feat: #3 add retrieve dataset endpoint

GenomicDataInfrastructure · Apr 8, 2024 · b1cab29 · b1cab29
1 parent 2bf215b
commit b1cab29
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Showing 19 changed files with 657 additions and 20 deletions.
diff --git a/_http/ckan.http b/_http/ckan.http
@@ -6,3 +6,6 @@ GET https://ckan-test.healthdata.nl/api/3/action/package_search?fq=&sort=score+d
 
 ###
 GET https://ckan-test.healthdata.nl/api/3/action/package_show?id=e1b3eff9-13eb-48b0-b180-7ecb76b84454
+
+###
+GET https://ckan-test.healthdata.nl/api/3/action/package_show?id=dummy
diff --git a/_http/discovery.http b/_http/discovery.http
@@ -22,5 +22,8 @@ Content-Type: application/json
     }]
 }
 
+###
+GET http://localhost:8080/api/v1/datasets/e1b3eff9-13eb-48b0-b180-7ecb76b84454
+
 ###
 GET http://localhost:8080/api/v1/datasets/dummy
diff --git a/...ava/io/github/genomicdatainfrastructure/discovery/api/DatasetNotFoundExceptionMapper.java b/...ava/io/github/genomicdatainfrastructure/discovery/api/DatasetNotFoundExceptionMapper.java
@@ -0,0 +1,34 @@
+// SPDX-FileCopyrightText: 2024 PNED G.I.E.
+//
+// SPDX-License-Identifier: Apache-2.0
+
+package io.github.genomicdatainfrastructure.discovery.api;
+
+import static jakarta.ws.rs.core.Response.Status.NOT_FOUND;
+
+import io.github.genomicdatainfrastructure.discovery.exceptions.DatasetNotFoundException;
+import io.github.genomicdatainfrastructure.discovery.model.ErrorResponse;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.ext.ExceptionMapper;
+import jakarta.ws.rs.ext.Provider;
+
+@Provider
+public class DatasetNotFoundExceptionMapper implements
+        ExceptionMapper<DatasetNotFoundException> {
+
+    @Override
+    public Response toResponse(DatasetNotFoundException exception) {
+        var errorResponse = new ErrorResponse(
+                "Dataset Not Found",
+                NOT_FOUND.getStatusCode(),
+                exception.getMessage()
+        );
+
+        return Response
+                .status(NOT_FOUND)
+                .entity(errorResponse)
+                .type(MediaType.APPLICATION_JSON)
+                .build();
+    }
+}
diff --git a/src/main/java/io/github/genomicdatainfrastructure/discovery/api/DatasetQueryApiImpl.java b/src/main/java/io/github/genomicdatainfrastructure/discovery/api/DatasetQueryApiImpl.java
@@ -8,6 +8,7 @@
 import io.github.genomicdatainfrastructure.discovery.model.DatasetsSearchResponse;
 import io.github.genomicdatainfrastructure.discovery.model.RetrievedDataset;
 import io.github.genomicdatainfrastructure.discovery.services.DatasetsSearchService;
+import io.github.genomicdatainfrastructure.discovery.services.RetrieveDatasetService;
 import io.quarkus.oidc.runtime.OidcJwtCallerPrincipal;
 import io.quarkus.security.identity.SecurityIdentity;
 import lombok.RequiredArgsConstructor;
@@ -17,16 +18,16 @@ public class DatasetQueryApiImpl implements DatasetQueryApi {
 
     private final SecurityIdentity identity;
     private final DatasetsSearchService datasetsSearchService;
+    private final RetrieveDatasetService retrievedDatasetService;
 
     @Override
     public DatasetsSearchResponse datasetSearch(DatasetSearchQuery datasetSearchQuery) {
-        return datasetsSearchService.search(accessToken(), datasetSearchQuery);
+        return datasetsSearchService.search(datasetSearchQuery, accessToken());
     }
 
