feat: #4 integrate with Beacon

_http/beacon.http

@@ -12,7 +12,7 @@ Content-Type: application/json
    "query":{
       "filters":[
          {
-            "id":"NCIT:C16352",
+            "id":"UBERON:0005352",
             "scope": "individual"
          }
       ],

_http/discovery.http

@@ -14,11 +14,29 @@ Content-Type: application/json
     }, {
         "facetGroup": "ckan",
         "facet": "theme",
-        "value": "http://purl.org/zonmw/covid19/10003"
+        "value": "http://purl.org/zonmw/covid19/10006"
     }, {
         "facetGroup": "ckan",
         "facet": "tags",
         "value": "COVID-19"
+    }, {
+        "facetGroup": "beacon",
+        "facet": "cellosaurus",
+        "value": "NCIT:C16352"
+    }]
+}
+
+###
+
+POST http://localhost:8080/api/v1/datasets/search
+Content-Type: application/json
+
+{
+    "query": "COVID",
+    "facets": [{
+        "facetGroup": "beacon",
+        "facet": "cellosaurus",
+        "value": "NCIT:C16352"
     }]
 }
 

pom.xml

@@ -1,8 +1,7 @@
-<?xml version="1.0"?>
-<project
-    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd"
-    xmlns="http://maven.apache.org/POM/4.0.0"
-    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <groupId>io.github.genomicdatainfrastructure</groupId>
     <artifactId>gdi-userportal-dataset-discovery-service</artifactId>
@@ -25,6 +24,7 @@
         <surefire.version>3.0.0-M7</surefire.version>
         <quarkus-wiremock.version>1.3.0</quarkus-wiremock.version>
         <jacoco-maven-plugin.version>0.8.11</jacoco-maven-plugin.version>
+        <commons-lang3.version>3.14.0</commons-lang3.version>
     </properties>
     <dependencyManagement>
         <dependencies>
@@ -77,10 +77,19 @@
             <artifactId>quarkus-openapi-generator</artifactId>
             <version>${quarkus-openapi-generator.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-lang3</artifactId>
+            <version>${commons-lang3.version}</version>
+        </dependency>
         <dependency>
             <groupId>io.quarkus</groupId>
             <artifactId>quarkus-oidc</artifactId>
         </dependency>
+        <dependency>
+            <groupId>io.quarkus</groupId>
+            <artifactId>quarkus-cache</artifactId>
+        </dependency>
         <dependency>
             <groupId>io.quarkus</groupId>
             <artifactId>quarkus-junit5</artifactId>

src/main/java/io/github/genomicdatainfrastructure/discovery/api/DatasetQueryApiImpl.java

@@ -7,7 +7,7 @@
 import io.github.genomicdatainfrastructure.discovery.model.DatasetSearchQuery;
 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.BeaconIndividualsSearchService;
 import io.github.genomicdatainfrastructure.discovery.services.RetrieveDatasetService;
 import io.quarkus.oidc.runtime.OidcJwtCallerPrincipal;
 import io.quarkus.security.identity.SecurityIdentity;
@@ -17,7 +17,7 @@
 public class DatasetQueryApiImpl implements DatasetQueryApi {
 
     private final SecurityIdentity identity;
-    private final DatasetsSearchService datasetsSearchService;
+    private final BeaconIndividualsSearchService datasetsSearchService;
     private final RetrieveDatasetService retrievedDatasetService;
 
     @Override

src/main/java/io/github/genomicdatainfrastructure/discovery/services/BeaconFilteringTermsService.java

