Added ListIdentifiers

fda-metadata-db/oai/src/main/java/at/tuwien/Identify.java

-package at.tuwien;
-
-import lombok.*;
-
-@Getter
-@Setter
-@ToString
-@Builder
-@AllArgsConstructor
-@NoArgsConstructor
-public class Identify {
-
-    private String repositoryName;
-
-    private String baseURL;
-
-    @Builder.Default
-    private String protocolVersion = "2.0";
-
-    private String adminEmail;
-
-    private String earliestDatestamp;
-
-    private String deletedRecord;
-
-    private String granularity;
-
-}

fda-metadata-db/oai/src/main/java/at/tuwien/OaiErrorType.java

+package at.tuwien;
+
+import lombok.Getter;
+
+@Getter
+public enum OaiErrorType {
+
+    BAD_VERB("badVerb", "Unknown verb"),
+    ID_DOES_NOT_EXIST("idDoesNotExist", "The value of the identifier argument is unknown or illegal in this repository."),
+    CANNOT_DISSEMINATE_FORMAT("cannotDisseminateFormat", "The metadata format identified by the value given for the metadataPrefix argument is not supported by the item or by the repository."),
+    NO_RECORDS_MATCH("noRecordsMatch", "The combination of the values of the from, until, set, and metadataPrefix arguments results in an empty list."),
+    NO_METADATA_FORMATS("noMetadataFormats", "There are no metadata formats available for the specified item."),
+    NO_SET_HIERARCHY("noSetHierarchy", "The repository does not support sets."),
+    BAD_RESUMPTION_TOKEN("badResumptionToken", "The value of the resumptionToken argument is invalid or expired."),
+    BAD_ARGUMENT("badArgument", "The request includes illegal arguments, is missing required arguments, includes a repeated argument, or values for arguments have an illegal syntax.");
+
+    private String errorCode;
+    private String errorText;
+
+    OaiErrorType(String errorCode, String errorText) {
+        this.errorCode = errorCode;
+        this.errorText = errorText;
+    }
+
+}

fda-metadata-db/oai/src/main/java/at/tuwien/OaiListIdentifiersParameters.java

+package at.tuwien;
+
+import lombok.*;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.time.DateUtils;
+
+import java.text.ParseException;
+import java.util.Date;
+
+@Getter
+@Setter
+@ToString
+@Builder
+@AllArgsConstructor
+@NoArgsConstructor
+public class OaiListIdentifiersParameters extends RequestParameters {
+
+    private static final String[] DATE_FORMATS = {"yyyy-MM-dd'T'HH:mm'Z'",
+            "yyyy-MM-dd'T'HH:mm:ss'Z'",
+            "yyyy-MM-dd"};
+    private String metadataPrefix;
+    private String from;
+    private String until;
+    private String set;
+    private String resumptionToken;
+
+    public Date getFromDate() throws ParseException {
+        if (StringUtils.isNotEmpty(from)) {
+            return DateUtils.parseDate(from, DATE_FORMATS);
+        }
+        return null;
+    }
+
+    public Date getUntilDate() throws ParseException {
+        if (StringUtils.isNotEmpty(until)) {
+            return DateUtils.parseDate(until, DATE_FORMATS);
+        }
+        return null;
+    }
+
+    @Override
+    public String getParametersString() {
+        StringBuilder builder = new StringBuilder();
+        appendIfNotEmpty(builder, "metadataPrefix", this.getMetadataPrefix());
+        appendIfNotEmpty(builder, "from", this.getFrom());
+        appendIfNotEmpty(builder, "until", this.getUntil());
+        appendIfNotEmpty(builder, "set", this.getSet());
+        appendIfNotEmpty(builder, "resumptionToken", this.getResumptionToken());
+        return builder.toString();
+    }
+
+}
\ No newline at end of file

fda-metadata-db/oai/src/main/java/at/tuwien/OaiListRecordsParameters.java

+package at.tuwien;
+
+import lombok.*;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.time.DateUtils;
+
+import java.text.ParseException;
+import java.util.Date;
+
+@Getter
+@Setter
+@ToString
+@Builder
+@AllArgsConstructor
+@NoArgsConstructor
+public class OaiListRecordsParameters extends RequestParameters {
+
+    private static final String[] DATE_FORMATS = {"yyyy-MM-dd'T'HH:mm'Z'",
+            "yyyy-MM-dd'T'HH:mm:ss'Z'",
+            "yyyy-MM-dd"};
+    private String metadataPrefix;
+    private String from;
+    private String until;
+    private String set;
+    private String resumptionToken;
+
+    public Date getFromDate() throws ParseException {
+        if (StringUtils.isNotEmpty(from)) {
+            return DateUtils.parseDate(from, DATE_FORMATS);
+        }
+        return null;
+    }
+
+    public Date getUntilDate() throws ParseException {
+        if (StringUtils.isNotEmpty(until)) {
+            return DateUtils.parseDate(until, DATE_FORMATS);
+        }
+        return null;
+    }
+
+    @Override
+    public String getParametersString() {
+        StringBuilder builder = new StringBuilder();
+        appendIfNotEmpty(builder, "metadataPrefix", this.getMetadataPrefix());
+        appendIfNotEmpty(builder, "from", this.getFrom());
+        appendIfNotEmpty(builder, "until", this.getUntil());
+        appendIfNotEmpty(builder, "set", this.getSet());
+        appendIfNotEmpty(builder, "resumptionToken", this.getResumptionToken());
+        return builder.toString();
+    }
+
+}
\ No newline at end of file

