#494 list institutions in GeoJson format

pom.xml

@@ -127,6 +127,7 @@
     <owasp-java-html-sanitizer.version>20200713.1</owasp-java-html-sanitizer.version>
     <super-csv.version>2.4.0</super-csv.version>
     <opencsv.version>5.7.1</opencsv.version>
+    <geojson.version>1.14</geojson.version>
 
     <!-- Test -->
     <junit.version>5.9.1</junit.version>
@@ -504,6 +505,11 @@
         <artifactId>feign-jackson</artifactId>
         <version>${feign.version}</version>
       </dependency>
+      <dependency>
+        <groupId>de.grundid.opendatalab</groupId>
+        <artifactId>geojson-jackson</artifactId>
+        <version>${geojson.version}</version>
+      </dependency>
 
       <dependency>
         <groupId>com.squareup.retrofit2</groupId>

registry-integration-tests/src/test/java/org/gbif/registry/ws/it/collections/resource/InstitutionResourceIT.java

@@ -13,15 +13,12 @@
  */
 package org.gbif.registry.ws.it.collections.resource;
 
-import liquibase.pro.packaged.I;
-
 import org.gbif.api.model.collections.Institution;
 import org.gbif.api.model.collections.InstitutionImportParams;
 import org.gbif.api.model.collections.merge.ConvertToCollectionParams;
 import org.gbif.api.model.collections.request.InstitutionSearchRequest;
 import org.gbif.api.model.collections.suggestions.InstitutionChangeSuggestion;
 import org.gbif.api.model.collections.suggestions.Type;
-import org.gbif.api.model.common.paging.Pageable;
 import org.gbif.api.model.common.paging.PagingRequest;
 import org.gbif.api.model.common.paging.PagingResponse;
 import org.gbif.api.model.registry.search.collections.KeyCodeNameResult;
@@ -47,6 +44,9 @@
 import java.util.List;
 import java.util.UUID;
 
+import org.geojson.Feature;
+import org.geojson.FeatureCollection;
+import org.geojson.Point;
 import org.junit.jupiter.api.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.mock.mockito.MockBean;
@@ -106,6 +106,27 @@ public void listTest() {
     assertEquals(institutions.size(), result.getResults().size());
   }
 
+  @Test
+  public void listAsGeoJsonTest() {
+    FeatureCollection featureCollection = new FeatureCollection();
+    Feature f1 = new Feature();
+    f1.setGeometry(new Point(12d, 50d));
+    f1.setProperty("name", "n1");
+    f1.setProperty("key", UUID.randomUUID().toString());
+    featureCollection.add(f1);
+    Feature f2 = new Feature();
+    f2.setGeometry(new Point(22d, 51d));
+    f2.setProperty("name", "n2");
+    f2.setProperty("key", UUID.randomUUID().toString());
+    featureCollection.add(f2);
+
+    when(institutionService.listGeojson(any(InstitutionSearchRequest.class)))
+        .thenReturn(featureCollection);
+
+    FeatureCollection result = getClient().listAsGeoJson(new InstitutionSearchRequest());
+    assertEquals(featureCollection.getFeatures().size(), result.getFeatures().size());
+  }
+
   @Test
   public void testSuggest() {
     KeyCodeNameResult r1 = new KeyCodeNameResult(UUID.randomUUID(), "c1", "n1");

registry-integration-tests/src/test/java/org/gbif/registry/ws/it/collections/service/InstitutionServiceIT.java

@@ -41,6 +41,7 @@
 import org.gbif.registry.service.collections.duplicates.InstitutionDuplicatesService;
 import org.gbif.ws.client.filter.SimplePrincipalProvider;
 
+import java.math.BigDecimal;
 import java.net.URI;
 import java.util.Arrays;
 import java.util.Collections;
@@ -49,6 +50,8 @@
 import javax.validation.ConstraintViolationException;
 import javax.validation.ValidationException;
 
