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com.ibm.fhir.persistence.jdbc.dao.impl.ParameterVisitorBatchDAO Maven / Gradle / Ivy
/*
* (C) Copyright IBM Corp. 2019, 2021
*
* SPDX-License-Identifier: Apache-2.0
*/
package com.ibm.fhir.persistence.jdbc.dao.impl;
import static com.ibm.fhir.persistence.jdbc.JDBCConstants.UTC;
import java.math.BigDecimal;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.sql.Timestamp;
import java.sql.Types;
import java.util.ArrayList;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
import com.ibm.fhir.persistence.exception.FHIRPersistenceException;
import com.ibm.fhir.persistence.jdbc.JDBCConstants;
import com.ibm.fhir.persistence.jdbc.dao.api.IResourceReferenceDAO;
import com.ibm.fhir.persistence.jdbc.dao.api.JDBCIdentityCache;
import com.ibm.fhir.persistence.jdbc.dto.CompositeParmVal;
import com.ibm.fhir.persistence.jdbc.dto.DateParmVal;
import com.ibm.fhir.persistence.jdbc.dto.ExtractedParameterValue;
import com.ibm.fhir.persistence.jdbc.dto.ExtractedParameterValueVisitor;
import com.ibm.fhir.persistence.jdbc.dto.LocationParmVal;
import com.ibm.fhir.persistence.jdbc.dto.NumberParmVal;
import com.ibm.fhir.persistence.jdbc.dto.QuantityParmVal;
import com.ibm.fhir.persistence.jdbc.dto.ReferenceParmVal;
import com.ibm.fhir.persistence.jdbc.dto.StringParmVal;
import com.ibm.fhir.persistence.jdbc.dto.TokenParmVal;
import com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceDataAccessException;
import com.ibm.fhir.persistence.jdbc.impl.ParameterTransactionDataImpl;
import com.ibm.fhir.schema.control.FhirSchemaConstants;
import com.ibm.fhir.search.util.ReferenceValue;
import com.ibm.fhir.search.util.ReferenceValue.ReferenceType;
import com.ibm.fhir.search.util.SearchUtil;
/**
* Batch insert into the parameter values tables. Avoids having to create one stored procedure
* per resource type, because the row type array approach apparently won't work with dynamic
* SQL (EXECUTE ... USING ...). Unfortunately this means we have more database round-trips, we
* don't have a choice.
*/
public class ParameterVisitorBatchDAO implements ExtractedParameterValueVisitor, AutoCloseable {
private static final Logger logger = Logger.getLogger(ParameterVisitorBatchDAO.class.getName());
// the connection to use for the inserts
private final Connection connection;
// the max number of rows we accumulate for a given statement before we submit the batch
private final int batchSize;
// FK to the logical resource for the parameters being added
private final long logicalResourceId;
// Maintainers: remember to close all statements in AutoCloseable#close()
private final String insertString;
private final PreparedStatement strings;
private int stringCount;
private final String insertNumber;
private final PreparedStatement numbers;
private int numberCount;
private final String insertDate;
private final PreparedStatement dates;
private int dateCount;
private final String insertQuantity;
private final PreparedStatement quantities;
private int quantityCount;
// rarely used so no need for {@code java.sql.PreparedStatement} or batching on this one
// even on Location resources its only there once by default
private final String insertLocation;
// Searchable string attributes stored at the system level
private final PreparedStatement systemStrings;
private int systemStringCount;
// Searchable date attributes stored at the system level
private final PreparedStatement systemDates;
private int systemDateCount;
// DAO for handling parameters stored as token values (including system-level token search params)
private final IResourceReferenceDAO resourceReferenceDAO;
// Collect a list of token values to process in one go
private final List tokenValueRecs = new ArrayList<>();
// The table prefix (resourceType)
private final String tablePrefix;
// The common cache for all our identity lookup needs
private final JDBCIdentityCache identityCache;
// If not null, we stash certain parameter data here for insertion later
private final ParameterTransactionDataImpl transactionData;
// tracks the number of composites so we know what next composite_id to use
int compositeIdCounter = 0;
// when set, this value is added as the composite_id value for each parameter we store
Integer currentCompositeId = null;
// Supports slightly more useful error messages if we hit a nested composite
String currentCompositeParameterName = null;
/**
* Public constructor
* @param c
* @param resourceId
*/
public ParameterVisitorBatchDAO(Connection c, String adminSchemaName, String tablePrefix, boolean multitenant, long logicalResourceId, int batchSize,
JDBCIdentityCache identityCache, IResourceReferenceDAO resourceReferenceDAO, ParameterTransactionDataImpl ptdi) throws SQLException {
if (batchSize < 1) {
throw new IllegalArgumentException("batchSize must be >= 1");
}
this.connection = c;
this.logicalResourceId = logicalResourceId;
this.batchSize = batchSize;
this.identityCache = identityCache;
this.resourceReferenceDAO = resourceReferenceDAO;
this.tablePrefix = tablePrefix;
this.transactionData = ptdi;
insertString = multitenant ?