     @Override
     public RetrievedDataset retrieveDataset(String id) {
-        return RetrievedDataset.builder()
-                .build();
+        return retrievedDatasetService.retrieve(id, accessToken());
     }
 
     private String accessToken() {

diff --git a/...va/io/github/genomicdatainfrastructure/discovery/exceptions/DatasetNotFoundException.java b/...va/io/github/genomicdatainfrastructure/discovery/exceptions/DatasetNotFoundException.java
@@ -0,0 +1,14 @@
+// SPDX-FileCopyrightText: 2024 PNED G.I.E.
+//
+// SPDX-License-Identifier: Apache-2.0
+
+package io.github.genomicdatainfrastructure.discovery.exceptions;
+
+public class DatasetNotFoundException extends RuntimeException {
+
+    private static final String MESSAGE = "Dataset %s not found";
+
+    public DatasetNotFoundException(String datasetId) {
+        super(MESSAGE.formatted(datasetId));
+    }
+}
diff --git a/...in/java/io/github/genomicdatainfrastructure/discovery/services/DatasetsSearchService.java b/...in/java/io/github/genomicdatainfrastructure/discovery/services/DatasetsSearchService.java
@@ -26,7 +26,7 @@ public DatasetsSearchService(
         this.ckanQueryApi = ckanQueryApi;
     }
 
-    public DatasetsSearchResponse search(String accessToken, DatasetSearchQuery query) {
+    public DatasetsSearchResponse search(DatasetSearchQuery query, String accessToken) {
         var response = ckanQueryApi.packageSearch(
                 query.getQuery(),
                 CkanFacetsQueryBuilder.buildFacetQuery(query.getFacets()),

