time.format.DateTimeFormatter;
 import lombok.RequiredArgsConstructor;
@@ -17,8 +18,8 @@ public class ApplicationConfig {
 
   public static final DateTimeFormatter FDO_FORMATTER = DateTimeFormatter.ofPattern(
       "yyyy-MM-dd'T'HH:mm:ss.SSSXXX").withZone(ZoneOffset.UTC);
-  public static final DateTimeFormatter DATACITE_FORMATTER = DateTimeFormatter.ofPattern("yyyy-MM-dd");
-
+  public static final DateTimeFormatter DATACITE_FORMATTER = DateTimeFormatter.ofPattern("yyyy-MM-dd")
+      .withZone(ZoneId.of("UTC"));
 
   @Bean
   public ObjectMapper objectMapper() {

src/main/java/eu/dissco/core/datacitepublisher/configuration/WebClientConfig.java

@@ -32,11 +32,8 @@ public WebClient dataciteClient() {
 
   @Bean("handle")
   public WebClient handleClient() {
-    ExchangeFilterFunction errorResponseFilter = ExchangeFilterFunction
-        .ofResponseProcessor(WebClientUtils::exchangeFilterResponseProcessor);
     return WebClient.builder()
         .baseUrl(handleProperties.getEndpoint())
-        .filter(errorResponseFilter)
         .build();
   }
 

src/main/java/eu/dissco/core/datacitepublisher/domain/EventType.java

@@ -1,10 +1,10 @@
 package eu.dissco.core.datacitepublisher.domain;
 
 import com.fasterxml.jackson.annotation.JsonProperty;
-import com.fasterxml.jackson.annotation.JsonPropertyOrder;
 
 public enum EventType {
   @JsonProperty("create") CREATE,
-  @JsonPropertyOrder("update") UPDATE;
+  @JsonProperty("update") UPDATE,
+  @JsonProperty("tombstone") TOMBSTONE;
 
 }

src/main/java/eu/dissco/core/datacitepublisher/domain/TombstoneEvent.java

@@ -0,0 +1,9 @@
+package eu.dissco.core.datacitepublisher.domain;
+
+import eu.dissco.core.datacitepublisher.domain.datacite.DcRelatedIdentifiers;
+import java.util.List;
+
+public record TombstoneEvent(String handle, List<DcRelatedIdentifiers> dcRelatedIdentifiersTombstone) {
+
+
+}

src/main/java/eu/dissco/core/datacitepublisher/domain/datacite/DcAttributes.java

@@ -1,23 +1,26 @@
 package eu.dissco.core.datacitepublisher.domain.datacite;
 
 import static com.fasterxml.jackson.annotation.JsonInclude.Include.NON_EMPTY;
-import static eu.dissco.core.datacitepublisher.domain.datacite.DataCiteConstants.DC_EVENT;
-import static eu.dissco.core.datacitepublisher.domain.datacite.DataCiteConstants.PUBLISHER;
-import static eu.dissco.core.datacitepublisher.domain.datacite.DataCiteConstants.SCHEMA_VERSION;
+import static eu.dissco.core.datacitepublisher.properties.DoiProperties.DC_EVENT;
+import static eu.dissco.core.datacitepublisher.properties.DoiProperties.SCHEMA_VERSION;
 
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonInclude;
 import java.util.List;
 import lombok.AccessLevel;
 import lombok.AllArgsConstructor;
 import lombok.Builder;
 import lombok.Getter;
 import lombok.Setter;
+import lombok.extern.jackson.Jacksonized;
 
 @Builder
 @AllArgsConstructor
 @Setter(value = AccessLevel.PACKAGE)
 @Getter
 @JsonInclude(NON_EMPTY)
+@Jacksonized
+@JsonIgnoreProperties(ignoreUnknown = true)
 public class DcAttributes {
 
   private String suffix;
@@ -33,7 +36,7 @@ public class DcAttributes {
   private List<DcRelatedIdentifiers> relatedIdentifiers; // tombstone pids; primary specimenObjectId; primaryMediaId
   private List<DcDescription> descriptions; // Specimen: Host + materialSampleType, Media: host + linked object type
   private String url; // human readable landing page
-  private final DcPublisher publisher = PUBLISHER;
+  private DcPublisher publisher;
   private final String schemaVersion = SCHEMA_VERSION;
   private final String event = DC_EVENT;
 

src/main/java/eu/dissco/core/datacitepublisher/domain/datacite/DcContributor.java