"INSERT INTO " + tablePrefix + "_str_values (mt_id, parameter_name_id, str_value, str_value_lcase, logical_resource_id, composite_id) VALUES (" + adminSchemaName + ".sv_tenant_id,?,?,?,?,?)"
:
"INSERT INTO " + tablePrefix + "_str_values (parameter_name_id, str_value, str_value_lcase, logical_resource_id, composite_id) VALUES (?,?,?,?,?)";
strings = c.prepareStatement(insertString);
insertNumber = multitenant ?
"INSERT INTO " + tablePrefix + "_number_values (mt_id, parameter_name_id, number_value, number_value_low, number_value_high, logical_resource_id, composite_id) VALUES (" + adminSchemaName + ".sv_tenant_id,?,?,?,?,?,?)"
:
"INSERT INTO " + tablePrefix + "_number_values (parameter_name_id, number_value, number_value_low, number_value_high, logical_resource_id, composite_id) VALUES (?,?,?,?,?,?)";
numbers = c.prepareStatement(insertNumber);
insertDate = multitenant ?
"INSERT INTO " + tablePrefix + "_date_values (mt_id, parameter_name_id, date_start, date_end, logical_resource_id, composite_id) VALUES (" + adminSchemaName + ".sv_tenant_id,?,?,?,?,?)"
:
"INSERT INTO " + tablePrefix + "_date_values (parameter_name_id, date_start, date_end, logical_resource_id, composite_id) VALUES (?,?,?,?,?)";
dates = c.prepareStatement(insertDate);
insertQuantity = multitenant ?
"INSERT INTO " + tablePrefix + "_quantity_values (mt_id, parameter_name_id, code_system_id, code, quantity_value, quantity_value_low, quantity_value_high, logical_resource_id, composite_id) VALUES (" + adminSchemaName + ".sv_tenant_id,?,?,?,?,?,?,?,?)"
:
"INSERT INTO " + tablePrefix + "_quantity_values (parameter_name_id, code_system_id, code, quantity_value, quantity_value_low, quantity_value_high, logical_resource_id, composite_id) VALUES (?,?,?,?,?,?,?,?)";
quantities = c.prepareStatement(insertQuantity);
insertLocation = multitenant ? "INSERT INTO " + tablePrefix + "_latlng_values (mt_id, parameter_name_id, latitude_value, longitude_value, logical_resource_id, composite_id) VALUES (" + adminSchemaName + ".sv_tenant_id,?,?,?,?,?)"
: "INSERT INTO " + tablePrefix + "_latlng_values (parameter_name_id, latitude_value, longitude_value, logical_resource_id, composite_id) VALUES (?,?,?,?,?)";
// System level string attributes
String insertSystemString = multitenant ?
"INSERT INTO str_values (mt_id, parameter_name_id, str_value, str_value_lcase, logical_resource_id) VALUES (" + adminSchemaName + ".sv_tenant_id,?,?,?,?)"
