From e130a5ec86d26ad446b9b6491c2f6829a8b46009 Mon Sep 17 00:00:00 2001
From: pkupczyk <pkupczyk>
Date: Mon, 14 Nov 2011 09:03:59 +0000
Subject: [PATCH] LMS-2655 - Create a unit test to check imaging db consistency
SVN: 23647
---
dbmigration/.classpath | 1 +
.../migration/SqlMigrationDataSource.java | 105 ++++++++++
.../SqlMigrationDataSourceFactory.java | 27 +++
.../migration/SqlMigrationTestAbstract.java | 189 ++++++++++++++++++
screening/.classpath | 1 +
.../db/ScreeningSqlMigrationTest.java | 55 +++++
.../sql/imaging/postgresql/002/schema-002.sql | 8 +-
.../migration/migration-016-017.sql | 1 +
8 files changed, 383 insertions(+), 4 deletions(-)
create mode 100644 dbmigration/source/java/ch/systemsx/cisd/dbmigration/migration/SqlMigrationDataSource.java
create mode 100644 dbmigration/source/java/ch/systemsx/cisd/dbmigration/migration/SqlMigrationDataSourceFactory.java
create mode 100644 dbmigration/source/java/ch/systemsx/cisd/dbmigration/migration/SqlMigrationTestAbstract.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/dataaccess/db/ScreeningSqlMigrationTest.java
diff --git a/dbmigration/.classpath b/dbmigration/.classpath
index ef01348da62..10cdfc7df48 100644
--- a/dbmigration/.classpath
+++ b/dbmigration/.classpath
@@ -22,5 +22,6 @@
<classpathentry kind="lib" path="/libraries/jmock/objenesis/objenesis-1.0.jar"/>
<classpathentry kind="lib" path="/libraries/cisd-base/cisd-base-test.jar" sourcepath="/libraries/cisd-base/cisd-base-src.zip"/>
<classpathentry kind="lib" path="/libraries/cisd-base/cisd-base.jar" sourcepath="/libraries/cisd-base/cisd-base-src.zip"/>
+ <classpathentry kind="lib" path="/libraries/apgdiff/apgdiff.jar" sourcepath="/libraries/apgdiff/src.zip"/>
<classpathentry kind="output" path="targets/classes"/>
</classpath>
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/migration/SqlMigrationDataSource.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/migration/SqlMigrationDataSource.java
new file mode 100644
index 00000000000..13bf5bce22d
--- /dev/null
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/migration/SqlMigrationDataSource.java
@@ -0,0 +1,105 @@
+package ch.systemsx.cisd.dbmigration.migration;
+
+import java.io.PrintWriter;
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.SQLException;
+
+import javax.sql.DataSource;
+
+import org.springframework.beans.factory.DisposableBean;
+
+public class SqlMigrationDataSource implements DataSource, DisposableBean
+{
+ private final String driver;
+
+ private final String url;
+
+ private final String owner;
+
+ private final String password;
+
+ private Connection connection;
+
+ SqlMigrationDataSource(final String driver, final String url, final String owner,
+ final String password)
+ {
+ this.driver = driver;
+ this.url = url;
+ this.owner = owner;
+ this.password = password;
+ }
+
+ public Connection getConnection() throws SQLException
+ {
+ if (connection != null && connection.isClosed() || connection == null)
+ {
+ try
+ {
+ Class.forName(driver);
+ } catch (final ClassNotFoundException ex)
+ {
+ throw new SQLException("Couldn't load driver " + driver);
+ }
+ final Connection c = DriverManager.getConnection(url, owner, password);
+ connection = c;
+ }
+ return connection;
+ }
+
+ public Connection getConnection(final String username, final String pw) throws SQLException
+ {
+ if (owner.equals(username) && password.equals(pw))
+ {
+ return getConnection();
+ }
+ throw new SQLException("Forbidden");
+ }
+
+ public int getLoginTimeout() throws SQLException
+ {
+ return 0;
+ }
+
+ public void setLoginTimeout(final int timeout) throws SQLException
+ {
+ throw new UnsupportedOperationException("setLoginTimeout");
+ }
+
+ public PrintWriter getLogWriter()
+ {
+ throw new UnsupportedOperationException("getLogWriter");
+ }
+
+ public void setLogWriter(final PrintWriter pw) throws SQLException
+ {
+ throw new UnsupportedOperationException("setLogWriter");
+ }
+
+ public void destroy() throws SQLException
+ {
+ if (connection != null)
+ {
+ connection.close();
+ connection = null;
+ }
+ }
+
+ @Override
+ public String toString()
+ {
