+/*
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.bin;
+import java.awt.image.BufferedImage;
import java.io.File;
import java.io.IOException;
-import java.lang.reflect.InvocationTargetException;
import java.nio.file.Files;
import java.util.Date;
import java.util.HashSet;
import java.util.Set;
+import javax.imageio.ImageIO;
import javax.swing.SwingUtilities;
import org.testng.Assert;
}
@AfterMethod(alwaysRun = true)
- public void tearDown()
+ public void tearDown()
{
try
{
public static void callJalviewMain(String[] args)
{
- if (Jalview.getInstance() != null)
+ callJalviewMain(args, false);
+ }
+
+ public static void callJalviewMain(String[] args, boolean newJalview)
+ {
+ if (!newJalview || Jalview.getInstance() != null)
{
Jalview.getInstance().doMain(args);
}
}
*/
- @Test(groups = "Functional", dataProvider = "cmdLines")
+ @Test(
+ groups =
+ { "Functional", "testTask3" },
+ dataProvider = "cmdLines",
+ singleThreaded = true)
+
public void commandsOpenTest(String cmdLine, boolean cmdArgs,
int numFrames, String[] sequences)
{
Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
"Overall command parse and operation is false");
- Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
+ Assert.assertEquals(Desktop.getDesktopAlignFrames().length, numFrames,
"Wrong number of AlignFrames");
if (sequences != null)
{
Set<String> openedSequenceNames = new HashSet<>();
- AlignFrame[] afs = Desktop.getAlignFrames();
+ AlignFrame[] afs = Desktop.getDesktopAlignFrames();
for (AlignFrame af : afs)
{
openedSequenceNames.addAll(
@Test(
groups =
- { "Functional", "testTask1" },
- dataProvider = "structureImageOutputFiles")
+ { "Functional", "testTask3" },
+ dataProvider = "structureImageOutputFiles",
+ singleThreaded = true)
public void structureImageOutputTest(String cmdLine, String[] filenames)
throws IOException
{
callJalviewMain(args);
Commands cmds = Jalview.getInstance().getCommands();
Assert.assertNotNull(cmds);
- File lastFile = null;
- for (String filename : filenames)
+ verifyIncreasingSize(cmdLine, filenames);
+ } catch (Exception x)
+ {
+ Assert.fail("Unexpected exception during structureImageOutputTest",
+ x);
+ } finally
+ {
+ cleanupFiles(filenames);
+ tearDown();
+ }
+ }
+
+ /**
+ * given two command lines, compare the output files produced - they should
+ * exist and be equal in size
+ */
+ @Test(
+ groups =
+ { "Functional", "testTask3" },
+ dataProvider = "compareHeadlessAndGUIOps",
+ singleThreaded = true)
+ public void headlessOrGuiImageOutputTest(String[] cmdLines,
+ String[] filenames) throws IOException
+ {
+ cleanupFiles(filenames);
+ try
+ {
+ for (String cmdLine : cmdLines)
{
- File file = new File(filename);
- Assert.assertTrue(file.exists(), "File '" + filename
- + "' was not created by '" + cmdLine + "'");
- Assert.assertTrue(file.isFile(), "File '" + filename
- + "' is not a file from '" + cmdLine + "'");
- Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
- + "' has no content from '" + cmdLine + "'");
- // make sure the successive output files get bigger!