:
"INSERT INTO str_values (parameter_name_id, str_value, str_value_lcase, logical_resource_id) VALUES (?,?,?,?)";
systemStrings = c.prepareStatement(insertSystemString);
// System level date attributes
String insertSystemDate = multitenant ?
"INSERT INTO date_values (mt_id, parameter_name_id, date_start, date_end, logical_resource_id) VALUES (" + adminSchemaName + ".sv_tenant_id,?,?,?,?)"
:
"INSERT INTO date_values (parameter_name_id, date_start, date_end, logical_resource_id) VALUES (?,?,?,?)";
systemDates = c.prepareStatement(insertSystemDate);
}
/**
* Look up the normalized id for the parameter, adding it to the parameter_names table if it doesn't yet exist
* @param parameterName
* @return
*/
protected int getParameterNameId(String parameterName) throws FHIRPersistenceException {
return identityCache.getParameterNameId(parameterName);
}
/**
* Looks up the code system. If it doesn't exist, adds it to the database
* @param codeSystem
* @return
*/
protected int getCodeSystemId(String codeSystem) throws FHIRPersistenceException {
return identityCache.getCodeSystemId(codeSystem);
}
@Override
public void visit(StringParmVal param) throws FHIRPersistenceException {
String parameterName = param.getName();
String value = param.getValueString();
while (value != null && value.getBytes().length > FhirSchemaConstants.MAX_SEARCH_STRING_BYTES) {
// keep chopping the string in half until its byte representation fits inside
// the VARCHAR
value = value.substring(0, value.length() / 2);
}
try {
int parameterNameId = getParameterNameId(parameterName);
if (isBase(param)) {
if (logger.isLoggable(Level.FINE)) {
logger.fine("systemStringValue: " + parameterName + "[" + parameterNameId + "], " + value);
}
systemStrings.setInt(1, parameterNameId);
if (value != null) {
systemStrings.setString(2, value);
systemStrings.setString(3, SearchUtil.normalizeForSearch(value));
}
else {
systemStrings.setNull(2, Types.VARCHAR);
systemStrings.setNull(3, Types.VARCHAR);
}
systemStrings.setLong(4, logicalResourceId);
systemStrings.addBatch();
if (++systemStringCount == this.batchSize) {
systemStrings.executeBatch();
systemStringCount = 0;
}
} else {
// standard resource property
if (logger.isLoggable(Level.FINE)) {
logger.fine("stringValue: " + parameterName + "[" + parameterNameId + "], " + value);
}
setStringParms(strings, parameterNameId, value);
strings.addBatch();
if (++stringCount == this.batchSize) {
strings.executeBatch();
stringCount = 0;
}
}
} catch (SQLException x) {
throw new FHIRPersistenceDataAccessException(parameterName + "=" + value, x);
}
}
private void setStringParms(PreparedStatement insert, int parameterNameId, String value) throws SQLException {
insert.setInt(1, parameterNameId);
if (value != null) {
insert.setString(2, value);
insert.setString(3, SearchUtil.normalizeForSearch(value));
} else {
insert.setNull(2, Types.VARCHAR);
insert.setNull(3, Types.VARCHAR);
}
insert.setLong(4, logicalResourceId);
setCompositeId(insert, 5);
}
/**
* Set the composite_id column value or null if required
* @param ps the statement
* @param idx the column index
* @throws SQLException
*/
private void setCompositeId(PreparedStatement ps, int idx) throws SQLException {
if (this.currentCompositeId != null) {
ps.setInt(idx, this.currentCompositeId);
} else {
ps.setNull(idx, Types.INTEGER);
}
}
@Override
public void visit(NumberParmVal param) throws FHIRPersistenceException {
String parameterName = param.getName();
BigDecimal value = param.getValueNumber();
BigDecimal valueLow = param.getValueNumberLow();
BigDecimal valueHigh = param.getValueNumberHigh();
try {
int parameterNameId = getParameterNameId(parameterName);
if (logger.isLoggable(Level.FINE)) {
logger.fine("numberValue: " + parameterName + "[" + parameterNameId + "], "
+ value + " [" + valueLow + ", " + valueHigh + "]");
}
setNumberParms(numbers, parameterNameId, value, valueLow, valueHigh);