fda-metadata-db/oai/src/main/java/at/tuwien/RequestParameters.java

+package at.tuwien;
+
+import org.apache.commons.lang3.StringUtils;
+
+public abstract class RequestParameters {
+
+    public abstract String getParametersString();
+
+    protected void appendIfNotEmpty(StringBuilder builder, String name, String value) {
+        if (StringUtils.isNotEmpty(value)) {
+            builder.append(name).append("=").append("\"").append(value).append("\" ");
+        }
+    }
+
+}

fda-metadata-service/Dockerfile

@@ -25,6 +25,7 @@ ENV METADATA_DB=fda
 ENV METADATA_USERNAME=postgres
 ENV METADATA_PASSWORD=postgres
 ENV GATEWAY_ENDPOINT=http://gateway-service:9095
+ENV PID_BASE="https://example.com/pid/"
 ENV REPOSITORY_NAME="Example Repository"
 ENV BASE_URL="https://example.com"
 ENV ADMIN_MAIL="noreply@example.com"

fda-metadata-service/pom.xml

@@ -74,6 +74,12 @@
             <version>${project.version}</version>
             <scope>compile</scope>
         </dependency>
+        <dependency>
+            <groupId>at.tuwien</groupId>
+            <artifactId>fda-metadata-db-querystore</artifactId>
+            <version>${project.version}</version>
+            <scope>compile</scope>
+        </dependency>
         <!-- IDE -->
         <dependency>
             <groupId>org.projectlombok</groupId>

fda-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/MetadataEndpoint.java

 package at.tuwien.endpoints;
 
+import at.tuwien.OaiErrorType;
+import at.tuwien.OaiListIdentifiersParameters;
+import at.tuwien.OaiListRecordsParameters;
 import at.tuwien.service.MetadataService;
 import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.Parameter;
 import lombok.extern.log4j.Log4j2;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.*;
-import org.springframework.web.util.UriComponentsBuilder;
 
-import java.net.URI;
+import javax.ws.rs.core.Response;
 
 @Log4j2
 @CrossOrigin(origins = "*")
@@ -23,15 +27,25 @@ public class MetadataEndpoint extends AbstractEndpoint {
         this.metadataService = metadataService;
     }
 
-    @GetMapping
+    @GetMapping(produces = "text/xml;charset=UTF-8")
     @Operation(summary = "Identify the repository")
-    public ResponseEntity<?> identify(UriComponentsBuilder uriComponentsBuilder) {
-        final URI uri = uriComponentsBuilder
-                .replacePath(null)
-                .replaceQuery(null)
-                .build().toUri();
-        final String document = metadataService.identify(uri.toString());
-        return ResponseEntity.ok(document);
+    public ResponseEntity<?> identify() {
+        return ResponseEntity.status(HttpStatus.BAD_REQUEST)
+                .body(metadataService.error(OaiErrorType.BAD_VERB));
+    }
+
+    @GetMapping(params = "verb=Identify", produces = "text/xml;charset=UTF-8")
+    @Operation(summary = "Identify the repository")
+    @Parameter(name = "verb", example = "Identify")
+    public ResponseEntity<?> identifyAlt() {
+        return ResponseEntity.ok(metadataService.identify());
+    }
+
+    @GetMapping(params = "verb=ListIdentifiers", produces = "text/xml;charset=UTF-8")
+    @Operation(summary = "List the identifiers")
+    @Parameter(name = "verb", example = "ListIdentifiers")
+    public ResponseEntity<?> listRecords(OaiListIdentifiersParameters parameters) {
+        return ResponseEntity.ok(metadataService.listIdentifiers(parameters));
     }
 
