Related identifier fix, some optical sugar with verified emails

fda-authentication-service/services/src/main/java/at/tuwien/config/JacksonConfig.java

+package at.tuwien.config;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.SerializationFeature;
+import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public class JacksonConfig {
+
+    @Bean
+    public ObjectMapper objectMapper() {
+        final ObjectMapper objectMapper = new ObjectMapper();
+        objectMapper.registerModule(new JavaTimeModule());
+        objectMapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false);
+        return objectMapper;
+    }
+
+}

fda-broker-service/services/src/main/java/at/tuwien/config/JacksonConfig.java

+package at.tuwien.config;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.SerializationFeature;
+import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public class JacksonConfig {
+
+    @Bean
+    public ObjectMapper objectMapper() {
+        final ObjectMapper objectMapper = new ObjectMapper();
+        objectMapper.registerModule(new JavaTimeModule());
+        objectMapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false);
+        return objectMapper;
+    }
+
+}

fda-container-service/services/src/main/java/at/tuwien/config/JacksonConfig.java

+package at.tuwien.config;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.SerializationFeature;
+import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public class JacksonConfig {
+
+    @Bean
+    public ObjectMapper objectMapper() {
+        final ObjectMapper objectMapper = new ObjectMapper();
+        objectMapper.registerModule(new JavaTimeModule());
+        objectMapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false);
+        return objectMapper;
+    }
+
+}

fda-database-service/services/src/main/java/at/tuwien/config/JacksonConfig.java

+package at.tuwien.config;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.SerializationFeature;
+import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public class JacksonConfig {
+
+    @Bean
+    public ObjectMapper objectMapper() {
+        final ObjectMapper objectMapper = new ObjectMapper();
+        objectMapper.registerModule(new JavaTimeModule());
+        objectMapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false);
+        return objectMapper;
+    }
+
+}

fda-document-service/services/src/main/java/at/tuwien/config/JacksonConfig.java

+package at.tuwien.config;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.SerializationFeature;
+import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public class JacksonConfig {
+
+    @Bean
+    public ObjectMapper objectMapper() {
+        final ObjectMapper objectMapper = new ObjectMapper();
+        objectMapper.registerModule(new JavaTimeModule());
+        objectMapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false);
+        return objectMapper;
+    }
+
+}

fda-gateway-service/gateway/src/main/java/at/tuwien/gatewayservice/config/JacksonConfig.java

+package at.tuwien.gatewayservice.config;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.SerializationFeature;
+import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public class JacksonConfig {
+
+    @Bean
+    public ObjectMapper objectMapper() {
+        final ObjectMapper objectMapper = new ObjectMapper();
+        objectMapper.registerModule(new JavaTimeModule());
+        objectMapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false);
+        return objectMapper;
+    }
+
+}

fda-identifier-service/rest-service/src/main/java/at/tuwien/endpoints/IdentifierEndpoint.java

@@ -51,7 +51,8 @@ public class IdentifierEndpoint {
             final Identifier identifier = identifierService.find(containerId, databaseId, qid);
             log.info("Found identifier with id {} filtered by query id {}", identifier.getId(), qid);
             log.debug("found identifier {} filtered by query id {}", identifier, qid);
-            return ResponseEntity.ok(List.of(identifierMapper.identifierToIdentifierDto(identifier)));
+            final IdentifierDto dto = identifierMapper.identifierToIdentifierDto(identifier);
+            return ResponseEntity.ok(List.of(dto));
         }
         final List<Identifier> identifiers = identifierService.findAll(containerId, databaseId);
         log.info("Found {} identifiers", identifiers.size());

fda-identifier-service/services/src/main/java/at/tuwien/config/JacksonConfig.java

 package at.tuwien.config;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.datatype.jdk8.Jdk8Module;
+import com.fasterxml.jackson.databind.SerializationFeature;
 import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -11,10 +11,10 @@ public class JacksonConfig {
 
