Work on migrator

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/TestUtil.java

@@ -20,30 +20,29 @@ package ca.uhn.fhir.jpa.util;
  * #L%
  */
 
-import static org.apache.commons.lang3.StringUtils.isBlank;
+import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
+import com.google.common.collect.ImmutableSet;
+import com.google.common.reflect.ClassPath;
+import com.google.common.reflect.ClassPath.ClassInfo;
+import org.apache.commons.lang3.Validate;
 
+import javax.persistence.*;
 import java.io.IOException;
 import java.lang.reflect.AnnotatedElement;
 import java.lang.reflect.Field;
 import java.util.HashSet;
 import java.util.Set;
 
-import javax.persistence.*;
+import static org.apache.commons.lang3.StringUtils.isBlank;
-
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
-import org.apache.commons.lang3.Validate;
-
-import com.google.common.collect.ImmutableSet;
-import com.google.common.reflect.ClassPath;
-import com.google.common.reflect.ClassPath.ClassInfo;
-
-import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 
 public class TestUtil {
 	private static final int MAX_LENGTH = 30;
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TestUtil.class);
 
-	/** non instantiable */
+	/**
+	 * non instantiable
+	 */
 	private TestUtil() {
 		super();
 	}
@@ -119,6 +118,7 @@ public class TestUtil {
 		Column column = ae.getAnnotation(Column.class);
 		if (column != null) {
 			assertNotADuplicateName(column.name(), null);
+			Validate.isTrue(column.unique() == false, "Should not use unique attribute on column (use named @UniqueConstraint instead) on " + ae.toString());
 		}
 
 		GeneratedValue gen = ae.getAnnotation(GeneratedValue.class);

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/DriverTypeEnum.java

@@ -11,11 +11,21 @@ import javax.annotation.Nonnull;
 
 /*-
  * #%L
- * Smile CDR - CDR
+ * HAPI FHIR JPA Server - Migration
  * %%
- * Copyright (C) 2016 - 2018 Simpatico Intelligent Systems Inc
+ * Copyright (C) 2014 - 2018 University Health Network
  * %%
- * All rights reserved.
+ * 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.
  * #L%
  */
 

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/JdbcUtils.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.migrate;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * 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.
+ * #L%
+ */
+
 import ca.uhn.fhir.jpa.migrate.taskdef.BaseTableColumnTypeTask;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.slf4j.Logger;
@@ -94,7 +114,7 @@ public class JdbcUtils {
 						case Types.VARCHAR:
 							return BaseTableColumnTypeTask.ColumnTypeEnum.STRING.getDescriptor(length);
 						case Types.BIGINT:
-							return BaseTableColumnTypeTask.ColumnTypeEnum.LONG.getDescriptor(length);
+							return BaseTableColumnTypeTask.ColumnTypeEnum.LONG.getDescriptor(null);
 						default:
 							throw new IllegalArgumentException("Don't know how to handle datatype: " + dataType);
 					}
@@ -110,6 +130,32 @@ public class JdbcUtils {
 	/**
 	 * Retrieve all index names
 	 */
+	public static Set<String> getForeignKeys(DriverTypeEnum.ConnectionProperties theConnectionProperties, String theTableName, String theForeignTable) throws SQLException {
+		DataSource dataSource = Objects.requireNonNull(theConnectionProperties.getDataSource());
+		Connection connection = dataSource.getConnection();
+		return theConnectionProperties.getTxTemplate().execute(t -> {
+			DatabaseMetaData metadata;
+			try {
+				metadata = connection.getMetaData();
+				ResultSet indexes = metadata.getCrossReference(null, null, theTableName, null, null, theForeignTable);
+
+				Set<String> columnNames = new HashSet<>();
+				while (indexes.next()) {
+					String fkName = indexes.getString("FK_NAME");
+					fkName = StringUtils.toUpperCase(fkName, Locale.US);
+					columnNames.add(fkName);
+				}
+
+				return columnNames;
+			} catch (SQLException e) {
+				throw new InternalErrorException(e);
+			}
+		});
+	}
+
+		/**
+        * Retrieve all index names
+        */
 	public static Set<String> getColumnNames(DriverTypeEnum.ConnectionProperties theConnectionProperties, String theTableName) throws SQLException {
 		DataSource dataSource = Objects.requireNonNull(theConnectionProperties.getDataSource());
 		Connection connection = dataSource.getConnection();
@@ -162,4 +208,35 @@ public class JdbcUtils {
 			}
 		});
 	}
+
+	public static boolean isColumnNullable(DriverTypeEnum.ConnectionProperties theConnectionProperties, String theTableName, String theColumnName) throws SQLException {
+		DataSource dataSource = Objects.requireNonNull(theConnectionProperties.getDataSource());
+		Connection connection = dataSource.getConnection();
+		//noinspection ConstantConditions
+		return theConnectionProperties.getTxTemplate().execute(t -> {
+			DatabaseMetaData metadata;
+			try {
+				metadata = connection.getMetaData();
+				ResultSet tables = metadata.getColumns(null, null, theTableName, theColumnName);
+
+				while (tables.next()) {
+					if (theColumnName.equals(tables.getString("COLUMN_NAME"))) {
+						String nullable = tables.getString("IS_NULLABLE");
+						if ("YES".equals(nullable)) {
+							return true;
+						} else if ("NO".equals(nullable)) {
+							return false;
+						} else {
+							throw new IllegalStateException("Unknown nullable: " + nullable);
+						}
+					}
+				}
+
+				throw new IllegalStateException("Did not find column " + theColumnName);
+			} catch (SQLException e) {
+				throw new InternalErrorException(e);
+			}
+		});
+
+	}
 }

