issue #334 - add db support for timestamp precision

1. added generic support in fhir-database-utils for passing precision
2. extended IDataBaseTypeAdapter to cover TIMESTAMP and default to
including the precision argument (i.e. `TIMESTAMP[(precision)]`)
3. override this default in Derby because it doesn't actually support
specifying the precision!
4. updated FhirSchemaGenerator to pass a precision of 6 (microsecond
precision to match our model)

Also added a "SimpleSchemaPrinter" class that has a single main method
for quickly printing the schema DDL.

Signed-off-by: Lee Surprenant <lmsurpre@us.ibm.com>

Author: lmsurpre

fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/api/IDatabaseTypeAdapter.java

@@ -34,4 +34,19 @@ public interface IDatabaseTypeAdapter {
      */
     public String varcharClause(int size);
 
+    /**
+     * Generate a clause for TIMESTAMP
+     * @param precision
+     * @return
+     * @implSpec the default implementation returns TIMESTAMP[(precision)]
+     *           and excludes the precision if it is null
+     */
+    default public String timestampClause(Integer precision) {
+        StringBuilder typeDef = new StringBuilder();
+        if (precision != null) {
+            typeDef.append("(" + precision + ")");
+        }
+        return typeDef.toString();
+    };
+
 }

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

@@ -203,6 +203,12 @@ public String blobClause(long size, int inlineSize) {
     public String varcharClause(int size) {
         return "VARCHAR(" + size + ")";
     }
+    
+    @Override
+    public String timestampClause(Integer precision) {
+        // Derby doesn't support the timestamp precision argument
+        return "TIMESTAMP";
+    }
 
     @Override
     public void createForeignKeyConstraint(String constraintName, String schemaName, String name, 

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

@@ -142,13 +142,12 @@ public String getUrl(Properties connectionProperties) {
             return "jdbc:derby:memory:" + adapter.getDatabase();
         }
         else {
-            return "jdbc:derby:" + adapter.getDatabase();            
+            return "jdbc:derby:" + adapter.getDatabase();
         }
     }
 
     @Override
     public boolean clobSupportsInline() {
         return false;
     }
-
 }

fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/model/ColumnDef.java

@@ -14,7 +14,7 @@ public class ColumnDef implements Comparable<ColumnDef> {
     private boolean nullable;
     private ColumnType columnType;
     private long size;
-    private int precision;
+    private Integer precision;
     private int inlineSize;
 
     /**
@@ -47,7 +47,7 @@ public long getSize() {
     public void setSize(long size) {
         this.size = size;
     }
-    public int getPrecision() {
+    public Integer getPrecision() {
         return precision;
     }
     public void setPrecision(int precision) {

fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/model/ColumnDefBuilder.java

@@ -156,7 +156,11 @@ protected List<ColumnBase> buildColumns() {
                 column = new DoubleColumn(cd.getName(), cd.isNullable());
                 break;
             case TIMESTAMP:
-                column = new TimestampColumn(cd.getName(), cd.isNullable());
+                if (cd.getPrecision() == null) {
+                    column = new TimestampColumn(cd.getName(), cd.isNullable());
+                } else {
+                    column = new TimestampColumn(cd.getName(), cd.isNullable(), cd.getPrecision());
+                }
                 break;
             case VARCHAR:
                 if (cd.getSize() > Integer.MAX_VALUE) {

fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/model/Table.java

@@ -261,6 +261,19 @@ public Builder addTimestampColumn(String columnName, boolean nullable) {
             columns.add(cd);
             return this;
         }
+        
+        public Builder addTimestampColumn(String columnName, int numberOfFractionalSecondDigits, boolean nullable) {
+            ColumnDef cd = new ColumnDef(columnName);
+            if (columns.contains(cd)) {
+                throw new IllegalArgumentException("Duplicate column: " + columnName);
+            }
+            
+            cd.setNullable(nullable);
+            cd.setColumnType(ColumnType.TIMESTAMP);
+            cd.setPrecision(numberOfFractionalSecondDigits);
+            columns.add(cd);
+            return this;
+        }
 
         public Builder addVarcharColumn(String columnName, int size, boolean nullable) {
             ColumnDef cd = new ColumnDef(columnName);
@@ -498,7 +511,11 @@ protected List<ColumnBase> buildColumns() {
                     column = new DoubleColumn(cd.getName(), cd.isNullable());
                     break;
                 case TIMESTAMP:
-                    column = new TimestampColumn(cd.getName(), cd.isNullable());
+                    if (cd.getPrecision() == null) {
+                        column = new TimestampColumn(cd.getName(), cd.isNullable());
+                    } else {
+                        column = new TimestampColumn(cd.getName(), cd.isNullable(), cd.getPrecision());
+                    }
                     break;
                 case VARCHAR:
                     if (cd.getSize() > Integer.MAX_VALUE) {

fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/model/TimestampColumn.java

