Merge pull request #2748 from IBM/issue-2747-utc-calendar

issue-2747 - thread safety for JDBC get/set timestamp UTC
LinuxForHealth · Sep 8, 2021 · af70782 · af70782
2 parents ad00a02 + 514bb92
commit af70782
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Showing 18 changed files with 130 additions and 50 deletions.
diff --git a/fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/query/BindVisitor.java b/fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/query/BindVisitor.java
@@ -28,7 +28,6 @@
  * for looser coupling.
  */
 public class BindVisitor implements BindMarkerNodeVisitor {
-    private static final Calendar UTC = Calendar.getInstance(TimeZone.getTimeZone("UTC"));
     private static final Logger logger = Logger.getLogger(BindVisitor.class.getName());
 
     // the statement to bind values to
@@ -40,6 +39,9 @@ public class BindVisitor implements BindMarkerNodeVisitor {
     // Keep track of the parameter index
     private int parameterIndex = 1;
 
+    // Do not make static - Calendar is not thread-safe
+    private final Calendar UTC = Calendar.getInstance(TimeZone.getTimeZone("UTC"));
+
     /**
      * Public constructor
      * @param ps

diff --git a/fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/version/SchemaConstants.java b/fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/version/SchemaConstants.java
@@ -19,7 +19,4 @@ public class SchemaConstants {
     public static final String OBJECT_TYPE = "OBJECT_TYPE";
     public static final String OBJECT_NAME = "OBJECT_NAME";
     public static final String SCHEMA_NAME = "SCHEMA_NAME";
-
-    public static final Calendar UTC = Calendar.getInstance(TimeZone.getTimeZone("UTC"));
-
 }
diff --git a/fhir-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/JDBCConstants.java b/fhir-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/JDBCConstants.java
@@ -119,9 +119,11 @@ public class JDBCConstants {
     public static final String DEFAULT_TOKEN_SYSTEM = "default-token-system";
 
     /**
-     * Calendar object to use while inserting Timestamp objects into the database.
+     * This Calendar object is not thread-safe! Use CalendarHelper#getCalendarForUTC() instead.
      */
-    public static final Calendar UTC = Calendar.getInstance(TimeZone.getTimeZone("UTC"));
+    // DO NOT USE
+    // public static final Calendar UTC = Calendar.getInstance(TimeZone.getTimeZone("UTC"));
+    // DO NOT USE
 
     /**
      * Maps search parameter types to the currently supported list of modifiers for that type.

diff --git a/...-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/ReindexResourceDAO.java b/...-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/ReindexResourceDAO.java
@@ -33,6 +33,7 @@
 import com.ibm.fhir.persistence.jdbc.dao.impl.ResourceDAOImpl;
 import com.ibm.fhir.persistence.jdbc.dto.ExtractedParameterValue;
 import com.ibm.fhir.persistence.jdbc.impl.ParameterTransactionDataImpl;
+import com.ibm.fhir.persistence.jdbc.util.CalendarHelper;
 import com.ibm.fhir.persistence.jdbc.util.ParameterTableSupport;
 
 /**
@@ -148,7 +149,7 @@ protected ResourceIndexRecord getResource(Instant reindexTstamp, Long logicalRes
             if (logicalResourceId != null) {
                 // specific resource by logical resource ID (primary key)
                 stmt.setLong(1, logicalResourceId);
-                stmt.setTimestamp(2, Timestamp.from(reindexTstamp));
+                stmt.setTimestamp(2, Timestamp.from(reindexTstamp), CalendarHelper.getCalendarForUTC());
             }
             ResultSet rs = stmt.executeQuery();
             if (rs.next()) {
@@ -208,13 +209,13 @@ protected ResourceIndexRecord getNextResource(SecureRandom random, Instant reind
                 if (resourceTypeId != null && logicalId != null) {
                     stmt.setInt(1, resourceTypeId);
                     stmt.setString(2, logicalId);
-                    stmt.setTimestamp(3, Timestamp.from(reindexTstamp));
+                    stmt.setTimestamp(3, Timestamp.from(reindexTstamp), CalendarHelper.getCalendarForUTC());
                 } else if (resourceTypeId != null) {
                     stmt.setInt(1, resourceTypeId);
-                    stmt.setTimestamp(2, Timestamp.from(reindexTstamp));
+                    stmt.setTimestamp(2, Timestamp.from(reindexTstamp), CalendarHelper.getCalendarForUTC());
                     stmt.setInt(3, offset);
                 } else {
-                    stmt.setTimestamp(1, Timestamp.from(reindexTstamp));
+                    stmt.setTimestamp(1, Timestamp.from(reindexTstamp), CalendarHelper.getCalendarForUTC());
                     stmt.setInt(2, offset);
                 }
                 ResultSet rs = stmt.executeQuery();
@@ -237,7 +238,7 @@ protected ResourceIndexRecord getNextResource(SecureRandom random, Instant reind
                         + "    AND reindex_txid = ? "; // make sure we have the txid we selected above
 
