Avoid creating unnecessary tables for Resource and DomainResource

resource types #713

- Checks for DOMAINRESOURCE and RESOURCE tables view
- Removes the artifacts
- Bonus: added fix for null condition on a code in
DefaultMemberMatchStrategy

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

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

@@ -2561,6 +2561,7 @@ private void applyTableRemovalForV0021() {
                     logger.info("V0021 Migration: Removing Abstract Tables from schema '" + schemaName + "'");
                     MigrateV0021AbstractTypeRemoval cmd = new MigrateV0021AbstractTypeRemoval(adapter, adminSchemaName, schemaName, forceUnusedTableRemoval);
                     adapter.runStatement(cmd);
+                    logger.info("V0021 Migration: Completed the Removal of the Abstract Tables from schema '" + schemaName + "'");
                 }
             } catch (DataAccessException x) {
                 // Something went wrong, so mark the transaction as failed

fhir-persistence-schema/src/main/java/com/ibm/fhir/schema/control/MigrateV0021AbstractTypeRemoval.java

@@ -14,6 +14,7 @@
 import java.util.Arrays;
 import java.util.List;
 import java.util.logging.Logger;
+import java.util.stream.Collectors;
 
 import com.ibm.fhir.database.utils.api.DataAccessException;
 import com.ibm.fhir.database.utils.api.IDatabaseAdapter;
@@ -34,6 +35,19 @@ public class MigrateV0021AbstractTypeRemoval implements IDatabaseStatement {
 
     private static final Logger LOG = Logger.getLogger(MigrateV0021AbstractTypeRemoval.class.getName());
 
+    private static final List<String> VALUE_TYPES = Arrays.asList(
+        "RESOURCE_TOKEN_REFS",
+        "DATE_VALUES",
+        "LATLNG_VALUES",
+        "NUMBER_VALUES",
+        "QUANTITY_VALUES",
+        "STR_VALUES",
+        "PROFILES",
+        "TAGS",
+        "SECURITY");
+
+    private static final List<String> VALUE_TYPES_LOWER = VALUE_TYPES.stream().map(s -> s.toLowerCase()).collect(Collectors.toList());
+
     // The Adapter
     private final IDatabaseAdapter adapter;
 
@@ -171,30 +185,16 @@ private void checkDataTables(IDatabaseTranslator translator, Connection c) {
      */
     private void removeBaseArtifacts(IDatabaseTranslator translator, Connection c) {
         List<String> tables = Arrays.asList("DOMAINRESOURCE_", "RESOURCE_");
-        List<String> valueTypes = Arrays.asList(
-                                        "DATE_VALUES",
-                                        "LATLNG_VALUES",
-                                        "NUMBER_VALUES",
-                                        "QUANTITY_VALUES",
-                                        "RESOURCE_TOKEN_REFS",
-                                        "STR_VALUES",
-                                        "PROFILES",
-                                        "TAGS",
-                                        "SECURITY");
+
 
         // Run across both tables
         for (String tablePrefix : tables) {
-            // Drop the Values Tables
-            for (String valueType : valueTypes) {
-                adapter.dropTable(schemaName, tablePrefix + valueType);
-            }
-
-            // Drop the supporting tables
-            adapter.dropTable(schemaName, tablePrefix + "logical_resources");
-            adapter.dropTable(schemaName, tablePrefix + "resources");
-
             // Drop the View for the Table
-            adapter.dropView(schemaName, tablePrefix + "_token_values_V");
+            if (translator.getType() == DbType.POSTGRESQL) {
+                runDropTableResourceGroup(translator, c, schemaName.toLowerCase(), tablePrefix.toLowerCase(), VALUE_TYPES_LOWER);
+            } else {
+                runDropTableResourceGroup(translator, c, schemaName, tablePrefix, VALUE_TYPES);
+            }
         }
 
         // Pattern for multitenant is to prefix tables with DRP_
@@ -206,8 +206,34 @@ private void removeBaseArtifacts(IDatabaseTranslator translator, Connection c) {
         // Drop the tables, when the tables don't exists the errors are swallowed
         // and logs print warnings saying the tables don't exist. That's OK.
         for (String deprecatedTable : UnusedTableRemovalNeedsV0021Migration.DEPRECATED_TABLES) {
-            adapter.dropTable(schemaName, prefix + deprecatedTable);
+            String table = prefix + deprecatedTable;
+            if (translator.getType() == DbType.POSTGRESQL) {
+                adapter.dropTable(schemaName.toLowerCase(), table.toLowerCase());
+            } else {
+                adapter.dropTable(schemaName, table);
+            }
+        }
+    }
+
+    /**
+     * run drop table resource group
+     * @param translator
+     * @param c
+     * @param schemaName
+     * @param tablePrefix
+     * @param valueTypes
+     */
+    public void runDropTableResourceGroup(IDatabaseTranslator translator, Connection c, String schemaName, String tablePrefix, List<String> valueTypes) {
+        adapter.dropView(schemaName, tablePrefix + "token_values_v");
+
+        // Drop the Values Tables
+        for (String valueType : valueTypes) {
+            adapter.dropTable(schemaName, tablePrefix + valueType);
         }
+
+        // Drop the supporting tables
+        adapter.dropTable(schemaName, tablePrefix + "logical_resources");
+        adapter.dropTable(schemaName, tablePrefix + "resources");
     }
 
