diff --git a/build.gradle b/build.gradle
index 73dade74c8031bc8a68fbb3d8072b19d7b3bd761..78832236939b32124502cb5dd2c27a64600aa4b7 100644
--- a/build.gradle
+++ b/build.gradle
@@ -7,7 +7,7 @@ def vSwagger = '2.4.0'
def vHibernate = '4.3.11.Final'
def vEhcache = '2.6.11'
def vJackson = '2.6.5'
-def vPostgreSQL = '9.4.1207'
+def vPostgreSQL = '9.4.1209.jre7'
def vServletApi = '3.1.0'
def vTomcat = '7.0.68'
def vCargo = '1.4.18'
diff --git a/src/main/java/org/nrg/xnat/configuration/OrmConfig.java b/src/main/java/org/nrg/xnat/configuration/OrmConfig.java
index fd4aa23e9eb2c13b47bf0aa0be2c7f24294165ff..519d95074b11158c87eafa4d996ffe50849107bc 100644
--- a/src/main/java/org/nrg/xnat/configuration/OrmConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/OrmConfig.java
@@ -18,6 +18,7 @@ import org.springframework.orm.hibernate4.HibernateTransactionManager;
import org.springframework.orm.hibernate4.LocalSessionFactoryBean;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.annotation.EnableTransactionManagement;
+import org.springframework.transaction.support.TransactionTemplate;
import javax.sql.DataSource;
import java.io.IOException;
@@ -26,9 +27,6 @@ import java.util.Properties;
@Configuration
@EnableTransactionManagement(proxyTargetClass = true)
public class OrmConfig {
-
- public static final String XNAT_ENTITIES_PACKAGES = "META-INF/xnat/entities/**/*-entity-packages.txt";
-
@Bean
public ImprovedNamingStrategy namingStrategy() {
return new PrefixedTableNamingStrategy("xhbm");
@@ -80,6 +78,12 @@ public class OrmConfig {
return new HibernateTransactionManager(sessionFactory(environment, dataSource).getObject());
}
+ @Bean
+ public TransactionTemplate transactionTemplate(final PlatformTransactionManager transactionManager) {
+ return new TransactionTemplate(transactionManager);
+ }
+
+ private static final String XNAT_ENTITIES_PACKAGES = "META-INF/xnat/entities/**/*-entity-packages.txt";
private static final Properties DEFAULT_HIBERNATE_PROPERTIES = new Properties() {{
setProperty("hibernate.dialect", "org.hibernate.dialect.PostgreSQL9Dialect");
setProperty("hibernate.hbm2ddl.auto", "update");
diff --git a/src/main/java/org/nrg/xnat/initialization/DatabaseConfig.java b/src/main/java/org/nrg/xnat/initialization/DatabaseConfig.java
index d4f2e81074eb65019a470b0ea81a4f75c669d0d6..4b717f6b528f5865e35ac65c0f831b7fe071bc6e 100644
--- a/src/main/java/org/nrg/xnat/initialization/DatabaseConfig.java
+++ b/src/main/java/org/nrg/xnat/initialization/DatabaseConfig.java
@@ -22,16 +22,6 @@ import java.util.Properties;
*/
@Configuration
public class DatabaseConfig {
-
- public static final String DEFAULT_DATASOURCE_URL = "jdbc:postgresql://localhost/xnat";
- public static final String DEFAULT_DATASOURCE_USERNAME = "xnat";
- public static final String DEFAULT_DATASOURCE_PASSWORD = "xnat";
- public static final String DEFAULT_DATASOURCE_CLASS = BasicDataSource.class.getName();
- public static final String DEFAULT_DATASOURCE_DRIVER = Driver.class.getName();
- public static final String DEFAULT_DATASOURCE_INITIAL_SIZE = "20";
- public static final String DEFAULT_DATASOURCE_MAX_TOTAL = "40";
- public static final String DEFAULT_DATASOURCE_MAX_IDLE = "10";
-
@Bean
public DataSource dataSource(final Environment environment) throws NrgServiceException {
final Properties properties = Beans.getNamespacedProperties(environment, "datasource", true);
@@ -117,4 +107,13 @@ public class DatabaseConfig {
}
private static final Logger _log = LoggerFactory.getLogger(DatabaseConfig.class);
+
+ private static final String DEFAULT_DATASOURCE_URL = "jdbc:postgresql://localhost/xnat";
+ private static final String DEFAULT_DATASOURCE_USERNAME = "xnat";
+ private static final String DEFAULT_DATASOURCE_PASSWORD = "xnat";
+ private static final String DEFAULT_DATASOURCE_CLASS = BasicDataSource.class.getName();
+ private static final String DEFAULT_DATASOURCE_DRIVER = Driver.class.getName();
+ private static final String DEFAULT_DATASOURCE_INITIAL_SIZE = "20";
+ private static final String DEFAULT_DATASOURCE_MAX_TOTAL = "40";
+ private static final String DEFAULT_DATASOURCE_MAX_IDLE = "10";
}
diff --git a/src/main/java/org/nrg/xnat/initialization/tasks/EncryptXnatPasswords.java b/src/main/java/org/nrg/xnat/initialization/tasks/EncryptXnatPasswords.java
index fbc9f06307285389fe59adca04a19ef67beb7b47..da4903621481ce2efee196b11f80c4999093201c 100644
--- a/src/main/java/org/nrg/xnat/initialization/tasks/EncryptXnatPasswords.java
+++ b/src/main/java/org/nrg/xnat/initialization/tasks/EncryptXnatPasswords.java
@@ -83,10 +83,11 @@ public class EncryptXnatPasswords extends AbstractInitializingTask {
}
return passwords;
}
+
final ShaPasswordEncoder encoder = new ShaPasswordEncoder(256);
}
- private static Logger logger = LoggerFactory.getLogger(EncryptXnatPasswords.class);
+ private static final Logger logger = LoggerFactory.getLogger(EncryptXnatPasswords.class);
private final JdbcTemplate _template;
}
diff --git a/src/main/java/org/nrg/xnat/initialization/tasks/MigrateDatabaseTables.java b/src/main/java/org/nrg/xnat/initialization/tasks/MigrateDatabaseTables.java
new file mode 100644
index 0000000000000000000000000000000000000000..c950f6ce928b1588b8b82ce38d89241478dbe3e0
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/initialization/tasks/MigrateDatabaseTables.java
@@ -0,0 +1,101 @@
+/*
+ * org.nrg.xnat.initialization.tasks.XnatPasswordEncrypter
+ * XNAT http://www.xnat.org
+ * Copyright (c) 2016, Washington University School of Medicine
+ * All Rights Reserved
+ *
+ * Released under the Simplified BSD.