numbers.addBatch();
if (++numberCount == this.batchSize) {
numbers.executeBatch();
numberCount = 0;
}
}
catch (SQLException x) {
throw new FHIRPersistenceDataAccessException(parameterName + "={" + value + " ["+ valueLow + "," + valueHigh + "}", x);
}
}
private void setNumberParms(PreparedStatement insert, int parameterNameId, BigDecimal value, BigDecimal valueLow, BigDecimal valueHigh) throws SQLException {
insert.setInt(1, parameterNameId);
insert.setBigDecimal(2, value);
insert.setBigDecimal(3, valueLow);
insert.setBigDecimal(4, valueHigh);
insert.setLong(5, logicalResourceId);
setCompositeId(insert, 6);
}
@Override
public void visit(DateParmVal param) throws FHIRPersistenceException {
String parameterName = param.getName();
Timestamp dateStart = param.getValueDateStart();
Timestamp dateEnd = param.getValueDateEnd();
try {
int parameterNameId = getParameterNameId(parameterName);
if (isBase(param)) {
// store as a system level search param
if (logger.isLoggable(Level.FINE)) {
logger.fine("systemDateValue: " + parameterName + "[" + parameterNameId + "], "
+ "[" + dateStart + ", " + dateEnd + "]");
}
// Insert record into the base level date attribute table
setDateParms(systemDates, parameterNameId, dateStart, dateEnd);
systemDates.addBatch();
if (++systemDateCount == this.batchSize) {
systemDates.executeBatch();
systemDateCount = 0;
}
} else {
if (logger.isLoggable(Level.FINE)) {
logger.fine("dateValue: " + parameterName + "[" + parameterNameId + "], "
+ "period: [" + dateStart + ", " + dateEnd + "]");
}
setDateParms(dates, parameterNameId, dateStart, dateEnd);
dates.addBatch();
if (++dateCount == this.batchSize) {
dates.executeBatch();
dateCount = 0;
}
}
} catch (SQLException x) {
throw new FHIRPersistenceDataAccessException(parameterName + "={" + dateStart + ", " + dateEnd + "}", x);
}
}
private void setDateParms(PreparedStatement insert, int parameterNameId, Timestamp dateStart, Timestamp dateEnd) throws SQLException {
insert.setInt(1, parameterNameId);
insert.setTimestamp(2, dateStart, UTC);
insert.setTimestamp(3, dateEnd, UTC);
insert.setLong(4, logicalResourceId);
setCompositeId(insert, 5);
}
@Override
public void visit(TokenParmVal param) throws FHIRPersistenceException {
String parameterName = param.getName();
String codeSystem = param.getValueSystem();
String tokenValue = param.getValueCode();
try {
int parameterNameId = getParameterNameId(parameterName);
boolean isSystemParam = isBase(param);
if (logger.isLoggable(Level.FINE)) {
logger.fine("tokenValue: " + parameterName + "[" + parameterNameId + "], "
+ codeSystem + ", " + tokenValue);
}
// Add the new token value to the collection we're building...what's the resourceTypeId?
final int resourceTypeId = identityCache.getResourceTypeId(param.getResourceType());
if (tokenValue == null) {
logger.info("tokenValue is NULL for: " + parameterName + "[" + parameterNameId + "], " + codeSystem);
}
// Issue 1683, for composites we now also record the current composite id (can be null)
ResourceTokenValueRec rec = new ResourceTokenValueRec(parameterNameId, param.getResourceType(), resourceTypeId, logicalResourceId, codeSystem, tokenValue, this.currentCompositeId, isSystemParam);
if (this.transactionData != null) {
this.transactionData.addValue(rec);
} else {
this.tokenValueRecs.add(rec);
}
} catch (FHIRPersistenceDataAccessException x) {
throw new FHIRPersistenceDataAccessException(parameterName + "=" + codeSystem + ":" + tokenValue, x);
}
}
@Override
public void visit(QuantityParmVal param) throws FHIRPersistenceException {
String parameterName = param.getName();
String code = param.getValueCode();
String codeSystem = param.getValueSystem();
BigDecimal quantityValue = param.getValueNumber();
BigDecimal quantityLow = param.getValueNumberLow();
BigDecimal quantityHigh = param.getValueNumberHigh();
// XXX why no check for isBase on this one?
