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/*
* (C) Copyright IBM Corp. 2017, 2021
*
* SPDX-License-Identifier: Apache-2.0
*/
package com.ibm.fhir.persistence.jdbc.dao.impl;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.Timestamp;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
import com.ibm.fhir.database.utils.api.IDatabaseTranslator;
import com.ibm.fhir.database.utils.common.CalendarHelper;
import com.ibm.fhir.database.utils.common.DatabaseTranslatorFactory;
import com.ibm.fhir.database.utils.model.DbType;
import com.ibm.fhir.database.utils.query.QueryUtil;
import com.ibm.fhir.database.utils.query.Select;
import com.ibm.fhir.model.resource.OperationOutcome.Issue;
import com.ibm.fhir.model.type.code.IssueType;
import com.ibm.fhir.model.util.FHIRUtil;
import com.ibm.fhir.persistence.exception.FHIRPersistenceException;
import com.ibm.fhir.persistence.jdbc.connection.FHIRDbFlavor;
import com.ibm.fhir.persistence.jdbc.dao.api.FHIRDbDAO;
import com.ibm.fhir.persistence.jdbc.dto.Resource;
import com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceDBCleanupException;
import com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceDBConnectException;
import com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceDataAccessException;
/**
* This class is a root Data Access Object for managing JDBC access to the FHIR database.
* As of 4.3.0, connection handling is factored out of the DAO and is instead the
* responsibility of the FHIRPersistenceJDBCImpl. Each DAO therefore requires a
* connection to be passed to it. This is good for separation of concerns, because the
* DAO code shouldn't care where the connection comes from. As each DAO is stateless,
* and lightweight, they can be created on-the-fly and handed a connection in the
* constructor. This pattern avoids polluting every method call with a connection
* parameter.
*/
public class FHIRDbDAOImpl implements FHIRDbDAO {
private static final Logger log = Logger.getLogger(FHIRDbDAOImpl.class.getName());
private static final String CLASSNAME = FHIRDbDAOImpl.class.getName();
private static final String NEWLINE = System.getProperty("line.separator");
// The connection the DAO operates against
private final Connection connection;
// The name of the FHIR data schema (containing the FHIR resource tables).
private final String schemaName;
// The type of database we are connected to. Perhaps should use translator instead?
private final FHIRDbFlavor flavor;
/**
* Constructs a DAO instance suitable for acquiring DB connections via JNDI from the app server.
*/
public FHIRDbDAOImpl(Connection connection, String schemaName, FHIRDbFlavor flavor) {
super();
this.connection = connection;
this.schemaName = schemaName;
this.flavor = flavor;
}
/**
* Getter for the connection being used by this DAO.
* @return
*/
@Override
public Connection getConnection() {
return this.connection;
}
/**
* Getter for the schema name we've been configured for
* @return
*/
public String getSchemaName() {
return this.schemaName;
}
@Override
public FHIRDbFlavor getFlavor() {
return this.flavor;
}
/**
* Convenience function to log the cause of an exception about to be thrown. This
* is useful when avoiding chaining the cause with the persistence exception, which
* could inadvertently leak sensitive information (details of the schema, for example)
*
* @param logger
* @param fx
* @param cause
* @return
*/
protected XT severe(Logger logger, XT fx, Throwable cause) {
logger.log(Level.SEVERE, fx.getMessage(), cause);
return fx;
}
/**
* Log the exception message here along with the cause stack. Return the
* exception fx to the caller so that it can be thrown easily.
*
* @param logger
* @param fx
* @param errorMessage
* @param cause
* @return
*/
protected XT severe(Logger logger, XT fx, String errorMessage,
Throwable cause) {
if (cause != null) {
logger.log(Level.SEVERE, fx.addProbeId(errorMessage), cause);
} else {
logger.log(Level.SEVERE, fx.addProbeId(errorMessage));
}
return fx;
}
/**
* Closes the passed PreparedStatement.
*
* @param stmt
* @param connection
*/
protected void cleanup(PreparedStatement stmt) {
final String METHODNAME = "cleanup(PreparedStatement, Connection)";
log.entering(CLASSNAME, METHODNAME);
FHIRPersistenceDBCleanupException ce;
if (stmt != null) {
try {
stmt.close();
} catch (Throwable e) {
ce = new FHIRPersistenceDBCleanupException("Failure closing PreparedStatement.", e);
log.log(Level.SEVERE, ce.getMessage(), ce);
}
}
log.exiting(CLASSNAME, METHODNAME);
}
/**
* Closes the passed ResultSet, PreparedStatement. We are no longer responsible
* for Connections so don't close them
*
* @param resultSet
* @param stmt
*/
protected void cleanup(ResultSet resultSet, PreparedStatement stmt) {
final String METHODNAME = "cleanup(PreparedStatement, Connection)";
log.entering(CLASSNAME, METHODNAME);
FHIRPersistenceDBCleanupException ce;
if (resultSet != null) {
try {
resultSet.close();
} catch (Throwable e) {
ce = new FHIRPersistenceDBCleanupException("Failure closing ResultSet.", e);
log.log(Level.SEVERE, ce.getMessage(), ce);
}
}
this.cleanup(stmt);
log.exiting(CLASSNAME, METHODNAME);
}
/**
* Creates and executes a PreparedStatement using the passed parameters that returns a collection of FHIR Data
* Transfer Objects of type T.
