DS-3489: Fixes after rebase on master

dspace-api/src/main/java/org/dspace/core/Context.java

@@ -7,16 +7,6 @@
  */
 package org.dspace.core;
 
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.EmptyStackException;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Locale;
-import java.util.Set;
-import java.util.Stack;
-import java.util.UUID;
-
 import org.apache.log4j.Logger;
 import org.dspace.authorize.ResourcePolicy;
 import org.dspace.content.DSpaceObject;
@@ -32,6 +22,10 @@ import org.dspace.storage.rdbms.DatabaseUtils;
 import org.dspace.utils.DSpace;
 import org.springframework.util.CollectionUtils;
 
+import java.sql.SQLException;
+import java.util.*;
+import java.util.concurrent.atomic.AtomicBoolean;
+
 /**
  * Class representing the context of a particular DSpace operation. This stores
  * information such as the current authenticated user and the database

dspace-api/src/main/java/org/dspace/storage/rdbms/DatabaseUtils.java

@@ -513,9 +513,15 @@ public class DatabaseUtils
                 log.info("Loading Flyway DB migrations from: " + StringUtils.join(scriptLocations, ", "));
                 flywaydb.setLocations(scriptLocations.toArray(new String[scriptLocations.size()]));
 
-                } catch (SQLException e) {
-                    log.error("Unable to setup Flyway against DSpace database", e);
-                }
+                // Set flyway callbacks (i.e. classes which are called post-DB migration and similar)
+                // In this situation, we have a Registry Updater that runs PRE-migration
+                // NOTE: DatabaseLegacyReindexer only indexes in Legacy Lucene & RDBMS indexes. It can be removed once those are obsolete.
+                List<FlywayCallback> flywayCallbacks = DSpaceServicesFactory.getInstance().getServiceManager().getServicesByType(FlywayCallback.class);
+                flywaydb.setCallbacks(flywayCallbacks.toArray(new FlywayCallback[flywayCallbacks.size()]));
+            }
+            catch(SQLException e)
+            {
+                log.error("Unable to setup Flyway against DSpace database", e);
             }
         }
 
@@ -600,11 +606,22 @@ public class DatabaseUtils
             // Setup Flyway API against our database
             Flyway flyway = setupFlyway(datasource);
 
+            // Set whethe Flyway will run migrations "out of order". By default, this is false,
+            // and Flyway ONLY runs migrations that have a higher version number.
+            flyway.setOutOfOrder(outOfOrder);
+
+            // If a target version was specified, tell Flyway to ONLY migrate to that version
+            // (i.e. all later migrations are left as "pending"). By default we always migrate to latest version.
+            if(!StringUtils.isBlank(targetVersion))
+            {
+                flyway.setTargetAsString(targetVersion);
+            }
+
             // Does the necessary Flyway table ("schema_version") exist in this database?
             // If not, then this is the first time Flyway has run, and we need to initialize
             // NOTE: search is case sensitive, as flyway table name is ALWAYS lowercase,
             // See: http://flywaydb.org/documentation/faq.html#case-sensitive
-            if (!tableExists(connection, flyway.getTable(), true))
+            if(!tableExists(connection, flyway.getTable(), true))
             {
                 // Try to determine our DSpace database version, so we know what to tell Flyway to do
                 String dbVersion = determineDBVersion(connection);
@@ -624,6 +641,7 @@ public class DatabaseUtils
                 }
             }
 
+            // Determine pending Database migrations
             MigrationInfo[] pending = flyway.info().pending();
 
             // As long as there are pending migrations, log them and run migrate()

dspace-spring-rest/src/main/java/org/dspace/app/rest/configuration/RESTSpringLoader.java

@@ -37,4 +37,4 @@ public class RESTSpringLoader implements SpringLoader {
             return new String[0];
         }
     }
-}
+}

dspace-spring-rest/src/main/java/org/dspace/app/rest/model/BaseObjectRest.java

@@ -9,9 +9,10 @@ package org.dspace.app.rest.model;
 
 import java.io.Serializable;
 
-import com.fasterxml.jackson.annotation.JsonIgnore;
 import org.springframework.hateoas.Identifiable;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
+
 /**
  * Base class for any REST resource that need to be addressable
  * 

dspace-spring-rest/src/main/java/org/dspace/app/rest/model/BrowseIndexRest.java

@@ -9,9 +9,10 @@ package org.dspace.app.rest.model;
 
 import java.util.List;
 
+import org.dspace.app.rest.RestResourceController;
+
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonProperty;
-import org.dspace.app.rest.RestResourceController;
 
 /**
  * The Browse Index REST Resource

dspace-spring-rest/src/main/java/org/dspace/app/rest/model/GroupRest.java

@@ -9,9 +9,10 @@ package org.dspace.app.rest.model;
 
 import java.util.List;
 
