Merge remote-tracking branch 'origin/dev' into dev

pom.xml

@@ -11,7 +11,7 @@
 
   <groupId>org.gbif.registry</groupId>
   <artifactId>registry-parent</artifactId>
-  <version>3.94.17-SNAPSHOT</version>
+  <version>3.95.0-SNAPSHOT</version>
   <name>GBIF Registry Parent</name>
   <description>GBIF Registry project</description>
 
@@ -84,7 +84,7 @@
     <spring-cloud-sleuth.version>2.2.8.RELEASE</spring-cloud-sleuth.version>
 
     <!-- GBIF -->
-    <gbif-api.version>1.10.0</gbif-api.version>
+    <gbif-api.version>1.11.0</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-cli/pom.xml

@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.gbif.registry</groupId>
     <artifactId>registry-parent</artifactId>
-    <version>3.94.17-SNAPSHOT</version>
+    <version>3.95.0-SNAPSHOT</version>
   </parent>
 
   <artifactId>registry-cli</artifactId>

registry-cli/src/main/java/org/gbif/registry/cli/datasetindex/SpringContextBuilder.java

@@ -13,13 +13,6 @@
  */
 package org.gbif.registry.cli.datasetindex;
 
-import com.fasterxml.jackson.core.JsonParser;
-import com.fasterxml.jackson.databind.DeserializationContext;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.deser.std.DateDeserializers;
-
-import com.fasterxml.jackson.databind.module.SimpleModule;
-
 import org.gbif.api.service.registry.DatasetService;
 import org.gbif.api.service.registry.InstallationService;
 import org.gbif.api.service.registry.NetworkService;
@@ -42,6 +35,9 @@
 import org.gbif.ws.client.ClientBuilder;
 import org.gbif.ws.json.JacksonJsonObjectMapperProvider;
 
+import java.io.IOException;
+import java.util.Date;
+
 import org.springframework.boot.actuate.autoconfigure.elasticsearch.ElasticSearchRestHealthContributorAutoConfiguration;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.autoconfigure.freemarker.FreeMarkerAutoConfiguration;
@@ -57,12 +53,14 @@
 import org.springframework.context.annotation.Primary;
 import org.springframework.core.env.MapPropertySource;
 
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.databind.DeserializationContext;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.deser.std.DateDeserializers;
+import com.fasterxml.jackson.databind.module.SimpleModule;
 import com.google.common.collect.ImmutableMap;
 import com.zaxxer.hikari.HikariDataSource;
 
-import java.io.IOException;
-import java.util.Date;
-
 public class SpringContextBuilder {
 
   private static EsClient.EsClientConfiguration toEsClientConfiguration(

registry-cli/src/main/java/org/gbif/registry/cli/doisynchronizer/DoiSynchronizer.java

@@ -30,6 +30,7 @@
 import org.gbif.registry.persistence.mapper.DoiMapper;
 import org.gbif.registry.persistence.mapper.OccurrenceDownloadMapper;
 import org.gbif.registry.persistence.mapper.UserMapper;
+import org.gbif.registry.persistence.mapper.params.DatasetListParams;
 
 import java.io.File;
 import java.io.IOException;
@@ -40,9 +41,6 @@
 
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.StringUtils;
-
-import org.gbif.registry.persistence.mapper.params.DatasetListParams;
-
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.context.ApplicationContext;

registry-cli/src/main/java/org/gbif/registry/cli/doisynchronizer/diagnostic/DoiDiagnostician.java

@@ -26,11 +26,10 @@
 import org.gbif.registry.persistence.mapper.DatasetMapper;
 import org.gbif.registry.persistence.mapper.DoiMapper;
 import org.gbif.registry.persistence.mapper.OccurrenceDownloadMapper;
+import org.gbif.registry.persistence.mapper.params.DatasetListParams;
 
 import java.util.stream.Collectors;
 
-import org.gbif.registry.persistence.mapper.params.DatasetListParams;
-
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

registry-directory/pom.xml

@@ -3,7 +3,7 @@
   <parent>
     <artifactId>registry-parent</artifactId>
     <groupId>org.gbif.registry</groupId>
-    <version>3.94.17-SNAPSHOT</version>
+    <version>3.95.0-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 

registry-doi/pom.xml

@@ -3,7 +3,7 @@
   <parent>
     <artifactId>registry-parent</artifactId>
     <groupId>org.gbif.registry</groupId>
-    <version>3.94.17-SNAPSHOT</version>
+    <version>3.95.0-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 

registry-domain/pom.xml

@@ -3,7 +3,7 @@
   <parent>
     <artifactId>registry-parent</artifactId>
     <groupId>org.gbif.registry</groupId>
-    <version>3.94.17-SNAPSHOT</version>
+    <version>3.95.0-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 