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/Migrator.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.migrate;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * 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.
+ * #L%
+ */
+
 import ca.uhn.fhir.jpa.migrate.taskdef.BaseTask;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.slf4j.Logger;

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/AddColumnTask.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.migrate.taskdef;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * 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.
+ * #L%
+ */
+
 import ca.uhn.fhir.jpa.migrate.JdbcUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/AddForeignKeyTask.java

@@ -0,0 +1,86 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * 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.
+ * #L%
+ */
+
+import ca.uhn.fhir.jpa.migrate.JdbcUtils;
+import org.apache.commons.lang3.Validate;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.SQLException;
+import java.util.Set;
+
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
+
+public class AddForeignKeyTask extends BaseTableColumnTask<AddForeignKeyTask> {
+
+	private static final Logger ourLog = LoggerFactory.getLogger(AddForeignKeyTask.class);
+	private String myConstraintName;
+	private String myForeignTableName;
+	private String myForeignColumnName;
+
+	public void setConstraintName(String theConstraintName) {
+		myConstraintName = theConstraintName;
+	}
+
+	public void setForeignTableName(String theForeignTableName) {
+		myForeignTableName = theForeignTableName;
+	}
+
+	public void setForeignColumnName(String theForeignColumnName) {
+		myForeignColumnName = theForeignColumnName;
+	}
+
+	@Override
+	public void validate() {
+		super.validate();
+
+		Validate.isTrue(isNotBlank(myConstraintName));
+		Validate.isTrue(isNotBlank(myForeignTableName));
+		Validate.isTrue(isNotBlank(myForeignColumnName));
+	}
+
+	@Override
+	public void execute() throws SQLException {
+
+		Set<String> existing = JdbcUtils.getForeignKeys(getConnectionProperties(), myForeignTableName, getTableName());
+		if (existing.contains(myConstraintName)) {
+			ourLog.info("Already have constraint named {} - No action performed", myConstraintName);
+			return;
+		}
+
+		String sql = null;
+		switch (getDriverType()) {
+			case MARIADB_10_1:
+			case MYSQL_5_7:
+				sql = "alter table " + getTableName() + " add constraint " + myConstraintName + " foreign key (" + getColumnName() + ") references " + myForeignTableName + " (" + myForeignColumnName + ")";
+				break;
+			case POSTGRES_9_4:
+			case DERBY_EMBEDDED:
+			case ORACLE_12C:
+			case MSSQL_2012:
+				sql = "alter table " + getTableName() + " add constraint " + myConstraintName + " foreign key (" + getColumnName() + ") references " + myForeignTableName;
+				break;
+		}
+		executeSql(sql);
+	}
+
+}

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/AddIndexTask.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.migrate.taskdef;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * 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.
+ * #L%
+ */
+
 import ca.uhn.fhir.jpa.migrate.JdbcUtils;
 import org.apache.commons.lang3.Validate;
 import org.slf4j.Logger;

