Execute settings migration as migration step + move all steps to migr…

…ation module
molgenis · Aug 20, 2015 · fc90982 · fc90982
1 parent 44e6d77
commit fc90982
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Showing 40 changed files with 281 additions and 127 deletions.
diff --git a/molgenis-app/src/main/java/org/molgenis/app/WebAppConfig.java b/molgenis-app/src/main/java/org/molgenis/app/WebAppConfig.java
@@ -13,30 +13,35 @@
 import org.molgenis.data.elasticsearch.config.EmbeddedElasticSearchConfig;
 import org.molgenis.data.elasticsearch.factory.EmbeddedElasticSearchServiceFactory;
 import org.molgenis.data.jpa.JpaRepositoryCollection;
-import org.molgenis.data.migrate.v1_9.Step14UpdateAttributeMapping;
 import org.molgenis.data.mysql.AsyncJdbcTemplate;
 import org.molgenis.data.mysql.MysqlRepository;
 import org.molgenis.data.mysql.MysqlRepositoryCollection;
 import org.molgenis.data.support.DataServiceImpl;
 import org.molgenis.data.system.RepositoryTemplateLoader;
-import org.molgenis.data.version.v1_5.Step1UpgradeMetaData;
-import org.molgenis.data.version.v1_5.Step2;
-import org.molgenis.data.version.v1_5.Step3AddOrderColumnToMrefTables;
-import org.molgenis.data.version.v1_5.Step4VarcharToText;
-import org.molgenis.data.version.v1_6.Step7UpgradeMetaDataTo1_6;
-import org.molgenis.data.version.v1_6.Step8VarcharToTextRepeated;
-import org.molgenis.data.version.v1_6.Step9MysqlTablesToInnoDB;
-import org.molgenis.data.version.v1_8.Step11ConvertNames;
-import org.molgenis.data.version.v1_8.Step12ChangeElasticsearchTokenizer;
-import org.molgenis.data.version.v1_9.Step15AddDefaultValue;
 import org.molgenis.dataexplorer.freemarker.DataExplorerHyperlinkDirective;
+import org.molgenis.migrate.version.v1_5.Step1UpgradeMetaData;
+import org.molgenis.migrate.version.v1_5.Step2;
+import org.molgenis.migrate.version.v1_5.Step3AddOrderColumnToMrefTables;
+import org.molgenis.migrate.version.v1_5.Step4VarcharToText;
+import org.molgenis.migrate.version.v1_5.Step5AlterDataexplorerMenuURLs;
+import org.molgenis.migrate.version.v1_5.Step6ChangeRScriptType;
+import org.molgenis.migrate.version.v1_6.Step7UpgradeMetaDataTo1_6;
+import org.molgenis.migrate.version.v1_6.Step8VarcharToTextRepeated;
+import org.molgenis.migrate.version.v1_6.Step9MysqlTablesToInnoDB;
+import org.molgenis.migrate.version.v1_8.Step10DeleteFormReferences;
+import org.molgenis.migrate.version.v1_8.Step11ConvertNames;
+import org.molgenis.migrate.version.v1_8.Step12ChangeElasticsearchTokenizer;
+import org.molgenis.migrate.version.v1_8.Step13RemoveCatalogueMenuEntries;
+import org.molgenis.migrate.version.v1_9.RuntimePropertyToAppSettingsMigrator;
+import org.molgenis.migrate.version.v1_9.RuntimePropertyToDataExplorerSettingsMigrator;
+import org.molgenis.migrate.version.v1_9.RuntimePropertyToGenomicDataSettingsMigrator;
+import org.molgenis.migrate.version.v1_9.RuntimePropertyToStaticContentMigrator;
+import org.molgenis.migrate.version.v1_9.Step14UpdateAttributeMapping;
+import org.molgenis.migrate.version.v1_9.Step15AddDefaultValue;
+import org.molgenis.migrate.version.v1_9.Step16RuntimePropertyToSettings;
 import org.molgenis.system.core.FreemarkerTemplateRepository;
 import org.molgenis.ui.MolgenisWebAppConfig;
 import org.molgenis.ui.menumanager.MenuManagerService;
-import org.molgenis.ui.migrate.v1_5.Step5AlterDataexplorerMenuURLs;
-import org.molgenis.ui.migrate.v1_5.Step6ChangeRScriptType;
-import org.molgenis.ui.migrate.v1_8.Step10DeleteFormReferences;
-import org.molgenis.ui.migrate.v1_8.Step13RemoveCatalogueMenuEntries;
 import org.molgenis.util.DependencyResolver;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -88,6 +93,18 @@ public class WebAppConfig extends MolgenisWebAppConfig
 	@Autowired
 	private EmbeddedElasticSearchServiceFactory embeddedElasticSearchServiceFactory;
 