registry-domain/src/main/java/org/gbif/registry/domain/ws/LegacyDataset.java

@@ -20,7 +20,9 @@
 import org.gbif.api.model.registry.Contact;
 import org.gbif.api.model.registry.Dataset;
 import org.gbif.api.model.registry.Endpoint;
+import org.gbif.api.util.VocabularyUtils;
 import org.gbif.api.vocabulary.ContactType;
+import org.gbif.api.vocabulary.DatasetSubtype;
 import org.gbif.api.vocabulary.DatasetType;
 import org.gbif.api.vocabulary.EndpointType;
 import org.gbif.api.vocabulary.Language;
@@ -73,6 +75,7 @@ public class LegacyDataset extends Dataset implements LegacyEntity {
   private String serviceTypes;
   private String serviceUrls;
   private DOI datasetDoi;
+  private String rawSubtype;
 
   // created from combination of fields after injection
   private Contact primaryContact;
@@ -141,6 +144,17 @@ public void setOrganizationKey(String organizationKey) {
     }
   }
 
+  @XmlTransient
+  @Nullable
+  public String getRawSubtype() {
+    return rawSubtype;
+  }
+
+  @ParamName(LegacyResourceConstants.SUBTYPE_PARAM)
+  public void setRawSubtype(String rawSubtype) {
+    this.rawSubtype = rawSubtype;
+  }
+
   /**
    * Get the publishing organization key. This is a required field in Registry2, and is required by
    * the web services. This method is not used but it is needed otherwise this Object can't be
@@ -634,6 +648,7 @@ public void prepare() {
     addArchiveEndpoint();
     addDataPackageEndpoint();
     setType(resolveType());
+    setSubtype(resolveSubtype());
   }
 
   /**
@@ -811,6 +826,18 @@ public DatasetType resolveType() {
     return DatasetType.METADATA;
   }
 
+  /**
+   * Return the DatasetSubtype from the string.
+   */
+  public DatasetSubtype resolveSubtype() {
+    try {
+      return VocabularyUtils.lookupEnum(rawSubtype, DatasetSubtype.class);
+    } catch (Exception e) {
+      LOG.error("Failed to resolve subtype", e);
+      return null;
+    }
+  }
+
   /**
    * Return a new GBIF API Dataset instance, derived from the LegacyDataset. Needed because of:
    * http://dev.gbif.org/issues/browse/REG-459
@@ -830,6 +857,7 @@ public Dataset toApiDataset() {
     dataset.setLogoUrl(getLogoUrl());
     dataset.setHomepage(getHomepage());
     dataset.setType(getType());
+    dataset.setSubtype(getSubtype());
     dataset.setDoi(datasetDoi);
     return dataset;
   }
@@ -853,7 +881,8 @@ public boolean equals(Object o) {
         && Objects.equal(primaryContact, that.primaryContact)
         && Objects.equal(emlEndpoint, that.emlEndpoint)
         && Objects.equal(archiveEndpoint, that.archiveEndpoint)
-        && Objects.equal(dataPackageEndpoint, that.dataPackageEndpoint);
+        && Objects.equal(dataPackageEndpoint, that.dataPackageEndpoint)
+        && Objects.equal(rawSubtype, that.rawSubtype);
   }
 
   @Generated
@@ -873,7 +902,8 @@ public int hashCode() {
         primaryContact,
         emlEndpoint,
         archiveEndpoint,
-        dataPackageEndpoint);
+        dataPackageEndpoint,
+        rawSubtype);
   }
 
   @Generated
@@ -893,6 +923,7 @@ public String toString() {
         .add("emlEndpoint", emlEndpoint)
         .add("archiveEndpoint", archiveEndpoint)
         .add("dataPackageEndpoint", dataPackageEndpoint)
+        .add("rawSubtype", rawSubtype)
         .toString();
   }
 }

registry-domain/src/main/java/org/gbif/registry/domain/ws/util/LegacyResourceConstants.java

@@ -49,6 +49,7 @@ public class LegacyResourceConstants {
   public static final String TYPE_DESCRIPTION_PARAM = "typeDescription";
   public static final String ACCESS_POINT_URL_PARAM = "accessPointURL";
   public static final String DOI_PARAM = "doi";
+  public static final String SUBTYPE_PARAM = "subtype";
 