@@ -1,5 +1,6 @@
 package eu.dissco.core.datacitepublisher.domain.datacite;
 
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import java.util.List;
 import lombok.AccessLevel;
 import lombok.AllArgsConstructor;
@@ -11,6 +12,7 @@
 @AllArgsConstructor
 @Setter(value = AccessLevel.PACKAGE)
 @Getter
+@JsonIgnoreProperties(ignoreUnknown = true)
 public class DcContributor {
 
   private String name;

src/main/java/eu/dissco/core/datacitepublisher/domain/datacite/DcCreator.java

@@ -1,5 +1,6 @@
 package eu.dissco.core.datacitepublisher.domain.datacite;
 
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import java.util.List;
 import lombok.AccessLevel;
 import lombok.AllArgsConstructor;
@@ -11,6 +12,7 @@
 @AllArgsConstructor
 @Setter(value = AccessLevel.PACKAGE)
 @Getter
+@JsonIgnoreProperties(ignoreUnknown = true)
 public class DcCreator {
   private final String nameType= "Organizational";
   private String name;

src/main/java/eu/dissco/core/datacitepublisher/domain/datacite/DcData.java

@@ -1,5 +1,6 @@
 package eu.dissco.core.datacitepublisher.domain.datacite;
 
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import lombok.AccessLevel;
 import lombok.AllArgsConstructor;
 import lombok.Builder;
@@ -10,6 +11,7 @@
 @AllArgsConstructor
 @Setter(value = AccessLevel.PACKAGE)
 @Getter
+@JsonIgnoreProperties(ignoreUnknown = true)
 public class DcData {
 
   private final String type = "dois";

src/main/java/eu/dissco/core/datacitepublisher/domain/datacite/DcDate.java

@@ -14,6 +14,6 @@
 @NoArgsConstructor
 public class DcDate {
   private String date;
-  private final String dateType = "Issued";
+  private String dateType;
 
 }

src/main/java/eu/dissco/core/datacitepublisher/domain/datacite/DcDescription.java

@@ -4,12 +4,14 @@
 import lombok.AllArgsConstructor;
 import lombok.Builder;
 import lombok.Getter;
+import lombok.NoArgsConstructor;
 import lombok.Setter;
 
 @Builder
 @AllArgsConstructor
 @Setter(value = AccessLevel.PACKAGE)
 @Getter
+@NoArgsConstructor
 public class DcDescription {
   private String description;
   private final String descriptionType = "TechnicalInfo";

src/main/java/eu/dissco/core/datacitepublisher/domain/datacite/DcPublisher.java

@@ -1,11 +1,13 @@
 package eu.dissco.core.datacitepublisher.domain.datacite;
 
+
 import lombok.Value;
 
 @Value
 public class DcPublisher {
-  String name = "Distributed System of Scientific Collections";
-  String publisherIdentifier = "https://ror.org/0566bfb96";
-  String publisherIdentifierScheme = UriScheme.ROR.getSchemeName();
-  String schemeUri = UriScheme.ROR.getUri();
+  String name;
+  String publisherIdentifier;
+  String publisherIdentifierScheme;
+  String schemeUri;
+
 }

src/main/java/eu/dissco/core/datacitepublisher/domain/datacite/DcRelatedIdentifiers.java

@@ -11,7 +11,7 @@
 @Setter(value = AccessLevel.PACKAGE)
 @Getter
 public class DcRelatedIdentifiers {
-  private String relationType;
+  private RelationType relationType;
   private String relatedIdentifier;
   private String relatedIdentifierType;
 }

src/main/java/eu/dissco/core/datacitepublisher/domain/datacite/DcTitle.java

@@ -4,12 +4,14 @@
 import lombok.AllArgsConstructor;
 import lombok.Builder;
 import lombok.Getter;
+import lombok.NoArgsConstructor;
 import lombok.Setter;
 
 @Builder
 @AllArgsConstructor
 @Setter(value = AccessLevel.PACKAGE)
 @Getter
+@NoArgsConstructor
 public class DcTitle {
   private String title;
 }

src/main/java/eu/dissco/core/datacitepublisher/domain/datacite/DcType.java

@@ -1,17 +1,22 @@
 package eu.dissco.core.datacitepublisher.domain.datacite;
 