+ return "MyDataSource[" + driver + ", " + url + ", " + owner + "]";
+ }
+
+ // NOTE: the following methods are needed because we compile with JDK 6 on Hudson
+ public boolean isWrapperFor(Class<?> arg0) throws SQLException
+ {
+ return false;
+ }
+
+ public <T> T unwrap(Class<T> arg0) throws SQLException
+ {
+ return null;
+ }
+
+}
\ No newline at end of file
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/migration/SqlMigrationDataSourceFactory.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/migration/SqlMigrationDataSourceFactory.java
new file mode 100644
index 00000000000..d69b0342c83
--- /dev/null
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/migration/SqlMigrationDataSourceFactory.java
@@ -0,0 +1,27 @@
+package ch.systemsx.cisd.dbmigration.migration;
+
+import javax.sql.DataSource;
+
+import ch.systemsx.cisd.dbmigration.IDataSourceFactory;
+
+public class SqlMigrationDataSourceFactory implements IDataSourceFactory
+{
+
+ public DataSource createDataSource(String driver, String url, String owner, String password)
+ {
+ return new SqlMigrationDataSource(driver, url, owner, password);
+ }
+
+ public void setMaxActive(int maxActive)
+ {
+ }
+
+ public void setMaxIdle(int maxIdle)
+ {
+ }
+
+ public void setMaxWait(long maxWait)
+ {
+ }
+
+}
\ No newline at end of file
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/migration/SqlMigrationTestAbstract.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/migration/SqlMigrationTestAbstract.java
new file mode 100644
index 00000000000..8ab6a17de86
--- /dev/null
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/migration/SqlMigrationTestAbstract.java
@@ -0,0 +1,189 @@
+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * 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 ch.systemsx.cisd.dbmigration.migration;
+
+import java.io.File;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterTest;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeTest;
+
+import cz.startnet.utils.pgdiff.PgDiff;
+import cz.startnet.utils.pgdiff.PgDiffArguments;
+
+import ch.systemsx.cisd.common.logging.LogInitializer;
+import ch.systemsx.cisd.dbmigration.DBMigrationEngine;
+import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
+import ch.systemsx.cisd.dbmigration.postgresql.DumpPreparator;
+
+/**
+ * Test cases for database migration.
+ *
+ * @author Piotr Kupczyk
+ */
+public abstract class SqlMigrationTestAbstract
+{
+
+ private File sqlScriptOutputDirectory;
+
+ protected abstract String getSqlScriptInputDirectory();
+
+ protected abstract String getSqlScriptOutputDirectory();
+
+ @BeforeClass(alwaysRun = true)
+ public void beforeClass() throws Exception
+ {
+ LogInitializer.init();
+ }
+
+ @BeforeTest(alwaysRun = true)
+ public void beforeTest() throws Exception
+ {
+ File dir = new File(getSqlScriptOutputDirectory());
+ if (!dir.exists())
+ {
+ dir.mkdir();
+ }
+ }
+
+ @AfterTest(alwaysRun = true)
+ public void afterTest() throws Exception
+ {
+ File dir = new File(getSqlScriptOutputDirectory());
+ if (dir.exists())
+ {
+ dir.delete();
+ }
+ }
+
+ public void test_migration(String firstVersion, String newestVersion) throws Exception
+ {
+ int firstVersionInt = Integer.valueOf(firstVersion);
+ int newestVersionInt = Integer.valueOf(newestVersion);
+
+ DatabaseConfigurationContext migrationContext = null;
+ DatabaseConfigurationContext scratchContext = null;
+
+ try
+ {
+
+ migrationContext = createMigrationDatabaseContext(true);
+ scratchContext = createScratchDatabaseContext();
+
+ // create first version of migration database
+ DBMigrationEngine.createOrMigrateDatabaseAndGetScriptProvider(migrationContext,
+ firstVersion);
+
+ migrationContext.setCreateFromScratch(false);
+
+ for (int version = firstVersionInt + 1; version <= newestVersionInt; version++)
+ {
+ String versionStr = String.format("%03d", version);
+
+ // migrate to the next version
+ DBMigrationEngine.createOrMigrateDatabaseAndGetScriptProvider(migrationContext,
+ versionStr);
+ dumpDatabaseSchema(migrationContext, getMigratedDatabaseSchemaFile());
+
+ // create next version from scratch
