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issue #426 fix for pipeline derby jdbc test error #432

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Merged
prb112 merged 4 commits into from
Nov 20, 2019
Merged

issue #426 fix for pipeline derby jdbc test error #432

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2243ded
Merge pull request #431 from IBM/master
albertwang-ibm Nov 19, 2019
91dea8c
issue #426 fix for derby jdbc pipeline error
albertwang-ibm Nov 19, 2019
83bfea8
issue #426 minor change
albertwang-ibm Nov 20, 2019
da60fbe
issue #426 change comments
albertwang-ibm Nov 20, 2019
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54 changes: 36 additions & 18 deletions fhir-database-utils/src/main/java/com/ibm/fhir/database/utils/derby/DerbyMaster.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand All @@ -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
Expand All @@ -47,18 +55,28 @@ public class DerbyMaster implements AutoCloseable {
*/
public DerbyMaster(String database) {
this.database = database;
try {

try (PrintWriter out = new PrintWriter(DERBY_PROPERTIES)){
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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) {
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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
Expand All @@ -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);
}
Expand All @@ -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();
Expand All @@ -110,7 +128,7 @@ private static void delete(File file) throws IOException {
file.delete();
}
}
}
}
else {
// if file exists, then delete it
file.delete();
Expand All @@ -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);
Expand All @@ -136,7 +154,7 @@ public Connection createConnection() throws SQLException {
}
catch (SQLException x) {
throw DERBY_TRANSLATOR.translate(x);
}
}

return connection;
}
Expand All @@ -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
Expand All @@ -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));
Expand All @@ -190,7 +208,7 @@ public void runWithAdapter(java.util.function.Consumer<IDatabaseAdapter> fn) {
catch (SQLException x) {
throw DERBY_TRANSLATOR.translate(x);
}

}

@Override
Expand Down
36 changes: 30 additions & 6 deletions ...stence-jdbc/src/test/java/com/ibm/fhir/persistence/jdbc/test/spec/R4JDBCExamplesTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;

Expand All @@ -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,
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transactionProvider);

// Overriding the JDBC ALL to Minimal.
// Unless the profile tells us differently
Expand Down Expand Up @@ -92,7 +115,8 @@ protected FHIRPersistenceContext createHistoryPersistenceContext() {

@Override
public FHIRPersistence getPersistenceImpl() throws Exception {
return new FHIRPersistenceJDBCImpl(this.properties, database);
// Return null to make sure the transaction operations in @BeforeMethod will be skipped
return null;
}

@Override
Expand Down
8 changes: 4 additions & 4 deletions ...rsistence/src/test/java/com/ibm/fhir/persistence/test/common/AbstractPersistenceTest.java
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Expand Up @@ -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();
}
}
Expand All @@ -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;
Expand Down