X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandLineOperations.java;h=9b94be9246aaac25655c17f9ab517783f558c3ea;hb=d5e758fa924437e30dc65b80a46cafcf4691da2f;hp=19bc165548664932ac3385253b0d2aa1086753d1;hpb=6bb79487bb8690d2880771df44d509fc441ece6c;p=jalview.git

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 19bc165..9b94be9 100644
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -1,79 +1,315 @@
+/*
+ * 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 static org.junit.Assert.*;
+import jalview.gui.JvOptionPane;
 
 import java.io.BufferedReader;
 import java.io.File;
+import java.io.IOException;
 import java.io.InputStreamReader;
+import java.util.ArrayList;
 
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.FileAssert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
 
 public class CommandLineOperations
 {
 
-  @BeforeClass
-  public static void setUpBeforeClass() throws Exception
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
   {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  @AfterClass
-  public static void tearDownAfterClass() throws Exception
+  private static final int TEST_TIMEOUT = 4500; // Note longer timeout needed on
+                                                // full test run than on
+                                                // individual tests
+
+  private static final int SETUP_TIMEOUT = 9000;
+
+  private static final int MINFILESIZE_SMALL = 2096;
+
+  private static final int MINFILESIZE_BIG = 4096;
+
+  private ArrayList<String> successfulCMDs = new ArrayList<>();
+
+  /***
+   * from
+   * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
+   * -using-javas-runtime-exec
+   * 
+   * @author jimp
+   * 
+   */
+  private static class Worker extends Thread
   {
+    private final Process process;
+
+    private BufferedReader outputReader;
+
+    private BufferedReader errorReader;
+
+    private Integer exit;
+
+    private Worker(Process process)
+    {
+      this.process = process;
+    }
+
+    @Override
+    public void run()
+    {
+      try
+      {
+        exit = process.waitFor();
+      } catch (InterruptedException ignore)
+      {
+        return;
+      }
+    }
+
+    public BufferedReader getOutputReader()
+    {
+      return outputReader;
+    }
+
+    public void setOutputReader(BufferedReader outputReader)
+    {
+      this.outputReader = outputReader;
+    }
+
+    public BufferedReader getErrorReader()
+    {
+      return errorReader;
+    }
+
+    public void setErrorReader(BufferedReader errorReader)
+    {
+      this.errorReader = errorReader;
+    }
   }
-/***
- * from http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when-using-javas-runtime-exec
- * @author jimp
- *
- */
-private static class Worker extends Thread {
-  private final Process process;
-  private Integer exit;
-  private Worker(Process process) {
-    this.process = process;
-  }
-  public void run() {
-    try { 
-      exit = process.waitFor();
-    } catch (InterruptedException ignore) {
-      return;
+
+  private Worker jalviewDesktopRunner(boolean withAwt, String cmd,
+          int timeout)
+  {
+    String cp_sep = ":";
+    if (System.getProperty("os.name").indexOf("Windows") >= 0)
+    {
+      cp_sep = ";";
+    }
+    String _cmd = "java "
+            + (withAwt ? "-Djava.awt.headless=true" : "")
+            + " -classpath \"./lib/*" + cp_sep
+            + "./classes\" jalview.bin.Jalview ";
+    System.out.println("CMD [" + cmd + "]");
+    Process ls2_proc = null;
+    Worker worker = null;
+    try
+    {
+      ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