                 try (PreparedStatement stmt = connection.prepareStatement(UPDATE)) {
-                    stmt.setTimestamp(1, Timestamp.from(reindexTstamp));
+                    stmt.setTimestamp(1, Timestamp.from(reindexTstamp), CalendarHelper.getCalendarForUTC());
                     stmt.setLong(2, result.getTransactionId() + 1L);
                     stmt.setLong(3, result.getLogicalResourceId());
                     stmt.setLong(4, result.getTransactionId());

diff --git a/...-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/FHIRDbDAOImpl.java b/...-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/FHIRDbDAOImpl.java
@@ -32,6 +32,7 @@
 import com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceDBCleanupException;
 import com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceDBConnectException;
 import com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceDataAccessException;
+import com.ibm.fhir.persistence.jdbc.util.CalendarHelper;
 
 /**
  * This class is a root Data Access Object for managing JDBC access to the FHIR database.
@@ -200,7 +201,7 @@ protected List<Resource> runQuery(String sql, Object... searchArgs)
             // 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], JDBCConstants.UTC);
+                    stmt.setTimestamp(i + 1, (Timestamp) searchArgs[i], CalendarHelper.getCalendarForUTC());
                 } else {
                     stmt.setObject(i + 1, searchArgs[i]);
                 }
@@ -263,7 +264,7 @@ protected int runCountQuery(String sql, Object... searchArgs)
             // 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], JDBCConstants.UTC);
+                    stmt.setTimestamp(i + 1, (Timestamp) searchArgs[i], CalendarHelper.getCalendarForUTC());
                 } else {
                     stmt.setObject(i + 1, searchArgs[i]);
                 }
@@ -474,7 +475,7 @@ protected List<String> runQuery_STR_VALUES(String sql, Object... searchArgs)
             // 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], JDBCConstants.UTC);
+                    stmt.setTimestamp(i + 1, (Timestamp) searchArgs[i], CalendarHelper.getCalendarForUTC());
                 } else {
                     stmt.setObject(i + 1, searchArgs[i]);
                 }

diff --git a/...nce-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/FetchPayloadsForIdsDAO.java b/...nce-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/FetchPayloadsForIdsDAO.java
@@ -23,6 +23,7 @@
 
 import com.ibm.fhir.persistence.ResourcePayload;
 import com.ibm.fhir.persistence.exception.FHIRPersistenceException;
+import com.ibm.fhir.persistence.jdbc.util.CalendarHelper;
 
 /**
  * DAO to fetch the payload objects for a list of resource ids
@@ -107,7 +108,7 @@ public void run(Connection c) throws FHIRPersistenceException {
                 // we can save a ton of CPU. The stream is closed by ResultSet (according to the docs). ResultSet
                 // will be closed when the PreparedStatement is closed
                 String logicalId = rs.getString(1);
-                Instant lastUpdated = Instant.ofEpochMilli(rs.getTimestamp(2).getTime());
+                Instant lastUpdated = rs.getTimestamp(2, CalendarHelper.getCalendarForUTC()).toInstant();
                 long resourceId = rs.getLong(3);
                 InputStream is = new GZIPInputStream(rs.getBinaryStream(4));
                 ResourcePayload rp =  new ResourcePayload(logicalId, lastUpdated, resourceId, is);

diff --git a/...ce-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/FetchResourceChangesDAO.java b/...ce-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/FetchResourceChangesDAO.java
@@ -23,13 +23,13 @@
 import com.ibm.fhir.persistence.ResourceChangeLogRecord;
 import com.ibm.fhir.persistence.ResourceChangeLogRecord.ChangeType;
 import com.ibm.fhir.persistence.exception.FHIRPersistenceException;
+import com.ibm.fhir.persistence.jdbc.util.CalendarHelper;
 