*
* @param sql - The SQL template to execute.
* @param searchArgs - An array of arguments to be substituted into the SQL template.
* @return List - A List of FHIR Data Transfer Objects resulting from the executed query.
* @throws FHIRPersistenceDataAccessException
* @throws FHIRPersistenceDBConnectException
*/
protected List runQuery(String sql, Object... searchArgs)
throws FHIRPersistenceDataAccessException, FHIRPersistenceDBConnectException {
final String METHODNAME = "runQuery";
log.entering(CLASSNAME, METHODNAME);
List fhirObjects = new ArrayList<>();
PreparedStatement stmt = null;
ResultSet resultSet = null;
String errMsg;
long dbCallStartTime;
double dbCallDuration;
try {
stmt = connection.prepareStatement(sql);
// Inject arguments into the prepared stmt.
for (int i = 0; i < searchArgs.length; i++) {
if (searchArgs[i] instanceof Timestamp) {
stmt.setTimestamp(i + 1, (Timestamp) searchArgs[i], CalendarHelper.getCalendarForUTC());
} else {
stmt.setObject(i + 1, searchArgs[i]);
}
}
dbCallStartTime = System.nanoTime();
resultSet = stmt.executeQuery();
dbCallDuration = (System.nanoTime() - dbCallStartTime) / 1e6;
// Transform the resultSet into a collection of Data Transfer Objects
fhirObjects = this.createDTOs(resultSet);
if (log.isLoggable(Level.FINE)) {
log.fine("Successfully retrieved FHIR objects; SQL=" + sql + NEWLINE + "searchArgs="
+ Arrays.toString(searchArgs) + " [took " + dbCallDuration + " ms]");
}
} catch (FHIRPersistenceException e) {
throw e;
} catch (Throwable e) {
// avoid leaking SQL because the exception message might be returned to a client
FHIRPersistenceDataAccessException fx =
new FHIRPersistenceDataAccessException("Failure retrieving FHIR objects");
errMsg = "Failure retrieving FHIR objects. SQL=" + sql + " searchArgs=" + Arrays.toString(searchArgs);
throw severe(log, fx, errMsg, e);
} finally {
this.cleanup(resultSet, stmt);
log.exiting(CLASSNAME, METHODNAME);
}
return fhirObjects;
}
/**
* Creates and executes a PreparedStatement for the passed sql containing a 'SELECT COUNT...'.
* The count value is extracted from the ResultSet and returned as an int.
*
* @param sql - The SQL SELECT COUNT template to execute.
* @param searchArgs - An array of arguments to be substituted into the SQL template.
* @return int - The count of results returned by the SQL query.
* @throws FHIRPersistenceDataAccessException
* @throws FHIRPersistenceDBConnectException
*/
protected int runCountQuery(String sql, Object... searchArgs)
throws FHIRPersistenceDataAccessException, FHIRPersistenceDBConnectException {
final String METHODNAME = "runCountQuery";
log.entering(CLASSNAME, METHODNAME);
int rowCount = 0;
PreparedStatement stmt = null;
ResultSet resultSet = null;
String errMsg =
"Failure retrieving count. SQL=" + sql + NEWLINE + " searchArgs=" + Arrays.toString(searchArgs);
long dbCallStartTime;
double dbCallDuration;
try {
if (log.isLoggable(Level.FINE)) {
log.fine("Count SQL = " + sql + NEWLINE + "; searchArgs="
+ Arrays.toString(searchArgs));
}
stmt = connection.prepareStatement(sql);
// Inject arguments into the prepared stmt.