-import com.fasterxml.jackson.annotation.JsonIgnore;
 import org.dspace.app.rest.RestResourceController;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
+
 /**
  * The Group REST Resource
  * 

dspace-spring-rest/src/main/java/org/dspace/app/rest/model/ItemRest.java

@@ -11,6 +11,8 @@ import java.util.Date;
 import java.util.List;
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonProperty.Access;
 
 /**
  * The Item REST Resource

dspace-spring-rest/src/main/java/org/dspace/app/rest/model/MetadataFieldRest.java

@@ -7,9 +7,10 @@
  */
 package org.dspace.app.rest.model;
 
-import com.fasterxml.jackson.annotation.JsonIgnore;
 import org.dspace.app.rest.RestResourceController;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
+
 /**
  * The MetadataField REST Resource
  * 

dspace-spring-rest/src/main/java/org/dspace/app/rest/model/MetadataSchemaRest.java

@@ -7,8 +7,12 @@
  */
 package org.dspace.app.rest.model;
 
+import java.util.List;
+
 import org.dspace.app.rest.RestResourceController;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
+
 /**
  * The MetadataSchema REST Resource
  * 

dspace-spring-rest/src/main/java/org/dspace/app/rest/model/RestModel.java

@@ -38,7 +38,4 @@ public interface RestModel extends Serializable {
 
 	@JsonIgnore
 	public Class getController();
-
-
-
 }

dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/BitstreamFormatRestRepository.java

@@ -21,6 +21,7 @@ import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.stereotype.Component;
 
+
 /**
  * This is the repository responsible to manage BitstreamFormat Rest object
  * 

dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/BrowseIndexRestRepository.java

@@ -7,12 +7,16 @@
  */
 package org.dspace.app.rest.repository;
 
+import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.List;
 
 import org.dspace.app.rest.converter.BrowseIndexConverter;
+import org.dspace.app.rest.converter.CollectionConverter;
 import org.dspace.app.rest.model.BrowseIndexRest;
+import org.dspace.app.rest.model.CollectionRest;
 import org.dspace.app.rest.model.hateoas.BrowseIndexResource;
+import org.dspace.app.rest.model.hateoas.CollectionResource;
 import org.dspace.browse.BrowseException;
 import org.dspace.browse.BrowseIndex;
 import org.dspace.core.Context;
@@ -20,6 +24,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageImpl;
 import org.springframework.data.domain.Pageable;
+import org.springframework.data.rest.webmvc.ResourceNotFoundException;
 import org.springframework.stereotype.Component;
 
 /**

dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/DSpaceRestRepository.java

@@ -11,7 +11,13 @@ import java.io.Serializable;
 
 import org.dspace.app.rest.model.RestModel;
 import org.dspace.app.rest.model.hateoas.DSpaceResource;
+import org.dspace.app.rest.utils.ContextUtil;
+import org.dspace.app.rest.utils.Utils;
 import org.dspace.core.Context;
+import org.dspace.services.RequestService;
+import org.dspace.services.model.Request;
+import org.dspace.utils.DSpace;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.domain.Sort;

dspace-spring-rest/src/main/java/org/dspace/app/rest/utils/ApplicationConfig.java

@@ -22,7 +22,6 @@ import org.springframework.data.web.config.EnableSpringDataWebSupport;
 @EnableSpringDataWebSupport
 @ComponentScan({ "org.dspace.app.rest.converter", "org.dspace.app.rest.repository", "org.dspace.app.rest.utils" })
 public class ApplicationConfig {
-
 	@Value("${dspace.dir}")
 	private String dspaceHome;
 

dspace-spring-rest/src/main/java/org/dspace/app/rest/utils/ContextUtil.java

@@ -7,11 +7,6 @@
  */
 package org.dspace.app.rest.utils;
 
-import java.sql.SQLException;
-
-import javax.servlet.ServletException;
-import javax.servlet.ServletRequest;
-
 import org.apache.log4j.Logger;
 import org.dspace.core.Context;
 

dspace-spring-rest/src/test/java/org/dspace/app/rest/builder/AbstractBuilder.java