// Skip anything with a null code
if (code == null || code.isEmpty()) {
if (logger.isLoggable(Level.FINE)) {
logger.fine("CODELESS QUANTITY (skipped): " + parameterName + "=" + code + ":" + codeSystem + "{" + quantityValue + ", " + quantityLow + ", " + quantityHigh + "}");
}
} else {
try {
int parameterNameId = getParameterNameId(parameterName);
if (logger.isLoggable(Level.FINE)) {
logger.fine("quantityValue: " + parameterName + "[" + parameterNameId + "], "
+ quantityValue + " [" + quantityLow + ", " + quantityHigh + "]");
}
setQuantityParms(quantities, parameterNameId, codeSystem, code, quantityValue, quantityLow, quantityHigh);
quantities.addBatch();
if (++quantityCount == batchSize) {
quantities.executeBatch();
quantityCount = 0;
}
} catch (FHIRPersistenceDataAccessException x) {
// wrap the exception so we have more context about the parameter causing the problem
throw new FHIRPersistenceDataAccessException(parameterName + "=" + code + ":" + codeSystem + "{" + quantityValue + ", " + quantityLow + ", " + quantityHigh + "}", x);
} catch (SQLException x) {
throw new FHIRPersistenceDataAccessException(parameterName + "=" + code + ":" + codeSystem + "{" + quantityValue + ", " + quantityLow + ", " + quantityHigh + "}", x);
}
}
}
private void setQuantityParms(PreparedStatement insert, int parameterNameId, String codeSystem, String code, BigDecimal quantityValue, BigDecimal quantityLow, BigDecimal quantityHigh)
throws SQLException, FHIRPersistenceException {
insert.setInt(1, parameterNameId);
insert.setInt(2, getCodeSystemId(codeSystem));
insert.setString(3, code);
insert.setBigDecimal(4, quantityValue);
insert.setBigDecimal(5, quantityLow);
insert.setBigDecimal(6, quantityHigh);
insert.setLong(7, logicalResourceId);
setCompositeId(insert, 8);
}
@Override
public void visit(LocationParmVal param) throws FHIRPersistenceException {
String parameterName = param.getName();
double lat = param.getValueLatitude();
double lng = param.getValueLongitude();
try {
PreparedStatement insert = connection.prepareStatement(insertLocation);
setLocationParms(insert, getParameterNameId(parameterName), lat, lng);
insert.executeUpdate();
} catch (SQLException x) {
throw new FHIRPersistenceDataAccessException(parameterName + "={" + lat + ", " + lng + "}", x);
}
}
private void setLocationParms(PreparedStatement insert, int parameterNameId, double lat, double lng) throws SQLException, FHIRPersistenceException {
insert.setInt(1, parameterNameId);
insert.setDouble(2, lat);
insert.setDouble(3, lng);
insert.setLong(4, logicalResourceId);
setCompositeId(insert, 5);
}
@Override
public void visit(CompositeParmVal compositeParameter) throws FHIRPersistenceException {
if (this.currentCompositeId != null) {
// no soup for you
logger.warning("A compositeParameter '" + currentCompositeParameterName + "' cannot itself contain a composite '" + compositeParameter.getName());
throw new FHIRPersistenceException("composite parameters cannot themselves contain composites");
}
// This composite is a collection of multiple parameters.