     @Bean
     public ObjectMapper objectMapper() {
-        return new ObjectMapper()
-                .findAndRegisterModules()
-                .registerModule(new JavaTimeModule())
-                .registerModule(new Jdk8Module());
+        final ObjectMapper objectMapper = new ObjectMapper();
+        objectMapper.registerModule(new JavaTimeModule());
+        objectMapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false);
+        return objectMapper;
     }
 
 }

fda-identifier-service/services/src/main/java/at/tuwien/mapper/DocumentMapper.java

@@ -78,6 +78,27 @@ public interface DocumentMapper {
                     .append("</language>");
         }
         builder.append("<resourceType resourceTypeGeneral=\"Dataset\">Dataset</resourceType>");
+        if (data.getRelated().size() > 0) {
+            builder.append("<relatedIdentifiers>");
+            data.getRelated()
+                    .forEach(related -> {
+                        builder.append("<relatedIdentifier");
+                        if (related.getType() != null) {
+                            builder.append(" relatedIdentifierType=\"")
+                                    .append(related.getType())
+                                    .append("\"");
+                        }
+                        if (related.getRelation() != null) {
+                            builder.append(" relationType=\"")
+                                    .append(related.getRelation())
+                                    .append("\"");
+                        }
+                        builder.append(">")
+                                .append(related.getValue())
+                                .append("</relatedIdentifier>");
+                    });
+            builder.append("</relatedIdentifiers>");
+        }
         if (database.getLicense() != null) {
             builder.append("<rightsList><rights xml:lang=\"en-US\" schemeURI=\"https://spdx.org/licenses/\" ")
                     .append("rightsIdentifierScheme=\"SPDX\" rightsIdentifier=\"")

fda-identifier-service/services/src/main/java/at/tuwien/mapper/IdentifierMapper.java

@@ -17,6 +17,10 @@ public interface IdentifierMapper {
     @Transactional
     Identifier identifierCreateDtoToIdentifier(IdentifierCreateDto data);
 
+    /* keep */
+    @Transactional
+    RelatedIdentifierDto relatedIdentifierToRelatedIdentifierDto(RelatedIdentifier data);
+
     @Transactional
     Identifier identifierDtoToIdentifier(IdentifierDto data);
 

fda-metadata-db/api/src/main/java/at/tuwien/api/container/ContainerCreateRequestDto.java

 package at.tuwien.api.container;
 
-import com.fasterxml.jackson.annotation.JsonProperty;
 import io.swagger.v3.oas.annotations.Parameter;
 import lombok.*;
 
 import javax.validation.constraints.NotBlank;
-import javax.validation.constraints.NotNull;
 
 @Getter
 @Setter

fda-metadata-db/api/src/main/java/at/tuwien/api/database/DatabaseDto.java

@@ -30,6 +30,10 @@ public class DatabaseDto {
     @Parameter(name = "database name", example = "Weather Australia")
     private String name;
 
+    @NotBlank
+    @Parameter(name = "database exchange")
+    private String exchange;
+
     @NotNull
     @Parameter(name = "database creator")
     private UserDto creator;

fda-metadata-db/api/src/main/java/at/tuwien/api/database/table/columns/ColumnCreateDto.java

@@ -37,14 +37,6 @@ public class ColumnCreateDto {
     @Parameter(name = "date format id", example = "1")
     private Long dfid;
 
-    @JsonProperty("decimal_digits_before")
-    @Parameter(name = "decimal digits before point", example = "3")
-    private Long decimalDigitsBefore;
-
-    @JsonProperty("decimal_digits_after")
-    @Parameter(name = "decimal digits after point", example = "0")
-    private Long decimalDigitsAfter;
-
     @NotNull
     @Parameter(name = "unique", example = "true")
     private Boolean unique = false;

fda-metadata-db/api/src/main/java/at/tuwien/api/identifier/CreatorCreateDto.java

@@ -5,6 +5,7 @@ import lombok.Builder;
 import lombok.Data;
 import lombok.Getter;
 import lombok.Setter;
+import lombok.extern.jackson.Jacksonized;
 
 import javax.validation.constraints.NotBlank;
 