@@ -12,17 +12,23 @@
  * Timestamp Column 
  */
 public class TimestampColumn extends ColumnBase {
-
     /**
-     * @param name
+     * The number of fractional second decimals to store or null to use the database's default
      */
+    private final Integer precision;
+
     public TimestampColumn(String name, boolean nullable) {
         super(name, nullable);
+        this.precision = null;
+    }
+    
+    public TimestampColumn(String name, boolean nullable, int precision) {
+        super(name, nullable);
+        this.precision = precision;
     }
 
     @Override
-    public String getTypeInfo(IDatabaseTypeAdapter translator) {
-        return "TIMESTAMP";
+    public String getTypeInfo(IDatabaseTypeAdapter adapter) {
+        return adapter.timestampClause(precision);
     }
-
 }

fhir-persistence-schema/.gitignore

@@ -1,3 +1,4 @@
 /derby/
 /derby.log
 /bin/
+/fhirschema.log

fhir-persistence-schema/src/main/java/com/ibm/fhir/schema/app/SimpleSchemaPrinter.java

@@ -0,0 +1,37 @@
+/*
+ * (C) Copyright IBM Corp. 2019
+ *
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+package com.ibm.fhir.schema.app;
+
+import com.ibm.fhir.database.utils.common.PrintTarget;
+
+import com.ibm.fhir.database.utils.db2.Db2Adapter;
+import com.ibm.fhir.database.utils.model.PhysicalDataModel;
+import com.ibm.fhir.schema.control.FhirSchemaGenerator;
+
+/**
+ * A simple main method for printing the DDL of the FHIR Server.
+ * For real work, use {@link Main}.
+ */
+public class SimpleSchemaPrinter {
+    private static final String SCHEMA_NAME = "FHIRAPP";
+    private static final String ADMIN_SCHEMA_NAME = "FHIRADMIN";
+    
+    public static void main(String[] args) {
+        // Create an instance of the service and use it to test creation
+        // of the FHIR schema
+        FhirSchemaGenerator gen = new FhirSchemaGenerator(ADMIN_SCHEMA_NAME, SCHEMA_NAME);
+        PhysicalDataModel model = new PhysicalDataModel();
+        gen.buildSchema(model);
+        
+        // Print the statements instead of executing them against a database
+        PrintTarget tgt = new PrintTarget(null, true);
+        
+        // Pretend that our target is a DB2 database
+        Db2Adapter adapter = new Db2Adapter(tgt);
+        model.apply(adapter);
+    }
+}

fhir-persistence-schema/src/main/java/com/ibm/fhir/schema/control/FhirSchemaGenerator.java

@@ -435,9 +435,9 @@ public void addResourceDateValues(PhysicalDataModel model) {
         Table tbl = Table.builder(schemaName, tableName)
                 .setTenantColumnName(MT_ID)
                 .addIntColumn(     PARAMETER_NAME_ID,      false)
-                .addTimestampColumn(      DATE_VALUE,      true)
-                .addTimestampColumn(      DATE_START,      true)
-                .addTimestampColumn(        DATE_END,      true)
+                .addTimestampColumn(      DATE_VALUE,6,    true)
+                .addTimestampColumn(      DATE_START,6,    true)
+                .addTimestampColumn(        DATE_END,6,    true)
                 .addBigIntColumn(LOGICAL_RESOURCE_ID,      false)
                 .addIndex(IDX + tableName + "_PVR", PARAMETER_NAME_ID, DATE_VALUE, LOGICAL_RESOURCE_ID)
                 .addIndex(IDX + tableName + "_RPV", LOGICAL_RESOURCE_ID, PARAMETER_NAME_ID, DATE_VALUE)