Merge branch 'dev'

pom.xml

@@ -84,7 +84,7 @@
     <spring-cloud-sleuth.version>2.2.8.RELEASE</spring-cloud-sleuth.version>
 
     <!-- GBIF -->
-    <gbif-api.version>1.12.8</gbif-api.version>
+    <gbif-api.version>1.12.10</gbif-api.version>
     <gbif-common.version>0.59</gbif-common.version>
     <gbif-common-mybatis.version>1.3</gbif-common-mybatis.version>
     <gbif-common-ws.version>1.25</gbif-common-ws.version>

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

@@ -528,7 +528,7 @@ public void listChangeSuggestionTest() {
     UUID entityKey = UUID.randomUUID();
     Pageable page = new PagingRequest();
 
-    when(getMockChangeSuggestionService().list(status, type, proposerEmail, entityKey, page))
+    when(getMockChangeSuggestionService().list(status, type, proposerEmail, entityKey, null, page))
         .thenReturn(
             new PagingResponse<>(
                 new PagingRequest(), 1L, Collections.singletonList(changeSuggestion)));

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

@@ -451,7 +451,6 @@ public void explicitMappingsTest() {
     params.setDatasetKey(d1.getKey());
     params.setInstitutionCode(i1.getCode());
     params.setCollectionCode(c5.getCode());
-    params.setDatasetKey(d1.getKey());
 
     // When
     LookupResult result = lookupService.lookup(params);
@@ -536,7 +535,6 @@ public void ambiguousExplicitMappingsTest() {
     params.setInstitutionId(occMappingI22.getIdentifier());
     params.setCollectionCode(occMappingC2.getCode());
     params.setCollectionId(occMappingC22.getIdentifier());
-    params.setDatasetKey(d1.getKey());
 
     // When
     LookupResult result = lookupService.lookup(params);
@@ -553,6 +551,39 @@ public void ambiguousExplicitMappingsTest() {
     assertEquals(Match.Status.AMBIGUOUS_EXPLICIT_MAPPINGS, collectionMatch.getStatus());
   }
 
+  @Test
+  public void explicitMappingsWithParentCodeTest() {
+    // State
+    Dataset d1 = createDataset();
+
+    OccurrenceMapping occMappingC1 = new OccurrenceMapping();
+    occMappingC1.setDatasetKey(d1.getKey());
+    occMappingC1.setParentCode(i1.getCode());
+    collectionService.addOccurrenceMapping(c1.getKey(), occMappingC1);
+
+    LookupParams params = new LookupParams();
+    params.setDatasetKey(d1.getKey());
+    params.setInstitutionCode(i1.getCode());
+    params.setInstitutionId(i1.getKey().toString());
+
+    // When
+    LookupResult result = lookupService.lookup(params);
+
+    // Should
+    assertNotNull(result.getInstitutionMatch());
+    Match<InstitutionMatched> institutionMatch = result.getInstitutionMatch();
+    assertEquals(Match.MatchType.EXACT, institutionMatch.getMatchType());
+    assertEquals(i1.getKey(), institutionMatch.getEntityMatched().getKey());
+    assertEquals(2, institutionMatch.getReasons().size());
+    assertEquals(Match.Status.ACCEPTED, institutionMatch.getStatus());
+
+    assertNotNull(result.getCollectionMatch());
+    Match<CollectionMatched> collectionMatch = result.getCollectionMatch();
+    assertEquals(Match.MatchType.EXPLICIT_MAPPING, collectionMatch.getMatchType());
+    assertEquals(c1.getKey(), collectionMatch.getEntityMatched().getKey());
+    assertEquals(Match.Status.ACCEPTED, collectionMatch.getStatus());
+  }
+
   @Test
   public void countryMatchTest() {
     // State

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

@@ -433,6 +433,11 @@ public void discardSuggestionTest() {
   public void listTest() {
     // State
     T entity = createEntity();
+
+    Address address = new Address();
+    address.setCountry(Country.DENMARK);
+    entity.setAddress(address);
+
     R suggestion = createEmptyChangeSuggestion();
     suggestion.setSuggestedEntity(entity);
     suggestion.setType(Type.CREATE);
@@ -442,8 +447,17 @@ public void listTest() {
     int suggKey1 = changeSuggestionService.createChangeSuggestion(suggestion);
 
