Address SQL syntax issue

hapi-fhir-cli/hapi-fhir-cli-app/pom.xml

@@ -43,6 +43,14 @@
 			<classifier>classes</classifier>
 		</dependency>
 
+		<!--
+		<dependency>
+			<groupId>com.oracle</groupId>
+			<artifactId>ojbc8g</artifactId>
+			<version>12.2.0.1</version>
+		</dependency>
+		-->
+
 	</dependencies>
 
 	<build>

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

@@ -50,7 +50,7 @@ public class JdbcUtils {
 				DatabaseMetaData metadata;
 				try {
 					metadata = connection.getMetaData();
-					ResultSet indexes = metadata.getIndexInfo(null, null, theTableName, false, true);
+					ResultSet indexes = metadata.getIndexInfo(connection.getCatalog(), connection.getSchema(), theTableName, false, true);
 
 					Set<String> indexNames = new HashSet<>();
 					while (indexes.next()) {
@@ -78,7 +78,7 @@ public class JdbcUtils {
 				DatabaseMetaData metadata;
 				try {
 					metadata = connection.getMetaData();
-					ResultSet indexes = metadata.getIndexInfo(null, null, theTableName, false, false);
+					ResultSet indexes = metadata.getIndexInfo(connection.getCatalog(), connection.getSchema(), theTableName, false, false);
 
 					while (indexes.next()) {
 						String indexName = indexes.getString("INDEX_NAME");
@@ -107,7 +107,9 @@ public class JdbcUtils {
 				DatabaseMetaData metadata;
 				try {
 					metadata = connection.getMetaData();
-					ResultSet indexes = metadata.getColumns(null, null, null, null);
+					String catalog = connection.getCatalog();
+					String schema = connection.getSchema();
+					ResultSet indexes = metadata.getColumns(catalog, schema, theTableName, null);
 
 					while (indexes.next()) {
 
@@ -158,7 +160,7 @@ public class JdbcUtils {
 				DatabaseMetaData metadata;
 				try {
 					metadata = connection.getMetaData();
-					ResultSet indexes = metadata.getCrossReference(null, null, theTableName, null, null, theForeignTable);
+					ResultSet indexes = metadata.getCrossReference(connection.getCatalog(), connection.getSchema(), theTableName, connection.getCatalog(), connection.getSchema(), theForeignTable);
 
 					Set<String> columnNames = new HashSet<>();
 					while (indexes.next()) {
@@ -194,7 +196,7 @@ public class JdbcUtils {
 				DatabaseMetaData metadata;
 				try {
 					metadata = connection.getMetaData();
-					ResultSet indexes = metadata.getColumns(null, null, null, null);
+					ResultSet indexes = metadata.getColumns(connection.getCatalog(), connection.getSchema(), theTableName, null);
 
 					Set<String> columnNames = new HashSet<>();
 					while (indexes.next()) {
@@ -223,7 +225,7 @@ public class JdbcUtils {
 				DatabaseMetaData metadata;
 				try {
 					metadata = connection.getMetaData();
-					ResultSet tables = metadata.getTables(null, null, null, null);
+					ResultSet tables = metadata.getTables(connection.getCatalog(), connection.getSchema(), null, null);
 
 					Set<String> columnNames = new HashSet<>();
 					while (tables.next()) {
@@ -254,7 +256,7 @@ public class JdbcUtils {
 				DatabaseMetaData metadata;
 				try {
 					metadata = connection.getMetaData();
-					ResultSet tables = metadata.getColumns(null, null, null, null);
+					ResultSet tables = metadata.getColumns(connection.getCatalog(), connection.getSchema(), theTableName, theColumnName);
 
 					while (tables.next()) {
 						String tableName = toUpperCase(tables.getString("TABLE_NAME"), Locale.US);