+ */
+package org.nrg.xnat.initialization.tasks;
+
+import com.google.common.base.Joiner;
+import org.nrg.framework.orm.DatabaseHelper;
+import org.nrg.framework.utilities.BasicXnatResourceLocator;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.core.io.Resource;
+import org.springframework.core.io.support.PropertiesLoaderUtils;
+import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.stereotype.Component;
+import org.springframework.transaction.support.TransactionTemplate;
+
+import java.io.IOException;
+import java.sql.SQLException;
+import java.sql.SQLWarning;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Properties;
+
+@Component
+public class MigrateDatabaseTables extends AbstractInitializingTask {
+ @Autowired
+ public MigrateDatabaseTables(final JdbcTemplate template, final TransactionTemplate transactionTemplate) {
+ super();
+ _db = new DatabaseHelper(template, transactionTemplate);
+ }
+
+ @Override
+ public String getTaskName() {
+ return "Migrate XNAT database tables";
+ }
+
+ @Override
+ public void run() {
+ try {
+ final Map<String, Map<String, String>> tables = new HashMap<>();
+ for (final Resource resource : BasicXnatResourceLocator.getResources("classpath*:META-INF/xnat/migration/**/*-tables.properties")) {
+ final Properties properties = PropertiesLoaderUtils.loadProperties(resource);
+ for (final String property : properties.stringPropertyNames()) {
+ final String[] atoms = property.split("\\.", 2);
+ if (atoms.length < 2) {
+ _log.error("The properties file {} contains a malformed key: {}. Keys in table migration properties files should take the form: \"table.column=column_type\".", resource.getFilename(), property);
+ continue;
+ }
+
+ final String table = atoms[0];
+ final String column = atoms[1];
+
+ final Map<String, String> columns;
+ if (tables.containsKey(table)) {
+ columns = tables.get(table);
+ } else {
+ columns = new HashMap<>();
+ tables.put(table, columns);
+ }
+ if (columns.containsKey(column)) {
+ _log.error("The properties for table {} defines the column {} as column type {}. This column has already been defined elsewhere as type: {}.", table, column, columns.get(column));
+ continue;
+ }
+ columns.put(column, properties.getProperty(property));
+ }
+ }
+ for (final String table : tables.keySet()) {
+ final Map<String, String> columns = tables.get(table);
+ for (final String column : columns.keySet()) {
+ final String value = columns.get(column);
+ try {
+ _db.setColumnDatatype(table, column, value);
+ } catch (SQLWarning e) {
+ final String message = e.getMessage();
+ if (message.startsWith(SQL_WARNING_TABLE)) {
+ _log.error("The table {} was defined, but that table doesn't appear to exist in the database. The following columns were to be checked: {}", table, Joiner.on(", ").join(columns.keySet()));
+ } else {
+ _log.error("The column {}.{} was defined, but that column doesn't appear to exist. Note that the table migration does not create new columns. The column was defined as: {}", table, column, value);
+ }
+ }
+ }
+ }
+ complete();
+ } catch (IOException e) {
+ _log.error("An error occurred attempting to read table migration properties files", e);
+ } catch (SQLException e) {
+ _log.error("An error occurred accessing the database", e);
+ }
+ }
+
+ private static final Logger _log = LoggerFactory.getLogger(MigrateDatabaseTables.class);
+ private static final String SQL_WARNING_TABLE = "The requested table";
+
+ private final DatabaseHelper _db;
+}
diff --git a/src/main/resources/META-INF/xnat/migration/xnat-1.6-tables.properties b/src/main/resources/META-INF/xnat/migration/xnat-1.6-tables.properties
new file mode 100644
index 0000000000000000000000000000000000000000..d7e0df9a0e3c9396d806467133b24728b38eb7c5
--- /dev/null
+++ b/src/main/resources/META-INF/xnat/migration/xnat-1.6-tables.properties
@@ -0,0 +1 @@
+xhbm_alias_token.secret=varchar(255)
\ No newline at end of file