 /**
  * Simple DAO to read records from the RESOURCE_CHANGE_LOG table
  */
 public class FetchResourceChangesDAO {
     private static final Logger logger = Logger.getLogger(FetchResourceChangesDAO.class.getName());
-    private static final Calendar UTC_CALENDAR = Calendar.getInstance(TimeZone.getTimeZone("UTC"));
 
     private final IDatabaseTranslator translator;
     private final String schemaName;
@@ -114,7 +114,7 @@ public List<ResourceChangeLogRecord> run(Connection c) throws FHIRPersistenceExc
         try (PreparedStatement ps = c.prepareStatement(SQL)) {
             int a = 1;
             if (this.fromTstamp != null) {
-                ps.setTimestamp(a++, Timestamp.from(this.fromTstamp), UTC_CALENDAR);
+                ps.setTimestamp(a++, Timestamp.from(this.fromTstamp), CalendarHelper.getCalendarForUTC());
             }
 
             if (this.afterResourceId != null) {
@@ -135,7 +135,7 @@ public List<ResourceChangeLogRecord> run(Connection c) throws FHIRPersistenceExc
                 default:
                     throw new FHIRPersistenceException("Invalid ChangeType in change log"); // DBA can find the bad row if it ever happens
                 }
-                ResourceChangeLogRecord record = new ResourceChangeLogRecord(rs.getString(2), rs.getString(3), rs.getInt(5), rs.getLong(1), rs.getTimestamp(4, UTC_CALENDAR).toInstant(), ct);
+                ResourceChangeLogRecord record = new ResourceChangeLogRecord(rs.getString(2), rs.getString(3), rs.getInt(5), rs.getLong(1), rs.getTimestamp(4, CalendarHelper.getCalendarForUTC()).toInstant(), ct);
                 result.add(record);
             }
         } catch (SQLException x) {

diff --git a/...e-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/FetchResourcePayloadsDAO.java b/...e-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/FetchResourcePayloadsDAO.java
@@ -27,6 +27,7 @@
 import com.ibm.fhir.persistence.ResourcePayload;
 import com.ibm.fhir.persistence.exception.FHIRPersistenceException;
 import com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceDataAccessException;
+import com.ibm.fhir.persistence.jdbc.util.CalendarHelper;
 
 /**
  * DAO to fetch resource ids using a time range and optional current resource id as a filter.
@@ -36,8 +37,6 @@
 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;
 
@@ -118,19 +117,19 @@ public ResourcePayload run(Connection c) throws FHIRPersistenceException {
 
             // Set the variables marking the start point of the scan
             if (this.fromLastUpdated != null) {
-                ps.setTimestamp(a++, Timestamp.from(this.fromLastUpdated), UTC_CALENDAR);
+                ps.setTimestamp(a++, Timestamp.from(this.fromLastUpdated), CalendarHelper.getCalendarForUTC());
             }
 
             // 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);
+                ps.setTimestamp(a++, Timestamp.from(this.toLastUpdated), CalendarHelper.getCalendarForUTC());
             }
 
             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();
+                Instant lastUpdated = rs.getTimestamp(2, CalendarHelper.getCalendarForUTC()).toInstant();
                 long resourceId = rs.getLong(3);
                 InputStream is = new GZIPInputStream(rs.getBinaryStream(4));
                 result = new ResourcePayload(logicalId, lastUpdated, resourceId, is);
@@ -192,12 +191,12 @@ public int count(Connection c) throws FHIRPersistenceException {
 
             // Set the variables marking the start point of the scan
             if (this.fromLastUpdated != null) {
-                ps.setTimestamp(a++, Timestamp.from(fromLastUpdated), UTC_CALENDAR);
+                ps.setTimestamp(a++, Timestamp.from(fromLastUpdated), CalendarHelper.getCalendarForUTC());
             }
 
