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/*
* (C) Copyright IBM Corp. 2021
*
* SPDX-License-Identifier: Apache-2.0
*/
package com.ibm.fhir.persistence.jdbc.dao.impl;
import static com.ibm.fhir.persistence.jdbc.JDBCConstants.DOT;
import java.io.IOException;
import java.io.InputStream;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Timestamp;
import java.time.Instant;
import java.util.Calendar;
import java.util.TimeZone;
import java.util.function.Function;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.zip.GZIPInputStream;
import com.ibm.fhir.database.utils.api.IDatabaseTranslator;
import com.ibm.fhir.persistence.ResourcePayload;
import com.ibm.fhir.persistence.exception.FHIRPersistenceException;
import com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceDataAccessException;
/**
* DAO to fetch resource ids using a time range and optional current resource id as a filter.
* Useful for scanning the database for new resources since a given timestamp (for example
* in export scenarios).
*/
public class FetchResourcePayloadsDAO {
private static final Logger logger = Logger.getLogger(FetchResourcePayloadsDAO.class.getName());
private static final Calendar UTC_CALENDAR = Calendar.getInstance(TimeZone.getTimeZone("UTC"));
// The FHIR data schema name
private final String schemaName;
// The name of the resource type (e.g. "Patient")
private final String resourceType;
// Start scanning from this timestamp. Never null
private final Instant fromLastUpdated;
// Scan up to this timestamp if given. Can be null.
private final Instant toLastUpdated;
// Consumer to process each of the records read
private final Function processor;
// The database translator to help tweak the syntax needed for different DB support
private final IDatabaseTranslator translator;
public FetchResourcePayloadsDAO(IDatabaseTranslator translator, String schemaName, String resourceType, Instant fromLastUpdated, Instant toLastUpdated,
Function processor) {
this.translator = translator;
this.schemaName = schemaName;
this.resourceType = resourceType;
this.fromLastUpdated = fromLastUpdated;
this.toLastUpdated = toLastUpdated;
this.processor = processor;
}
/**
* Run the query, feeding each result row to the consumer
* @param c
* @return the last record processed
* @throws FHIRPersistenceException
*/
public ResourcePayload run(Connection c) throws FHIRPersistenceException {
ResourcePayload result = null;
final String lrTableName = resourceType + "_logical_resources";
final String rTableName = resourceType + "_resources";
StringBuilder query = new StringBuilder();
query.append("SELECT lr.logical_id, r.last_updated, r.resource_id, r.data FROM ");
query.append(schemaName).append(DOT).append(rTableName).append(" AS r, ");
query.append(schemaName).append(DOT).append(lrTableName).append(" AS lr ");
query.append(" WHERE r.is_deleted = 'N' ");
query.append(" AND lr.current_resource_id = r.resource_id ");
// Add the predicate for the optoional start
// thiss aligns with the Bulk Data Specification.
if (this.fromLastUpdated != null) {
query.append(" AND r.last_updated >= ? ");
}
// Add the predicate for the optional end-stop
if (this.toLastUpdated != null) {
query.append(" AND r.last_updated <= ? ");
}
// It is crucial to ORDER BY both the last_updated timestamp and the resource_id so that
// the scan can continue from where it left off. Unfortunately the index on last_updated
// doesn't include resource_id, so a fetch from the table is unavoidable.
query.append(" ORDER BY r.last_updated ");
// For Postgres, the LIMIT is absolutely required to make sure we get a sort-free scan (the ORDER BY
// is supported by an index, so the database should be able to start feeding results back immediately
// without having to first gather everything for a sort, which makes this a whole lot faster and more
// scalable. With this LIMIT, it does mean that we have to call this query more frequently, but because
// it is so cheap, this doesn't hurt us.
query.append(translator.limit(Integer.toString(1000)));
final String select = query.toString();
if (logger.isLoggable(Level.FINE)) {
logger.fine("Fetch resource payload query: " + select);
}
try (PreparedStatement ps = c.prepareStatement(select)) {
int a = 1;
// Set the variables marking the start point of the scan
if (this.fromLastUpdated != null) {
ps.setTimestamp(a++, Timestamp.from(this.fromLastUpdated), UTC_CALENDAR);
}
// And where we want the scan to stop (e.g. exporting a limited time range)
if (this.toLastUpdated != null) {
ps.setTimestamp(a++, Timestamp.from(this.toLastUpdated), UTC_CALENDAR);
}
ResultSet rs = ps.executeQuery();
while (rs.next()) {
// make sure we get the timestamp as a UTC value
String logicalId = rs.getString(1);
Instant lastUpdated = rs.getTimestamp(2, UTC_CALENDAR).toInstant();
long resourceId = rs.getLong(3);
InputStream is = new GZIPInputStream(rs.getBinaryStream(4));
result = new ResourcePayload(logicalId, lastUpdated, resourceId, is);
Boolean cont = processor.apply(result);
if (cont == null || !cont) {
// the processor has asked us to stop
break;
}
}
} catch (IOException x) {
logger.log(Level.SEVERE, "query: " + select + "[fromLastUpdated=" + fromLastUpdated + ", toLastUpdated=" + toLastUpdated + "]", x);
throw new FHIRPersistenceDataAccessException("FetchResourceIds query failed");
} catch (SQLException x) {
logger.log(Level.SEVERE, "query: " + select + "[fromLastUpdated=" + fromLastUpdated + ", toLastUpdated=" + toLastUpdated + "]", x);
throw new FHIRPersistenceDataAccessException("FetchResourceIds query failed");
}
// the last ResultPayload to be processed is returned as a convenience to the caller
return result;
}
/**
* Get a count of the resources matching the filter predicates...for debugging...slows
* things down a lot
* @param c
* @return
* @throws FHIRPersistenceException
*/
public int count(Connection c) throws FHIRPersistenceException {
int result;
final String lrTableName = resourceType + "_logical_resources";
final String rTableName = resourceType + "_resources";
StringBuilder query = new StringBuilder();
query.append("SELECT count(*) FROM ");
query.append(schemaName).append(DOT).append(rTableName).append(" AS r, ");
query.append(schemaName).append(DOT).append(lrTableName).append(" AS lr ");
query.append(" WHERE r.is_deleted = 'N' ");
query.append(" AND lr.current_resource_id = r.resource_id ");
query.append(" AND r.last_updated >= ? ");
// Add the predicate for the optional end-stop
if (this.toLastUpdated != null) {
query.append(" AND r.last_updated <= ? ");
}
final String select = query.toString();
if (logger.isLoggable(Level.FINE)) {
Timestamp from = Timestamp.from(fromLastUpdated);
logger.fine("Resource count query: " + select + "; [" + fromLastUpdated + "]");
}
try (PreparedStatement ps = c.prepareStatement(select)) {
int a = 1;
// Set the variables marking the start point of the scan
ps.setTimestamp(a++, Timestamp.from(fromLastUpdated), UTC_CALENDAR);
// And where we want the scan to stop (e.g. exporting a limited time range)
if (this.toLastUpdated != null) {
ps.setTimestamp(a++, Timestamp.from(this.toLastUpdated), UTC_CALENDAR);
}
ResultSet rs = ps.executeQuery();
if (rs.next()) {
result = rs.getInt(1);
} else {
throw new IllegalStateException("no count result"); // not gonna happen
}
} catch (SQLException x) {
logger.log(Level.SEVERE, "query: " + select + "[fromLastUpdated=" + fromLastUpdated + ", toLastUpdated=" + toLastUpdated + "]", x);
throw new FHIRPersistenceDataAccessException("FetchResourceIds query failed");
}
return result;
}
}