@@ -12,16 +12,7 @@ import org.dspace.authorize.factory.AuthorizeServiceFactory;
 import org.dspace.authorize.service.AuthorizeService;
 import org.dspace.authorize.service.ResourcePolicyService;
 import org.dspace.content.factory.ContentServiceFactory;
-import org.dspace.content.service.BitstreamFormatService;
-import org.dspace.content.service.BitstreamService;
-import org.dspace.content.service.BundleService;
-import org.dspace.content.service.CollectionService;
-import org.dspace.content.service.CommunityService;
-import org.dspace.content.service.DSpaceObjectService;
-import org.dspace.content.service.InstallItemService;
-import org.dspace.content.service.ItemService;
-import org.dspace.content.service.WorkspaceItemService;
-import org.dspace.core.Constants;
+import org.dspace.content.service.*;
 import org.dspace.core.Context;
 import org.dspace.discovery.IndexingService;
 import org.dspace.eperson.factory.EPersonServiceFactory;
@@ -63,6 +54,15 @@ public abstract class AbstractBuilder<T, S> {
     static AuthorizeService authorizeService;
     static ResourcePolicyService resourcePolicyService;
     static IndexingService indexingService;
+    static RegistrationDataService registrationDataService;
+    static VersionHistoryService versionHistoryService;
+    static ClaimedTaskService claimedTaskService;
+    static InProgressUserService inProgressUserService;
+    static PoolTaskService poolTaskService;
+    static WorkflowItemRoleService workflowItemRoleService;
+    static MetadataFieldService metadataFieldService;
+    static MetadataSchemaService metadataSchemaService;
+    static SiteService siteService;
 
     protected Context context;
 
@@ -89,6 +89,18 @@ public abstract class AbstractBuilder<T, S> {
         authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
         resourcePolicyService = AuthorizeServiceFactory.getInstance().getResourcePolicyService();
         indexingService = DSpaceServicesFactory.getInstance().getServiceManager().getServiceByName(IndexingService.class.getName(),IndexingService.class);
+        registrationDataService = EPersonServiceFactory.getInstance().getRegistrationDataService();
+        versionHistoryService = VersionServiceFactory.getInstance().getVersionHistoryService();
+        metadataFieldService = ContentServiceFactory.getInstance().getMetadataFieldService();
+        metadataSchemaService = ContentServiceFactory.getInstance().getMetadataSchemaService();
+        siteService = ContentServiceFactory.getInstance().getSiteService();
+
+        // Temporarily disabled
+        // TODO find a way to be able to test the XML and "default" workflow at the same time
+        //claimedTaskService = XmlWorkflowServiceFactoryImpl.getInstance().getClaimedTaskService();
+        //inProgressUserService = XmlWorkflowServiceFactoryImpl.getInstance().getInProgressUserService();
+        //poolTaskService = XmlWorkflowServiceFactoryImpl.getInstance().getPoolTaskService();
+        //workflowItemRoleService = XmlWorkflowServiceFactoryImpl.getInstance().getWorkflowItemRoleService();
     }
 
 
@@ -106,6 +118,15 @@ public abstract class AbstractBuilder<T, S> {
         resourcePolicyService = null;
         indexingService = null;
         bitstreamFormatService = null;
+        registrationDataService = null;
+        versionHistoryService = null;
+        claimedTaskService = null;
+        inProgressUserService = null;
+        poolTaskService = null;
+        workflowItemRoleService = null;
+        metadataFieldService = null;
+        metadataSchemaService = null;
+        siteService = null;
     }
 
     public static void cleanupObjects() throws Exception {

dspace-spring-rest/src/test/java/org/dspace/app/rest/matcher/ItemMatcher.java

@@ -45,7 +45,8 @@ public class ItemMatcher {
                 hasJsonPath("$._links.self.href", startsWith(REST_SERVER_URL)),
                 hasJsonPath("$._links.bitstreams.href", startsWith(REST_SERVER_URL)),
                 hasJsonPath("$._links.owningCollection.href", startsWith(REST_SERVER_URL)),
-                hasJsonPath("$._links.templateItemOf.href", startsWith(REST_SERVER_URL))
+                hasJsonPath("$._links.templateItemOf.href", startsWith(REST_SERVER_URL)),
+                hasJsonPath("$._links.self.href", startsWith(REST_SERVER_URL))
         );
     }
 

dspace-spring-rest/src/test/java/org/dspace/app/rest/test/AbstractDSpaceIntegrationTest.java

@@ -107,6 +107,5 @@ public class AbstractDSpaceIntegrationTest
         return System.getProperty("dspace.dir");
 
     }
-
 }
 

dspace-spring-rest/src/test/java/org/dspace/app/rest/test/AbstractIntegrationTestWithDatabase.java

@@ -9,12 +9,12 @@ package org.dspace.app.rest.test;
 
 import static org.junit.Assert.fail;
 
-import java.io.IOException;
 import java.sql.SQLException;
 import java.util.Arrays;
 
 import org.apache.log4j.Logger;
 import org.dspace.app.launcher.ScriptLauncher;
+import org.dspace.app.rest.builder.AbstractBuilder;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Community;
 import org.dspace.core.Context;
@@ -28,10 +28,6 @@ import org.junit.After;
 import org.junit.Before;
 import org.junit.BeforeClass;
 
-import java.sql.SQLException;
-
-import static org.junit.Assert.fail;
-
 /**
  * Abstract Test class that will initialize the in-memory database
  */