 }

fda-metadata-service/rest-service/src/main/resources/application-docker.yml

@@ -35,6 +35,7 @@ eureka:
   client.serviceUrl.defaultZone: http://discovery-service:9090/eureka/
 fda:
   ready.path: ./ready
+  pid.base: "${PID_BASE}"
   gateway.endpoint: "${GATEWAY_ENDPOINT}"
 dbrepo:
   repository-name: "${REPOSITORY_NAME}"

fda-metadata-service/rest-service/src/main/resources/application-local.yml

@@ -35,10 +35,11 @@ eureka:
   client.serviceUrl.defaultZone: http://localhost:9090/eureka/
 fda:
   ready.path: ./ready
+  pid.base: https://example.com/pid/
   gateway.endpoint: http://localhost:9095
 dbrepo:
   repository-name: TU Wien Database Repository
-  base-url: https://dbrepo.ossdip.at
+  base-url: https://dbrepo.ossdip.at/api/oai
   admin-email: noreply@example.com
   earliest-datestamp: 2022-09-17T16:09:00Z
   deleted-record: persistent

fda-metadata-service/rest-service/src/main/resources/application.yml

@@ -39,6 +39,7 @@ eureka:
   client.serviceUrl.defaultZone: http://discovery-service:9090/eureka/
 fda:
   ready.path: ./ready
+  pid.base: "${PID_BASE}"
   gateway.endpoint: "${GATEWAY_ENDPOINT}"
 dbrepo:
   repository-name: "${REPOSITORY_NAME}"

fda-metadata-service/rest-service/src/main/resources/templates/_header.xml

+<?xml version='1.0' encoding='UTF-8'?>
+<OAI-PMH xmlns='http://www.openarchives.org/OAI/2.0/' xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance'
+         xsi:schemaLocation='http://www.openarchives.org/OAI/2.0/ http://www.openarchives.org/OAI/2.0/OAI-PMH.xsd'>
+    <responseDate>[[${responseDate}]]</responseDate>
+    [(${request})]
+    [(${body})]
+</OAI-PMH>
\ No newline at end of file

fda-metadata-service/rest-service/src/main/resources/templates/error.xml

+<error th:attr="code=${code}">[[${message}]]</error>
\ No newline at end of file

fda-metadata-service/rest-service/src/main/resources/templates/identify.xml

-<?xml version='1.0' encoding='UTF-8'?>
-<OAI-PMH xmlns='http://www.openarchives.org/OAI/2.0/' xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance'
-         xsi:schemaLocation='http://www.openarchives.org/OAI/2.0/ http://www.openarchives.org/OAI/2.0/OAI-PMH.xsd'>
-    <responseDate>[[${responseDate}]]</responseDate>
-    <request verb="Identify">[[${request}]]</request>
 <Identify>
     <repositoryName>[[${repositoryName}]]</repositoryName>
     <baseURL>[[${baseURL}]]</baseURL>
@@ -12,4 +7,3 @@
     <deletedRecord>[[${deletedRecord}]]</deletedRecord>
     <granularity>[[${granularity}]]</granularity>
 </Identify>
\ No newline at end of file
-</OAI-PMH>
\ No newline at end of file

fda-metadata-service/rest-service/src/main/resources/templates/record.xml

+<header>
+    <identifier>[[${identifier}]]</identifier>
+    <datestamp>[[${datestamp}]]</datestamp>
+</header>
\ No newline at end of file

fda-metadata-service/services/src/main/java/at/tuwien/config/MetadataConfig.java

@@ -26,4 +26,7 @@ public class MetadataConfig {
     @Value("${dbrepo.granularity}")
     private String granularity;
 
+    @Value("${fda.pid.base}")
+    private String pidBase;
+
 }

fda-metadata-service/services/src/main/java/at/tuwien/exception/InvalidPrefixException.java

+package at.tuwien.exception;
+
+import org.springframework.http.HttpStatus;
+import org.springframework.web.bind.annotation.ResponseStatus;
+
+@ResponseStatus(code = HttpStatus.BAD_REQUEST)
+public class InvalidPrefixException extends Exception {
+
+    public InvalidPrefixException(String msg) {
+        super(msg);
+    }
+
+    public InvalidPrefixException(String msg, Throwable thr) {
+        super(msg, thr);
+    }
+
+    public InvalidPrefixException(Throwable thr) {
+        super(thr);
+    }
+}

fda-metadata-service/services/src/main/java/at/tuwien/mapper/MetadataMapper.java

+package at.tuwien.mapper;
+
+import org.mapstruct.Mapper;
+
+import java.time.Instant;
+import java.time.ZoneId;
+import java.time.format.DateTimeFormatter;
+
+
+@Mapper(componentModel = "spring")
+public interface MetadataMapper {
+
+    org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(MetadataMapper.class);
+
+    default String instantToDatestamp(Instant data) {
+        return DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss'Z'")
+                .withZone(ZoneId.systemDefault())
+                .format(data);
+    }
+
+}

fda-metadata-service/services/src/main/java/at/tuwien/repository/jpa/IdentifierRepository.java

+package at.tuwien.repository.jpa;
+
+import at.tuwien.entities.identifier.Identifier;
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.stereotype.Repository;
+
+@Repository
+public interface IdentifierRepository extends JpaRepository<Identifier, Long> {
+}

fda-metadata-service/services/src/main/java/at/tuwien/service/IdentifierService.java

+package at.tuwien.service;
+
+import at.tuwien.entities.identifier.Identifier;
+
+import java.util.List;
+
+public interface IdentifierService {
+    List<Identifier> findAll();
+}