+    } catch (IOException e1)
+    {
+      e1.printStackTrace();
+    }
+    if (ls2_proc != null)
+    {
+      BufferedReader outputReader = new BufferedReader(
+              new InputStreamReader(ls2_proc.getInputStream()));
+      BufferedReader errorReader = new BufferedReader(
+              new InputStreamReader(ls2_proc.getErrorStream()));
+      worker = new Worker(ls2_proc);
+      worker.start();
+      try
+      {
+        worker.join(timeout);
+      } catch (InterruptedException e)
+      {
+        // e.printStackTrace();
+      }
+      worker.setOutputReader(outputReader);
+      worker.setErrorReader(errorReader);
     }
+    return worker;
   }
-}
-  @Test
-  public void testHeadlessModeEPS() throws Exception
+
+  @BeforeTest(alwaysRun = true)
+  public void initialize()
   {
-    String jalview_input = "examples/uniref50.fa";
-    String jalview_output = "test_uniref50_out.eps";
-    String cmd = "java -Djava.awt.headless=true -Djava.ext.dirs=./lib -classpath ./classes jalview.bin.Jalview -nodisplay -open "+ jalview_input + " -eps " + jalview_output;
-
-    System.out.println("###############Jalview CMD: " + cmd);
-    Process ls2_proc = Runtime.getRuntime().exec(cmd);
-    BufferedReader outputReader = new BufferedReader(new InputStreamReader(ls2_proc.getInputStream()));
-        
-    BufferedReader errorReader = new BufferedReader(new InputStreamReader(ls2_proc.getErrorStream()));
-    Worker worker = new Worker(ls2_proc);
-    worker.start();
-    worker.join(9000);
-    System.out.println("Output:  ");
-    String ln=null;
-    while ((ln=outputReader.readLine())!=null) {
+    new CommandLineOperations();
+  }
+
+  @BeforeTest(alwaysRun = true)
+  public void setUpForHeadlessCommandLineInputOperations()
+          throws IOException
+  {
+    String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo "
+            + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com "
+            + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
+    Worker worker = jalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
+    String ln = null;
+    while ((ln = worker.getOutputReader().readLine()) != null)
+    {
       System.out.println(ln);
+      successfulCMDs.add(ln);
     }
-    
-    System.out.println("Error:  " );
-    while ((ln=errorReader.readLine())!=null) {
+  }
+
+  @BeforeTest(alwaysRun = true)
+  public void setUpForCommandLineInputOperations() throws IOException
+  {
+    String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
+    Worker worker = jalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
+    String ln = null;
+    int count = 0;
+    while ((ln = worker.getErrorReader().readLine()) != null)
+    {
       System.out.println(ln);
+      successfulCMDs.add(ln);
+      if (++count > 5)
+      {
+        break;
+      }
     }
-    assertTrue("Didn't create an output EPS file.", new File("test_uniref50_out.eps").exists());
-    assertTrue("Didn't create an EPS file with any content", new File("test_uniref50_out.eps").length()>4096);
-    if (worker.exit == null){
+    if (worker != null && worker.exit == null)
+    {
       worker.interrupt();
       Thread.currentThread().interrupt();
-      ls2_proc.destroy();
-      fail("Jalview did not exit after EPS generation (try running test again to verify - timeout at 9000ms).");
-}
+      worker.process.destroy();
+    }
+  }
+
+  @Test(groups = { "Functional" }, dataProvider = "allInputOpearationsData")
+  public void testAllInputOperations(String expectedString,
+          String failureMsg)
+  {
+    Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
   }
 
+  @Test(
+    groups = { "Functional" },
+    dataProvider = "headlessModeOutputOperationsData")
+  public void testHeadlessModeOutputOperations(String harg, String type,
+          String fileName, boolean withAWT, int expectedMinFileSize,
+          int timeout)
+  {
+    String cmd = harg + type + " " + fileName;
+    // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
+    File file = new File(fileName);
+    Worker worker = jalviewDesktopRunner(withAWT, cmd, timeout);
+
+    FileAssert.assertFile(file, "Didn't create an output" + type
+            + " file.[" + harg + "]");
+    FileAssert.assertMinLength(new File(fileName), expectedMinFileSize);
+    if (worker != null && worker.exit == null)
+    {
+      worker.interrupt();
+      Thread.currentThread().interrupt();
+      worker.process.destroy();
+      Assert.fail("Jalview did not exit after "
+              + type
+              + " generation (try running test again to verify - timeout at "
+              + SETUP_TIMEOUT + "ms). ["
+              + harg + "]");
+    }
+    new File(fileName).delete();
+  }
+
+  @DataProvider(name = "allInputOpearationsData")
+  public Object[][] getHeadlessModeInputParams()
+  {
+    return new Object[][] {
+        // headless mode input operations
+        { "CMD [-color zappo] executed successfully!",
+            "Failed command : -color zappo" },
+        { "CMD [-props FILE] executed successfully!",
+            "Failed command : -props File" },
+        { "CMD [-sortbytree] executed successfully!",
+            "Failed command : -sortbytree" },
+        {
+            "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
+            "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
+        { "CMD [-open examples/uniref50.fa] executed successfully!",
+            "Failed command : -open examples/uniref50.fa" },
+        { "CMD [-nosortbytree] executed successfully!",
+            "Failed command : -nosortbytree" },
+        { "CMD [-dasserver nickname=www.test.com] executed successfully!",
+            "Failed command : -dasserver nickname=www.test.com" },
+        {
+            "CMD [-features examples/testdata/plantfdx.features]  executed successfully!",
+            "Failed command : -features examples/testdata/plantfdx.features" },
+        {
+            "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
+            "Failed command : -annotations examples/testdata/plantfdx.annotations" },
+        {
+            "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
+            "Failed command : -tree examples/testdata/uniref50_test_tree" },
+        // non headless mode input operations
+        { "CMD [-nousagestats] executed successfully!",
+            "Failed command : -nousagestats" },
+        { "CMD [-noquestionnaire] executed successfully!",
+            "Failed command : -noquestionnaire nickname=www.test.com" } };
+
+  }
+
+  @DataProvider(name = "headlessModeOutputOperationsData")
+  public static Object[][] getHeadlessModeOutputParams()
+  {
+    return new Object[][] {
+        { "nodisplay -open examples/uniref50.fa", " -eps",
+            "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
+        { "nodisplay -open examples/uniref50.fa", " -eps",
+            "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
+        { "nogui -open examples/uniref50.fa", " -eps",
+            "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
+        { "nogui -open examples/uniref50.fa", " -eps",
+            "test_uniref50_out.eps", false, MINFILESIZE_BIG, TEST_TIMEOUT },
+        { "headless -open examples/uniref50.fa", " -eps",
+            "test_uniref50_out.eps", true, MINFILESIZE_BIG, TEST_TIMEOUT },
+        { "headless -open examples/uniref50.fa", " -svg",
+            "test_uniref50_out.svg", false, MINFILESIZE_BIG, TEST_TIMEOUT },
+        { "headless -open examples/uniref50.fa", " -png",
+            "test_uniref50_out.png", true, MINFILESIZE_BIG, TEST_TIMEOUT },
+        { "headless -open examples/uniref50.fa", " -html",
+            "test_uniref50_out.html", true, MINFILESIZE_BIG, TEST_TIMEOUT },
+        { "headless -open examples/uniref50.fa", " -fasta",
+            "test_uniref50_out.mfa", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
+        { "headless -open examples/uniref50.fa", " -clustal",
+            "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
+        { "headless -open examples/uniref50.fa", " -msf",
+            "test_uniref50_out.msf", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
+        { "headless -open examples/uniref50.fa", " -pileup",
+            "test_uniref50_out.aln", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
+        { "headless -open examples/uniref50.fa", " -pir",
+            "test_uniref50_out.pir", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
+        { "headless -open examples/uniref50.fa", " -pfam",
+            "test_uniref50_out.pfam", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
+        { "headless -open examples/uniref50.fa", " -blc",
+            "test_uniref50_out.blc", true, MINFILESIZE_SMALL, TEST_TIMEOUT },
+        { "headless -open examples/uniref50.fa", " -jalview",
+            "test_uniref50_out.jvp", true, MINFILESIZE_SMALL, TEST_TIMEOUT }, };
+  }
 }