issue #426 fix for derby jdbc pipeline error

Signed-off-by: Albert Wang <xuwang@us.ibm.com>

Author: albertwang-ibm

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

@@ -7,7 +7,9 @@
 package com.ibm.fhir.database.utils.derby;
 
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.io.PrintWriter;
 import java.sql.Connection;
 import java.sql.DriverManager;
 import java.sql.SQLException;
@@ -28,17 +30,23 @@
  * Set up an instance of Derby for use with unit tests
  */
 public class DerbyMaster implements AutoCloseable {
-    
+
     private static final Logger logger = Logger.getLogger(DerbyMaster.class.getName());
-    
+
     // The directory holding our derby databases
     private static final String DERBY_DIR = "derby/";
 
+    // The derby properties file
+    private static final String DERBY_PROPERTIES = DERBY_DIR + "derby.properties";
+
     // The translator to help us out with Derby syntax
     private static final IDatabaseTranslator DERBY_TRANSLATOR = new DerbyTranslator();
-    
+
     // The name of the database we manage
-    private final String database;    
+    private final String database;
+
+    // Controls if we run derby in debugging mode which enables more logs.
+    private final boolean debugging = false;
 
     /**
      * Public constructor
@@ -47,18 +55,28 @@ public class DerbyMaster implements AutoCloseable {
      */
     public DerbyMaster(String database) {
         this.database = database;
-                
-        try {
+
+        try (PrintWriter out = new PrintWriter(DERBY_PROPERTIES)){
             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) {
+                out.println("derby.language.logQueryPlan=true");
+                out.println("derby.language.logStatementText=true");
+                out.println("derby.locks.deadlockTrace=true");
+                out.println("derby.infolog.append=true");
+            }
         }
         catch (ClassNotFoundException e) {
             throw new IllegalStateException(e);
+        } catch (FileNotFoundException e1) {
+            logger.warning("Failed to create derby.properties file!");
         }
-        
+
         dropDatabase(database);
-        
+
     }
-    
+
     /**
      * Drop the contents of the database on disk. Must reside in the derby/ directory
      * as a simple check against accidentally wiping the wrong files
@@ -68,13 +86,13 @@ public static void dropDatabase(String database) {
         if (!database.startsWith(DERBY_DIR)) {
             throw new IllegalArgumentException("Derby databases must start with: " + DERBY_DIR);
         }
-        
+
         try {
             File dir = new File(database);
             if (dir.exists()) {
                 delete(dir);
             }
-        } 
+        }
         catch (IOException e) {
             throw new IllegalStateException("Failed to delete derby DB: " + database, e);
         }
@@ -92,7 +110,7 @@ private static void delete(File file) throws IOException {
             //directory is empty, then delete it
             if (file.list().length == 0) {
                 file.delete();
-            } 
+            }
             else {
                 // list all the directory contents
                 String files[] = file.list();
@@ -110,7 +128,7 @@ private static void delete(File file) throws IOException {
                     file.delete();
                 }
             }
-        } 
+        }
         else {
             // if file exists, then delete it
             file.delete();
@@ -126,7 +144,7 @@ private static void delete(File file) throws IOException {
     public Connection createConnection() throws SQLException {
         logger.info("Opening connection to Derby database: " + database);
         Connection connection;
-        try {   
+        try {
             // Make sure the Derby driver is loaded
                 Properties properties = new Properties();
                 DerbyPropertyAdapter adapter = new DerbyPropertyAdapter(properties);
@@ -136,7 +154,7 @@ public Connection createConnection() throws SQLException {
         }
         catch (SQLException x) {
             throw DERBY_TRANSLATOR.translate(x);
-        } 
+        }
 
         return connection;
     }
@@ -148,7 +166,7 @@ public Connection createConnection() throws SQLException {
     public IDatabaseTranslator getTranslator() {
         return DERBY_TRANSLATOR;
     }
-    
+
     /**
      * Ask the schema to apply itself to our target (adapter pattern)
      * @param pdm
@@ -167,7 +185,7 @@ public void runWithAdapter(java.util.function.Consumer<IDatabaseAdapter> fn) {
             try (Connection c = createConnection()) {
                 try {
                     JdbcTarget target = new JdbcTarget(c);
-                    
+
                     if (logger.isLoggable(Level.FINE)) {
                         // Decorate the target so that we print all the DDL before executing
                         PrintTarget printer = new PrintTarget(target, logger.isLoggable(Level.FINE));
@@ -190,7 +208,7 @@ public void runWithAdapter(java.util.function.Consumer<IDatabaseAdapter> fn) {
         catch (SQLException x) {
             throw DERBY_TRANSLATOR.translate(x);
         }
-        
+
     }
 
     @Override

fhir-persistence-jdbc/src/test/java/com/ibm/fhir/persistence/jdbc/test/spec/R4JDBCExamplesTest.java