@@ -0,0 +1,76 @@
+// SPDX-FileCopyrightText: 2024 PNED G.I.E.
+//
+// SPDX-License-Identifier: Apache-2.0
+
+package io.github.genomicdatainfrastructure.discovery.services;
+
+import static java.util.Optional.ofNullable;
+import static java.util.stream.Collectors.toMap;
+
+import org.eclipse.microprofile.rest.client.inject.RestClient;
+import io.github.genomicdatainfrastructure.discovery.model.Facet;
+import io.github.genomicdatainfrastructure.discovery.model.FacetGroup;
+import io.github.genomicdatainfrastructure.discovery.model.ValueLabel;
+import io.github.genomicdatainfrastructure.discovery.remote.beacon.api.BeaconQueryApi;
+import io.github.genomicdatainfrastructure.discovery.remote.beacon.model.BeaconFilteringTermsResponse;
+import io.github.genomicdatainfrastructure.discovery.remote.beacon.model.BeaconFilteringTermsResponseContent;
+import io.github.genomicdatainfrastructure.discovery.remote.beacon.model.BeaconResource;
+import io.quarkus.cache.CacheResult;
+import jakarta.enterprise.context.ApplicationScoped;
+import java.util.List;
+import java.util.ArrayList;
+
+@ApplicationScoped
+public class BeaconFilteringTermsService {
+
+    private static final String DEFAULT_SCOPE = "individual";
+
+    private final BeaconQueryApi beaconQueryApi;
+
+    public BeaconFilteringTermsService(
+            @RestClient BeaconQueryApi beaconQueryApi
+    ) {
+        this.beaconQueryApi = beaconQueryApi;
+    }
+
+    @CacheResult(cacheName = "beacon-facet-group-cache")
+    public FacetGroup listFilteringTerms(String authorization) {
+        var filteringTerms = beaconQueryApi.listFilteringTerms(authorization);
+
+        var nonNullFilteringTermsResponse = ofNullable(filteringTerms)
+                .map(BeaconFilteringTermsResponse::getResponse)
+                .filter(it -> it.getFilteringTerms() != null && it.getResources() != null)
+                .orElseGet(BeaconFilteringTermsResponseContent::new);
+
+        var facetsMappedByName = nonNullFilteringTermsResponse.getResources().stream()
+                .filter(it -> it.getName() != null && !it.getName().isBlank())
+                .collect(toMap(
+                        BeaconResource::getName,
+                        it -> Facet.builder()
+                                .key(it.getId())
+                                .label(it.getName())
+                                .values(new ArrayList<>())
+                                .build()
+                ));
+
+        nonNullFilteringTermsResponse.getFilteringTerms().stream()
+                .filter(it -> it.getLabel() != null && !it.getLabel().isBlank())
+                .filter(it -> it.getId() != null && !it.getId().isBlank())
+                .filter(it -> it.getScopes() != null && it.getScopes().contains(DEFAULT_SCOPE))
+                .filter(it -> facetsMappedByName.containsKey(it.getType()))
+                .forEach(filteringTerm -> {
+                    var facet = facetsMappedByName.get(filteringTerm.getType());
+                    var values = facet.getValues();
+                    values.add(ValueLabel.builder()
+                            .value(filteringTerm.getId())
+                            .label(filteringTerm.getLabel())
+                            .build());
+                });
+
+        return FacetGroup.builder()
+                .key("beacon")
+                .label("Data")
+                .facets(List.copyOf(facetsMappedByName.values()))
+                .build();
+    }
+}

src/main/java/io/github/genomicdatainfrastructure/discovery/services/BeaconIndividualsSearchService.java