+ DBMigrationEngine.createOrMigrateDatabaseAndGetScriptProvider(scratchContext,
+ versionStr);
+ dumpDatabaseSchema(scratchContext, getScratchDatabaseSchemaFile());
+
+ // check whether migrated and scratch version are equal
+ assertDatabaseSchemasEqual(getMigratedDatabaseSchemaFile(),
+ getScratchDatabaseSchemaFile());
+ }
+
+ } finally
+ {
+ if (migrationContext != null)
+ {
+ migrationContext.closeConnections();
+ }
+ if (scratchContext != null)
+ {
+ scratchContext.closeConnections();
+ }
+ }
+ }
+
+ private DatabaseConfigurationContext createDatabaseContext(String dbKind,
+ boolean createFromScratch)
+ {
+ DatabaseConfigurationContext context = new DatabaseConfigurationContext();
+ context.setDatabaseEngineCode("postgresql");
+ context.setBasicDatabaseName("openbis");
+ context.setDatabaseKind(dbKind);
+ context.setScriptFolder(getSqlScriptInputDirectory());
+ context.initDataSourceFactory(new SqlMigrationDataSourceFactory());
+ context.setCreateFromScratch(createFromScratch);
+ return context;
+ }
+
+ private DatabaseConfigurationContext createMigrationDatabaseContext(boolean createFromScratch)
+ {
+ return createDatabaseContext("test_migration_migrated", createFromScratch);
+ }
+
+ private DatabaseConfigurationContext createScratchDatabaseContext()
+ {
+ return createDatabaseContext("test_migration_scratch", true);
+ }
+
+ private File getMigratedDatabaseSchemaFile()
+ {
+ return new File(sqlScriptOutputDirectory, "migratedDatabaseSchema.sql");
+ }
+
+ private File getScratchDatabaseSchemaFile()
+ {
+ return new File(sqlScriptOutputDirectory, "scratchDatabaseSchema.sql");
+ }
+
+ private void dumpDatabaseSchema(final DatabaseConfigurationContext configurationContext,
+ final File migratedSchemaFile)
+ {
+ final boolean dumpSuccessful =
+ DumpPreparator.createDatabaseSchemaDump(configurationContext.getDatabaseName(),
+ migratedSchemaFile);
+ AssertJUnit.assertTrue("dump of db failed: " + configurationContext.getDatabaseName(),
+ dumpSuccessful);
+ }
+
+ private void assertDatabaseSchemasEqual(final File currentSchemaFile,
+ final File expectedSchemaFile)
+ {
+ final StringWriter writer = new StringWriter();
+ final PgDiffArguments arguments = new PgDiffArguments();
+ arguments.setOldDumpFile(currentSchemaFile.getAbsolutePath());
+ arguments.setNewDumpFile(expectedSchemaFile.getAbsolutePath());
+ arguments.setIgnoreFunctionWhitespace(true);
+ arguments.setIgnoreStartWith(true);
+ PgDiff.createDiff(new PrintWriter(writer), arguments);
+
+ String delta = writer.toString();
+ delta = delta == null ? "" : delta;
+
+ AssertJUnit.assertEquals("The migrated schema is not identical to the scratch one. "
+ + "Consider attaching following script to the migration file.", "", delta);
+ }
+
+}
diff --git a/screening/.classpath b/screening/.classpath
index 6d09234b064..feeaf400b2f 100644
--- a/screening/.classpath
+++ b/screening/.classpath
@@ -51,5 +51,6 @@
<classpathentry kind="lib" path="/libraries/gxt2.2.5/gxt.jar"/>
<classpathentry kind="lib" path="/libraries/gwt2.4/validation-api-1.0.0.GA-sources.jar"/>
<classpathentry kind="lib" path="/libraries/gwt2.4/validation-api-1.0.0.GA.jar"/>
+ <classpathentry kind="lib" path="/libraries/apgdiff/apgdiff.jar" sourcepath="/libraries/apgdiff/src.zip"/>
<classpathentry kind="output" path="targets/www/WEB-INF/classes"/>
</classpath>
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/dataaccess/db/ScreeningSqlMigrationTest.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/dataaccess/db/ScreeningSqlMigrationTest.java
new file mode 100644
index 00000000000..733dd0a5f29
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/dataaccess/db/ScreeningSqlMigrationTest.java
@@ -0,0 +1,55 @@
+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * 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 ch.systemsx.cisd.openbis.dss.generic.server.dataaccess.db;
+
+import java.io.File;
+
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.dbmigration.migration.SqlMigrationTestAbstract;
+import ch.systemsx.cisd.openbis.dss.etl.ImagingDatabaseVersionHolder;
+
+/**
+ * Test cases for database migration.