-import static eu.dissco.core.datacitepublisher.domain.datacite.DataCiteConstants.RESOURCE_TYPE_GENERAL;
 
+import static eu.dissco.core.datacitepublisher.properties.DoiProperties.RESOURCE_TYPE_GENERAL;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import lombok.AccessLevel;
 import lombok.AllArgsConstructor;
 import lombok.Builder;
 import lombok.Getter;
+import lombok.NoArgsConstructor;
 import lombok.Setter;
 
 @Builder
 @AllArgsConstructor
 @Setter(value = AccessLevel.PACKAGE)
 @Getter
+@NoArgsConstructor
+@JsonIgnoreProperties(ignoreUnknown = true)
 public class DcType {
 
   private String resourceType;

src/main/java/eu/dissco/core/datacitepublisher/domain/datacite/RelationType.java

@@ -0,0 +1,40 @@
+package eu.dissco.core.datacitepublisher.domain.datacite;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+public enum RelationType {
+  @JsonProperty("IsCitedBy") IS_CITED_BY,
+  @JsonProperty("Cites") CITES,
+  @JsonProperty("IsSupplementTo") IS_SUPPLEMENT_TO,
+  @JsonProperty("IsSupplementedBy") IS_SUPPLEMENTED_BY,
+  @JsonProperty("IsContinuedBy") IS_CONTINUED_BY,
+  @JsonProperty("Continues") CONTINUES,
+  @JsonProperty("IsDescribedBy") IS_DESCRIBED_BY,
+  @JsonProperty("Describes") DESCRIBES,
+  @JsonProperty("HasMetadata") HAS_METADATA,
+  @JsonProperty("IsMetadataFor") IS_METADATA_FOR,
+  @JsonProperty("HasVersion") HAS_VERSION,
+  @JsonProperty("IsVersionOf") IS_VERSION_OF,
+  @JsonProperty("IsNewVersionOf") IS_NEW_VERSION_OF,
+  @JsonProperty("IsPreviousVersionOf") IS_PREVIOUS_VERSION_OF,
+  @JsonProperty("IsPartOf") IS_PART_OF,
+  @JsonProperty("HasPart") HAS_PART,
+  @JsonProperty("IsPublishedIn") IS_PUBLISHED_IN,
+  @JsonProperty("IsReferencedBy") IS_REFERENCED_BY,
+  @JsonProperty("References") REFERENCES,
+  @JsonProperty("IsDocumentedBy") IS_DOCUMENTED_BY,
+  @JsonProperty("Documents") DOCUMENTS,
+  @JsonProperty("IsCompiledBy") IS_COMPILED_BY,
+  @JsonProperty("Compiles") COMPILES,
+  @JsonProperty("IsVariantFormOf") IS_VARIANT_FORM_OF,
+  @JsonProperty("IsOriginalFormOf") IS_ORIGINAL_FORM_OF,
+  @JsonProperty("IsIdenticalTo") IS_IDENTICAL_TO,
+  @JsonProperty("IsReviewedBy") IS_REVIEWED_BY,
+  @JsonProperty("Reviews") REVIEWS,
+  @JsonProperty("IsDerivedFrom") IS_DERIVED_FROM,
+  @JsonProperty("IsSourceOf") IS_SOURCE_OF,
+  @JsonProperty("IsRequiredBy") IS_REQUIRED_BY,
+  @JsonProperty("Requires") REQUIRES,
+  @JsonProperty("IsObsoletedBy") IS_OBSOLETED_BY,
+  @JsonProperty("Obsoletes") OBSOLETES;
+}

src/main/java/eu/dissco/core/datacitepublisher/exceptions/InvalidFdoProfileReceivedException.java

@@ -0,0 +1,10 @@
+package eu.dissco.core.datacitepublisher.exceptions;
+
+public class InvalidFdoProfileReceivedException extends InvalidRequestException {
+
+  public InvalidFdoProfileReceivedException() {
+    super();
+  }
+
+
+}

src/main/java/eu/dissco/core/datacitepublisher/exceptions/InvalidRequestException.java

@@ -0,0 +1,8 @@
+package eu.dissco.core.datacitepublisher.exceptions;
+
+public class InvalidRequestException extends Exception {
+  public InvalidRequestException(){
+    super();
+  }
+
+}