+	@Autowired
+	private RuntimePropertyToAppSettingsMigrator runtimePropertyToAppSettingsMigrator;
+
+	@Autowired
+	private RuntimePropertyToGenomicDataSettingsMigrator runtimePropertyToGenomicDataSettingsMigrator;
+
+	@Autowired
+	private RuntimePropertyToDataExplorerSettingsMigrator runtimePropertyToDataExplorerSettingsMigrator;
+
+	@Autowired
+	private RuntimePropertyToStaticContentMigrator runtimePropertyToStaticContentMigrator;
+
 	@Override
 	public ManageableRepositoryCollection getBackend()
 	{
@@ -124,6 +141,9 @@ public void addUpgrades()
 		upgradeService.addUpgrade(new Step13RemoveCatalogueMenuEntries(dataSource));
 		upgradeService.addUpgrade(new Step14UpdateAttributeMapping(dataSource));
 		upgradeService.addUpgrade(new Step15AddDefaultValue(dataSource, searchService, jpaRepositoryCollection));
+		upgradeService.addUpgrade(new Step16RuntimePropertyToSettings(runtimePropertyToAppSettingsMigrator,
+				runtimePropertyToGenomicDataSettingsMigrator, runtimePropertyToDataExplorerSettingsMigrator,
+				runtimePropertyToStaticContentMigrator));
 	}
 
 	@Override

diff --git a/molgenis-core-ui/pom.xml b/molgenis-core-ui/pom.xml
@@ -237,11 +237,6 @@
 			<version>1.3</version>
 			<scope>test</scope>
 		</dependency>
-		<dependency>
-			<groupId>org.molgenis</groupId>
-			<artifactId>molgenis-data-migrate</artifactId>
-			<version>${project.version}</version>
-		</dependency>
 		<dependency>
 			<groupId>com.google.auto.value</groupId>
 			<artifactId>auto-value</artifactId>

diff --git a/molgenis-core-ui/src/main/java/org/molgenis/ui/MolgenisWebAppConfig.java b/molgenis-core-ui/src/main/java/org/molgenis/ui/MolgenisWebAppConfig.java
@@ -42,8 +42,8 @@
 import org.molgenis.data.validation.EntityAttributesValidator;
 import org.molgenis.data.validation.IndexedRepositoryValidationDecorator;
 import org.molgenis.data.validation.RepositoryValidationDecorator;
-import org.molgenis.data.version.MolgenisUpgradeService;
 import org.molgenis.file.FileStore;
+import org.molgenis.framework.MolgenisUpgradeService;
 import org.molgenis.framework.db.WebAppDatabasePopulator;
 import org.molgenis.framework.db.WebAppDatabasePopulatorService;
 import org.molgenis.framework.ui.MolgenisPluginRegistry;

diff --git a/...olgenis/data/version/MolgenisUpgrade.java → ...g/molgenis/framework/MolgenisUpgrade.java b/...olgenis/data/version/MolgenisUpgrade.java → ...g/molgenis/framework/MolgenisUpgrade.java
@@ -1,4 +1,4 @@
-package org.molgenis.data.version;
+package org.molgenis.framework;
 
 /**
  * Base class for Molgenis upgrade steps.