@@ -0,0 +1,163 @@
+// SPDX-FileCopyrightText: 2024 PNED G.I.E.
+//
+// SPDX-License-Identifier: Apache-2.0
+
+package io.github.genomicdatainfrastructure.discovery.services;
+
+import static java.util.Optional.ofNullable;
+import static java.util.function.Predicate.not;
+import static java.util.stream.Collectors.toCollection;
+
+import org.eclipse.microprofile.rest.client.inject.RestClient;
+import io.github.genomicdatainfrastructure.discovery.model.DatasetSearchQuery;
+import io.github.genomicdatainfrastructure.discovery.model.DatasetSearchQueryFacet;
+import io.github.genomicdatainfrastructure.discovery.model.DatasetsSearchResponse;
+import io.github.genomicdatainfrastructure.discovery.model.FacetGroup;
+import io.github.genomicdatainfrastructure.discovery.remote.beacon.api.BeaconQueryApi;
+import io.github.genomicdatainfrastructure.discovery.remote.beacon.model.BeaconIndividualsRequest;
+import io.github.genomicdatainfrastructure.discovery.remote.beacon.model.BeaconIndividualsRequestMeta;
+import io.github.genomicdatainfrastructure.discovery.remote.beacon.model.BeaconIndividualsRequestQuery;
+import io.github.genomicdatainfrastructure.discovery.remote.beacon.model.BeaconIndividualsRequestQueryFilter;
+import io.github.genomicdatainfrastructure.discovery.remote.beacon.model.BeaconIndividualsRequestQueryPagination;
+import io.github.genomicdatainfrastructure.discovery.remote.beacon.model.BeaconIndividualsResponse;
+import io.github.genomicdatainfrastructure.discovery.remote.beacon.model.BeaconIndividualsResponseContent;
+import io.github.genomicdatainfrastructure.discovery.remote.beacon.model.BeaconResultSet;
+import io.github.genomicdatainfrastructure.discovery.remote.keycloak.api.KeycloakQueryApi;
+import jakarta.enterprise.context.ApplicationScoped;
+import jakarta.inject.Inject;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+
+@ApplicationScoped
+public class BeaconIndividualsSearchService {
+
+    private static final String BEACON_FACET_GROUP = "beacon";
+    private static final String BEACON_IDP_ALIAS = "LSAAI";
+    private static final String BEARER_PATTERN = "Bearer %s";
+    private static final String BEACON_DATASET_TYPE = "dataset";
+    private static final String CKAN_FACET_GROUP = "ckan";
+    private static final String CKAN_IDENTIFIER_FIELD = "identifier";
+    private static final String SCOPE = "individual";
+    private static final String INCLUDE_RESULTSET_RESPONSES = "HIT";
+    private static final String REQUESTED_GRANULARITY = "count";
+
+    private final BeaconQueryApi beaconQueryApi;
+    private final KeycloakQueryApi keycloakQueryApi;
+    private final DatasetsSearchService datasetsSearchService;
+    private final BeaconFilteringTermsService beaconFilteringTermsService;
+
+    @Inject
+    public BeaconIndividualsSearchService(
+            @RestClient BeaconQueryApi beaconQueryApi,
+            @RestClient KeycloakQueryApi keycloakQueryApi,
+            DatasetsSearchService datasetsSearchService,
+            BeaconFilteringTermsService beaconFilteringTermsService
+    ) {
+        this.beaconQueryApi = beaconQueryApi;
+        this.keycloakQueryApi = keycloakQueryApi;
+        this.datasetsSearchService = datasetsSearchService;
+        this.beaconFilteringTermsService = beaconFilteringTermsService;
+    }
+
+    public DatasetsSearchResponse search(DatasetSearchQuery query, String accessToken) {
+        if (accessToken == null) {
+            return datasetsSearchService.search(query, accessToken);
+        }
+        var beaconAuthorization = retrieveAuthorization(accessToken);
+        var beaconResponse = queryOnBeacon(beaconAuthorization, query);
+        var enhancedQuery = enhanceQueryFacets(query, beaconResponse);
+        var datasetsReponse = datasetsSearchService.search(enhancedQuery, accessToken);
+        return enhanceDatasetsResponse(beaconAuthorization, datasetsReponse, beaconResponse);
+    }
+
+    private String retrieveAuthorization(String accessToken) {
+        var keycloakAuthorization = BEARER_PATTERN.formatted(accessToken);
+        var response = keycloakQueryApi.retriveIdpTokens(BEACON_IDP_ALIAS, keycloakAuthorization);
+        return BEARER_PATTERN.formatted(response.getAccessToken());
+    }
+
+    private List<BeaconResultSet> queryOnBeacon(
+            String beaconAuthorization,
+            DatasetSearchQuery query
+    ) {
+        var beaconFilters = ofNullable(query.getFacets()).orElseGet(List::of)
+                .stream()
+                .filter(it -> BEACON_FACET_GROUP.equals(it.getFacetGroup()))
+                .map(DatasetSearchQueryFacet::getValue)
+                .filter(not(String::isBlank))
+                .map(it -> BeaconIndividualsRequestQueryFilter.builder()
+                        .id(it)
+                        .scope(SCOPE)
+                        .build())
+                .toList();
+
+        var beaconQuery = BeaconIndividualsRequest.builder()
+                .meta(new BeaconIndividualsRequestMeta())
+                .query(BeaconIndividualsRequestQuery.builder()
+                        .includeResultsetResponses(INCLUDE_RESULTSET_RESPONSES)
+                        .requestedGranularity(REQUESTED_GRANULARITY)
+                        .testMode(false)
+                        .pagination(new BeaconIndividualsRequestQueryPagination())
+                        .filters(beaconFilters)
+                        .build())
+                .build();
+
+        var response = beaconQueryApi.listIndividuals(beaconAuthorization, beaconQuery);
+
+        return ofNullable(response)
+                .map(BeaconIndividualsResponse::getResponse)
+                .map(BeaconIndividualsResponseContent::getResultSets)
+                .orElseGet(List::of)
+                .stream()
+                .filter(it -> BEACON_DATASET_TYPE.equals(it.getSetType()) &&
+                        it.getResultsCount() > 0
+                )
+                .toList();
+    }
+
+    private DatasetSearchQuery enhanceQueryFacets(
+            DatasetSearchQuery query,
+            List<BeaconResultSet> resultSets
+    ) {
+        var enhancedFacets = resultSets.stream()
+                .map(BeaconResultSet::getId)
+                .map(it -> DatasetSearchQueryFacet.builder()
+                        .facetGroup(CKAN_FACET_GROUP)
+                        .facet(CKAN_IDENTIFIER_FIELD)
+                        .value(it)
+                        .build())
+                .collect(toCollection(ArrayList::new));
+
+        if (query.getFacets() != null) {
+            enhancedFacets.addAll(query.getFacets());
+        }
+
+        return query.toBuilder()
+                .facets(enhancedFacets)
+                .build();
+    }
+
+    private DatasetsSearchResponse enhanceDatasetsResponse(
+            String beaconAuthorization,
+            DatasetsSearchResponse datasetsReponse,
+            List<BeaconResultSet> resultSets
+    ) {
+        var facetGroupCount = new HashMap<String, Integer>();
+        facetGroupCount.put("beacon", resultSets.size());
+        if (datasetsReponse.getFacetGroupCount() != null) {
+            facetGroupCount.putAll(datasetsReponse.getFacetGroupCount());
+        }
+
+        var facetGroups = new ArrayList<FacetGroup>();
+        facetGroups.add(beaconFilteringTermsService.listFilteringTerms(beaconAuthorization));
+        if (datasetsReponse.getFacetGroups() != null) {
+            facetGroups.addAll(datasetsReponse.getFacetGroups());
+        }
+
+        return datasetsReponse.toBuilder()
+                .facetGroupCount(facetGroupCount)
+                .facetGroups(facetGroups)
+                .build();
+    }
+}