for (int i = 0; i < searchArgs.length; i++) {
if (searchArgs[i] instanceof Timestamp) {
stmt.setTimestamp(i + 1, (Timestamp) searchArgs[i], CalendarHelper.getCalendarForUTC());
} else {
stmt.setObject(i + 1, searchArgs[i]);
}
}
dbCallStartTime = System.nanoTime();
resultSet = stmt.executeQuery();
dbCallDuration = (System.nanoTime() - dbCallStartTime) / 1e6;
if (resultSet.next()) {
rowCount = resultSet.getInt(1);
if (log.isLoggable(Level.FINE)) {
log.fine("Successfully retrieved count; count=" + rowCount + " [took "
+ dbCallDuration + " ms]");
}
} else {
// Don't emit the SQL text in an exception - it risks returning it to the client in a response
FHIRPersistenceDataAccessException fx =
new FHIRPersistenceDataAccessException("Server error: failure retrieving count");
throw severe(log, fx, errMsg, null);
}
} catch (FHIRPersistenceException e) {
throw e;
} catch (Throwable e) {
// Don't emit the SQL text in an exception - it risks returning it to the client in a response
FHIRPersistenceDataAccessException fx =
new FHIRPersistenceDataAccessException("Server error: failure retrieving count");
throw severe(log, fx, errMsg, e);
} finally {
this.cleanup(resultSet, stmt);
log.exiting(CLASSNAME, METHODNAME);
}
return rowCount;
}
/**
* Creates and executes a PreparedStatement for the passed sql containing a 'SELECT COUNT...'.
* The count value is extracted from the ResultSet and returned as an int.
*
* @param countQuery - The SQL SELECT COUNT statement and bind variables to execute.
* @return int - The count of results returned by the SQL query.
* @throws FHIRPersistenceDataAccessException
* @throws FHIRPersistenceDBConnectException
*/
protected int runCountQuery(Select countQuery)
throws FHIRPersistenceDataAccessException, FHIRPersistenceDBConnectException {
final String METHODNAME = "runCountQuery";
log.entering(CLASSNAME, METHODNAME);
int rowCount = 0;
long dbCallStartTime;
double dbCallDuration;
// Query string is FINE logged inside prepareSelect, so no need to log again here
try (PreparedStatement stmt = QueryUtil.prepareSelect(connection, countQuery, getTranslator())) {
dbCallStartTime = System.nanoTime();
ResultSet resultSet = stmt.executeQuery();
dbCallDuration = (System.nanoTime() - dbCallStartTime) / 1e6;
if (resultSet.next()) {
rowCount = resultSet.getInt(1);
if (log.isLoggable(Level.FINE)) {
log.fine("Successfully retrieved count; count=" + rowCount + " [took "
+ dbCallDuration + " ms]");
}
} else {
// Don't emit the SQL text in an exception - it risks returning it to the client in a response
FHIRPersistenceDataAccessException fx =
new FHIRPersistenceDataAccessException("Server error: failure retrieving count");
throw severe(log, fx, countQuery.toDebugString(), null);
}
} catch (FHIRPersistenceException e) {
throw e;
} catch (Throwable e) {
// Don't emit the SQL text in an exception - it risks returning it to the client in a response
FHIRPersistenceDataAccessException fx =
new FHIRPersistenceDataAccessException("Server error: failure retrieving count");
throw severe(log, fx, countQuery.toDebugString(), e);
} finally {
log.exiting(CLASSNAME, METHODNAME);
}
return rowCount;
}
/**
* Retrieve the FHIR objects by executing the given {@link Select} statement
* @param select
* @return
* @throws FHIRPersistenceDataAccessException
* @throws FHIRPersistenceDBConnectException
*/
protected List runQuery(Select select)
throws FHIRPersistenceDataAccessException, FHIRPersistenceDBConnectException {
final String METHODNAME = "runQuery";
log.entering(CLASSNAME, METHODNAME);
List fhirObjects = new ArrayList<>();
ResultSet resultSet = null;
long dbCallStartTime;
double dbCallDuration;
try (PreparedStatement stmt = QueryUtil.prepareSelect(connection, select, getTranslator())) {
dbCallStartTime = System.nanoTime();
resultSet = stmt.executeQuery();
dbCallDuration = (System.nanoTime() - dbCallStartTime) / 1e6;
// Transform the resultSet into a collection of Data Transfer Objects
fhirObjects = this.createDTOs(resultSet);
if (log.isLoggable(Level.FINE)) {
log.fine("Successfully retrieved FHIR objects [took " + dbCallDuration + " ms]");
}
} catch (FHIRPersistenceException e) {
throw e;
} catch (Throwable e) {
// avoid leaking SQL because the exception message might be returned to a client
FHIRPersistenceDataAccessException fx =
new FHIRPersistenceDataAccessException("Failure retrieving FHIR objects");
throw severe(log, fx, select.toDebugString(), e);
} finally {
log.exiting(CLASSNAME, METHODNAME);
}
return fhirObjects;
}
/**
* An method for creating a collection of Data Transfer Objects of type T from the contents of the passed ResultSet.
*
* @param resultSet A ResultSet containing FHIR persistent object data.
* @return List - A collection of FHIR Data Transfer objects of the same type.
* @throws FHIRPersistenceDataAccessException
*/
protected List createDTOs(ResultSet resultSet) throws FHIRPersistenceDataAccessException {
final String METHODNAME = "createDTOs";
log.entering(CLASSNAME, METHODNAME);
Resource dto;
List dtoList = new ArrayList();
try {
// Some queries include the resource type id, which we need to know
// when fetching offloaded payloads.
boolean hasResourceTypeId = resultSet.getMetaData().getColumnCount() == 9;
while (resultSet.next()) {
dto = this.createDTO(resultSet, hasResourceTypeId);
if (dto != null) {
dtoList.add(dto);
}
}
} catch (Throwable e) {
// Don't chain the cause, because we might leak secrets
FHIRPersistenceDataAccessException fx = new FHIRPersistenceDataAccessException("Failure creating DTOs.");
throw severe(log, fx, e);
} finally {
log.exiting(CLASSNAME, METHODNAME);
}
return dtoList;
}
/**
* A method for creating a Data Transfer Object of type T from the contents of the passed ResultSet.
*
* @param resultSet A ResultSet containing FHIR persistent object data.
* @return T - An instance of type T, which is a FHIR Data Transfer Object.
* @throws FHIRPersistenceDataAccessException
*/
protected Resource createDTO(ResultSet resultSet, boolean hasResourceTypeId) throws FHIRPersistenceDataAccessException {
// Can be overridden by subclasses that need to return DTOs.
return null;
}
@Override
public boolean isDb2Database() {
return this.flavor.getType() == DbType.DB2;
}
protected FHIRPersistenceDataAccessException buildExceptionWithIssue(String msg, IssueType issueType)
throws FHIRPersistenceDataAccessException {
Issue ooi = FHIRUtil.buildOperationOutcomeIssue(msg, issueType);
return new FHIRPersistenceDataAccessException(msg).withIssue(ooi);
}
protected FHIRPersistenceDBConnectException buildFHIRPersistenceDBConnectException(String msg, IssueType issueType)
throws FHIRPersistenceDBConnectException {
Issue ooi = FHIRUtil.buildOperationOutcomeIssue(msg, issueType);
return new FHIRPersistenceDBConnectException(msg).withIssue(ooi);
}
/**
* Creates and executes a PreparedStatement using the passed parameters that returns a collection of String values.
*
* @param sql - The SQL template to execute.
* @param searchArgs - An array of arguments to be substituted into the SQL template.
* @return List - A List of strings resulting from the executed query.
* @throws FHIRPersistenceDataAccessException
* @throws FHIRPersistenceDBConnectException
*/
protected List runQuery_STR_VALUES(String sql, Object... searchArgs)
throws FHIRPersistenceDataAccessException, FHIRPersistenceDBConnectException {
final String METHODNAME = "runQuery_STR_VALUES";
log.entering(CLASSNAME, METHODNAME);
List strValues = new ArrayList();
PreparedStatement stmt = null;
ResultSet resultSet = null;
String errMsg;
long dbCallStartTime;
double dbCallDuration;
try {
stmt = connection.prepareStatement(sql);
// Inject arguments into the prepared stmt.
for (int i = 0; i < searchArgs.length; i++) {
if (searchArgs[i] instanceof Timestamp) {
stmt.setTimestamp(i + 1, (Timestamp) searchArgs[i], CalendarHelper.getCalendarForUTC());
} else {
stmt.setObject(i + 1, searchArgs[i]);
}
}
dbCallStartTime = System.nanoTime();
resultSet = stmt.executeQuery();
dbCallDuration = (System.nanoTime() - dbCallStartTime) / 1e6;
while (resultSet.next()) {
strValues.add(resultSet.getString(1));
}
if (log.isLoggable(Level.FINE)) {
log.fine("Successfully retrieved string values. SQL=" + sql + " searchArgs="
+ Arrays.toString(searchArgs) + " executionTime=" + dbCallDuration + "ms");
}
} catch (Throwable e) {
// avoid leaking SQL because the exception message might be returned to a client
FHIRPersistenceDataAccessException fx =
new FHIRPersistenceDataAccessException("Failure retrieving string values");
errMsg = "Failure retrieving string values. SQL=" + sql + " searchArgs=" + Arrays.toString(searchArgs);
throw severe(log, fx, errMsg, e);
} finally {
this.cleanup(resultSet, stmt);
log.exiting(CLASSNAME, METHODNAME);
}
return strValues;
}
/**
* Get the translator appropriate for the flavor of database we are using
* @return
*/
protected IDatabaseTranslator getTranslator() {
return DatabaseTranslatorFactory.getTranslator(this.flavor.getType());
}
}