diff --git a/molgenis-core/src/main/java/org/molgenis/framework/MolgenisUpgradeService.java b/molgenis-core/src/main/java/org/molgenis/framework/MolgenisUpgradeService.java
@@ -0,0 +1,8 @@
+package org.molgenis.framework;
+
+public interface MolgenisUpgradeService
+{
+	boolean upgrade();
+
+	public void addUpgrade(MolgenisUpgrade upgrade);
+}
diff --git a/molgenis-data-import/pom.xml b/molgenis-data-import/pom.xml
@@ -72,6 +72,11 @@
 			<artifactId>molgenis-data-jpa</artifactId>
 			<version>${project.version}</version>
 		</dependency>
+		<dependency>
+            <groupId>org.molgenis</groupId>
+            <artifactId>molgenis-data-mysql</artifactId>
+            <version>${project.version}</version>
+        </dependency>
 		<dependency>
 			<groupId>org.molgenis</groupId>
 			<artifactId>molgenis-security</artifactId>

diff --git a/molgenis-data-migrate/pom.xml b/molgenis-data-migrate/pom.xml
@@ -33,5 +33,20 @@
 			<artifactId>molgenis-security-core</artifactId>
 			<version>${project.version}</version>
 		</dependency>
+		<dependency>
+            <groupId>org.molgenis</groupId>
+            <artifactId>molgenis-core-ui</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+		<dependency>
+            <groupId>org.molgenis</groupId>
+            <artifactId>molgenis-dataexplorer</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.molgenis</groupId>
+            <artifactId>molgenis-scripts</artifactId>
+            <version>${project.version}</version>
+        </dependency>
 	</dependencies>
 </project>
diff --git a/...molgenis/data/version/MigrationUtils.java → ...genis/migrate/version/MigrationUtils.java b/...molgenis/data/version/MigrationUtils.java → ...genis/migrate/version/MigrationUtils.java
@@ -1,4 +1,4 @@
-package org.molgenis.data.version;
+package org.molgenis.migrate.version;
 
 import java.io.File;
 import java.io.FileInputStream;

diff --git a/.../data/version/MolgenisUpgradeService.java → ...e/version/MolgenisUpgradeServiceImpl.java b/.../data/version/MolgenisUpgradeService.java → ...e/version/MolgenisUpgradeServiceImpl.java
@@ -1,8 +1,12 @@
-package org.molgenis.data.version;
+package org.molgenis.migrate.version;
+
+import static com.google.common.base.Preconditions.checkNotNull;
 
 import java.util.ArrayList;
 import java.util.List;
 
+import org.molgenis.framework.MolgenisUpgrade;
+import org.molgenis.framework.MolgenisUpgradeService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -14,17 +18,17 @@
  * Gets the current version from the {@link MolgenisVersionService}.
  */
 @Service
-public class MolgenisUpgradeService
+public class MolgenisUpgradeServiceImpl implements MolgenisUpgradeService
 {
 	private final Logger LOG = LoggerFactory.getLogger(getClass());
 
 	private final MolgenisVersionService versionService;
 	private final List<MolgenisUpgrade> upgrades = new ArrayList<>();
 
 	@Autowired
-	public MolgenisUpgradeService(MolgenisVersionService versionService)
+	public MolgenisUpgradeServiceImpl(MolgenisVersionService versionService)
 	{
-		this.versionService = versionService;
+		this.versionService = checkNotNull(versionService);
 	}
 
 	public void addUpgrade(MolgenisUpgrade upgrade)
@@ -37,16 +41,17 @@ public void addUpgrade(MolgenisUpgrade upgrade)
 	 * 
 	 * @return true if an upgrade was necessary, false if not
 	 */
+	@Override
 	public boolean upgrade()
 	{
 		if (versionService.getMolgenisVersionFromServerProperties() < MolgenisVersionService.CURRENT_VERSION)
 		{
 			LOG.info("MetaData version:{}, current version:{} upgrade needed",
 					versionService.getMolgenisVersionFromServerProperties(), MolgenisVersionService.CURRENT_VERSION);
 
