/*
* Copyright (C) 2013 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.IOException;
import java.io.InputStreamReader;
import java.io.PrintStream;
import java.util.Map;
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 org.junit.Assert;
import org.junit.Before;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TestRule;
import org.junit.rules.TestWatcher;
import org.junit.runner.Description;
/**
*
* @author dyuen
*/
public class ExtendedPluginTest extends PluginTest {
protected ByteArrayOutputStream errStream = null;
protected Pattern errorPattern = Pattern.compile("ERROR|error|Error|FATAL|fatal|Fatal|WARN|warn|Warn");
protected ByteArrayOutputStream outStream = null;
protected Pattern swidPattern = Pattern.compile("SWID: ([\\d]+)");
protected PrintStream systemErr = System.err;
protected PrintStream systemOut = System.out;
@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());
}
}
};
public ExtendedPluginTest() {
}
protected void checkErrors(String s) {
Matcher matcher = errorPattern.matcher(s);
systemErr.println("~~~~~~~~~~" + s);
Assert.assertFalse("Output contains errors:" + s, matcher.find());
// systemErr.println("~~~~~~~~~~"+matcher.group());
}
/**
* Run an instance with an error and/or failure expected
*/
protected 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.
*/
protected void checkExpectedIncorrectParameters() {
checkReturnValue(ReturnValue.SUCCESS, instance.parse_parameters());
checkReturnValue(ReturnValue.SUCCESS, instance.init());
checkReturnValue(ReturnValue.INVALIDPARAMETERS, instance.do_run());
}
protected void checkFields(Map<String, String> expectedFields) {
String out = getOut();
for (String s : out.split("\n")) {
String[] tokens = s.split("\t");
Assert.assertTrue("Unknown field exists: " + s, expectedFields.containsKey(tokens[0]));
Assert.assertEquals("Field has different parameter type than expected", expectedFields.get(tokens[0]), tokens[1]);
}
}
// //////////////////////////////////////////////////////////////////////////
protected String getAndCheckSwid(String s) {
return getAndCheckSwid(s, 1);
}
protected String getAndCheckSwid(String s, int index) throws NumberFormatException {
Matcher match = swidPattern.matcher(s);
for (int i = 0; i < index; i++) {
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;
}
public String getErr() {
return parsePrintStream(errStream);
}
public String getOut() {
return parsePrintStream(outStream);
}
public 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(MetadataTest.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();
}
@Before
@Override
public void setUp() {
super.setUp();
if (instance != null) {
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) {
// systemErr.append(csq);
return super.append(csq);
}
@Override
public void print(String s) {
// systemErr.print(s);
super.print(s);
}
};
System.setOut(pso);
System.setErr(pse);
}
@Override
public void tearDown() {
super.tearDown();
}
@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));
}
}