@@ -6,20 +6,24 @@
 
 package com.ibm.fhir.persistence.jdbc.test.spec;
 
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Properties;
 
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeSuite;
 import org.testng.annotations.Test;
 
+import com.ibm.fhir.database.utils.api.ITransactionProvider;
+import com.ibm.fhir.database.utils.pool.PoolConnectionProvider;
+import com.ibm.fhir.database.utils.transaction.SimpleTransactionProvider;
 import com.ibm.fhir.model.spec.test.R4ExamplesDriver;
 import com.ibm.fhir.model.spec.test.R4ExamplesDriver.TestType;
 import com.ibm.fhir.model.test.TestUtil;
 import com.ibm.fhir.persistence.FHIRPersistence;
 import com.ibm.fhir.persistence.context.FHIRHistoryContext;
 import com.ibm.fhir.persistence.context.FHIRPersistenceContext;
 import com.ibm.fhir.persistence.context.FHIRPersistenceContextFactory;
-import com.ibm.fhir.persistence.jdbc.impl.FHIRPersistenceJDBCImpl;
 import com.ibm.fhir.persistence.test.common.AbstractPersistenceTest;
 import com.ibm.fhir.schema.derby.DerbyFhirDatabase;
 
@@ -44,10 +48,29 @@ public void bootstrapAndLoad() {
 
     @Test(groups = { "jdbc-seed" })
     public void perform() throws Exception {
-
-        R4JDBCExamplesProcessor processor = new R4JDBCExamplesProcessor(persistence,
-            () -> createPersistenceContext(),
-            () -> createHistoryPersistenceContext());
+        // Use connection pool and transaction provider to make sure the resource operations
+        // of each resource are committed after the processing is finished, and because this
+        // testng test process the samples one by one, so set the connection pool size to 1.
+        PoolConnectionProvider connectionPool = new PoolConnectionProvider(database, 1);
+        ITransactionProvider transactionProvider = new SimpleTransactionProvider(connectionPool);
+        List<ITestResourceOperation> operations = new ArrayList<>();
+        operations.add(new CreateOperation());
+        operations.add(new ReadOperation());
+        operations.add(new UpdateOperation());
+        operations.add(new UpdateOperation());
+        operations.add(new ReadOperation());
+        operations.add(new VReadOperation());
+        operations.add(new HistoryOperation(3));
+        operations.add(new DeleteOperation());
+        operations.add(new DeleteOperation());
+        operations.add(new HistoryOperation(4));
+        R4JDBCExamplesProcessor processor = new R4JDBCExamplesProcessor(
+                operations,
+                this.properties,
+                connectionPool,
+                null,
+                null,
+                transactionProvider);
 
         // Overriding the JDBC ALL to Minimal.
         // Unless the profile tells us differently
@@ -92,7 +115,8 @@ protected FHIRPersistenceContext createHistoryPersistenceContext() {
 
     @Override
     public FHIRPersistence getPersistenceImpl() throws Exception {
-        return new FHIRPersistenceJDBCImpl(this.properties, database);
+        //return new FHIRPersistenceJDBCImpl(this.properties, database);
+        return null;
     }
 
     @Override

fhir-persistence/src/test/java/com/ibm/fhir/persistence/test/common/AbstractPersistenceTest.java

@@ -86,14 +86,14 @@ public void setUp() throws Exception {
 
     @BeforeMethod(alwaysRun = true)
     public void startTrx() throws Exception{
-        if (persistence.isTransactional()) {
+        if (persistence != null && persistence.isTransactional()) {
             persistence.getTransaction().begin();
         }
     }
 
     @AfterMethod(alwaysRun = true)
     public void commitTrx() throws Exception{
-        if (persistence.isTransactional()) {
+        if (persistence != null && persistence.isTransactional()) {
             persistence.getTransaction().commit();
         }
     }
@@ -117,11 +117,11 @@ protected List<Resource> runQueryTest(Class<? extends Resource> resourceType, St
     protected List<Resource> runQueryTest(Class<? extends Resource> resourceType, Map<String, List<String>> queryParms) throws Exception {
         return runQueryTest(resourceType, queryParms, null);
     }
-    
+
     protected List<Resource> runQueryTest(Class<? extends Resource> resourceType, Map<String, List<String>> queryParms, Integer maxPageSize) throws Exception {
         return runQueryTest(SearchUtil.parseQueryParameters(resourceType, queryParms), resourceType, queryParms, maxPageSize).getResource();
     }
-    
+
     protected MultiResourceResult<Resource> runQueryTest(FHIRSearchContext searchContext, Class<? extends Resource> resourceType, Map<String, List<String>> queryParms, Integer maxPageSize) throws Exception {
         // ensure that all the query parameters were processed into search parameters (needed because the server ignores invalid params by default)
         int expectedCount = 0;