   // request / response value names
   public static final String ADMINISTRATIVE_CONTACT_TYPE = "administrative";

registry-events/pom.xml

@@ -3,7 +3,7 @@
   <parent>
     <artifactId>registry-parent</artifactId>
     <groupId>org.gbif.registry</groupId>
-    <version>3.94.17-SNAPSHOT</version>
+    <version>3.95.0-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 

registry-examples/pom.xml

@@ -3,12 +3,12 @@
   <parent>
     <artifactId>registry-parent</artifactId>
     <groupId>org.gbif.registry</groupId>
-    <version>3.94.17-SNAPSHOT</version>
+    <version>3.95.0-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 
   <artifactId>registry-examples</artifactId>
-  <version>3.94.17-SNAPSHOT</version>
+  <version>3.95.0-SNAPSHOT</version>
 
   <packaging>jar</packaging>
 

registry-identity/pom.xml

@@ -3,7 +3,7 @@
   <parent>
     <artifactId>registry-parent</artifactId>
     <groupId>org.gbif.registry</groupId>
-    <version>3.94.17-SNAPSHOT</version>
+    <version>3.95.0-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 

registry-integration-tests/pom.xml

@@ -3,7 +3,7 @@
   <parent>
     <artifactId>registry-parent</artifactId>
     <groupId>org.gbif.registry</groupId>
-    <version>3.94.17-SNAPSHOT</version>
+    <version>3.95.0-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 

registry-integration-tests/src/test/java/org/gbif/registry/ws/it/DatasetIT.java

@@ -51,7 +51,6 @@
 import org.gbif.registry.ws.client.InstallationClient;
 import org.gbif.registry.ws.client.NodeClient;
 import org.gbif.registry.ws.client.OrganizationClient;
-import org.gbif.registry.ws.provider.networkEntitiesList.BaseRequestSearchParamsHandlerMethodArgumentResolver;
 import org.gbif.registry.ws.resources.DatasetResource;
 import org.gbif.utils.file.FileUtils;
 import org.gbif.ws.NotFoundException;

registry-integration-tests/src/test/java/org/gbif/registry/ws/it/InstallationIT.java

@@ -17,16 +17,12 @@
 import org.gbif.api.model.registry.Identifier;
 import org.gbif.api.model.registry.Installation;
 import org.gbif.api.model.registry.MachineTag;
-import org.gbif.api.model.registry.Node;
 import org.gbif.api.model.registry.Organization;
-import org.gbif.api.model.registry.search.DatasetRequestSearchParams;
 import org.gbif.api.model.registry.search.InstallationRequestSearchParams;
-import org.gbif.api.model.registry.search.OrganizationRequestSearchParams;
 import org.gbif.api.service.registry.InstallationService;
 import org.gbif.api.service.registry.NodeService;
 import org.gbif.api.service.registry.OrganizationService;
 import org.gbif.api.util.Range;
-import org.gbif.api.vocabulary.Country;
 import org.gbif.api.vocabulary.IdentifierType;
 import org.gbif.api.vocabulary.InstallationType;
 import org.gbif.registry.search.test.EsManageServer;

registry-integration-tests/src/test/java/org/gbif/registry/ws/it/NetworkIT.java

@@ -20,13 +20,10 @@
 import org.gbif.api.model.registry.Installation;
 import org.gbif.api.model.registry.MachineTag;
 import org.gbif.api.model.registry.Network;
-import org.gbif.api.model.registry.Node;
 import org.gbif.api.model.registry.Organization;
 import org.gbif.api.model.registry.search.NetworkRequestSearchParams;
-import org.gbif.api.model.registry.search.NodeRequestSearchParams;
 import org.gbif.api.service.registry.DatasetService;
 import org.gbif.api.service.registry.NetworkService;
-import org.gbif.api.service.registry.NodeService;
 import org.gbif.api.util.Range;
 import org.gbif.api.vocabulary.IdentifierType;
 import org.gbif.registry.identity.service.IdentityService;

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

@@ -1,3 +1,16 @@
+/*
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package org.gbif.registry.ws.it.collections.service.batch;
 
 import org.gbif.api.model.collections.Address;

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

@@ -1,3 +1,16 @@
+/*
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package org.gbif.registry.ws.it.collections.service.batch;
 
 import org.gbif.api.model.collections.Collection;

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

@@ -1,3 +1,16 @@
+/*
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package org.gbif.registry.ws.it.collections.service.batch;
 
 import org.gbif.api.model.collections.Collection;

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

@@ -1,3 +1,16 @@
+/*
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package org.gbif.registry.ws.it.collections.service.batch;
 
 import org.gbif.api.model.collections.CollectionEntityType;

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

@@ -1,3 +1,16 @@
+/*
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package org.gbif.registry.ws.it.collections.service.batch;
 
 import org.gbif.api.model.collections.CollectionEntityType;