diff --git a/src/main/java/io/github/genomicdatainfrastructure/discovery/services/PackageShowMapper.java b/src/main/java/io/github/genomicdatainfrastructure/discovery/services/PackageShowMapper.java
@@ -0,0 +1,105 @@
+// SPDX-FileCopyrightText: 2024 PNED G.I.E.
+//
+// SPDX-License-Identifier: Apache-2.0
+
+package io.github.genomicdatainfrastructure.discovery.services;
+
+import java.util.List;
+import java.util.Objects;
+
+import io.github.genomicdatainfrastructure.discovery.model.RetrievedDataset;
+import io.github.genomicdatainfrastructure.discovery.model.RetrievedDistribution;
+import io.github.genomicdatainfrastructure.discovery.model.ValueLabel;
+import io.github.genomicdatainfrastructure.discovery.remote.ckan.model.CkanOrganization;
+import io.github.genomicdatainfrastructure.discovery.remote.ckan.model.CkanPackage;
+import io.github.genomicdatainfrastructure.discovery.remote.ckan.model.CkanResource;
+
+import static java.util.Optional.ofNullable;
+import static java.util.function.Predicate.not;
+
+import java.time.LocalDateTime;
+import java.time.format.DateTimeFormatter;
+
+public class PackageShowMapper {
+
+    public static final DateTimeFormatter DATE_FORMATTER = DateTimeFormatter.ofPattern(
+            "yyyy-MM-dd'T'HH:mm:ss.SSSSSS"
+    );
+
+    private PackageShowMapper() {
+        // Utility class
+    }
+
+    public static RetrievedDataset from(CkanPackage ckanPackage) {
+        var catalogue = ofNullable(ckanPackage.getOrganization())
+                .map(CkanOrganization::getTitle)
+                .orElse(null);
+
+        return RetrievedDataset.builder()
+                .id(ckanPackage.getId())
+                .identifier(ckanPackage.getIdentifier())
+                .title(ckanPackage.getName())
+                .description(ckanPackage.getNotes())
+                .themes(values(ckanPackage.getTheme()))
+                .publisherName(ckanPackage.getPublisherName())
+                .catalogue(catalogue)
+                .createdAt(parse(ckanPackage.getMetadataCreated()))
+                .modifiedAt(parse(ckanPackage.getMetadataModified()))
+                .url(ckanPackage.getUrl())
+                .languages(values(ckanPackage.getLanguage()))
+                .contact(value(ckanPackage.getContactUri()))
+                .hasVersions(values(ckanPackage.getHasVersion()))
+                .accessRights(value(ckanPackage.getAccessRights()))
+                .conformsTo(values(ckanPackage.getConformsTo()))
+                .provenance(ckanPackage.getProvenance())
+                .spatial(value(ckanPackage.getSpatialUri()))
+                .distributions(distributions(ckanPackage))
+                .build();
+    }
+
+    private static List<ValueLabel> values(List<String> values) {
+        return ofNullable(values)
+                .orElseGet(List::of)
+                .stream()
+                .map(PackageShowMapper::value)
+                .filter(Objects::nonNull)
+                .toList();
+    }
+
+    private static ValueLabel value(String value) {
+        return ofNullable(value)
+                .filter(Objects::nonNull)
+                .filter(not(String::isBlank))
+                .map(it -> ValueLabel.builder()
+                        .value(it)
+                        .label(it)
+                        .build())
+                .orElse(null);
+    }
+
+    private static LocalDateTime parse(String date) {
+        return ofNullable(date)
+                .map(it -> LocalDateTime.parse(it, DATE_FORMATTER))
+                .orElse(null);
+    }
+
+    private static List<RetrievedDistribution> distributions(CkanPackage ckanPackage) {
+        return ofNullable(ckanPackage.getResources())
+                .orElseGet(List::of)
+                .stream()
+                .map(PackageShowMapper::distribution)
+                .toList();
+    }
+
+    private static RetrievedDistribution distribution(CkanResource ckanResource) {
+        return RetrievedDistribution.builder()
+                .id(ckanResource.getId())
+                .title(ckanResource.getName())
+                .description(ckanResource.getDescription())
+                .format(value(ckanResource.getFormat()))
+                .uri(ckanResource.getUri())
+                .createdAt(parse(ckanResource.getCreated()))
+                .modifiedAt(parse(ckanResource.getLastModified()))
+                .build();
+    }
+}
diff --git a/.../io/github/genomicdatainfrastructure/discovery/services/PackagesSearchResponseMapper.java b/.../io/github/genomicdatainfrastructure/discovery/services/PackagesSearchResponseMapper.java
@@ -16,11 +16,12 @@
 import io.github.genomicdatainfrastructure.discovery.remote.ckan.model.PackagesSearchResult;
 import java.util.List;
 import java.util.Map;
-
+import java.util.Objects;
 import java.time.format.DateTimeFormatter;
 import java.time.LocalDateTime;
 
 import static java.util.Optional.ofNullable;
+import static java.util.function.Predicate.not;
 
