Merge pull request #506 from IBM/issue-255-lastupdated

Improve Date Time support and _lastUpdated behavior #255 #258 #437

Author: lmsurpre

fhir-core/src/main/java/com/ibm/fhir/core/FHIRUtilities.java

@@ -8,6 +8,7 @@
 
 import java.sql.Timestamp;
 import java.text.SimpleDateFormat;
+import java.time.ZoneId;
 import java.util.Base64;
 import java.util.Date;
 import java.util.TimeZone;
@@ -117,7 +118,7 @@ public static boolean isEncoded(String s) {
      * @return
      */
     public static Timestamp convertToTimestamp(java.time.ZonedDateTime zdt) {
-        return new Timestamp(zdt.toInstant().toEpochMilli());
+        return Timestamp.from(zdt.withZoneSameInstant(ZoneId.of("UTC")).toInstant());
     }
 
 

fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/derby/DerbyMaster.java

@@ -46,7 +46,7 @@ public class DerbyMaster implements AutoCloseable {
     private final String database;
 
     // Controls if we run derby in debugging mode which enables more logs.
-    private final boolean debugging = false;
+    private static final boolean DEBUG = false;
 
     /**
      * Public constructor
@@ -60,7 +60,7 @@ public DerbyMaster(String database) {
             Class.forName(DERBY_TRANSLATOR.getDriverClassName());
             // This speeds up sequence fetching by pre-creating 1000 instead of the default 100.
             out.println("derby.language.sequence.preallocator=1000");
-            if (debugging) {
+            if (DEBUG) {
                 out.println("derby.language.logQueryPlan=true");
                 out.println("derby.language.logStatementText=true");
                 out.println("derby.locks.deadlockTrace=true");

fhir-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/JDBCConstants.java

@@ -11,15 +11,15 @@
 import java.util.Map;
 
 import com.ibm.fhir.search.SearchConstants.Modifier;
-import com.ibm.fhir.search.SearchConstants.Prefix;
 import com.ibm.fhir.search.SearchConstants.Type;
 
 public class JDBCConstants {
     /**
-     * The maximum number of components allowed within a search parameter of type composite
+     * The maximum number of components allowed within a search parameter of type
+     * composite
      */
     public static final int MAX_NUM_OF_COMPOSITE_COMPONENTS = 3;
-    
+
     // Constants for the IBM FHIR Server database schema
     public static final String STR_VALUE = "STR_VALUE";
     public static final String STR_VALUE_LCASE = "STR_VALUE_LCASE";
@@ -35,15 +35,14 @@ public class JDBCConstants {
     public static final String DATE_END = "DATE_END";
     public static final String LATITUDE_VALUE = "LATITUDE_VALUE";
     public static final String LONGITUDE_VALUE = "LONGITUDE_VALUE";
-    
+
     // Generic SQL query string constants
     public static final String DOT = ".";
+    public static final char DOT_CHAR = '.';
     public static final String WHERE = " WHERE ";
     public static final String PARAMETER_TABLE_ALIAS = "pX";
     public static final String LEFT_PAREN = "(";
     public static final String RIGHT_PAREN = ")";
-    public static final String AND = " AND ";
-    public static final String OR = " OR ";
     public static final String BIND_VAR = "?";
     public static final String PERCENT_WILDCARD = "%";
     public static final String UNDERSCORE_WILDCARD = "_";
@@ -60,25 +59,49 @@ public class JDBCConstants {
     public static final String ON = " ON ";
     public static final String JOIN = " JOIN ";
     public static final String LEFT_JOIN = " LEFT JOIN ";
-    public static final String COMBINED_RESULTS = " COMBINED_RESULTS";
+    public static final String COMBINED_RESULTS = ") COMBINED_RESULTS";
+    public static final String COMMA = " , ";
+    public static final char COMMA_CHAR = ',';
+    public static final char QUOTE = '\'';
+    public static final char PATH_CHAR = '/';
+    
+    // JDBC Operators
+    public static final String EQ = " = ";
+    public static final String LIKE = " LIKE ";
+    public static final String IN =" IN ";
+    public static final String LT = " < ";
+    public static final String LTE = " <= ";
+    public static final String GT = " > "; 
+    public static final String GTE = " >= ";
+    public static final String NE = " <> ";
+    public static final String OR = " OR ";
+    public static final String AND = " AND ";
+    
+    // ASC/DESC
+    public static final String ORDER_BY = " ORDER BY ";
+    public static final String ASCENDING = "ASC";
+    public static final String DESCENDING = "DESC";
+    
+    public static final String DEFAULT_ORDERING = " ORDER BY RESOURCE_ID ASC ";
+    public static final String DEFAULT_ORDERING_WITH_TABLE = " ORDER BY R.RESOURCE_ID ASC ";
+    
+    // MIN / MAX 
+    public static final String MAX = "MAX";
+    public static final String MIN = "MIN";
 
     /**
-     * Maps search parameter types to the currently supported list of modifiers for that type.
+     * Maps search parameter types to the currently supported list of modifiers for
+     * that type.
      */
-    public static Map<Type, List<Modifier>> supportedModifiersMap;
+    public static final Map<Type, List<Modifier>> supportedModifiersMap;
 
     /**
      * Maps Parameter modifiers to SQL operators.
      */
-    public static Map<Modifier, JDBCOperator> modifierOperatorMap;
-
-    /**
-     * Maps Parameter value prefix operators to SQL operators.
-     */
-    public static Map<Prefix, JDBCOperator> prefixOperatorMap;
+    public static final Map<Modifier, String> modifierOperatorMap;
 
     static {
-        supportedModifiersMap = new HashMap<Type, List<Modifier>>();
+        supportedModifiersMap = new HashMap<>();
         supportedModifiersMap.put(Type.STRING, Arrays.asList(Modifier.EXACT, Modifier.CONTAINS, Modifier.MISSING));
         supportedModifiersMap.put(Type.REFERENCE, Arrays.asList(Modifier.TYPE, Modifier.MISSING));
         supportedModifiersMap.put(Type.URI, Arrays.asList(Modifier.BELOW, Modifier.ABOVE, Modifier.MISSING));
@@ -90,56 +113,14 @@ public class JDBCConstants {
         supportedModifiersMap.put(Type.SPECIAL, Arrays.asList(Modifier.MISSING));
 
         modifierOperatorMap = new HashMap<>();
-        modifierOperatorMap.put(Modifier.ABOVE, JDBCOperator.GT);
-        modifierOperatorMap.put(Modifier.BELOW, JDBCOperator.LT);
-        modifierOperatorMap.put(Modifier.CONTAINS, JDBCOperator.LIKE);
-        modifierOperatorMap.put(Modifier.EXACT, JDBCOperator.EQ);
-        modifierOperatorMap.put(Modifier.NOT, JDBCOperator.NE);
-
-        prefixOperatorMap = new HashMap<>();
-        prefixOperatorMap.put(Prefix.EQ, JDBCOperator.EQ);
-        prefixOperatorMap.put(Prefix.GE, JDBCOperator.GTE);
-        prefixOperatorMap.put(Prefix.GT, JDBCOperator.GT);
-        prefixOperatorMap.put(Prefix.LE, JDBCOperator.LTE);
-        prefixOperatorMap.put(Prefix.LT, JDBCOperator.LT);
-        prefixOperatorMap.put(Prefix.NE, JDBCOperator.NE);
-        prefixOperatorMap.put(Prefix.SA, JDBCOperator.GT);
-        prefixOperatorMap.put(Prefix.EB, JDBCOperator.LT);
-        prefixOperatorMap.put(Prefix.AP, JDBCOperator.EQ);
+        modifierOperatorMap.put(Modifier.ABOVE, GT);
+        modifierOperatorMap.put(Modifier.BELOW, LT);
+        modifierOperatorMap.put(Modifier.CONTAINS, LIKE);
+        modifierOperatorMap.put(Modifier.EXACT, EQ);
+        modifierOperatorMap.put(Modifier.NOT, NE);
     }
 
-    /**
-     * An enumeration of SQL query operators.
-     */
-    public static enum JDBCOperator {
-        EQ(" = "), 
-        LIKE(" LIKE "), 
-        IN(" IN "), 
-        LT(" < "), 
-        LTE(" <= "),
-        GT(" > "), 
-        GTE(" >= "),
-        NE(" <> "), 
-        OR(" OR "),
-        AND(" AND ");
-        
-        private String value = null;
-        
-        JDBCOperator(String value) {
-            this.value = value;
-        }
-        
-        public String value() {
-            return value;
-        }
-        
-        public static JDBCOperator fromValue(String value) {
-            for (JDBCOperator operator : JDBCOperator.values()) {
-                if (operator.value.equalsIgnoreCase(value)) {
-                    return operator;
-                }
-            }
-            throw new IllegalArgumentException("No constant with value " + value + " found.");
-        }
+    private JDBCConstants() {
+        // Hide the constructor
     }
-}
+}

fhir-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/api/FHIRDbDAO.java

@@ -15,11 +15,11 @@
  */
 public interface FHIRDbDAO {
 
-    String FHIRDB_JNDI_NAME_DEFAULT = "jdbc/fhirDB";
-    String PROPERTY_DB_DRIVER = "dbDriverName";
-    String PROPERTY_DB_URL = "dbUrl";
-    String PROPERTY_DB2_USER = "user";
-    String PROPERTY_DB2_PSWD = "password";
+    public static final String FHIRDB_JNDI_NAME_DEFAULT = "jdbc/fhirDB";
+    public static final String PROPERTY_DB_DRIVER = "dbDriverName";
+    public static final String PROPERTY_DB_URL = "dbUrl";
+    public static final String PROPERTY_DB2_USER = "user";
+    public static final String PROPERTY_DB2_PSWD = "password";
 
     /**
      * Acquires and returns a JDBC database connection to the FHIR database.

fhir-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/api/ParameterDAO.java

@@ -97,7 +97,7 @@ public interface ParameterDAO extends FHIRDbDAO {
      * @param codeSystemId The id corresponding to the code system name.
      * @throws FHIRPersistenceException
      */
-    void addCodeSystemsCacheCandidate(String codeSystemName, Integer codeSystemId) throws FHIRPersistenceException;    
+    void addCodeSystemsCacheCandidate(String codeSystemName, Integer codeSystemId) throws FHIRPersistenceException;
 
     /**
      * Adds a parameter name / parameter id pair to a candidate collection for population into the ParameterNamesCache.

fhir-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/api/ResourceDAO.java

@@ -13,7 +13,6 @@
 import com.ibm.fhir.persistence.context.FHIRPersistenceContext;
 import com.ibm.fhir.persistence.exception.FHIRPersistenceException;
 import com.ibm.fhir.persistence.exception.FHIRPersistenceVersionIdMismatchException;
-import com.ibm.fhir.persistence.jdbc.dto.StringParmVal;
 import com.ibm.fhir.persistence.jdbc.dto.ExtractedParameterValue;
 import com.ibm.fhir.persistence.jdbc.dto.Resource;
 import com.ibm.fhir.persistence.jdbc.exception.FHIRPersistenceDBConnectException;

fhir-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/FHIRDbDAOImpl.java

@@ -140,7 +140,7 @@ public Connection getConnection() throws FHIRPersistenceDBConnectException {
             }
             else if (this.connectionProvider != null) {
                 try {
-                    connection = connectionProvider.getConnection();                    
+                    connection = connectionProvider.getConnection();
                 }
                 catch (SQLException x) {
                     FHIRPersistenceDBConnectException fx = new FHIRPersistenceDBConnectException("Failed to acquire database connection from provider");
@@ -361,7 +361,7 @@ protected List<Resource> runQuery(String sql, Object... searchArgs) throws FHIRP
             connection = this.getConnection();
             stmt = connection.prepareStatement(sql);
             // Inject arguments into the prepared stmt.
-            for (int i = 0; i <searchArgs.length;  i++) {
+            for (int i = 0; i <searchArgs.length; i++) {
                 stmt.setObject(i+1, searchArgs[i]);
             }
             dbCallStartTime = System.nanoTime();
@@ -404,20 +404,20 @@ protected List<Resource> runQuery(String sql, Object... searchArgs) throws FHIRP
     protected int runCountQuery(String sql, Object... searchArgs) throws FHIRPersistenceDataAccessException, FHIRPersistenceDBConnectException {
         final String METHODNAME = "runCountQuery";
         log.entering(CLASSNAME, METHODNAME);
-        
+
         int rowCount = 0;
         Connection connection = null;
         PreparedStatement stmt = null;
         ResultSet resultSet = null;
         String errMsg = "Failure retrieving count. SQL=" + sql + NEWLINE + "  searchArgs=" + Arrays.toString(searchArgs);
         long dbCallStartTime;
         double dbCallDuration;
-                        
+
         try {
             connection = this.getConnection();
             stmt = connection.prepareStatement(sql);
             // Inject arguments into the prepared stmt.
-            for (int i = 0; i <searchArgs.length;  i++) {
+            for (int i = 0; i <searchArgs.length; i++) {
                 stmt.setObject(i+1, searchArgs[i]);
             }
             dbCallStartTime = System.nanoTime();

fhir-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/ParameterVisitorBatchDAO.java

@@ -74,7 +74,7 @@ public class ParameterVisitorBatchDAO implements ExtractedParameterValueVisitor,
     private final PreparedStatement quantities;
     private int quantityCount;
 
-    // rarely used so no need for PreparedStatement or batching on this one;
+    // 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;
 
@@ -338,8 +338,8 @@ public void visit(DateParmVal param) throws FHIRPersistenceException {
             }
             else {
                 if (logger.isLoggable(Level.FINE)) {
-                    logger.fine("dateValue: " + parameterName + "[" + parameterNameId + "], "
-                            + date + " [" + dateStart + ", " + dateEnd + "]");
+                    logger.fine("dateValue: " + parameterName + "[" + parameterNameId + "], value: [" 
+                            + date + "], period: [" + dateStart + ", " + dateEnd + "]");
                 }
 
                 setDateParms(dates, parameterNameId, date, dateStart, dateEnd);

fhir-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/dao/impl/ResourceDAOImpl.java

@@ -453,10 +453,9 @@ public void addResourceTypeCacheCandidate(String resourceType, Integer resourceT
 
     }
 
-    @Override
     public Resource insert(Resource resource, List<ExtractedParameterValue> parameters, ParameterDAO parameterDao)
             throws FHIRPersistenceDataAccessException, FHIRPersistenceDBConnectException, FHIRPersistenceVersionIdMismatchException {
-            final String METHODNAME = "insert(Resource, List<Parameter>";
+            final String METHODNAME = "insert(Resource, List<ExtractedParameterValue>";
             log.entering(CLASSNAME, METHODNAME);
 
             try {
@@ -770,4 +769,4 @@ public List<String> searchStringValues(SqlQueryData queryData)
             log.exiting(CLASSNAME, METHODNAME);
         }
     }
-}
+}

fhir-persistence-jdbc/src/main/java/com/ibm/fhir/persistence/jdbc/derby/FhirRefSequenceDAOImpl.java

@@ -36,7 +36,7 @@ public int nextValue() throws SQLException {
         try (PreparedStatement stmt = conn.prepareStatement(SEQ)) {
             ResultSet rs = stmt.executeQuery();
             if (rs.next()) {
-                result = rs.getInt(1);                    
+                result = rs.getInt(1);
             }
             else {
                 // not gonna happen