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/AddTableTask.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.migrate.taskdef;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * 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.
+ * #L%
+ */
+
 import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
 import ca.uhn.fhir.jpa.migrate.JdbcUtils;
 import org.apache.commons.lang3.Validate;

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ArbitrarySqlTask.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.migrate.taskdef;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * 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.
+ * #L%
+ */
+
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.jdbc.core.ColumnMapRowMapper;

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTableColumnTask.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.migrate.taskdef;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * 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.
+ * #L%
+ */
+
 import org.apache.commons.lang3.Validate;
 import org.thymeleaf.util.StringUtils;
 

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTableColumnTypeTask.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.migrate.taskdef;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * 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.
+ * #L%
+ */
+
 import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
 import org.apache.commons.lang3.Validate;
 import org.springframework.util.Assert;
@@ -33,12 +53,12 @@ public abstract class BaseTableColumnTypeTask<T extends BaseTableTask> extends B
 		setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.ORACLE_12C, "varchar2(?)");
 		setColumnType(ColumnTypeEnum.STRING, DriverTypeEnum.POSTGRES_9_4, "varchar(?)");
 
-		setColumnType(ColumnTypeEnum.DATE_TIMESTAMPT, DriverTypeEnum.DERBY_EMBEDDED, "timestamp");
+		setColumnType(ColumnTypeEnum.DATE_TIMESTAMP, DriverTypeEnum.DERBY_EMBEDDED, "timestamp");
-		setColumnType(ColumnTypeEnum.DATE_TIMESTAMPT, DriverTypeEnum.MARIADB_10_1, "datetime(6)");
+		setColumnType(ColumnTypeEnum.DATE_TIMESTAMP, DriverTypeEnum.MARIADB_10_1, "datetime(6)");
-		setColumnType(ColumnTypeEnum.DATE_TIMESTAMPT, DriverTypeEnum.MYSQL_5_7, "datetime(6)");
+		setColumnType(ColumnTypeEnum.DATE_TIMESTAMP, DriverTypeEnum.MYSQL_5_7, "datetime(6)");
-		setColumnType(ColumnTypeEnum.DATE_TIMESTAMPT, DriverTypeEnum.MSSQL_2012, "datetime2");
+		setColumnType(ColumnTypeEnum.DATE_TIMESTAMP, DriverTypeEnum.MSSQL_2012, "datetime2");
-		setColumnType(ColumnTypeEnum.DATE_TIMESTAMPT, DriverTypeEnum.ORACLE_12C, "timestamp");
+		setColumnType(ColumnTypeEnum.DATE_TIMESTAMP, DriverTypeEnum.ORACLE_12C, "timestamp");
-		setColumnType(ColumnTypeEnum.DATE_TIMESTAMPT, DriverTypeEnum.POSTGRES_9_4, "timestamp");
+		setColumnType(ColumnTypeEnum.DATE_TIMESTAMP, DriverTypeEnum.POSTGRES_9_4, "timestamp");
 	}
 
 	public ColumnTypeEnum getColumnType() {
@@ -93,7 +113,7 @@ public abstract class BaseTableColumnTypeTask<T extends BaseTableTask> extends B
 	}
 
 	protected String getSqlNotNull() {
-		return isNullable() ? "" : " not null";
+		return isNullable() ? " null" : " not null";
 	}
 
 	public Long getColumnLength() {
@@ -121,7 +141,7 @@ public abstract class BaseTableColumnTypeTask<T extends BaseTableTask> extends B
 				return "varchar(" + theColumnLength + ")";
 			}
 		},
-		DATE_TIMESTAMPT{
+		DATE_TIMESTAMP {
 			@Override
 			public String getDescriptor(Long theColumnLength) {
 				Assert.isTrue(theColumnLength == null, "Must not supply a column length");

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTableTask.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.migrate.taskdef;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * 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.
+ * #L%
+ */
+
 import org.apache.commons.lang3.Validate;
 
 public abstract class BaseTableTask<T extends BaseTableTask> extends BaseTask {

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/BaseTask.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.migrate.taskdef;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * 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.
+ * #L%
+ */
+
 import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
 import org.intellij.lang.annotations.Language;
 import org.slf4j.Logger;