+import org.geojson.FeatureCollection;
+import org.geojson.Point;
 import org.junit.jupiter.api.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 
@@ -58,6 +61,7 @@
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertNull;
 import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 /** Tests the {@link InstitutionService}. */
 public class InstitutionServiceIT extends BaseCollectionEntityServiceIT<Institution> {
@@ -671,4 +675,45 @@ public void lockMasterSourceFieldsTest() {
     institutionService.deleteMasterSourceMetadata(institutionKey);
     assertDoesNotThrow(() -> institutionService.delete(institutionKey));
   }
+
+  @Test
+  public void listAsGeoJsonTest() {
+    Institution institution1 = testData.newEntity();
+    institution1.setCode("c1");
+    institution1.setName("n1");
+    institution1.setLatitude(new BigDecimal(12));
+    institution1.setLongitude(new BigDecimal(2));
+    UUID key1 = institutionService.create(institution1);
+
+    Institution institution2 = testData.newEntity();
+    institution2.setCode("c2");
+    institution2.setName("n2");
+    institution2.setLatitude(new BigDecimal(23));
+    institution2.setLongitude(new BigDecimal(70));
+    UUID key2 = institutionService.create(institution2);
+
+    Institution institution3 = testData.newEntity();
+    institution3.setCode("c3");
+    institution3.setName("n3");
+    UUID key3 = institutionService.create(institution3);
+
+    assertEquals(
+        2,
+        institutionService
+            .listGeojson(InstitutionSearchRequest.builder().build())
+            .getFeatures()
+            .size());
+    FeatureCollection featuresC1 =
+        institutionService.listGeojson(InstitutionSearchRequest.builder().code("c1").build());
+    assertEquals(1, featuresC1.getFeatures().size());
+    assertTrue(featuresC1.getFeatures().get(0).getGeometry() instanceof Point);
+    assertEquals(2, featuresC1.getFeatures().get(0).getProperties().size());
+    assertEquals("n1", featuresC1.getFeatures().get(0).getProperty("name"));
+    assertEquals(
+        12d,
+        ((Point) featuresC1.getFeatures().get(0).getGeometry()).getCoordinates().getLatitude());
+    assertEquals(
+        2d,
+        ((Point) featuresC1.getFeatures().get(0).getGeometry()).getCoordinates().getLongitude());
+  }
 }

registry-persistence/src/main/java/org/gbif/registry/persistence/config/MyBatisConfiguration.java

@@ -62,6 +62,7 @@
 import org.gbif.registry.persistence.mapper.collections.dto.CollectionMatchedDto;
 import org.gbif.registry.persistence.mapper.collections.dto.DuplicateDto;
 import org.gbif.registry.persistence.mapper.collections.dto.DuplicateMetadataDto;
+import org.gbif.registry.persistence.mapper.collections.dto.InstitutionGeoJsonDto;
 import org.gbif.registry.persistence.mapper.collections.dto.InstitutionMatchedDto;
 import org.gbif.registry.persistence.mapper.collections.dto.MasterSourceOrganizationDto;
 import org.gbif.registry.persistence.mapper.collections.dto.SearchDto;
@@ -156,6 +157,9 @@ ConfigurationCustomizer mybatisConfigCustomizer() {
       configuration
           .getTypeAliasRegistry()
           .registerAlias("InstitutionMatchedDto", InstitutionMatchedDto.class);
+      configuration
+          .getTypeAliasRegistry()
+          .registerAlias("InstitutionGeoJsonDto", InstitutionGeoJsonDto.class);
       configuration
           .getTypeAliasRegistry()
           .registerAlias("CollectionMatchedDto", CollectionMatchedDto.class);
@@ -165,7 +169,9 @@ ConfigurationCustomizer mybatisConfigCustomizer() {
       configuration
           .getTypeAliasRegistry()
           .registerAlias("MasterSourceOrganizationDto", MasterSourceOrganizationDto.class);
-      configuration.getTypeAliasRegistry().registerAlias("OrganizationContactDto", OrganizationContactDto.class);
+      configuration
+          .getTypeAliasRegistry()
+          .registerAlias("OrganizationContactDto", OrganizationContactDto.class);
 
       configuration.getTypeAliasRegistry().registerAlias("UriTypeHandler", UriTypeHandler.class);
       configuration.getTypeAliasRegistry().registerAlias("UuidTypeHandler", UuidTypeHandler.class);

registry-persistence/src/main/java/org/gbif/registry/persistence/mapper/collections/InstitutionMapper.java

@@ -14,8 +14,8 @@
 package org.gbif.registry.persistence.mapper.collections;
 
 import org.gbif.api.model.collections.Institution;
-import org.gbif.api.model.common.paging.Pageable;
 import org.gbif.api.model.registry.search.collections.KeyCodeNameResult;
+import org.gbif.registry.persistence.mapper.collections.dto.InstitutionGeoJsonDto;
 import org.gbif.registry.persistence.mapper.collections.dto.InstitutionMatchedDto;
 import org.gbif.registry.persistence.mapper.collections.params.InstitutionSearchParams;
 
@@ -48,4 +48,6 @@ public interface InstitutionMapper
 
   void convertToCollection(
       @Param("institutionKey") UUID institutionKey, @Param("collectionKey") UUID collectionKey);
+
+  List<InstitutionGeoJsonDto> listGeoJson(@Param("params") InstitutionSearchParams searchParams);
 }

registry-persistence/src/main/java/org/gbif/registry/persistence/mapper/collections/dto/InstitutionGeoJsonDto.java