 public class PackagesSearchResponseMapper {
 
@@ -120,10 +121,19 @@ private static List<ValueLabel> values(List<String> values) {
         return ofNullable(values)
                 .orElseGet(List::of)
                 .stream()
+                .map(PackagesSearchResponseMapper::value)
+                .filter(Objects::nonNull)
+                .toList();
+    }
+
+    private static ValueLabel value(String value) {
+        return ofNullable(value)
+                .filter(Objects::nonNull)
+                .filter(not(String::isBlank))
                 .map(it -> ValueLabel.builder()
                         .value(it)
                         .label(it)
                         .build())
-                .toList();
+                .orElse(null);
     }
 }
diff --git a/...n/java/io/github/genomicdatainfrastructure/discovery/services/RetrieveDatasetService.java b/...n/java/io/github/genomicdatainfrastructure/discovery/services/RetrieveDatasetService.java
@@ -0,0 +1,44 @@
+// SPDX-FileCopyrightText: 2024 PNED G.I.E.
+//
+// SPDX-License-Identifier: Apache-2.0
+
+package io.github.genomicdatainfrastructure.discovery.services;
+
+import org.eclipse.microprofile.rest.client.inject.RestClient;
+
+import io.github.genomicdatainfrastructure.discovery.exceptions.DatasetNotFoundException;
+import io.github.genomicdatainfrastructure.discovery.model.RetrievedDataset;
+import io.github.genomicdatainfrastructure.discovery.remote.ckan.api.CkanQueryApi;
+import io.github.genomicdatainfrastructure.discovery.remote.ckan.model.CkanPackageShowResponse;
+import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.inject.Inject;
+import jakarta.ws.rs.WebApplicationException;
+
+@ApplicationScoped
+public class RetrieveDatasetService {
+
+    private final CkanQueryApi ckanQueryApi;
+
+    @Inject
+    public RetrieveDatasetService(
+            @RestClient CkanQueryApi ckanQueryApi
+    ) {
+        this.ckanQueryApi = ckanQueryApi;
+    }
+
+    public RetrievedDataset retrieve(String id, String accessToken) {
+        var response = retrieveCkanPackage(id, accessToken);
+        return PackageShowMapper.from(response.getResult());
+    }
+
+    public CkanPackageShowResponse retrieveCkanPackage(String id, String accessToken) {
+        try {
+            return ckanQueryApi.packageShow(id, accessToken);
+        } catch (WebApplicationException e) {
+            if (e.getResponse().getStatus() == 404) {
+                throw new DatasetNotFoundException(id);
+            }
+            throw e;
+        }
+    }
+}
diff --git a/src/main/openapi/ckan.yaml b/src/main/openapi/ckan.yaml
@@ -98,7 +98,13 @@ paths:
           content:
             application/json:
               schema:
-                $ref: "#/components/schemas/CkanPackage"
+                $ref: "#/components/schemas/CkanPackageShowResponse"
+        "404":
+          description: The package not found
+          content:
+            application/json:
+              schema:
+                $ref: "#/components/schemas/CkanErrorResponse"
 components:
   schemas:
     PackagesSearchResponse:
@@ -232,3 +238,26 @@ components:
         - name
         - description
         - created
+    CkanPackageShowResponse:
+      type: object
+      properties:
+        help:
+          type: string
+        success:
+          type: boolean
+        result:
+          $ref: "#/components/schemas/CkanPackage"
+    CkanErrorResponse:
+      type: object
+      properties:
+        help:
+          type: string
+        success:
+          type: boolean
+        error:
+          type: object
+          properties:
+            __type:
+              type: string
+            message:
+              type: string
diff --git a/src/main/openapi/discovery.yaml b/src/main/openapi/discovery.yaml
@@ -65,12 +65,6 @@ paths:
             application/json:
               schema:
                 $ref: "#/components/schemas/RetrievedDataset"
-        "403":
-          description: Dataset is not visible to the user
-          content:
-            application/json:
-              schema:
-                $ref: "#/components/schemas/ErrorResponse"
         "404":
           description: Dataset not found
           content:
@@ -229,7 +223,7 @@ components:
         hasVersions:
           type: array
           items:
-            type: string
+            $ref: "#/components/schemas/ValueLabel"
           title: Has Versions
         accessRights:
           $ref: "#/components/schemas/ValueLabel"
@@ -269,7 +263,7 @@ components:
           type: string
           title: Description
         format:
-          type: string
+          $ref: "#/components/schemas/ValueLabel"
           title: Format
         uri:
           type: string

diff --git a/src/test/java/io/github/genomicdatainfrastructure/discovery/api/RetrieveDatasetIT.java b/src/test/java/io/github/genomicdatainfrastructure/discovery/api/RetrieveDatasetIT.java
@@ -0,0 +1,11 @@
+// SPDX-FileCopyrightText: 2024 PNED G.I.E.
+//
+// SPDX-License-Identifier: Apache-2.0
+
+package io.github.genomicdatainfrastructure.discovery.api;
+
+import io.quarkus.test.junit.QuarkusIntegrationTest;
+
+@QuarkusIntegrationTest
+public class RetrieveDatasetIT extends RetrieveDatasetTest {
+}