/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview 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.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import static org.junit.Assert.*;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
+import java.io.BufferedInputStream;
+import java.io.ByteArrayInputStream;
import java.io.File;
+import java.io.FileInputStream;
import java.io.IOException;
+import java.io.InputStream;
+import java.io.StringBufferInputStream;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
+import jalview.gui.JvOptionPane;
/**
* @author jimp
- *
+ *
*/
public class FileIOTester
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
/**
* @throws java.lang.Exception
*/
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
+ Cache.initLogger();
}
/**
* @throws java.lang.Exception
*/
- @AfterClass
+ @AfterClass(alwaysRun = true)
public static void tearDownAfterClass() throws Exception
{
}
+
// TODO: make a better/more comprehensive test harness for identify/io
-
- final static File ALIGN_FILE = new File("test/jalview/io/test_gz_fasta.gz");
- final static File NOTGZALIGN_FILE = new File("test/jalview/io/test_gz_fasta_notgz.gz");
- private void assertValidFormat(String fmt, String src, FileParse fp)
+ final static File ALIGN_FILE = new File(
+ "test/jalview/io/test_gz_fasta.gz");
+
+ final static File NOTGZALIGN_FILE = new File(
+ "test/jalview/io/test_gz_fasta_notgz.gz");
+
+ final static File STARS_FA_FILE1 = new File(
+ "test/jalview/io/test_fasta_stars.fa");
+
+ final static File STARS_FA_FILE2 = new File(
+ "test/jalview/io/test_fasta_stars2.fa");
+
+ private void assertValidFormat(FileFormatI fmt, String src, FileParse fp)
+ throws FileFormatException
{
- assertTrue("Couldn't resolve "+src+" as a valid file",fp.isValid());
- String type = new IdentifyFile().Identify(fp);
- assertTrue("Data from '"+src+"' Expected to be '"+fmt+"' identified as '"+type+"'",type.equalsIgnoreCase(fmt));
+ AssertJUnit.assertTrue("Couldn't resolve " + src + " as a valid file",
+ fp.isValid());
+ FileFormatI type = new IdentifyFile().identify(fp);
+ AssertJUnit.assertSame("Data from '" + src + "' Expected to be '" + fmt
+ + "' identified as '" + type + "'", type, fmt);
}
- @Test
+
+ @Test(groups = { "Functional" })
+ public void testStarsInFasta1() throws IOException
+ {
+ String uri;
+ FileParse fp = new FileParse(
+ uri = STARS_FA_FILE1.getAbsoluteFile().toString(),
+ DataSourceType.FILE);
+ assertValidFormat(FileFormat.Fasta, uri, fp);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testStarsInFasta2() throws IOException
+ {
+ String uri;
+ FileParse fp = new FileParse(
+ uri = STARS_FA_FILE2.getAbsoluteFile().toString(),
+ DataSourceType.FILE);
+ assertValidFormat(FileFormat.Fasta, uri, fp);
+ }
+
+ @Test(groups = { "Functional" })
public void testGzipIo() throws IOException
- {
+ {
String uri;
- FileParse fp = new FileParse(uri=ALIGN_FILE.getAbsoluteFile().toURI().toString(),AppletFormatAdapter.URL);
- assertValidFormat("FASTA", uri, fp);
+ FileParse fp = new FileParse(
+ uri = ALIGN_FILE.getAbsoluteFile().toURI().toString(),
+ DataSourceType.URL);
+ assertValidFormat(FileFormat.Fasta, uri, fp);
}
- @Test
+ @Test(groups = { "Functional" })
public void testGziplocalFileIO() throws IOException
{
String filepath;
- FileParse fp = new FileParse(filepath=ALIGN_FILE.getAbsoluteFile().toString(), AppletFormatAdapter.FILE);
- assertValidFormat("FASTA",filepath, fp);
+ FileParse fp = new FileParse(
+ filepath = ALIGN_FILE.getAbsoluteFile().toString(),
+ DataSourceType.FILE);
+ assertValidFormat(FileFormat.Fasta, filepath, fp);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testIsGzipInputStream() throws IOException
+ {
+ InputStream is = new FileInputStream(ALIGN_FILE);
+
+ /*
+ * first try fails - FileInputStream does not support mark/reset
+ */
+ assertFalse(FileParse.isGzipStream(is));
+
+ /*
+ * wrap in a BufferedInputStream and try again
+ */
+ is = new BufferedInputStream(is, 16);
+ assertTrue(FileParse.isGzipStream(is));
+
+ /*
+ * check recognition of non-gzipped input
+ */
+ assertFalse(FileParse.isGzipStream(new BufferedInputStream(
+ new ByteArrayInputStream("NOT A GZIP".getBytes()))));
}
- @Test
+
+ @Test(groups = { "Functional" })
public void testNonGzipURLIO() throws IOException
{
String uri;
- FileParse fp = new FileParse(uri=NOTGZALIGN_FILE.getAbsoluteFile().toURI().toString(),AppletFormatAdapter.URL);
- assertValidFormat("FASTA",uri, fp);
+ FileParse fp = new FileParse(
+ uri = NOTGZALIGN_FILE.getAbsoluteFile().toURI().toString(),
+ DataSourceType.URL);
+ assertValidFormat(FileFormat.Fasta, uri, fp);
}
- @Test
+
+ @Test(groups = { "Functional" })
public void testNonGziplocalFileIO() throws IOException
{
String filepath;
- FileParse fp = new FileParse(filepath=NOTGZALIGN_FILE.getAbsoluteFile().toString(), AppletFormatAdapter.FILE);
- assertValidFormat("FASTA",filepath, fp);
+ FileParse fp = new FileParse(
+ filepath = NOTGZALIGN_FILE.getAbsoluteFile().toString(),
+ DataSourceType.FILE);
+ assertValidFormat(FileFormat.Fasta, filepath, fp);
}
}