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/CalculateHashesTask.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.migrate.taskdef;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * 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.
+ * #L%
+ */
+
 import ca.uhn.fhir.util.StopWatch;
 import com.google.common.collect.ForwardingMap;
 import org.apache.commons.lang3.Validate;

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/DropIndexTask.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.migrate.taskdef;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * 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.
+ * #L%
+ */
+
 import ca.uhn.fhir.jpa.migrate.JdbcUtils;
 import org.apache.commons.lang3.Validate;
 import org.slf4j.Logger;

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/LogStartSectionWithMessageTask.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.migrate.taskdef;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * 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.
+ * #L%
+ */
+
 import org.apache.commons.lang3.StringUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/taskdef/ModifyColumnTask.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.migrate.taskdef;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * 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.
+ * #L%
+ */
+
 import ca.uhn.fhir.jpa.migrate.JdbcUtils;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.slf4j.Logger;
@@ -16,39 +36,55 @@ public class ModifyColumnTask extends BaseTableColumnTypeTask<ModifyColumnTask>
 	public void execute() {
 
 		String existingType;
+		boolean nullable;
 		try {
 			existingType = JdbcUtils.getColumnType(getConnectionProperties(), getTableName(), getColumnName());
+			nullable = JdbcUtils.isColumnNullable(getConnectionProperties(), getTableName(), getColumnName());
 		} catch (SQLException e) {
 			throw new InternalErrorException(e);
 		}
 
 		String wantedType = getColumnType().getDescriptor(getColumnLength());
-		if (existingType.equals(wantedType)) {
+		boolean alreadyOfCorrectType = existingType.equals(wantedType);
-			ourLog.info("Column {} on table {} is already of type {} - No action performed", getColumnName(), getTableName(), wantedType);
+		boolean alreadyCorrectNullable = isNullable() == nullable;
+		if (alreadyOfCorrectType && alreadyCorrectNullable) {
+			ourLog.info("Column {} on table {} is already of type {} and has nullable {} - No action performed", getColumnName(), getTableName(), wantedType, nullable);
 			return;
 		}
 
 		String type = getSqlType();
 		String notNull = getSqlNotNull();
 
-		String sql;
+		String sql = null;
 		String sqlNotNull = null;
 		switch (getDriverType()) {
 			case DERBY_EMBEDDED:
+				if (!alreadyOfCorrectType) {
 					sql = "alter table " + getTableName() + " alter column " + getColumnName() + " set data type " + type;
+				}
+				if (!alreadyCorrectNullable) {
+					sqlNotNull = "alter table " + getTableName() + " alter column " + getColumnName() + notNull;
+				}
 				break;
 			case MARIADB_10_1:
 			case MYSQL_5_7:
 				sql = "alter table " + getTableName() + " modify column " + getColumnName() + " " + type + notNull;
 				break;
 			case POSTGRES_9_4:
+				if (!alreadyOfCorrectType) {
 					sql = "alter table " + getTableName() + " alter column " + getColumnName() + " type " + type;
-				if (isNullable() == false) {
+				}
+				if (!alreadyCorrectNullable) {
+					if (isNullable()) {
+						sqlNotNull = "alter table " + getTableName() + " alter column " + getColumnName() + " set null";
+					} else {
 						sqlNotNull = "alter table " + getTableName() + " alter column " + getColumnName() + " set not null";
 					}
+				}
 				break;
 			case ORACLE_12C:
-				sql = "alter table " + getTableName() + " modify " + getColumnName() + " " + type + notNull;
+				String oracleNullableStmt = !alreadyCorrectNullable ? notNull : "";
+				sql = "alter table " + getTableName() + " modify ( " + getColumnName() + " " + type + oracleNullableStmt + " )";
 				break;
 			case MSSQL_2012:
 				sql = "alter table " + getTableName() + " alter column " + getColumnName() + " " + type + notNull;
@@ -58,7 +94,9 @@ public class ModifyColumnTask extends BaseTableColumnTypeTask<ModifyColumnTask>
 		}
 
 		ourLog.info("Updating column {} on table {} to type {}", getColumnName(), getTableName(), type);
+		if (sql != null) {
 			executeSql(sql);
+		}
 
 		if (sqlNotNull != null) {
 			ourLog.info("Updating column {} on table {} to not null", getColumnName(), getTableName());

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.migrate.tasks;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * 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.
+ * #L%
+ */
+
 import ca.uhn.fhir.jpa.dao.DaoConfig;
 import ca.uhn.fhir.jpa.entity.*;
 import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
@@ -11,7 +31,7 @@ import ca.uhn.fhir.jpa.migrate.tasks.api.BaseMigrationTasks;
 import ca.uhn.fhir.util.VersionEnum;
 
 @SuppressWarnings({"UnstableApiUsage", "SqlNoDataSourceInspection", "SpellCheckingInspection"})
-public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks {
+public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 
 	/**
 	 * Constructor
@@ -259,7 +279,7 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks {
 		trmConcept
 			.addColumn("CONCEPT_UPDATED")
 			.nullable()
-			.type(BaseTableColumnTypeTask.ColumnTypeEnum.DATE_TIMESTAMPT);
+			.type(BaseTableColumnTypeTask.ColumnTypeEnum.DATE_TIMESTAMP);
 		trmConcept
 			.addIndex("IDX_CONCEPT_UPDATED")
 			.unique(false)

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/api/BaseMigrationTasks.java

@@ -1,11 +1,30 @@
 package ca.uhn.fhir.jpa.migrate.tasks.api;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2018 University Health Network
+ * %%
+ * 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.
+ * #L%
+ */
+
 import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
 import ca.uhn.fhir.jpa.migrate.taskdef.*;
-import ca.uhn.fhir.jpa.migrate.tasks.HapiFhirJpaMigrationTasks;
-import ca.uhn.fhir.util.VersionEnum;
 import com.google.common.collect.Multimap;
 import com.google.common.collect.MultimapBuilder;
+import org.apache.commons.lang3.EnumUtils;
 import org.apache.commons.lang3.Validate;
 import org.intellij.lang.annotations.Language;
 
@@ -14,24 +33,25 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 
-public class BaseMigrationTasks {
+public class BaseMigrationTasks<T extends Enum> {
-	private Multimap<VersionEnum, BaseTask<?>> myTasks = MultimapBuilder.hashKeys().arrayListValues().build();
+	private Multimap<T, BaseTask<?>> myTasks = MultimapBuilder.hashKeys().arrayListValues().build();
 
-	public List<BaseTask<?>> getTasks(@Nonnull VersionEnum theFrom, @Nonnull VersionEnum theTo) {
+	@SuppressWarnings("unchecked")
+	public List<BaseTask<?>> getTasks(@Nonnull T theFrom, @Nonnull T theTo) {
 		Validate.notNull(theFrom);
 		Validate.notNull(theTo);
 		Validate.isTrue(theFrom.ordinal() < theTo.ordinal(), "From version must be lower than to version");
 
 		List<BaseTask<?>> retVal = new ArrayList<>();
-		for (VersionEnum nextVersion : VersionEnum.values()) {
+		for (Object nextVersion : EnumUtils.getEnumList(theFrom.getClass())) {
-			if (nextVersion.ordinal() <= theFrom.ordinal()) {
+			if (((T)nextVersion).ordinal() <= theFrom.ordinal()) {
 				continue;
 			}
-			if (nextVersion.ordinal() > theTo.ordinal()) {
+			if (((T)nextVersion).ordinal() > theTo.ordinal()) {
 				continue;
 			}
 
-			Collection<BaseTask<?>> nextValues = myTasks.get(nextVersion);
+			Collection<BaseTask<?>> nextValues = myTasks.get((T)nextVersion);
 			if (nextValues != null) {
 				retVal.addAll(nextValues);
 			}
@@ -40,16 +60,16 @@ public class BaseMigrationTasks {
 		return retVal;
 	}
 
-	protected HapiFhirJpaMigrationTasks.Builder forVersion(VersionEnum theVersion) {
+	protected Builder forVersion(T theVersion) {
-		return new HapiFhirJpaMigrationTasks.Builder(theVersion);
+		return new Builder(theVersion);
 	}
 
 	protected class Builder {
 
-		private final VersionEnum myVersion;
+		private final T myVersion;
 		private String myTableName;
 
-		Builder(VersionEnum theVersion) {
+		Builder(T theVersion) {
 			myVersion = theVersion;
 		}
 
@@ -68,14 +88,16 @@ public class BaseMigrationTasks {
 			return new BuilderAddTable();
 		}
 