             // 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);
+                ps.setTimestamp(a++, Timestamp.from(this.toLastUpdated), CalendarHelper.getCalendarForUTC());
             }
 
             ResultSet rs = ps.executeQuery();

diff --git a/...e-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/ParameterVisitorBatchDAO.java b/...e-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/ParameterVisitorBatchDAO.java
@@ -7,7 +7,6 @@
 package com.ibm.fhir.persistence.jdbc.dao.impl;
 
 import static com.ibm.fhir.config.FHIRConfiguration.PROPERTY_SEARCH_ENABLE_LEGACY_WHOLE_SYSTEM_SEARCH_PARAMS;
-import static com.ibm.fhir.persistence.jdbc.JDBCConstants.UTC;
 import static com.ibm.fhir.search.SearchConstants.PROFILE;
 import static com.ibm.fhir.search.SearchConstants.SECURITY;
 import static com.ibm.fhir.search.SearchConstants.TAG;
@@ -19,6 +18,7 @@
 import java.sql.Timestamp;
 import java.sql.Types;
 import java.util.ArrayList;
+import java.util.Calendar;
 import java.util.List;
 import java.util.logging.Level;
 import java.util.logging.Logger;
@@ -40,6 +40,7 @@
 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.persistence.jdbc.util.CalendarHelper;
 import com.ibm.fhir.persistence.jdbc.util.CanonicalSupport;
 import com.ibm.fhir.schema.control.FhirSchemaConstants;
 import com.ibm.fhir.search.util.ReferenceValue;
@@ -415,6 +416,7 @@ public void visit(DateParmVal param) throws FHIRPersistenceException {
     }
 
     private void setDateParms(PreparedStatement insert, int parameterNameId, Timestamp dateStart, Timestamp dateEnd) throws SQLException {
+        final Calendar UTC = CalendarHelper.getCalendarForUTC();
         insert.setInt(1, parameterNameId);
         insert.setTimestamp(2, dateStart, UTC);
         insert.setTimestamp(3, dateEnd, UTC);

diff --git a/...ersistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/ResourceDAOImpl.java b/...ersistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/ResourceDAOImpl.java
@@ -8,7 +8,6 @@
 
 import static com.ibm.fhir.persistence.jdbc.JDBCConstants.END;
 import static com.ibm.fhir.persistence.jdbc.JDBCConstants.THEN;
-import static com.ibm.fhir.persistence.jdbc.JDBCConstants.UTC;
 import static com.ibm.fhir.persistence.jdbc.JDBCConstants.WHEN;
 
 import java.sql.CallableStatement;
@@ -48,6 +47,7 @@
 import com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceDataAccessException;
 import com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceFKVException;
 import com.ibm.fhir.persistence.jdbc.impl.ParameterTransactionDataImpl;
+import com.ibm.fhir.persistence.jdbc.util.CalendarHelper;
 import com.ibm.fhir.persistence.jdbc.util.ResourceTypesCache;
 import com.ibm.fhir.persistence.jdbc.util.ResourceTypesCacheUpdater;
 import com.ibm.fhir.persistence.jdbc.util.SqlQueryData;
@@ -262,7 +262,7 @@ protected Resource createDTO(ResultSet resultSet) throws FHIRPersistenceDataAcce
             }
             resource.setId(resultSet.getLong(IDX_RESOURCE_ID));
             resource.setLogicalResourceId(resultSet.getLong(IDX_LOGICAL_RESOURCE_ID));
-            resource.setLastUpdated(resultSet.getTimestamp(IDX_LAST_UPDATED));
+            resource.setLastUpdated(resultSet.getTimestamp(IDX_LAST_UPDATED, CalendarHelper.getCalendarForUTC()));
             resource.setLogicalId(resultSet.getString(IDX_LOGICAL_ID));
             resource.setVersionId(resultSet.getInt(IDX_VERSION_ID));
             resource.setDeleted(resultSet.getString(IDX_IS_DELETED).equals("Y") ? true : false);
@@ -466,7 +466,7 @@ public List<Long> searchForIds(SqlQueryData queryData) throws FHIRPersistenceDat
             for (int i = 0; i < queryData.getBindVariables().size(); i++) {
                 Object object = queryData.getBindVariables().get(i);
                 if (object instanceof Timestamp) {
-                    stmt.setTimestamp(i + 1, (Timestamp) object, JDBCConstants.UTC);
+                    stmt.setTimestamp(i + 1, (Timestamp) object, CalendarHelper.getCalendarForUTC());
                 } else {
                     stmt.setObject(i + 1, object);
                 }
@@ -582,7 +582,7 @@ public Resource insert(Resource resource, List<ExtractedParameterValue> paramete
             }
 