+ *
+ * @author Piotr Kupczyk
+ */
+public class ScreeningSqlMigrationTest extends SqlMigrationTestAbstract
+{
+
+ @Test(groups =
+ { "slow" })
+ public void test_migration()
+ throws Exception
+ {
+ test_migration("001",
+ new ImagingDatabaseVersionHolder().getDatabaseVersion());
+ }
+
+ @Override
+ protected String getSqlScriptInputDirectory()
+ {
+ return "source" + File.separator + "sql" + File.separator + "imaging";
+ }
+
+ @Override
+ protected String getSqlScriptOutputDirectory()
+ {
+ return "targets" + File.separator + "unit-test-wd";
+ }
+
+}
diff --git a/screening/source/sql/imaging/postgresql/002/schema-002.sql b/screening/source/sql/imaging/postgresql/002/schema-002.sql
index 29a34a7b0ca..8b28913b3dc 100644
--- a/screening/source/sql/imaging/postgresql/002/schema-002.sql
+++ b/screening/source/sql/imaging/postgresql/002/schema-002.sql
@@ -182,15 +182,15 @@ CREATE TABLE FEATURE_VALUES (
VALUES BYTEA NOT NULL,
FD_ID TECH_ID NOT NULL,
- DS_ID TECH_ID NOT NULL,
+ --DS_ID TECH_ID NOT NULL,
PRIMARY KEY (ID),
- CONSTRAINT FK_FEATURE_VALUES_1 FOREIGN KEY (FD_ID) REFERENCES FEATURE_DEFS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
- CONSTRAINT FK_FEATURE_VALUES_2 FOREIGN KEY (DS_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+ CONSTRAINT FK_FEATURE_VALUES_1 FOREIGN KEY (FD_ID) REFERENCES FEATURE_DEFS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+ --CONSTRAINT FK_FEATURE_VALUES_2 FOREIGN KEY (DS_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE
-- This constaint does not make any sense. Leave it out for now.
-- CONSTRAINT FEATURE_VALUES_UK_1 UNIQUE(Z_in_M, T_in_SEC)
);
CREATE INDEX FEATURE_VALUES_FD_IDX ON FEATURE_VALUES(FD_ID);
-CREATE INDEX FEATURE_VALUES_DS_IDX ON FEATURE_VALUES(DS_ID);
+--CREATE INDEX FEATURE_VALUES_DS_IDX ON FEATURE_VALUES(DS_ID);
CREATE INDEX FEATURE_VALUES_Z_AND_T_IDX ON FEATURE_VALUES(Z_in_M, T_in_SEC);
diff --git a/screening/source/sql/imaging/postgresql/migration/migration-016-017.sql b/screening/source/sql/imaging/postgresql/migration/migration-016-017.sql
index 383b68b9383..f36529af24a 100644
--- a/screening/source/sql/imaging/postgresql/migration/migration-016-017.sql
+++ b/screening/source/sql/imaging/postgresql/migration/migration-016-017.sql
@@ -25,6 +25,7 @@ ALTER TABLE ACQUIRED_IMAGES DROP CONSTRAINT FK_IMAGES_3;
ALTER TABLE ACQUIRED_IMAGES ADD CONSTRAINT FK_IMAGES_3 FOREIGN KEY (IMG_ID) REFERENCES IMAGES (ID) ON DELETE SET NULL ON UPDATE CASCADE;
ALTER TABLE ACQUIRED_IMAGES DROP CONSTRAINT FK_IMAGES_4;
ALTER TABLE ACQUIRED_IMAGES ADD CONSTRAINT FK_IMAGES_4 FOREIGN KEY (THUMBNAIL_ID) REFERENCES IMAGES (ID) ON DELETE SET NULL ON UPDATE CASCADE;
+ALTER TABLE acquired_images ADD CONSTRAINT fk_images_img_or_thumb_arc_ck CHECK (IMG_ID IS NOT NULL OR THUMBNAIL_ID IS NOT NULL);
CREATE OR REPLACE FUNCTION DELETE_UNUSED_NULLED_IMAGES() RETURNS trigger AS $$
BEGIN
--
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