- if (lastFile != null)
- Assert.assertTrue(Files.size(file.toPath()) > Files
- .size(lastFile.toPath()));
+ CommandLineOperations.Worker runner = CommandLineOperations
+ .getJalviewDesktopRunner(false, cmdLine, 1000);
+ long timeOut = 10000;
+ while (runner.isAlive() && timeOut > 0)
+ {
+ Thread.sleep(25);
+ timeOut -= 25;
+ }
}
+ verifyOrderedFileSet(cmdLines[0] + " vs " + cmdLines[1], filenames,
+ false);
} catch (Exception x)
{
Assert.fail("Unexpected exception during structureImageOutputTest",
}
}
- @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
+ @DataProvider(name = "compareHeadlessAndGUIOps")
+ public Object[][] compareHeadlessAndGUIOps()
+ {
+ return new Object[][] {
+ new Object[]
+ { new String[] { "--open examples/uniref50.fa "
+ + "--structure [seqid=FER1_SPIOL,tempfac=plddt,showssannotations,structureviewer=jmol]"
+ + "examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image="
+ + testfiles
+ + "test-al-pae-ss-gui.png --overwrite --gui --quit",
+ "--open examples/uniref50.fa "
+ + "--structure [seqid=FER1_SPIOL,tempfac=plddt,showssannotations,structureviewer=jmol]"
+ + "examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json --image="
+ + testfiles
+ + "test-al-pae-ss-nogui.png --overwrite --nogui"
+
+ }, new String[] { testfiles + "test-al-pae-ss-gui.png",
+ testfiles + "test-al-pae-ss-nogui.png", } } };
+ }
+
+ private static void verifyIncreasingSize(String cmdLine,
+ String[] filenames) throws Exception
+ {
+ verifyOrderedFileSet(cmdLine, filenames, true);
+ }
+
+ private static void verifyOrderedFileSet(String cmdLine,
+ String[] filenames, boolean increasingSize) throws Exception
+ {
+ File lastFile = null;
+ for (String filename : filenames)
+ {
+ File file = new File(filename);
+ Assert.assertTrue(file.exists(), "File '" + filename
+ + "' was not created by '" + cmdLine + "'");
+ Assert.assertTrue(file.isFile(), "File '" + filename
+ + "' is not a file from '" + cmdLine + "'");
+ Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
+ + "' has no content from '" + cmdLine + "'");
+ // make sure the successive output files get bigger!
+ if (lastFile != null)
+ {
+ waitForLastWrite(file, 25);
+
+ if (increasingSize)
+ {
+ Assert.assertTrue(
+ Files.size(file.toPath()) > Files.size(lastFile.toPath()),
+ "Expected " + file.toPath() + " to be larger than "
+ + lastFile.toPath());
+ }
+ else
+ {
+ Assert.assertEquals(Files.size(file.toPath()),
+ Files.size(lastFile.toPath()),
+ "New file " + file.toPath()
+ + " (actual size) not same as last file's size "
+ + lastFile.toString());
+ }
+ }
+ // remember it for next file
+ lastFile = file;
+ }
+
+ }
+
+ private static long waitForLastWrite(File file, int i) throws IOException
+ {
+ long lastSize, stableSize = Files.size(file.toPath());
+ // wait around until we are sure the file has been completely written.
+ do
+ {
+ lastSize = stableSize;
+ try
+ {
+ Thread.sleep(i);
+ } catch (Exception x)
+ {
+ }
+ stableSize = Files.size(file.toPath());
+ } while (stableSize != lastSize);
+ return stableSize;
+ }
+
+ @Test(
+ groups = "Functional",
+ dataProvider = "argfileOutputFiles",
+ singleThreaded = true)
+
public void argFilesGlobAndSubstitutionsTest(String cmdLine,
String[] filenames) throws IOException
{
+ "' has no content from '" + cmdLine + "'");
// make sure the successive output files get bigger!
if (lastFile != null)
+ {
Assert.assertTrue(Files.size(file.toPath()) > Files
.size(lastFile.toPath()));
+ System.out.println("this file: " + file + " +"
+ + Files.size(file.toPath()) + " greater than "
+ + Files.size(lastFile.toPath()));
+ }
+ // remember it for next file
+ lastFile = file;
}
} catch (Exception x)
{
{ testfiles + "/structureimage1.png",
testfiles + "/structureimage2.png",
testfiles + "/structureimage3.png" } },
+ { "--gui --nonews --nosplash --open examples/1gaq.txt --append ./examples/3W5V.pdb "
+ + "--structure examples/1gaq.txt --seqid \"1GAQ|A\" "
+ + "--structureimage " + testfiles
+ + "/1gaq.png --structure examples/3W5V.pdb "
+ + "--seqid \"3W5V|A\" --structureimage " + testfiles
+ + "/3w5v.png --overwrite",
+
+ new String[]
+ { testfiles + "/1gaq.png",
+ testfiles + "/3w5v.png" } },
+ { "--headless --noquit --open ./examples/1gaq.txt --append ./examples/3W5V.pdb "
+ + "--structure examples/1gaq.txt --seqid \"1GAQ|A\" "
+ + "--structureimage " + testfiles
+ + "/1gaq.png --structure examples/3W5V.pdb "
+ + "--seqid \"3W5V|A\" --structureimage " + testfiles