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.migrate;
  * 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.
@@ -28,6 +28,7 @@ import org.slf4j.LoggerFactory;
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Objects;
 
 public class Migrator {
 
@@ -40,6 +41,7 @@ public class Migrator {
 	private DriverTypeEnum.ConnectionProperties myConnectionProperties;
 	private int myChangesCount;
 	private boolean myDryRun;
+	private List<BaseTask.ExecutedStatement> myExecutedStatements = new ArrayList<>();
 
 	public int getChangesCount() {
 		return myChangesCount;
@@ -74,7 +76,7 @@ public class Migrator {
 
 		myConnectionProperties = myDriverType.newConnectionProperties(myConnectionUrl, myUsername, myPassword);
 		try {
-			for (BaseTask next : myTasks) {
+			for (BaseTask<?> next : myTasks) {
 				next.setDriverType(myDriverType);
 				next.setConnectionProperties(myConnectionProperties);
 				next.setDryRun(myDryRun);
@@ -85,12 +87,33 @@ public class Migrator {
 				}
 
 				myChangesCount += next.getChangesCount();
+				myExecutedStatements.addAll(next.getExecutedStatements());
 			}
 		} finally {
 			myConnectionProperties.close();
 		}
 
 		ourLog.info("Finished migration of {} tasks", myTasks.size());
+
+		if (myDryRun) {
+			StringBuilder statementBuilder = new StringBuilder();
+			String lastTable = null;
+			for (BaseTask.ExecutedStatement next : myExecutedStatements) {
+				if (!Objects.equals(lastTable, next.getTableName())) {
+					statementBuilder.append("\n\n-- Table: ").append(next.getTableName()).append("\n");
+					lastTable = next.getTableName();
+				}
+
+				statementBuilder.append(next.getSql()).append(";\n");
+
+				for (Object nextArg : next.getArguments()) {
+					statementBuilder.append("  -- Arg: ").append(nextArg).append("\n");
+				}
+			}
+
+			ourLog.info("SQL that would be executed:\n\n***********************************\n{}***********************************", statementBuilder);
+		}
+
 	}
 
 }

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

@@ -46,9 +46,22 @@ public class AddColumnTask extends BaseTableColumnTypeTask<AddColumnTask> {
 			nullable = "";
 		}
 
-		String sql = "alter table " + getTableName() + " add column " + getColumnName() + " " + type + " " + nullable;
+		String sql = "";
+		switch (getDriverType()) {
+			case DERBY_EMBEDDED:
+			case MARIADB_10_1:
+			case MYSQL_5_7:
+			case POSTGRES_9_4:
+				sql = "alter table " + getTableName() + " add column " + getColumnName() + " " + type + " " + nullable;
+				break;
+			case MSSQL_2012:
+			case ORACLE_12C:
+				sql = "alter table " + getTableName() + " add " + getColumnName() + " " + type + " " + nullable;
+				break;
+		}
+
 		ourLog.info("Adding column {} of type {} to table {}", getColumnName(), type, getTableName());
-		executeSql(sql);
+		executeSql(getTableName(), sql);
 	}
 
 }

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

@@ -83,7 +83,7 @@ public class AddForeignKeyTask extends BaseTableColumnTask<AddForeignKeyTask> {
 
 
 		try {
-			executeSql(sql);
+			executeSql(getTableName(), sql);
 		} catch (Exception e) {
 			if (e.toString().contains("already exists")) {
 				ourLog.warn("Index {} already exists", myConstraintName);

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

@@ -67,12 +67,13 @@ public class AddIndexTask extends BaseTableTask<AddIndexTask> {
 			return;
 		}
 
-		String unique = myUnique ? "UNIQUE " : "";
+		String unique = myUnique ? "unique " : "";
 		String columns = String.join(", ", myColumns);
-		String sql = "CREATE " + unique + " INDEX " + myIndexName + " ON " + getTableName() + "(" + columns + ")";
+		String sql = "create " + unique + "index " + myIndexName + " on " + getTableName() + "(" + columns + ")";
+		String tableName = getTableName();
 
 		try {
-			executeSql(sql);
+			executeSql(tableName, sql);
 		} catch (Exception e) {
 			if (e.toString().contains("already exists")) {
 				ourLog.warn("Index {} already exists", myIndexName);

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.migrate.taskdef;
  * 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.
@@ -38,11 +38,13 @@ public class ArbitrarySqlTask extends BaseTask<ArbitrarySqlTask> {
 
 	private static final Logger ourLog = LoggerFactory.getLogger(ArbitrarySqlTask.class);
 	private final String myDescription;
+	private final String myTableName;
 	private List<Task> myTask = new ArrayList<>();
 	private int myBatchSize = 1000;
 	private String myExecuteOnlyIfTableExists;
 
-	public ArbitrarySqlTask(String theDescription) {
+	public ArbitrarySqlTask(String theTableName, String theDescription) {
+		myTableName = theTableName;
 		myDescription = theDescription;
 	}
 
@@ -104,7 +106,6 @@ public class ArbitrarySqlTask extends BaseTask<ArbitrarySqlTask> {
 		@Override
 		public void execute() {
 			if (isDryRun()) {
-				logDryRunSql(mySql);
 				return;
 			}
 

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

@@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.migrate.taskdef;
  * 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.
@@ -28,6 +28,10 @@ import org.springframework.jdbc.core.JdbcTemplate;
 import org.springframework.transaction.support.TransactionTemplate;
 
 import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
 
 public abstract class BaseTask<T extends BaseTask> {
 
@@ -37,6 +41,7 @@ public abstract class BaseTask<T extends BaseTask> {
 	private String myDescription;
 	private int myChangesCount;
 	private boolean myDryRun;
+	private List<ExecutedStatement> myExecutedStatements = new ArrayList<>();
 
 	public boolean isDryRun() {
 		return myDryRun;
@@ -56,29 +61,36 @@ public abstract class BaseTask<T extends BaseTask> {
 		return (T) this;
 	}
 
+	public List<ExecutedStatement> getExecutedStatements() {
+		return myExecutedStatements;
+	}
+
 	public int getChangesCount() {
 		return myChangesCount;
 	}
 
-	public void executeSql(@Language("SQL") String theSql, Object... theArguments) {
+	/**
-		if (isDryRun()) {
+	 * @param theTableName This is only used for logging currently
-			logDryRunSql(theSql);
+	 * @param theSql       The SQL statement
-			return;
+	 * @param theArguments The SQL statement arguments
+	 */
+	public void executeSql(String theTableName, @Language("SQL") String theSql, Object... theArguments) {
+		if (isDryRun() == false) {
+			Integer changes = getConnectionProperties().getTxTemplate().execute(t -> {
+				JdbcTemplate jdbcTemplate = getConnectionProperties().newJdbcTemplate();
+				int changesCount = jdbcTemplate.update(theSql, theArguments);
+				ourLog.info("SQL \"{}\" returned {}", theSql, changesCount);
+				return changesCount;
+			});
+
+			myChangesCount += changes;
 		}
 
-		Integer changes = getConnectionProperties().getTxTemplate().execute(t -> {
+		captureExecutedStatement(theTableName, theSql, theArguments);
-			JdbcTemplate jdbcTemplate = getConnectionProperties().newJdbcTemplate();
-			int changesCount = jdbcTemplate.update(theSql, theArguments);
-			ourLog.info("SQL \"{}\" returned {}", theSql, changesCount);
-			return changesCount;
-		});
-
-		myChangesCount += changes;
-
 	}
 
-	protected void logDryRunSql(@Language("SQL") String theSql) {
+	protected void captureExecutedStatement(String theTableName, @Language("SQL") String theSql, Object[] theArguments) {
-		ourLog.info("WOULD EXECUTE SQL: {}", theSql);
+		myExecutedStatements.add(new ExecutedStatement(theTableName, theSql, theArguments));
 	}
 
 	public DriverTypeEnum.ConnectionProperties getConnectionProperties() {
@@ -108,4 +120,28 @@ public abstract class BaseTask<T extends BaseTask> {
 	}
 
 	public abstract void execute() throws SQLException;
+
+	public static class ExecutedStatement {
+		private final String mySql;
+		private final List<Object> myArguments;
+		private final String myTableName;
+
+		public ExecutedStatement(String theDescription, String theSql, Object[] theArguments) {
+			myTableName = theDescription;
+			mySql = theSql;
+			myArguments = theArguments != null ? Arrays.asList(theArguments) : Collections.emptyList();
+		}
+
+		public String getTableName() {
+			return myTableName;
+		}
+
+		public String getSql() {
+			return mySql;
+		}
+
+		public List<Object> getArguments() {
+			return myArguments;
+		}
+	}
 }

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

@@ -162,7 +162,7 @@ public class CalculateHashesTask extends BaseTableColumnTask<CalculateHashesTask
 
 					// Generate update SQL
 					StringBuilder sqlBuilder = new StringBuilder();
-					List<Long> arguments = new ArrayList<>();
+					List<Number> arguments = new ArrayList<>();
 					sqlBuilder.append("UPDATE ");
 					sqlBuilder.append(getTableName());
 					sqlBuilder.append(" SET ");
@@ -174,7 +174,7 @@ public class CalculateHashesTask extends BaseTableColumnTask<CalculateHashesTask
 						arguments.add(nextNewValueEntry.getValue());
 					}
 					sqlBuilder.append(" WHERE SP_ID = ?");
-					arguments.add((Long) nextRow.get("SP_ID"));
+					arguments.add((Number) nextRow.get("SP_ID"));
 
 					// Apply update SQL
 					newJdbcTemnplate().update(sqlBuilder.toString(), arguments.toArray());

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

@@ -42,7 +42,7 @@ public class DropColumnTask extends BaseTableColumnTask<DropColumnTask> {
 
 		String sql = "alter table " + getTableName() + " drop column " + getColumnName();
 		ourLog.info("Dropping column {} on table {}", getColumnName(), getTableName());
-		executeSql(sql);
+		executeSql(getTableName(), sql);
 	}
 
 }

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

@@ -63,15 +63,15 @@ public class DropIndexTask extends BaseTableTask<DropIndexTask> {
 			switch (getDriverType()) {
 				case MYSQL_5_7:
 				case MARIADB_10_1:
-					sql = "ALTER TABLE " + getTableName() + " DROP INDEX " + myIndexName;
+					sql = "alter table " + getTableName() + " drop index " + myIndexName;
 					break;
 				case DERBY_EMBEDDED:
-					sql = "DROP INDEX " + myIndexName;
+					sql = "drop index " + myIndexName;
 					break;
 				case POSTGRES_9_4:
 				case ORACLE_12C:
 				case MSSQL_2012:
-					sql = "ALTER TABLE " + getTableName() + " DROP CONSTRAINT " + myIndexName;
+					sql = "alter table " + getTableName() + " drop constraint " + myIndexName;
 					break;
 			}
 		} else {
@@ -79,19 +79,19 @@ public class DropIndexTask extends BaseTableTask<DropIndexTask> {
 			switch (getDriverType()) {
 				case MYSQL_5_7:
 				case MARIADB_10_1:
-					sql = "ALTER TABLE " + getTableName() + " DROP INDEX " + myIndexName;
+					sql = "alter table " + getTableName() + " drop index " + myIndexName;
 					break;
 				case POSTGRES_9_4:
 				case DERBY_EMBEDDED:
 				case ORACLE_12C:
-					sql = "DROP INDEX " + myIndexName;
+					sql = "drop index " + myIndexName;
 					break;
 				case MSSQL_2012:
-					sql = "DROP INDEX " + getTableName() + "." + myIndexName;
+					sql = "drop index " + getTableName() + "." + myIndexName;
 					break;
 			}
 		}
-		executeSql(sql);
+		executeSql(getTableName(), sql);
 
 	}
 

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

@@ -95,12 +95,12 @@ public class ModifyColumnTask extends BaseTableColumnTypeTask<ModifyColumnTask>
 
 		ourLog.info("Updating column {} on table {} to type {}", getColumnName(), getTableName(), type);
 		if (sql != null) {
-			executeSql(sql);
+			executeSql(getTableName(), sql);
 		}
 
 		if (sqlNotNull != null) {
 			ourLog.info("Updating column {} on table {} to not null", getColumnName(), getTableName());
-			executeSql(sqlNotNull);
+			executeSql(getTableName(), sqlNotNull);
 		}
 	}
 

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

@@ -322,7 +322,7 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 			.unique(false)
 			.withColumns("HASH_PRESENCE");
 
-		ArbitrarySqlTask consolidateSearchParamPresenceIndexesTask = new ArbitrarySqlTask("Consolidate search parameter presence indexes");
+		ArbitrarySqlTask consolidateSearchParamPresenceIndexesTask = new ArbitrarySqlTask("HFJ_SEARCH_PARM", "Consolidate search parameter presence indexes");
 		consolidateSearchParamPresenceIndexesTask.setExecuteOnlyIfTableExists("HFJ_SEARCH_PARM");
 		consolidateSearchParamPresenceIndexesTask.setBatchSize(1);
 