-		public void startSectionWithMessage(String theMessage) {
+		public Builder startSectionWithMessage(String theMessage) {
 			Validate.notBlank(theMessage);
 			addTask(new LogStartSectionWithMessageTask(theMessage));
+			return this;
 		}
 
 		public class BuilderWithTableName {
 			private String myIndexName;
 			private String myColumnName;
+			private String myForeignKeyName;
 
 			public String getTableName() {
 				return myTableName;
@@ -108,6 +130,11 @@ public class BaseMigrationTasks {
 				return new BuilderModifyColumnWithName();
 			}
 
+			public BuilderAddForeignKey addForeignKey(String theForeignKeyName) {
+				myForeignKeyName = theForeignKeyName;
+				return new BuilderAddForeignKey();
+			}
+
 			public class BuilderAddIndexWithName {
 				private boolean myUnique;
 
@@ -163,8 +190,15 @@ public class BaseMigrationTasks {
 
 				public class BuilderModifyColumnWithNameAndNullable {
 
+					public void withType(BaseTableColumnTypeTask.ColumnTypeEnum theColumnType) {
+						withType(theColumnType, 0);
+					}
+
 					public void withType(BaseTableColumnTypeTask.ColumnTypeEnum theColumnType, int theLength) {
 						if (theColumnType == BaseTableColumnTypeTask.ColumnTypeEnum.STRING) {
+							if (theLength == 0) {
+								throw new IllegalArgumentException("Can not specify length 0 for column of type " + theColumnType);
+							}
 							ModifyColumnTask task = new ModifyColumnTask();
 							task.setColumnName(myColumnName);
 							task.setTableName(myTableName);
@@ -172,13 +206,32 @@ public class BaseMigrationTasks {
 							task.setNullable(myNullable);
 							task.setColumnType(theColumnType);
 							addTask(task);
-						} else {
+						} else if (theLength > 0){
 							throw new IllegalArgumentException("Can not specify length for column of type " + theColumnType);
 						}
 					}
 
 				}
 			}
+
+			public class BuilderAddForeignKey extends BuilderModifyColumnWithName {
+				public BuilderAddForeignKeyToColumn toColumn(String theColumnName) {
+					myColumnName = theColumnName;
+					return new BuilderAddForeignKeyToColumn();
+				}
+
+				public class BuilderAddForeignKeyToColumn {
+					public void references(String theForeignTable, String theForeignColumn) {
+						AddForeignKeyTask task = new AddForeignKeyTask();
+						task.setTableName(myTableName);
+						task.setConstraintName(myForeignKeyName);
+						task.setColumnName(myColumnName);
+						task.setForeignTableName(theForeignTable);
+						task.setForeignColumnName(theForeignColumn);
+						addTask(task);
+					}
+				}
+			}
 		}
 
 		public class BuilderAddTable {

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/AddForeignKeyTaskTest.java

@@ -0,0 +1,39 @@
+package ca.uhn.fhir.jpa.migrate.taskdef;
+
+import ca.uhn.fhir.jpa.migrate.JdbcUtils;
+import org.hamcrest.Matchers;
+import org.junit.Test;
+
+import java.sql.SQLException;
+
+import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.hamcrest.Matchers.empty;
+import static org.junit.Assert.assertThat;
+
+public class AddForeignKeyTaskTest extends BaseTest {
+
+	@Test
+	public void testAddForeignKey() throws SQLException {
+		executeSql("create table HOME (PID bigint not null, TEXTCOL varchar(255), primary key (PID))");
+		executeSql("create table FOREIGNTBL (PID bigint not null, HOMEREF bigint)");
+		assertThat(JdbcUtils.getForeignKeys(getConnectionProperties(), "HOME", "FOREIGNTBL"), empty());
+
+		AddForeignKeyTask task = new AddForeignKeyTask();
+		task.setTableName("FOREIGNTBL");
+		task.setColumnName("HOMEREF");
+		task.setConstraintName("FK_HOME_FOREIGN");
+		task.setForeignColumnName("PID");
+		task.setForeignTableName("HOME");
+		getMigrator().addTask(task);
+
+		getMigrator().migrate();
+
+		assertThat(JdbcUtils.getForeignKeys(getConnectionProperties(), "HOME", "FOREIGNTBL"), Matchers.contains("FK_HOME_FOREIGN"));
+
+		// Make sure additional calls don't crash
+		getMigrator().migrate();
+		getMigrator().migrate();
+	}
+
+
+}