src/main/java/io/github/genomicdatainfrastructure/discovery/services/DatasetsSearchService.java

@@ -15,7 +15,7 @@
 @ApplicationScoped
 public class DatasetsSearchService {
 
-    private static final String FACETS_QUERY = "[\"access_rights\",\"theme\",\"tags\",\"spatial_uri\",\"organization\",\"publisher_name\",\"res_format\"]";
+    private static final String SELECTED_FACETS = "[\"access_rights\",\"theme\",\"tags\",\"spatial_uri\",\"organization\",\"publisher_name\",\"res_format\"]";
 
     private final CkanQueryApi ckanQueryApi;
 
@@ -27,15 +27,18 @@ public DatasetsSearchService(
     }
 
     public DatasetsSearchResponse search(DatasetSearchQuery query, String accessToken) {
+        var facetsQuery = CkanFacetsQueryBuilder.buildFacetQuery(query.getFacets());
+
         var response = ckanQueryApi.packageSearch(
                 query.getQuery(),
-                CkanFacetsQueryBuilder.buildFacetQuery(query.getFacets()),
+                facetsQuery,
                 query.getSort(),
                 query.getRows(),
                 query.getStart(),
-                FACETS_QUERY,
+                SELECTED_FACETS,
                 accessToken
         );
+
         return PackagesSearchResponseMapper.from(response);
     }
 }

src/main/java/io/github/genomicdatainfrastructure/discovery/services/PackagesSearchResponseMapper.java

@@ -34,10 +34,13 @@ private PackagesSearchResponseMapper() {
     }
 
     public static DatasetsSearchResponse from(PackagesSearchResponse response) {
+        var count = count(response.getResult());
+
         return DatasetsSearchResponse.builder()
-                .count(count(response.getResult()))
+                .count(count)
                 .facetGroups(facetGroups(response.getResult()))
                 .results(results(response.getResult()))
+                .facetGroupCount(Map.of("ckan", count))
                 .build();
     }
 
@@ -58,7 +61,7 @@ private static List<FacetGroup> facetGroups(PackagesSearchResult result) {
     private static FacetGroup facetGroup(Map<String, CkanFacet> facets) {
         return FacetGroup.builder()
                 .key("ckan")
-                .label("Metadata")
+                .label("DCAT-AP")
                 .facets(facets.entrySet().stream()
                         .map(PackagesSearchResponseMapper::facet)
                         .toList())