@@ -338,7 +338,7 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 			String resType = (String) t.get("RES_TYPE");
 			String paramName = (String) t.get("PARAM_NAME");
 			Long hash = SearchParamPresent.calculateHashPresence(resType, paramName, present);
-			consolidateSearchParamPresenceIndexesTask.executeSql("update HFJ_RES_PARAM_PRESENT set HASH_PRESENCE = ? where PID = ?", hash, pid);
+			consolidateSearchParamPresenceIndexesTask.executeSql("HFJ_RES_PARAM_PRESENT", "update HFJ_RES_PARAM_PRESENT set HASH_PRESENCE = ? where PID = ?", hash, pid);
 		});
 		version.addTask(consolidateSearchParamPresenceIndexesTask);
 

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

@@ -19,7 +19,7 @@ public class ArbitrarySqlTaskTest extends BaseTest {
 		executeSql("insert into HFJ_RES_PARAM_PRESENT (PID, SP_ID, SP_PRESENT, HASH_PRESENT) values (100, 1, true, null)");
 		executeSql("insert into HFJ_RES_PARAM_PRESENT (PID, SP_ID, SP_PRESENT, HASH_PRESENT) values (101, 2, true, null)");
 
-		ArbitrarySqlTask task = new ArbitrarySqlTask("Consolidate search parameter presence indexes");
+		ArbitrarySqlTask task = new ArbitrarySqlTask("HFJ_RES_PARAM_PRESENT", "Consolidate search parameter presence indexes");
 		task.setExecuteOnlyIfTableExists("hfj_search_parm");
 		task.setBatchSize(1);
 		String sql = "SELECT " +
@@ -34,7 +34,7 @@ public class ArbitrarySqlTaskTest extends BaseTest {
 			String resType = (String) t.get("RES_TYPE");
 			String paramName = (String) t.get("PARAM_NAME");
 			Long hash = SearchParamPresent.calculateHashPresence(resType, paramName, present);
-			task.executeSql("update HFJ_RES_PARAM_PRESENT set HASH_PRESENT = ? where PID = ?", hash, pid);
+			task.executeSql("HFJ_RES_PARAM_PRESENT", "update HFJ_RES_PARAM_PRESENT set HASH_PRESENT = ? where PID = ?", hash, pid);
 		});
 
 		getMigrator().addTask(task);
@@ -53,11 +53,11 @@ public class ArbitrarySqlTaskTest extends BaseTest {
 
 	@Test
 	public void testExecuteOnlyIfTableExists() {
-		ArbitrarySqlTask task = new ArbitrarySqlTask("Consolidate search parameter presence indexes");
+		ArbitrarySqlTask task = new ArbitrarySqlTask("HFJ_RES_PARAM_PRESENT", "Consolidate search parameter presence indexes");
 		task.setBatchSize(1);
 		String sql = "SELECT * FROM HFJ_SEARCH_PARM";
 		task.addQuery(sql, ArbitrarySqlTask.QueryModeEnum.BATCH_UNTIL_NO_MORE, t -> {
-			task.executeSql("update HFJ_RES_PARAM_PRESENT set FOOFOOOFOO = null");
+			task.executeSql("HFJ_RES_PARAM_PRESENT", "update HFJ_RES_PARAM_PRESENT set FOOFOOOFOO = null");
 		});
 		task.setExecuteOnlyIfTableExists("hfj_search_parm");
 

src/changes/changes.xml

@@ -97,6 +97,11 @@
 				including support for either allowing the operation response to proceed unchallenged,
 				or authorizing the contents of the response.
 			</action>
+			<action type="add">
+				An invalid SQL syntax issue has been fixed when running the CLI JPA Migrator tool against 
+				Oracle or SQL Server. In addition, when using the "Dry Run" option, all generated SQL
+				statements will be logged at the end of the run.
+			</action>
 		</release>
 		<release version="3.6.0" date="2018-11-12" description="Food">
 			<action type="add">