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/ModifyColumnTest.java

@@ -5,9 +5,7 @@ import org.junit.Test;
 
 import java.sql.SQLException;
 
-import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.junit.Assert.*;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertThat;
 
 public class ModifyColumnTest extends BaseTest {
 
@@ -27,6 +25,90 @@ public class ModifyColumnTest extends BaseTest {
 		getMigrator().migrate();
 
 		assertEquals("varchar(300)", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
+
+		// Make sure additional migrations don't crash
+		getMigrator().migrate();
+		getMigrator().migrate();
+
+	}
+
+	@Test
+	public void testColumnMakeNullable() throws SQLException {
+		executeSql("create table SOMETABLE (PID bigint not null, TEXTCOL varchar(255) not null)");
+		assertFalse(JdbcUtils.isColumnNullable(getConnectionProperties(), "SOMETABLE", "PID"));
+		assertFalse(JdbcUtils.isColumnNullable(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
+		assertEquals("bigint", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "PID"));
+		assertEquals("varchar(255)", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
+
+		// PID
+		ModifyColumnTask task = new ModifyColumnTask();
+		task.setTableName("SOMETABLE");
+		task.setColumnName("PID");
+		task.setColumnType(AddColumnTask.ColumnTypeEnum.LONG);
+		task.setNullable(true);
+		getMigrator().addTask(task);
+
+		// STRING
+		task = new ModifyColumnTask();
+		task.setTableName("SOMETABLE");
+		task.setColumnName("TEXTCOL");
+		task.setColumnType(AddColumnTask.ColumnTypeEnum.STRING);
+		task.setNullable(true);
+		task.setColumnLength(255);
+		getMigrator().addTask(task);
+
+		// Do migration
+		getMigrator().migrate();
+
+		assertTrue(JdbcUtils.isColumnNullable(getConnectionProperties(), "SOMETABLE", "PID"));
+		assertTrue(JdbcUtils.isColumnNullable(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
+		assertEquals("bigint", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "PID"));
+		assertEquals("varchar(255)", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
+
+		// Make sure additional migrations don't crash
+		getMigrator().migrate();
+		getMigrator().migrate();
+
+
+	}
+
+	@Test
+	public void testColumnMakeNotNullable() throws SQLException {
+		executeSql("create table SOMETABLE (PID bigint, TEXTCOL varchar(255))");
+		assertTrue(JdbcUtils.isColumnNullable(getConnectionProperties(), "SOMETABLE", "PID"));
+		assertTrue(JdbcUtils.isColumnNullable(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
+		assertEquals("bigint", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "PID"));
+		assertEquals("varchar(255)", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
+
+		// PID
+		ModifyColumnTask task = new ModifyColumnTask();
+		task.setTableName("SOMETABLE");
+		task.setColumnName("PID");
+		task.setColumnType(AddColumnTask.ColumnTypeEnum.LONG);
+		task.setNullable(false);
+		getMigrator().addTask(task);
+
+		// STRING
+		task = new ModifyColumnTask();
+		task.setTableName("SOMETABLE");
+		task.setColumnName("TEXTCOL");
+		task.setColumnType(AddColumnTask.ColumnTypeEnum.STRING);
+		task.setNullable(false);
+		task.setColumnLength(255);
+		getMigrator().addTask(task);
+
+		// Do migration
+		getMigrator().migrate();
+
+		assertFalse(JdbcUtils.isColumnNullable(getConnectionProperties(), "SOMETABLE", "PID"));
+		assertFalse(JdbcUtils.isColumnNullable(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
+		assertEquals("bigint", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "PID"));
+		assertEquals("varchar(255)", JdbcUtils.getColumnType(getConnectionProperties(), "SOMETABLE", "TEXTCOL"));
+
+		// Make sure additional migrations don't crash
+		getMigrator().migrate();
+		getMigrator().migrate();
+
 	}
 
 }

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasksTest.java

@@ -9,4 +9,6 @@ public class HapiFhirJpaMigrationTasksTest {
 		new HapiFhirJpaMigrationTasks();
 	}
 
+
+
 }