@@ -12,6 +13,7 @@ import javax.validation.constraints.NotBlank;
 @Getter
 @Setter
 @Builder
+@Jacksonized
 public class CreatorCreateDto {
 
     @NotBlank

fda-metadata-db/api/src/main/java/at/tuwien/api/identifier/IdentifierCreateDto.java

@@ -6,6 +6,7 @@ import lombok.Builder;
 import lombok.Data;
 import lombok.Getter;
 import lombok.Setter;
+import lombok.extern.jackson.Jacksonized;
 
 import javax.validation.constraints.NotBlank;
 import javax.validation.constraints.NotNull;
@@ -16,6 +17,7 @@ import java.util.List;
 @Getter
 @Setter
 @Builder
+@Jacksonized
 public class IdentifierCreateDto {
 
     @NotNull

fda-metadata-db/api/src/main/java/at/tuwien/api/identifier/IdentifierDto.java

@@ -50,10 +50,9 @@ public class IdentifierDto {
     @Parameter(name = "query normalized")
     private String queryNormalized;
 
-    @NotNull
-    @JsonProperty("related_identifiers")
+    @JsonProperty("related")
     @Parameter(name = "related identifiers")
-    private List<RelatedIdentifierDto> relatedIdentifiers;
+    private List<RelatedIdentifierDto> related;
 
     @NotBlank
     @JsonProperty("query_hash")

fda-metadata-db/api/src/main/java/at/tuwien/api/identifier/RelatedIdentifierCreateDto.java

@@ -2,6 +2,7 @@ package at.tuwien.api.identifier;
 
 import io.swagger.v3.oas.annotations.Parameter;
 import lombok.*;
+import lombok.extern.jackson.Jacksonized;
 
 import javax.validation.constraints.NotNull;
 
@@ -9,6 +10,7 @@ import javax.validation.constraints.NotNull;
 @Getter
 @Setter
 @Builder
+@Jacksonized
 public class RelatedIdentifierCreateDto {
 
     @NotNull

fda-metadata-db/api/src/main/java/at/tuwien/api/identifier/RelatedIdentifierDto.java

 package at.tuwien.api.identifier;
 
 import at.tuwien.api.user.UserDto;
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import io.swagger.v3.oas.annotations.Parameter;
 import lombok.*;
@@ -17,6 +18,7 @@ public class RelatedIdentifierDto {
     @NotNull
     private Long id;
 
+    @JsonIgnore
     @NotNull
     private Long iid;
 
@@ -31,6 +33,7 @@ public class RelatedIdentifierDto {
     private RelationTypeDto relation;
 
     @ToString.Exclude
+    @JsonIgnore
     @NotNull
     private UserDto creator;
 

fda-metadata-db/entities/src/main/java/at/tuwien/entities/identifier/Identifier.java

@@ -88,6 +88,12 @@ public class Identifier {
     @Enumerated(EnumType.STRING)
     private VisibilityType visibility = VisibilityType.SELF;
 
+    @OneToMany(fetch = FetchType.LAZY, cascade = CascadeType.MERGE)
+    @JoinColumns({
+            @JoinColumn(name = "iid", referencedColumnName = "id", insertable = false, updatable = false)
+    })
+    private List<RelatedIdentifier> related;
+
     @Column
     private String doi;
 

fda-query-service/services/src/main/java/at/tuwien/config/JacksonConfig.java

+package at.tuwien.config;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.SerializationFeature;
+import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public class JacksonConfig {
+
+    @Bean
+    public ObjectMapper objectMapper() {
+        final ObjectMapper objectMapper = new ObjectMapper();
+        objectMapper.registerModule(new JavaTimeModule());
+        objectMapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false);
+        return objectMapper;
+    }
+
+}