-			upgrades.stream()
-					.filter(upgrade -> upgrade.getFromVersion() >= versionService
-							.getMolgenisVersionFromServerProperties()).forEach(this::runUpgrade);
+			upgrades.stream().filter(
+					upgrade -> upgrade.getFromVersion() >= versionService.getMolgenisVersionFromServerProperties())
+					.forEach(this::runUpgrade);
 
 			versionService.updateToCurrentVersion();
 

diff --git a/.../data/version/MolgenisVersionService.java → ...grate/version/MolgenisVersionService.java b/.../data/version/MolgenisVersionService.java → ...grate/version/MolgenisVersionService.java
@@ -1,4 +1,4 @@
-package org.molgenis.data.version;
+package org.molgenis.migrate.version;
 
 import java.io.FileOutputStream;
 import java.io.IOException;
@@ -39,7 +39,7 @@
 @Service
 public class MolgenisVersionService
 {
-	public static final int CURRENT_VERSION = 15;
+	public static final int CURRENT_VERSION = 16;
 
 	private static final Logger LOG = LoggerFactory.getLogger(MolgenisVersionService.class);
 

diff --git a/...te/v1_4/AttributeMetaDataMetaData1_4.java → ...on/v1_4/AttributeMetaDataMetaData1_4.java b/...te/v1_4/AttributeMetaDataMetaData1_4.java → ...on/v1_4/AttributeMetaDataMetaData1_4.java
@@ -1,4 +1,4 @@
-package org.molgenis.data.meta.migrate.v1_4;
+package org.molgenis.migrate.version.v1_4;
 
 import static org.molgenis.MolgenisFieldTypes.BOOL;
 import static org.molgenis.MolgenisFieldTypes.MREF;

diff --git a/...grate/v1_4/EntityMetaDataMetaData1_4.java → ...rsion/v1_4/EntityMetaDataMetaData1_4.java b/...grate/v1_4/EntityMetaDataMetaData1_4.java → ...rsion/v1_4/EntityMetaDataMetaData1_4.java
@@ -1,4 +1,4 @@
-package org.molgenis.data.meta.migrate.v1_4;
+package org.molgenis.migrate.version.v1_4;
 
 import static org.molgenis.MolgenisFieldTypes.BOOL;
 import static org.molgenis.MolgenisFieldTypes.MREF;

diff --git a/...meta/migrate/v1_4/PackageMetaData1_4.java → ...rate/version/v1_4/PackageMetaData1_4.java b/...meta/migrate/v1_4/PackageMetaData1_4.java → ...rate/version/v1_4/PackageMetaData1_4.java
@@ -1,4 +1,4 @@
-package org.molgenis.data.meta.migrate.v1_4;
+package org.molgenis.migrate.version.v1_4;
 
 import static org.molgenis.MolgenisFieldTypes.MREF;
 import static org.molgenis.MolgenisFieldTypes.TEXT;

diff --git a/...ata/meta/migrate/v1_4/TagMetaData1_4.java → .../migrate/version/v1_4/TagMetaData1_4.java b/...ata/meta/migrate/v1_4/TagMetaData1_4.java → .../migrate/version/v1_4/TagMetaData1_4.java
@@ -1,4 +1,4 @@
-package org.molgenis.data.meta.migrate.v1_4;
+package org.molgenis.migrate.version.v1_4;
 
 import org.molgenis.data.support.DefaultEntityMetaData;
 

diff --git a/...ta/version/v1_5/Step1UpgradeMetaData.java → ...te/version/v1_5/Step1UpgradeMetaData.java b/...ta/version/v1_5/Step1UpgradeMetaData.java → ...te/version/v1_5/Step1UpgradeMetaData.java
@@ -1,4 +1,4 @@
-package org.molgenis.data.version.v1_5;
+package org.molgenis.migrate.version.v1_5;
 
 import static org.molgenis.data.support.QueryImpl.EQ;
 