@@ -0,0 +1,15 @@
+package org.gbif.registry.persistence.mapper.collections.dto;
+
+import java.math.BigDecimal;
+import java.util.UUID;
+
+import lombok.Data;
+
+@Data
+public class InstitutionGeoJsonDto {
+
+  private UUID key;
+  private String name;
+  private BigDecimal latitude;
+  private BigDecimal longitude;
+}

registry-persistence/src/main/resources/org/gbif/registry/persistence/mapper/collections/InstitutionMapper.xml

@@ -26,6 +26,10 @@
     <result property="alternativeCodes" column="alternative_codes" typeHandler="org.gbif.mybatis.type.StringArrayTypeHandler"/>
   </resultMap>
 
+  <resultMap id="INSTITUTION_GEOJSON_DTO_MAP" type="InstitutionGeoJsonDto" autoMapping="true">
+    <id property="key" column="key"/>
+  </resultMap>
+
   <sql id="INSTITUTION_WRITE_FIELDS">
     key, code, name, description, type, active, email, phone, homepage, catalog_url, api_url, institutional_governance, discipline,
     latitude, longitude, mailing_address_key, address_key, additional_names, founding_date, geographic_description,
@@ -207,6 +211,22 @@
     <include refid="LIST_FILTER"/>
   </select>
 
+  <!-- returns only the fields needed for geojson -->
+  <select id="listGeoJson" resultType="InstitutionGeoJsonDto"  resultMap="INSTITUTION_GEOJSON_DTO_MAP" parameterType="Pageable">
+    SELECT DISTINCT ON (<if test="params.query != null" >ts_rank_cd(i.fulltext_search, query), </if>
+    <if test="params.fuzzyName != null" >similarity_score, </if> i.key)
+    i.key, i.name, i.latitude, i.longitude
+    <if test="params.fuzzyName != null" >,similarity(i.name, #{params.fuzzyName,jdbcType=VARCHAR}) AS similarity_score</if>
+    <include refid="LIST_FILTER"/>
+    AND i.latitude IS NOT NULL AND i.longitude IS NOT NULL
+    ORDER BY <if test="params.query != null" >ts_rank_cd(i.fulltext_search, query) DESC, </if>
+    <if test="params.fuzzyName != null" >similarity_score DESC, </if>
+    i.key
+    <if test="params.page != null" >
+      LIMIT #{params.page.limit} OFFSET #{params.page.offset}
+    </if>
+  </select>
+
   <sql id="LIST_FILTER">
     FROM institution i
     <if test="params.query != null" >

registry-service/pom.xml

@@ -64,6 +64,10 @@
       <groupId>com.opencsv</groupId>
       <artifactId>opencsv</artifactId>
     </dependency>
+    <dependency>
+      <groupId>de.grundid.opendatalab</groupId>
+      <artifactId>geojson-jackson</artifactId>
+    </dependency>
 
     <!-- Test dependencies -->
     <dependency>

registry-service/src/main/java/org/gbif/registry/service/collections/DefaultInstitutionService.java

@@ -40,6 +40,7 @@
 import org.gbif.registry.persistence.mapper.collections.InstitutionMapper;
 import org.gbif.registry.persistence.mapper.collections.MasterSourceSyncMetadataMapper;
 import org.gbif.registry.persistence.mapper.collections.OccurrenceMappingMapper;
+import org.gbif.registry.persistence.mapper.collections.dto.InstitutionGeoJsonDto;
 import org.gbif.registry.persistence.mapper.collections.params.InstitutionSearchParams;
 import org.gbif.registry.service.WithMyBatis;
 import org.gbif.registry.service.collections.converters.InstitutionConverter;
@@ -53,6 +54,9 @@
 import javax.validation.Validator;
 import javax.validation.groups.Default;
 
+import org.geojson.Feature;
+import org.geojson.FeatureCollection;
+import org.geojson.Point;
 import org.jetbrains.annotations.NotNull;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.security.access.annotation.Secured;
@@ -128,39 +132,43 @@ private PagingResponse<Institution> listInternal(
 
     Pageable page = searchRequest.getPage() == null ? new PagingRequest() : searchRequest.getPage();
 
+    InstitutionSearchParams params = buildSearchParams(searchRequest, deleted, page);
+
+    long total = institutionMapper.count(params);
+    return new PagingResponse<>(page, total, institutionMapper.list(params));
+  }
+
+  private InstitutionSearchParams buildSearchParams(
+      InstitutionSearchRequest searchRequest, boolean deleted, Pageable page) {
     String query =
         searchRequest.getQ() != null
             ? Strings.emptyToNull(CharMatcher.WHITESPACE.trimFrom(searchRequest.getQ()))
             : searchRequest.getQ();
 
