merged develop into release/1.0-develop

manually resolve merge conflicts

.env.template

@@ -3,6 +3,8 @@
 USER_ID=<user id of system user>
 GROUP_ID=<group id of system user>
 
+ORCID_SANDBOX_AUTHENTICATION=<true or false; true=>use the Sandbox Orcid, false=>use the Production Orcid.  Defaults to false.>
+
 # Authentication variables
 OAUTH_CLIENT_ID=<oauth app client id>
 OAUTH_CLIENT_SECRET=<ouath_client_secret goes here>

src/main/java/org/breedinginsight/db/migration/V1_32_0__Set_Dev_Admin_Email.java

@@ -0,0 +1,87 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * 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.breedinginsight.db.migration;
+
+import lombok.extern.slf4j.Slf4j;
+import org.breedinginsight.daos.UserDAO;
+import org.flywaydb.core.api.migration.BaseJavaMigration;
+import org.flywaydb.core.api.migration.Context;
+import org.jooq.DSLContext;
+
+import javax.inject.Inject;
+import java.sql.SQLException;
+import java.sql.Statement;
+import java.util.*;
+
+@Slf4j
+public class V1_32_0__Set_Dev_Admin_Email extends BaseJavaMigration {
+
+    @Inject
+    private DSLContext dsl;
+    @Inject
+    private UserDAO userDAO;
+
+    final private String ORCID_SANDBOX_AUTHENTICATION = "orcid-sandbox-authentication";
+
+    public void migrate(Context context) throws Exception {
+        Map<String, String> placeholders = context.getConfiguration().getPlaceholders();
+        boolean isOrcidSandboxAuthentication =  Boolean.parseBoolean( placeholders.get(ORCID_SANDBOX_AUTHENTICATION) );
+        updateDevAdminUser(context, isOrcidSandboxAuthentication);
+        //Must delete user "Chris Tucker" before adding the new Constraint (User "Chris Tucker" is added by migration V0.5.2__populate-user-data.sql.
+        // It would violate the new constraint)
+        // PS -- We miss Chris Tucker.
+        deleteUserChris(context);
+        addConstraint(context);
+    }
+
+    private void updateDevAdminUser(Context context, boolean isOrcidSandboxAuthentication) throws SQLException {
+        String biDevAdminUserEmail = isOrcidSandboxAuthentication ?
+                "[email protected]" : "[email protected]";
+        try (Statement update = context.getConnection().createStatement()) {
+            String sql = "UPDATE bi_user SET email='" + biDevAdminUserEmail + "' WHERE NULLIF(email,'') IS NULL AND bi_user.name='BI-DEV Admin'";
+            log.debug(sql);
+            update.executeUpdate(sql);
+        }
+    }
+
+    private void deleteUserChris(Context context) throws SQLException {
+        try (Statement delete = context.getConnection().createStatement()) {
+            String sql = "DELETE FROM bi_user WHERE name = 'Chris Tucker'  AND email IS NULL";
+            log.debug(sql);
+            delete.executeUpdate(sql);
+        }
+    }
+
+    private void addConstraint(Context context) throws SQLException {
+        final String CONSTRAINT_NAME = "email_orcid";
+        // First, drop the constraint if it already exist.
+        try (Statement altTable = context.getConnection().createStatement()) {
+            String sql = "ALTER TABLE bi_user DROP CONSTRAINT IF EXISTS "+ CONSTRAINT_NAME;
+            log.debug(sql);
+            altTable.executeUpdate(sql);
+        }
+
+        // Add new constraint
+        try (Statement altTable = context.getConnection().createStatement()) {
+            String sql = "ALTER TABLE bi_user\n" +
+                    "ADD CONSTRAINT " +CONSTRAINT_NAME+ " CHECK ( (email IS NOT NULL ) OR (orcid IS NULL) ) ;";
+            log.debug(sql);
+            altTable.executeUpdate(sql);
+        }
+    }
+}

src/main/java/org/breedinginsight/services/validators/TraitValidatorService.java

@@ -228,6 +228,7 @@ public ValidationErrors checkTraitFieldsFormat(List<Trait> traits, TraitValidato
         }
         return errors;
     }
+
     public List<Trait> checkDuplicateTraitsExistingByName(UUID programId, List<Trait> traits){
 
         List<Trait> duplicates = new ArrayList<>();

src/main/resources/application.yml

@@ -110,6 +110,7 @@ flyway:
       placeholders:
         default-url: ${brapi.server.default-url}
         brapi-reference-source: ${brapi.server.reference-source}
+        orcid-sandbox-authentication: ${ORCID_SANDBOX_AUTHENTICATION:false}
       out-of-order: true
 jooq:
   datasources:

src/main/resources/version.properties

@@ -14,5 +14,6 @@
 # limitations under the License.
 #
 
-version=v1.0.0+872
-versionInfo=https://github.com/Breeding-Insight/bi-api/commit/8b73c45263b416ed0944240f6da23c2810cdd11c
+
+version=v1.1.0+887
+versionInfo=https://github.com/Breeding-Insight/bi-api/commit/b7d65b01c976e1c729ef9bb450143e63dad4c014

src/test/java/org/breedinginsight/api/v1/controller/metadata/MetadataFilterIntegrationTest.java

@@ -132,7 +132,7 @@ public void getDataResponseMetadataFilterSuccess() {
 
         // Check our page numbers weren't altered by the filtered
         assertEquals(1, data.getAsJsonPrimitive("totalPages").getAsInt(), "Default total pages is incorrect");
-        assertEquals(38, data.getAsJsonPrimitive("totalCount").getAsInt(), "Default total count is incorrect");
+        assertEquals(37, data.getAsJsonPrimitive("totalCount").getAsInt(), "Default total count is incorrect");
         assertEquals(50, data.getAsJsonPrimitive("pageSize").getAsInt(), "Default page size is incorrect");
         assertEquals(1, data.getAsJsonPrimitive("currentPage").getAsInt(), "Default current page is incorrect");
     }