     /**

fhir-persistence-schema/src/main/java/com/ibm/fhir/schema/control/UnusedTableRemovalNeedsV0021Migration.java

@@ -15,6 +15,7 @@
 
 import com.ibm.fhir.database.utils.api.IDatabaseSupplier;
 import com.ibm.fhir.database.utils.api.IDatabaseTranslator;
+import com.ibm.fhir.database.utils.model.DbType;
 
 /**
  * Checks to see if any of the tables exist in the target database.
@@ -87,7 +88,7 @@ public Boolean run(IDatabaseTranslator translator, Connection c) {
      * @return
      */
     public boolean checkDb2(IDatabaseTranslator translator, Connection c) {
-        final String sql = "SELECT tabname FROM SYSCAT.TABLES TABS"
+        final String sql = "SELECT 1 FROM SYSCAT.TABLES TABS"
                 + " WHERE TABS.tabschema = ? "
                 + "     AND TABS.tabname in ( " + addParameterMarkers(TABLE_COUNT) + " )";
         return hasTables(translator, c, sql);
@@ -103,7 +104,7 @@ public boolean checkDb2(IDatabaseTranslator translator, Connection c) {
     public boolean checkDerby(IDatabaseTranslator translator, Connection c) {
         // Grab the list of tables for the configured schema from the Derby sys catalog
         final String sql = ""
-                + "SELECT tables.tablename FROM sys.systables AS tables "
+                + "SELECT 1 FROM sys.systables AS tables "
                 + "  JOIN sys.sysschemas AS schemas "
                 + "    ON (tables.schemaid = schemas.schemaid) "
                 + " WHERE schemas.schemaname = ?"
@@ -122,8 +123,8 @@ public boolean checkPostgres(IDatabaseTranslator translator, Connection c) {
         // Grab the list of tables for the configured schema from the PostgreSQL schema
         // catalog
         final String sql = ""
-                + "SELECT table_name FROM information_schema.tables "
-                + " WHERE table_schema = ?"
+                + "SELECT 1 FROM information_schema.tables "
+                + " WHERE table_schema = lower(?)"
                 + "     AND table_name in (" + addParameterMarkers(TABLE_COUNT) + ")";
         return hasTables(translator, c, sql);
     }
@@ -157,7 +158,11 @@ private boolean hasTables(IDatabaseTranslator translator, Connection c, final St
             ps.setString(i++, schemaName);
 
             for (String deprecatedTable : DEPRECATED_TABLES) {
-                ps.setString(i++, deprecatedTable);
+                if (translator.getType() == DbType.POSTGRESQL) {
+                    ps.setString(i++, deprecatedTable.toLowerCase());
+                } else {
+                    ps.setString(i++, deprecatedTable);
+                }
             }
             ResultSet rs = ps.executeQuery();
             return rs.next();

fhir-persistence-schema/src/test/java/com/ibm/fhir/schema/derby/DerbyFhirDatabaseTest.java

@@ -9,7 +9,6 @@
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertNotNull;
-import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertTrue;
 
 import java.sql.Connection;
@@ -31,7 +30,6 @@
 import com.ibm.fhir.database.utils.model.PhysicalDataModel;
 import com.ibm.fhir.database.utils.pool.PoolConnectionProvider;
 import com.ibm.fhir.database.utils.transaction.SimpleTransactionProvider;
-import com.ibm.fhir.database.utils.version.CreateVersionHistory;
 import com.ibm.fhir.database.utils.version.CreateWholeSchemaVersion;
 import com.ibm.fhir.database.utils.version.VersionHistoryService;
 import com.ibm.fhir.schema.app.Main;
@@ -62,7 +60,7 @@ public void testFhirSchema() throws Exception {
         try (DerbyFhirDatabase db = new DerbyFhirDatabase(DB_NAME)) {
             System.out.println("FHIR database exists.");
             checkDatabase(db, db.getSchemaName());
-            
+
             // Test the schema drop
             testDrop(db, db.getSchemaName());
         }
@@ -87,9 +85,9 @@ protected void testDrop(IConnectionProvider cp, String schemaName) throws SQLExc
             FhirSchemaGenerator gen = new FhirSchemaGenerator(ADMIN_SCHEMA_NAME, schemaName, false);
             gen.buildSchema(pdm);
             pdm.drop(adapter, FhirSchemaGenerator.SCHEMA_GROUP_TAG, FhirSchemaGenerator.FHIRDATA_GROUP);
-            
+
             CreateWholeSchemaVersion.dropTable(schemaName, adapter);
-            
+
             // Check that the schema is empty
             List<SchemaInfoObject> schemaObjects = adapter.listSchemaObjects(schemaName);
             boolean schemaIsEmpty = schemaObjects.isEmpty();
@@ -100,7 +98,7 @@ protected void testDrop(IConnectionProvider cp, String schemaName) throws SQLExc
             }
             assertTrue(schemaIsEmpty);
         }
-        
+
         // Now we're all done we can finally clean up the version-history for
         // our schema. Make sure we don't get a version for an object we know
         // we created
@@ -137,10 +135,10 @@ protected void checkDatabase(IConnectionProvider cp, String schemaName) throws S
                 JdbcTarget tgt = new JdbcTarget(c);
                 DerbyAdapter adapter = new DerbyAdapter(tgt);
                 checkRefSequence(adapter);
-                
+
                 // Check that we have the correct number of tables. This will need to be updated
                 // whenever tables, views or sequences are added or removed
-                assertEquals(adapter.listSchemaObjects(schemaName).size(), 1943);
+                assertEquals(adapter.listSchemaObjects(schemaName).size(), 1917);
                 c.commit();
             } catch (Throwable t) {
                 c.rollback();

fhir-persistence-schema/src/test/java/com/ibm/fhir/schema/derby/DerbySchemaVersionsTest.java

@@ -3,7 +3,7 @@
  *
  * SPDX-License-Identifier: Apache-2.0
  */
- 
+
 package com.ibm.fhir.schema.derby;
 
 import static org.testng.Assert.assertEquals;
@@ -27,7 +27,7 @@
 public class DerbySchemaVersionsTest {
     private static final String TARGET_DIR = "target/derby/";
     private static final String SCHEMA_NAME = "APP";
-    
+
     @Test
     public void test() throws Exception {
         String dbPath = TARGET_DIR + "fhirdb";
@@ -41,18 +41,18 @@ public void test() throws Exception {
             PoolConnectionProvider connectionPool = new PoolConnectionProvider(cp, 10);
             ITransactionProvider transactionProvider = new SimpleTransactionProvider(connectionPool);
             SchemaVersionsManager svm = new SchemaVersionsManager(db.getTranslator(), connectionPool, transactionProvider, SCHEMA_NAME);
-            
+
             svm.updateSchemaVersionId(FhirSchemaVersion.V0001);
             assertEquals(svm.getVersionForSchema(), FhirSchemaVersion.V0001.vid());
             svm.updateSchemaVersionId(FhirSchemaVersion.V0002);
             assertEquals(svm.getVersionForSchema(), FhirSchemaVersion.V0002.vid());
             svm.updateSchemaVersionId(FhirSchemaVersion.V0003);
             assertEquals(svm.getVersionForSchema(), FhirSchemaVersion.V0003.vid());
-            
+
             // Make sure we can correctly determine the latest schema version value
             svm.updateSchemaVersion();
-            assertEquals(svm.getVersionForSchema(), FhirSchemaVersion.V0020.vid());
-            
+            assertEquals(svm.getVersionForSchema(), FhirSchemaVersion.V0021.vid());
+
             assertTrue(svm.isLatestSchema());
        }
     }

operation/fhir-operation-member-match/src/main/java/com/ibm/fhir/operation/davinci/hrex/provider/strategy/DefaultMemberMatchStrategy.java

@@ -255,8 +255,9 @@ private void addIdValue(Identifier identifier) {
                 // If there is  more than one Coding it has to be MB.
                 for (Coding coding : identifier.getType().getCoding()) {
                     if (coding.getSystem() != null
-                            &&  "http://terminology.hl7.org/CodeSystem/v2-0203"
+                            && "http://terminology.hl7.org/CodeSystem/v2-0203"
                                     .equals(coding.getSystem().getValue())
+                            && coding.getCode() != null
                             && "MB".equals(coding.getCode().getValue())) {
                         // We only want to extract the code system v2-0203 with MB
                         Uri sys = identifier.getSystem();