-    InstitutionSearchParams params =
-        InstitutionSearchParams.builder()
-            .query(query)
-            .code(searchRequest.getCode())
-            .name(searchRequest.getName())
-            .alternativeCode(searchRequest.getAlternativeCode())
-            .machineTagNamespace(searchRequest.getMachineTagNamespace())
-            .machineTagName(searchRequest.getMachineTagName())
-            .machineTagValue(searchRequest.getMachineTagValue())
-            .identifierType(searchRequest.getIdentifierType())
-            .identifier(searchRequest.getIdentifier())
-            .country(searchRequest.getCountry())
-            .city(searchRequest.getCity())
-            .fuzzyName(searchRequest.getFuzzyName())
-            .active(searchRequest.getActive())
-            .type(searchRequest.getType())
-            .institutionalGovernance(searchRequest.getInstitutionalGovernance())
-            .disciplines(searchRequest.getDisciplines())
-            .masterSourceType(searchRequest.getMasterSourceType())
-            .numberSpecimens(parseNumberSpecimensParameter(searchRequest.getNumberSpecimens()))
-            .displayOnNHCPortal(searchRequest.getDisplayOnNHCPortal())
-            .replacedBy(searchRequest.getReplacedBy())
-            .deleted(deleted)
-            .page(page)
-            .build();
-
-    long total = institutionMapper.count(params);
-    return new PagingResponse<>(page, total, institutionMapper.list(params));
+    return InstitutionSearchParams.builder()
+        .query(query)
+        .code(searchRequest.getCode())
+        .name(searchRequest.getName())
+        .alternativeCode(searchRequest.getAlternativeCode())
+        .machineTagNamespace(searchRequest.getMachineTagNamespace())
+        .machineTagName(searchRequest.getMachineTagName())
+        .machineTagValue(searchRequest.getMachineTagValue())
+        .identifierType(searchRequest.getIdentifierType())
+        .identifier(searchRequest.getIdentifier())
+        .country(searchRequest.getCountry())
+        .city(searchRequest.getCity())
+        .fuzzyName(searchRequest.getFuzzyName())
+        .active(searchRequest.getActive())
+        .type(searchRequest.getType())
+        .institutionalGovernance(searchRequest.getInstitutionalGovernance())
+        .disciplines(searchRequest.getDisciplines())
+        .masterSourceType(searchRequest.getMasterSourceType())
+        .numberSpecimens(parseNumberSpecimensParameter(searchRequest.getNumberSpecimens()))
+        .displayOnNHCPortal(searchRequest.getDisplayOnNHCPortal())
+        .replacedBy(searchRequest.getReplacedBy())
+        .deleted(deleted)
+        .page(page)
+        .build();
   }
 
   @Override
@@ -225,4 +233,23 @@ public UUID createFromOrganization(UUID organizationKey, String institutionCode)
 
     return institutionKey;
   }
+
+  @Override
+  public FeatureCollection listGeojson(InstitutionSearchRequest searchRequest) {
+    List<InstitutionGeoJsonDto> dtos =
+        institutionMapper.listGeoJson(buildSearchParams(searchRequest, false, null));
+
+    FeatureCollection featureCollection = new FeatureCollection();
+    dtos.forEach(
+        dto -> {
+          Feature feature = new Feature();
+          feature.setProperty("key", dto.getKey());
+          feature.setProperty("name", dto.getName());
+          feature.setGeometry(
+              new Point(dto.getLongitude().doubleValue(), dto.getLatitude().doubleValue()));
+          featureCollection.add(feature);
+        });
+
+    return featureCollection;
+  }
 }

registry-ws-client/src/main/java/org/gbif/registry/ws/client/collections/InstitutionClient.java

@@ -18,13 +18,13 @@
 import org.gbif.api.model.collections.merge.ConvertToCollectionParams;
 import org.gbif.api.model.collections.request.InstitutionSearchRequest;
 import org.gbif.api.model.collections.suggestions.InstitutionChangeSuggestion;
-import org.gbif.api.model.common.paging.Pageable;
 import org.gbif.api.model.common.paging.PagingResponse;
 import org.gbif.api.model.registry.search.collections.KeyCodeNameResult;
 
 import java.util.List;
 import java.util.UUID;
 
+import org.geojson.FeatureCollection;
 import org.springframework.cloud.openfeign.SpringQueryMap;
 import org.springframework.http.MediaType;
 import org.springframework.web.bind.annotation.PathVariable;
@@ -42,6 +42,13 @@ public interface InstitutionClient
   @ResponseBody
   PagingResponse<Institution> list(@SpringQueryMap InstitutionSearchRequest searchRequest);
 
+  @RequestMapping(
+      method = RequestMethod.GET,
+      value = "geojson",
+      produces = MediaType.APPLICATION_JSON_VALUE)
+  @ResponseBody
+  FeatureCollection listAsGeoJson(@SpringQueryMap InstitutionSearchRequest searchRequest);
+
   @RequestMapping(
       method = RequestMethod.GET,
       value = "deleted",