+ + "/3w5v.png --overwrite",
+
+ new String[]
+ { testfiles + "/1gaq.png", testfiles + "/3w5v.png" } }
+
/*
*/
//
public static boolean lookForSequenceName(String sequenceName)
{
- AlignFrame[] afs = Desktop.getAlignFrames();
+ AlignFrame[] afs = Desktop.getDesktopAlignFrames();
for (AlignFrame af : afs)
{
for (String name : af.getViewport().getAlignment().getSequenceNames())
};
}
+ @Test(
+ groups =
+ { "Functional", "testTask3" },
+ dataProvider = "structureImageAnnotationsOutputFiles",
+ singleThreaded = true)
+ public void structureImageAnnotationsOutputTest(String cmdLine,
+ String filename, int height) throws IOException
+ {
+ cleanupFiles(new String[] { filename });
+ String[] args = (cmdLine).split("\\s+");
+ callJalviewMain(args, true); // Create new instance of Jalview each time for
+ // linkedIds
+
+ BufferedImage img = ImageIO.read(new File(filename));
+ Assert.assertEquals(height, img.getHeight(), "Output image '" + filename
+ + "' is not in the expected height range, possibly because of the wrong number of annotations");
+
+ cleanupFiles(new String[] { filename });
+ tearDown();
+ }
+
+ @DataProvider(name = "structureImageAnnotationsOutputFiles")
+ public Object[][] structureImageAnnotationsOutputFiles()
+ {
+ String filename = "test/jalview/bin/argparser/testfiles/test_annotations.png";
+ return new Object[][] {
+ //
+ { "--headless --nonews --nosplash --overwrite --open=./examples/uniref50.fa "
+ + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ + "--seqid=FER1_SPIOL --structureviewer=jmol "
+ + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ + "--image=" + filename + " " + "--tempfac=plddt "
+ + "--noshowssannotations " + "--noshowannotations", //
+ filename, //
+ 252 }, //
+ { "--headless --nonews --nosplash --overwrite --open=./examples/uniref50.fa "
+ + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ + "--seqid=FER1_SPIOL --structureviewer=jmol "
+ + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ + "--image=" + filename + " " + "--tempfac=plddt "
+ + "--showssannotations " + "--noshowannotations", //
+ filename, //
+ 368 }, //
+ { "--headless --nonews --nosplash --overwrite --open=./examples/uniref50.fa "
+ + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ + "--seqid=FER1_SPIOL --structureviewer=jmol "
+ + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ + "--image=" + filename + " " + "--tempfac=plddt "
+ + "--noshowssannotations " + "--showannotations", //
+ filename, //
+ 524 }, //
+ { "--headless --nonews --nosplash --overwrite --open=./examples/uniref50.fa "
+ + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ + "--seqid=FER1_SPIOL --structureviewer=jmol "
+ + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ + "--image=" + filename + " " + "--tempfac=plddt "
+ + "--showssannotations " + "--showannotations", //
+ filename, //
+ 660 }, //
+ { "--gui --nonews --nosplash --overwrite --open=./examples/uniref50.fa "
+ + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ + "--seqid=FER1_SPIOL --structureviewer=jmol "
+ + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ + "--image=" + filename + " " + "--tempfac=plddt "
+ + "--noshowssannotations " + "--noshowannotations", //
+ filename, //
+ 252 }, //
+ { "--gui --nonews --nosplash --overwrite --open=./examples/uniref50.fa "
+ + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ + "--seqid=FER1_SPIOL --structureviewer=jmol "
+ + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ + "--image=" + filename + " " + "--tempfac=plddt "
+ + "--showssannotations " + "--noshowannotations", //
+ filename, //
+ 368 }, //
+ { "--gui --nonews --nosplash --overwrite --open=./examples/uniref50.fa "
+ + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ + "--seqid=FER1_SPIOL --structureviewer=jmol "
+ + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ + "--image=" + filename + " " + "--tempfac=plddt "
+ + "--noshowssannotations " + "--showannotations", //
+ filename, //
+ 524 }, //
+ { "--gui --nonews --nosplash --overwrite --open=./examples/uniref50.fa "
+ + "--structure=examples/AlphaFold/AF-P00221-F1-model_v4.pdb "
+ + "--seqid=FER1_SPIOL --structureviewer=jmol "
+ + "--paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ + "--image=" + filename + " " + "--tempfac=plddt "
+ + "--showssannotations " + "--showannotations", //
+ filename, //
+ 660 }, //
+ };
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff