/*
* Copyright (C) 2012 SeqWare
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package net.sourceforge.seqware.pipeline.plugins;
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.PrintStream;
import java.util.Arrays;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import net.sourceforge.seqware.common.module.ReturnValue;
import net.sourceforge.seqware.common.util.testtools.BasicTestDatabaseCreator;
import static net.sourceforge.seqware.pipeline.plugins.PluginTest.metadata;
import org.apache.commons.dbutils.handlers.ArrayHandler;
import org.junit.Assert;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Rule;
import org.junit.Test;
import org.junit.contrib.java.lang.system.ExpectedSystemExit;
import org.junit.rules.TestRule;
import org.junit.rules.TestWatcher;
import org.junit.runner.Description;
/**
* Runs the tests for the GenericMetadataSaver plugin
*
* @author dyuen
*/
public class GenericMetadataSaverTest extends PluginTest {
private ByteArrayOutputStream outStream = null;
private ByteArrayOutputStream errStream = null;
private Pattern swidPattern = Pattern.compile("SWID: ([\\d]+)");
private Pattern errorPattern = Pattern.compile("ERROR|error|Error|FATAL|fatal|Fatal|WARN|warn|Warn");
private PrintStream systemErr = System.err;
/**
* This allows us to intercept and ignore the various System.exit calls within runner so they don't take down the tests as well
*/
@Rule
public final ExpectedSystemExit exit = ExpectedSystemExit.none();
@BeforeClass
public static void beforeClass() {
BasicTestDatabaseCreator.resetDatabaseWithUsers();
}
@Before
@Override
public void setUp() {
super.setUp();
instance = new ModuleRunner();
instance.setMetadata(metadata);
outStream = new ByteArrayOutputStream();
errStream = new ByteArrayOutputStream();
PrintStream pso = new PrintStream(outStream);
PrintStream pse = new PrintStream(errStream) {
@Override
public PrintStream append(CharSequence csq) {
return super.append(csq);
}
@Override
public void print(String s) {
super.print(s);
}
};
System.setOut(pso);
System.setErr(pse);
}
@Override
public void tearDown() {
super.tearDown();
}
public GenericMetadataSaverTest() {
}
private String getOut() {
return parsePrintStream(outStream);
}
private String getErr() {
return parsePrintStream(errStream);
}
private String parsePrintStream(ByteArrayOutputStream stream) {
StringBuilder sb = new StringBuilder();
BufferedReader r = null;
try {
ByteArrayInputStream inStream = new ByteArrayInputStream(stream.toByteArray());
r = new BufferedReader(new InputStreamReader(inStream));
String s = r.readLine();
while (s != null) {
s = s.trim();
// remove any blank lines
if (s.isEmpty()) {
s = r.readLine();
continue;
}
if (s.endsWith("[")) {
while (s != null && !s.contains("]")) {
sb.append(s);
s = r.readLine();
}
}
sb.append(s).append("\n");
s = r.readLine();
}
} catch (IOException ex) {
Logger.getLogger(GenericMetadataSaverTest.class.getName()).log(Level.SEVERE, null, ex);
} finally {
if (r != null) {
try {
r.close();
} catch (IOException ex) {
systemErr.println("Couldn't close System.out reader" + ex.getMessage());
}
}
}
return sb.toString();
}
private void checkErrors(String s) {
Matcher matcher = errorPattern.matcher(s);
systemErr.println("~~~~~~~~~~" + s);
Assert.assertFalse("Output contains errors:" + s, matcher.find());
}
@Test
public void testMatcher() {
String string = "[SeqWare Pipeline] ERROR [2012/11/01 15:53:51] | "
+ "MetadataWS.findObject with search string /288023 encountered error "
+ "Internal Server Error\nExperiment: null\nSWID: 6740";
Matcher match = swidPattern.matcher(string);
Assert.assertTrue(match.find());
Assert.assertEquals("6740", match.group(1));
match = errorPattern.matcher(string);
Assert.assertTrue(match.find());
Assert.assertEquals("ERROR", match.group(0));
}
@Test
public void testSaveNonExistingFileFail() {
exit.expectSystemExitWithStatus(ReturnValue.FILENOTREADABLE);
instance.setParams(Arrays.asList("--module", "net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver",
"--metadata-parent-accession", "10", "--", "--gms-output-file", "text::text/plain::/abcdefghijklmnop/test.txt",
"--gms-algorithm", "UploadText"));
String s = getOut();
checkExpectedFailure();
}
@Test
public void testSaveNonExistingFile() throws IOException {
exit.expectSystemExitWithStatus(ReturnValue.SUCCESS);
launchPlugin("--module", "net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver", "--metadata-parent-accession", "10",
"--", "--gms-output-file", "text::text/plain::/tmp/abcdefghijklmnop/xyz", "--gms-algorithm", "UploadText",
"--gms-suppress-output-file-check");
String s = getOut();
String swid = getAndCheckSwid(s);
int accession = Integer.valueOf(swid);
// check that file records and processing were created properly
BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator();
Object[] runQuery = dbCreator
.runQuery(
new ArrayHandler(),
"select file_path, meta_type, algorithm from file f, processing_files pf, processing p WHERE f.file_id = pf.file_id AND pf.processing_id = p.processing_id AND p.sw_accession == ?",
accession);
Assert.assertTrue("values not found", runQuery.length == 3);
Assert.assertTrue("file_path value incorrect", runQuery[0].equals("/tmp/abcdefghijklmnop/xyz"));
Assert.assertTrue("meta_type value incorrect", runQuery[1].equals("text/plain"));
Assert.assertTrue("algorithm value incorrect", runQuery[2].equals("UploadText"));
}
@Test
public void testSaveExistingFile() throws IOException {
exit.expectSystemExitWithStatus(ReturnValue.SUCCESS);
File createTempFile = File.createTempFile("output", "txt");
createTempFile.createNewFile();
launchPlugin("--module", "net.sourceforge.seqware.pipeline.modules.GenericMetadataSaver", "--metadata-parent-accession", "10",
"--", "--gms-output-file", "text::text/plain::" + createTempFile.getAbsolutePath(), "--gms-algorithm", "UploadText");
String s = getOut();
String swid = getAndCheckSwid(s);
int accession = Integer.valueOf(swid);
// check that file records and processing were created properly
BasicTestDatabaseCreator dbCreator = new BasicTestDatabaseCreator();
Object[] runQuery = dbCreator
.runQuery(
new ArrayHandler(),
"select file_path, meta_type, algorithm from file f, processing_files pf, processing p WHERE f.file_id = pf.file_id AND pf.processing_id = p.processing_id AND p.sw_accession == ?",
accession);
Assert.assertTrue("values not found", runQuery.length == 3);
Assert.assertTrue("file_path value incorrect", runQuery[0].equals(createTempFile.getAbsolutePath()));
Assert.assertTrue("meta_type value incorrect", runQuery[1].equals("text/plain"));
Assert.assertTrue("algorithm value incorrect", runQuery[2].equals("UploadText"));
}
// //////////////////////////////////////////////////////////////////////////
private String getAndCheckSwid(String s) throws NumberFormatException {
Matcher match = swidPattern.matcher(s);
Assert.assertTrue("SWID not found in output.", match.find());
String swid = match.group(1);
Assert.assertFalse("The SWID was empty", swid.trim().isEmpty());
Integer.parseInt(swid.trim());
return swid;
}
@Rule
public TestRule watchman = new TestWatcher() {
// This doesn't catch logs that are sent to Log4J
@Override
protected void succeeded(Description d) {
// do not fail on tests that intend on failing
if (!d.getMethodName().endsWith("Fail")) {
checkErrors(getErr());
checkErrors(getOut());
}
}
};
/**
* Run an instance with an error and/or failure expected
*/
private void checkExpectedFailure() {
checkReturnValue(ReturnValue.SUCCESS, instance.parse_parameters());
checkReturnValue(ReturnValue.SUCCESS, instance.init());
checkReturnValue(ReturnValue.FAILURE, instance.do_run());
}
/**
* Run an instance with incorrect parameters expected.
*/
private void checkExpectedIncorrectParameters() {
checkReturnValue(ReturnValue.SUCCESS, instance.parse_parameters());
checkReturnValue(ReturnValue.SUCCESS, instance.init());
checkReturnValue(ReturnValue.INVALIDPARAMETERS, instance.do_run());
}
}