             lastUpdated = resource.getLastUpdated();
-            stmt.setTimestamp(4, lastUpdated, UTC);
+            stmt.setTimestamp(4, lastUpdated, CalendarHelper.getCalendarForUTC());
             stmt.setString(5, resource.isDeleted() ? "Y": "N");
             stmt.setInt(6, resource.getVersionId());
             stmt.setString(7, parameterHashB64);

diff --git a/...rsistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/RetrieveIndexDAO.java b/...rsistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/RetrieveIndexDAO.java
@@ -22,14 +22,13 @@
 import com.ibm.fhir.database.utils.api.IDatabaseTranslator;
 import com.ibm.fhir.persistence.exception.FHIRPersistenceException;
 import com.ibm.fhir.persistence.jdbc.FHIRPersistenceJDBCCache;
+import com.ibm.fhir.persistence.jdbc.util.CalendarHelper;
 
 /**
  * Simple DAO to retrieve index IDs (i.e. logical resource IDs) from the LOGICAL_RESOURCES table.
  */
 public class RetrieveIndexDAO {
     private static final Logger logger = Logger.getLogger(RetrieveIndexDAO.class.getName());
-    private static final Calendar UTC_CALENDAR = Calendar.getInstance(TimeZone.getTimeZone("UTC"));
-
     private final IDatabaseTranslator translator;
     private final String schemaName;
     private final String resourceTypeName;
@@ -109,7 +108,7 @@ public List<Long> run(Connection c) throws FHIRPersistenceException {
                 ps.setString(i++, resourceTypeName);
             }
             if (notModifiedAfter != null) {
-                ps.setTimestamp(i++, Timestamp.from(notModifiedAfter), UTC_CALENDAR);
+                ps.setTimestamp(i++, Timestamp.from(notModifiedAfter), CalendarHelper.getCalendarForUTC());
             }
             if (afterLogicalResourceId != null) {
                 ps.setLong(i++, afterLogicalResourceId);

diff --git a/...-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/derby/DerbyResourceDAO.java b/...-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/derby/DerbyResourceDAO.java
@@ -6,15 +6,14 @@
 
 package com.ibm.fhir.persistence.jdbc.derby;
 
-import static com.ibm.fhir.persistence.jdbc.JDBCConstants.UTC;
-
 import java.io.InputStream;
 import java.sql.Connection;
 import java.sql.PreparedStatement;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.sql.SQLIntegrityConstraintViolationException;
 import java.sql.Timestamp;
+import java.util.Calendar;
 import java.util.List;
 import java.util.UUID;
 import java.util.logging.Level;
@@ -40,6 +39,7 @@
 import com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceDataAccessException;
 import com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceFKVException;
 import com.ibm.fhir.persistence.jdbc.impl.ParameterTransactionDataImpl;
+import com.ibm.fhir.persistence.jdbc.util.CalendarHelper;
 import com.ibm.fhir.persistence.jdbc.util.ParameterTableSupport;
 import com.ibm.fhir.persistence.jdbc.util.ResourceTypesCache;
 
@@ -207,6 +207,7 @@ public Resource  insert(Resource resource, List<ExtractedParameterValue> paramet
     public long storeResource(String tablePrefix, List<ExtractedParameterValue> parameters, String p_logical_id, InputStream p_payload, Timestamp p_last_updated, boolean p_is_deleted,
         String p_source_key, Integer p_version, String p_parameterHashB64, Connection conn, ParameterDAO parameterDao) throws Exception {
 
+        final Calendar UTC = CalendarHelper.getCalendarForUTC();
         final String METHODNAME = "storeResource() for " + tablePrefix + " resource";
         logger.entering(CLASSNAME, METHODNAME);