List component = compositeParameter.getComponent();
this.currentCompositeId = this.compositeIdCounter++;
this.currentCompositeParameterName = compositeParameter.getName();
for (ExtractedParameterValue val : component) {
val.accept(this);
}
// Clear the currentCompositeId value so we no longer associate it with other parameters
this.currentCompositeId = null;
this.currentCompositeParameterName = null;
}
@Override
public void close() throws Exception {
// flush any stragglers, remembering to reset each count because
// close() should be idempotent.
try {
if (stringCount > 0) {
strings.executeBatch();
stringCount = 0;
}
if (numberCount > 0) {
numbers.executeBatch();
numberCount = 0;
}
if (dateCount > 0) {
dates.executeBatch();
dateCount = 0;
}
if (quantityCount > 0) {
quantities.executeBatch();
quantityCount = 0;
}
if (systemStringCount > 0) {
systemStrings.executeBatch();
systemStringCount = 0;
}
if (systemDateCount > 0) {
systemDates.executeBatch();
systemDateCount = 0;
}
} catch (SQLException x) {
SQLException batchException = x.getNextException();
if (batchException != null) {
// We're really interested in the underlying cause here
throw batchException;
}
else {
throw x;
}
}
// Process any tokens and references we've collected along the way
if (!tokenValueRecs.isEmpty()) {
this.resourceReferenceDAO.addCommonTokenValues(this.tablePrefix, tokenValueRecs);
}
closeStatement(strings);
closeStatement(numbers);
closeStatement(dates);
closeStatement(quantities);
closeStatement(systemStrings);
closeStatement(systemDates);
}
/**
* Quietly close the given statement
* @param ps
*/
private void closeStatement(PreparedStatement ps) {
try {
ps.close();
} catch (SQLException x) {
logger.warning("failed to close statement");
}
}
private boolean isBase(ExtractedParameterValue param) {
return "Resource".equals(param.getBase());
}
@Override
public void visit(ReferenceParmVal rpv) throws FHIRPersistenceException {
if (rpv.getRefValue() == null) {
return;
}
final String resourceType = this.tablePrefix;
int parameterNameId = getParameterNameId(rpv.getName());
Integer resourceTypeId = identityCache.getResourceTypeId(resourceType);
if (resourceTypeId == null) {
// resourceType is not sensitive, so it's OK to include in the exception message
throw new FHIRPersistenceException("Resource type not found in cache: '" + resourceType + "'");
}
// The ReferenceValue has already been processed to convert the reference to
// the required standard form, ready for insertion as a token value.
ReferenceValue refValue = rpv.getRefValue();
// Ignore references containing only a "display" element (apparently supported by the spec,
// but contains nothing useful to store because there's no searchable value).
String refResourceType = refValue.getTargetResourceType();
String refLogicalId = refValue.getValue();
Integer refVersion = refValue.getVersion();
ResourceTokenValueRec rec;
if (refValue.getType() == ReferenceType.DISPLAY_ONLY || refValue.getType() == ReferenceType.INVALID) {
// protect against code regression. Invalid/improper references should be
// filtered out already.
logger.warning("Invalid reference parameter type: '" + resourceType + "." + rpv.getName() + "' type=" + refValue.getType().name());
throw new IllegalArgumentException("Invalid reference parameter value. See server log for details.");
}
// reference params are never system-level
final boolean isSystemParam = false;
if (refResourceType != null) {
// Store a token value configured as a reference to another resource
rec = new ResourceTokenValueRec(parameterNameId, resourceType, resourceTypeId, logicalResourceId, refResourceType, refLogicalId, refVersion, this.currentCompositeId, isSystemParam);
} else {
// stored as a token with the default system
rec = new ResourceTokenValueRec(parameterNameId, resourceType, resourceTypeId, logicalResourceId, JDBCConstants.DEFAULT_TOKEN_SYSTEM, refLogicalId, this.currentCompositeId, isSystemParam);
}
if (this.transactionData != null) {
this.transactionData.addValue(rec);
} else {
this.tokenValueRecs.add(rec);
}
}
}