@@ -19,13 +19,13 @@
 import org.molgenis.data.meta.MetaDataServiceImpl;
 import org.molgenis.data.meta.PackageMetaData;
 import org.molgenis.data.meta.TagMetaData;
-import org.molgenis.data.meta.migrate.v1_4.AttributeMetaDataMetaData1_4;
-import org.molgenis.data.meta.migrate.v1_4.EntityMetaDataMetaData1_4;
 import org.molgenis.data.mysql.AsyncJdbcTemplate;
 import org.molgenis.data.mysql.MysqlRepository;
 import org.molgenis.data.mysql.MysqlRepositoryCollection;
 import org.molgenis.data.support.DataServiceImpl;
-import org.molgenis.data.version.MolgenisUpgrade;
+import org.molgenis.framework.MolgenisUpgrade;
+import org.molgenis.migrate.version.v1_4.AttributeMetaDataMetaData1_4;
+import org.molgenis.migrate.version.v1_4.EntityMetaDataMetaData1_4;
 import org.molgenis.security.core.runas.RunAsSystemProxy;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

diff --git a/...org/molgenis/data/version/v1_5/Step2.java → .../molgenis/migrate/version/v1_5/Step2.java b/...org/molgenis/data/version/v1_5/Step2.java → .../molgenis/migrate/version/v1_5/Step2.java
@@ -1,4 +1,4 @@
-package org.molgenis.data.version.v1_5;
+package org.molgenis.migrate.version.v1_5;
 
 import static org.molgenis.data.elasticsearch.util.MapperTypeSanitizer.sanitizeMapperType;
 
@@ -30,9 +30,9 @@
 import org.molgenis.data.meta.MetaDataServiceImpl;
 import org.molgenis.data.support.DefaultAttributeMetaData;
 import org.molgenis.data.support.DefaultEntityMetaData;
-import org.molgenis.data.version.MolgenisUpgrade;
 import org.molgenis.fieldtypes.MrefField;
 import org.molgenis.fieldtypes.XrefField;
+import org.molgenis.framework.MolgenisUpgrade;
 import org.molgenis.util.DependencyResolver;
 import org.springframework.jdbc.core.JdbcTemplate;
 

diff --git a/...v1_5/Step3AddOrderColumnToMrefTables.java → ...v1_5/Step3AddOrderColumnToMrefTables.java b/...v1_5/Step3AddOrderColumnToMrefTables.java → ...v1_5/Step3AddOrderColumnToMrefTables.java
@@ -1,4 +1,4 @@
-package org.molgenis.data.version.v1_5;
+package org.molgenis.migrate.version.v1_5;
 
 import javax.sql.DataSource;
 
@@ -10,8 +10,8 @@
 import org.molgenis.data.mysql.MysqlRepository;
 import org.molgenis.data.mysql.MysqlRepositoryCollection;
 import org.molgenis.data.support.DataServiceImpl;
-import org.molgenis.data.version.MolgenisUpgrade;
 import org.molgenis.fieldtypes.MrefField;
+import org.molgenis.framework.MolgenisUpgrade;
 import org.molgenis.security.core.runas.RunAsSystemProxy;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

diff --git a/...data/version/v1_5/Step4VarcharToText.java → ...rate/version/v1_5/Step4VarcharToText.java b/...data/version/v1_5/Step4VarcharToText.java → ...rate/version/v1_5/Step4VarcharToText.java
@@ -1,13 +1,13 @@
-package org.molgenis.data.version.v1_5;
+package org.molgenis.migrate.version.v1_5;
 
 import javax.sql.DataSource;
 
 import org.molgenis.data.AttributeMetaData;
 import org.molgenis.data.EntityMetaData;
 import org.molgenis.data.Repository;
 import org.molgenis.data.RepositoryCollection;
-import org.molgenis.data.version.MolgenisUpgrade;
 import org.molgenis.fieldtypes.StringField;
+import org.molgenis.framework.MolgenisUpgrade;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.dao.DataAccessException;

diff --git a/.../v1_5/Step5AlterDataexplorerMenuURLs.java → .../v1_5/Step5AlterDataexplorerMenuURLs.java b/.../v1_5/Step5AlterDataexplorerMenuURLs.java → .../v1_5/Step5AlterDataexplorerMenuURLs.java
@@ -1,4 +1,4 @@
-package org.molgenis.ui.migrate.v1_5;
+package org.molgenis.migrate.version.v1_5;
 
 import static org.molgenis.data.support.QueryImpl.EQ;
 import static org.molgenis.ui.menu.MenuItemType.MENU;
@@ -12,7 +12,7 @@
 import org.elasticsearch.common.base.Joiner;
 import org.elasticsearch.common.base.Joiner.MapJoiner;
 import org.molgenis.data.Repository;
-import org.molgenis.data.version.MolgenisUpgrade;
+import org.molgenis.framework.MolgenisUpgrade;
 import org.molgenis.system.core.RuntimeProperty;
 import org.molgenis.ui.menu.Menu;
 import org.molgenis.ui.menu.MenuItem;

diff --git a/.../migrate/v1_5/Step6ChangeRScriptType.java → .../version/v1_5/Step6ChangeRScriptType.java b/.../migrate/v1_5/Step6ChangeRScriptType.java → .../version/v1_5/Step6ChangeRScriptType.java
@@ -1,4 +1,4 @@
-package org.molgenis.ui.migrate.v1_5;
+package org.molgenis.migrate.version.v1_5;
 
 import static com.google.common.collect.Iterables.transform;
 
@@ -15,7 +15,7 @@
 import org.molgenis.data.support.DataServiceImpl;
 import org.molgenis.data.support.MapEntity;
 import org.molgenis.data.support.QueryImpl;
-import org.molgenis.data.version.MolgenisUpgrade;
+import org.molgenis.framework.MolgenisUpgrade;
 import org.molgenis.script.Script;
 import org.molgenis.script.ScriptParameter;
 import org.molgenis.script.ScriptType;

diff --git a/...rsion/v1_6/Step7UpgradeMetaDataTo1_6.java → ...rsion/v1_6/Step7UpgradeMetaDataTo1_6.java b/...rsion/v1_6/Step7UpgradeMetaDataTo1_6.java → ...rsion/v1_6/Step7UpgradeMetaDataTo1_6.java
@@ -1,4 +1,4 @@
-package org.molgenis.data.version.v1_6;
+package org.molgenis.migrate.version.v1_6;
 
 import java.util.Arrays;
 import java.util.List;
@@ -13,7 +13,7 @@
 import org.molgenis.data.mysql.MysqlRepository;
 import org.molgenis.data.mysql.MysqlRepositoryCollection;
 import org.molgenis.data.support.DataServiceImpl;
-import org.molgenis.data.version.MolgenisUpgrade;
+import org.molgenis.framework.MolgenisUpgrade;
 import org.molgenis.security.core.runas.RunAsSystemProxy;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

diff --git a/...sion/v1_6/Step8VarcharToTextRepeated.java → ...sion/v1_6/Step8VarcharToTextRepeated.java b/...sion/v1_6/Step8VarcharToTextRepeated.java → ...sion/v1_6/Step8VarcharToTextRepeated.java
@@ -1,4 +1,4 @@
-package org.molgenis.data.version.v1_6;
+package org.molgenis.migrate.version.v1_6;
 
 import java.util.List;
 import java.util.Map;
@@ -14,13 +14,13 @@
 import org.molgenis.data.mysql.MysqlRepository;
 import org.molgenis.data.mysql.MysqlRepositoryCollection;
 import org.molgenis.data.support.DataServiceImpl;
-import org.molgenis.data.version.MolgenisUpgrade;
 import org.molgenis.fieldtypes.CategoricalField;
 import org.molgenis.fieldtypes.CategoricalMrefField;
 import org.molgenis.fieldtypes.FieldType;
 import org.molgenis.fieldtypes.MrefField;
 import org.molgenis.fieldtypes.StringField;
 import org.molgenis.fieldtypes.XrefField;
+import org.molgenis.framework.MolgenisUpgrade;
 import org.molgenis.security.core.runas.RunAsSystemProxy;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;