     T entity2 = createEntity();
+    Address address2 = new Address();
+    address2.setCountry(Country.DENMARK);
+    entity2.setAddress(address2);
+
     UUID entity2Key = collectionEntityService.create(entity2);
     R suggestion2 = createEmptyChangeSuggestion();
+
+    Address addressSugg = new Address();
+    addressSugg.setCountry(Country.SPAIN);
+    entity2.setAddress(addressSugg);
+
     suggestion2.setSuggestedEntity(entity2);
     suggestion2.setEntityKey(entity2Key);
     suggestion2.setType(Type.UPDATE);
@@ -454,26 +468,38 @@ public void listTest() {
 
     // When
     PagingResponse<R> results =
-        changeSuggestionService.list(Status.APPLIED, null, null, null, DEFAULT_PAGE);
+        changeSuggestionService.list(Status.APPLIED, null, null, null, null, DEFAULT_PAGE);
     // Then
     assertEquals(0, results.getResults().size());
     assertEquals(0, results.getCount());
 
     // When
-    results = changeSuggestionService.list(null, Type.CREATE, null, null, DEFAULT_PAGE);
+    results = changeSuggestionService.list(null, Type.CREATE, null, null, null, DEFAULT_PAGE);
     // Then
     assertEquals(1, results.getResults().size());
     assertEquals(1, results.getCount());
 
     // When
-    results = changeSuggestionService.list(null, null, null, entity2Key, DEFAULT_PAGE);
+    results = changeSuggestionService.list(null, null, null, entity2Key, null, DEFAULT_PAGE);
     // Then
     assertEquals(1, results.getResults().size());
     assertEquals(1, results.getCount());
 
+    // When
+    results = changeSuggestionService.list(null, null, null, null, Country.DENMARK, DEFAULT_PAGE);
+    // Then
+    assertEquals(2, results.getResults().size());
+    assertEquals(2, results.getCount());
+
+    // When
+    results = changeSuggestionService.list(null, null, null, null, Country.SPAIN, DEFAULT_PAGE);
+    // Then
+    assertEquals(0, results.getResults().size());
+    assertEquals(0, results.getCount());
+
     // When - user with no rights can't see the proposer email
     resetSecurityContext("user", UserRole.USER);
-    results = changeSuggestionService.list(null, null, null, entity2Key, DEFAULT_PAGE);
+    results = changeSuggestionService.list(null, null, null, entity2Key, null, DEFAULT_PAGE);
     // Then
     assertTrue(results.getResults().stream().allMatch(v -> v.getProposerEmail() == null));
   }
@@ -587,15 +613,14 @@ public void updateContactsTest() {
     assertTrue(applied.getContactPersons().stream().anyMatch(c -> c.getFirstName().equals("11")));
     assertTrue(applied.getContactPersons().stream().anyMatch(c -> c.getFirstName().equals("22")));
 
-
     entity = collectionEntityService.get(entityKey);
 
     // suggestion to change contact1
     entity.getContactPersons().stream()
-      .filter(c -> c.getKey().equals(contact1.getKey()))
-      .findFirst()
-      .get()
-      .setModifiedBy("11");
+        .filter(c -> c.getKey().equals(contact1.getKey()))
+        .findFirst()
+        .get()
+        .setModifiedBy("11");
 
     R suggestion3 = createEmptyChangeSuggestion();
     suggestion3.setSuggestedEntity(entity);

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

@@ -17,6 +17,7 @@
 import org.gbif.api.model.collections.suggestions.Status;
 import org.gbif.api.model.collections.suggestions.Type;
 import org.gbif.api.model.common.paging.Pageable;
+import org.gbif.api.vocabulary.Country;
 import org.gbif.registry.persistence.mapper.collections.dto.ChangeSuggestionDto;
 
 import java.util.List;
@@ -43,14 +44,16 @@ List<ChangeSuggestionDto> list(
       @Param("entityType") CollectionEntityType entityType,
       @Param("proposerEmail") String proposerEmail,
       @Param("entityKey") UUID entityKey,
+      @Param("country") Country country,
       @Nullable @Param("page") Pageable page);
 
   long count(
       @Param("status") Status status,
       @Param("type") Type type,
       @Param("entityType") CollectionEntityType entityType,
       @Param("proposerEmail") String proposerEmail,
-      @Param("entityKey") UUID entityKey);
+      @Param("entityKey") UUID entityKey,
+      @Param("country") Country country);
 
   void update(ChangeSuggestionDto suggestion);
 }

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

@@ -26,6 +26,7 @@ public interface LookupMapper<T extends EntityMatchedDto> {
 
   List<T> lookup(
       @Nullable @Param("code") String code,
+      @Nullable @Param("parentCode") String parentCode,
       @Nullable @Param("identifier") String identifier,
       @Nullable @Param("key") UUID key,
       @Nullable @Param("datasetKey") UUID datasetKey);

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

@@ -50,8 +50,5 @@ public class ChangeSuggestionDto {
   private String nameNewInstitutionConvertedCollection;
   private Date modified;
   private String modifiedBy;
-
-  // this field is not persisted in the DB. It stores the country that has to be taken into account
-  // to check the user permissions
   private Country countryScope;
 }

registry-persistence/src/main/resources/liquibase/128-suggestions-country.xml

@@ -0,0 +1,13 @@
+<databaseChangeLog
+    xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-2.0.xsd">
+
+  <changeSet id="128" author="mlopez" runInTransaction="false">
+    <sql splitStatements="false" stripComments="false">
+      <![CDATA[
+        ALTER TABLE change_suggestion ADD COLUMN entity_country CHAR(2) CHECK (assert_min_length(entity_country, 2));
+      ]]>
+    </sql>
+  </changeSet>
+</databaseChangeLog>

registry-persistence/src/main/resources/liquibase/129-parent-code-occurrence-mapping.xml

@@ -0,0 +1,13 @@
+<databaseChangeLog
+    xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-2.0.xsd">
+
+  <changeSet id="129" author="mlopez" runInTransaction="false">
+    <sql splitStatements="false" stripComments="false">
+      <![CDATA[
+        ALTER TABLE occurrence_mapping ADD COLUMN parent_code varchar CHECK (assert_min_length(code, 1));
+      ]]>
+    </sql>
+  </changeSet>
+</databaseChangeLog>

registry-persistence/src/main/resources/liquibase/master.xml

@@ -133,4 +133,6 @@
   <include file="liquibase/125-occurrence-counts-grscicoll.xml" />
   <include file="liquibase/126-wikidata-ncbi-identifier-types.xml" />
   <include file="liquibase/127-organization-country-not-null.xml" />
+  <include file="liquibase/128-suggestions-country.xml" />
+  <include file="liquibase/129-parent-code-occurrence-mapping.xml" />
 </databaseChangeLog>

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

@@ -7,19 +7,20 @@
     <id property="key" column="key"/>
     <result property="comments" column="comments" typeHandler="StringArrayTypeHandler"/>
     <result property="changes" column="changes" typeHandler="SuggestedChangesTypeHandler"/>
+    <result property="countryScope" column="entity_country"/>
   </resultMap>
 
   <sql id="SUGGESTION_WRITE_FIELDS">
     entity_type, entity_key, type, status, proposed, proposed_by, proposer_email, changes, comments,
     suggested_entity, merge_target_key, institution_converted_collection, name_new_institution_converted_collection,
-    modified, modified_by
+    modified, modified_by, entity_country
   </sql>
 
   <sql id="SUGGESTION_READ_FIELDS">
     cs.key, cs.entity_type, cs.entity_key, cs.type, cs.status, cs.proposed, cs.proposed_by, cs.proposer_email, cs. applied,
     cs.applied_by, cs.discarded_by, cs.discarded, cs.suggested_entity, cs.comments,
     cs.merge_target_key, cs.changes, cs.institution_converted_collection, cs.name_new_institution_converted_collection,
-    cs.modified, cs.modified_by
+    cs.modified, cs.modified_by, cs.entity_country
   </sql>
 
   <sql id="SUGGESTION_PARAMS_CREATE">
@@ -37,7 +38,8 @@
     #{institutionConvertedCollection,jdbcType=OTHER},
     #{nameNewInstitutionConvertedCollection,jdbcType=VARCHAR},
     now(), <!-- modified -->
-    #{modifiedBy,jdbcType=VARCHAR}
+    #{modifiedBy,jdbcType=VARCHAR},
+    #{countryScope,jdbcType=VARCHAR}
   </sql>
 
   <sql id="SUGGESTION_PARAMS_UPDATE">
@@ -51,7 +53,8 @@
     discarded_by = #{discardedBy,jdbcType=INTEGER},
     applied = #{applied,jdbcType=OTHER},
     applied_by = #{appliedBy,jdbcType=INTEGER},
-    entity_key = #{entityKey,jdbcType=INTEGER}
+    entity_key = #{entityKey,jdbcType=INTEGER},
+    entity_country = #{countryScope,jdbcType=VARCHAR}
   </sql>
 
   <insert id="create" parameterType="ChangeSuggestionDto" useGeneratedKeys="true" keyProperty="key">
@@ -94,6 +97,9 @@
       <if test="entityKey != null">
         AND cs.entity_key = #{entityKey,jdbcType=OTHER}
       </if>
+      <if test="country != null">
+        AND cs.entity_country = #{country,jdbcType=VARCHAR}
+      </if>
     </where>
     ORDER BY cs.proposed DESC
     <if test="page != null">
@@ -120,6 +126,9 @@
       <if test="entityKey != null">
         AND cs.entity_key = #{entityKey,jdbcType=OTHER}
       </if>
+      <if test="country != null">
+        AND cs.entity_country = #{country,jdbcType=VARCHAR}
+      </if>
     </where>
   </select>
 

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

@@ -523,6 +523,7 @@
           INNER JOIN occurrence_mapping om ON om.key = com.occurrence_mapping_key
           WHERE c.deleted is null AND om.dataset_key = #{datasetKey,jdbcType=OTHER}
           <if test="code != null"> AND (om.code IS NULL OR om.code = #{code,jdbcType=VARCHAR})</if>
+          <if test="parentCode != null"> AND (om.parent_code IS NULL OR om.parent_code = #{parentCode,jdbcType=VARCHAR})</if>
           <if test="identifier != null"> AND (om.identifier IS NULL OR om.identifier = #{identifier,jdbcType=VARCHAR})</if>
       </if>
     </trim>) AS matches

registry-service/README.md

@@ -39,6 +39,7 @@ when there are more than 1 possible combination within a dataset. This allows us
 - All the occurrences from the dataset X have to be mapped to the institution I
 - All the occurrences from the dataset X and code Y have to be mapped to the institution I
 - All the occurrences from the dataset X, code Y and identifier Z have to be mapped to the institution I
+- For collections only, all the occurrences from the dataset X and parentCode Y(this is the institution code) have to be mapped to the collection C
 
 There can be as many combinations as needed.
 

registry-service/src/main/java/org/gbif/registry/service/collections/lookup/matchers/BaseMatcher.java

@@ -203,17 +203,18 @@ private static String cleanString(String value) {
     return !Strings.isNullOrEmpty(value) ? value.trim() : null;
   }
 
-  protected List<T> getDbMatches(String codeParam, String identifierParam, UUID datasetKey) {
+  protected List<T> getDbMatches(String codeParam, String parentCodeParam, String identifierParam, UUID datasetKey) {
     String code = cleanString(codeParam);
+    String parentCode = cleanString(parentCodeParam);
     String identifier = cleanString(identifierParam);
 
-    if (code == null && identifier == null) {
+    if (code == null && identifier == null && datasetKey == null) {
       return Collections.emptyList();
     }
 
     UUID key = parseUUID(identifier);
 
-    return getLookupMapper().lookup(code, identifier, key, datasetKey);
+    return getLookupMapper().lookup(code, parentCode, identifier, key, datasetKey);
   }
 
   protected Match<R> createMatch(