JAL-629 sort files from java glob for predictability. reduce maxdepth of walkfiletree

[jalview.git] / test / jalview / bin / CommandsTest.java

diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index b37c6e3..f7805fe 100644 (file)
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.java
@@ -1,5 +1,8 @@
 package jalview.bin;
 
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
 import java.util.Date;
 import java.util.HashSet;
 import java.util.Set;
@@ -19,6 +22,12 @@ import jalview.util.ArrayUtils;
 @Test(singleThreaded = true)
 public class CommandsTest
 {
+  private static final String testfiles = "test/jalview/bin/argparser/testfiles";
+
+  private static final String png1 = testfiles + "/dir1/test1.png";
+
+  private static final String png2 = testfiles + "/dir2/test1.png";
+
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
@@ -48,6 +57,19 @@ public class CommandsTest
       Desktop.instance.closeAll_actionPerformed(null);
   }
 
+  /* --setprop currently disabled
+  @Test(groups = "Functional")
+  public void setpropsTest()
+  {
+    String MOSTLY_HARMLESS = "MOSTLY_HARMLESS";
+    String cmdLine = "--setprop=" + MOSTLY_HARMLESS + "=Earth";
+    String[] args = cmdLine.split("\\s+");
+    Jalview.main(args);
+    Assert.assertEquals(Cache.getDefault(MOSTLY_HARMLESS, "Magrathea"),
+            "Earth");
+  }
+  */
+
   @Test(groups = "Functional", dataProvider = "cmdLines")
   public void commandsOpenTest(String cmdLine, boolean cmdArgs,
           int numFrames, String[] sequences)
@@ -86,6 +108,28 @@ public class CommandsTest
             lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
   }
 
+  @Test(groups = "Functional")
+  public void argFilesGlobAndSubstitutionsTest() throws IOException
+  {
+    cleanupArgfilesImages();
+    String cmdLine = "--argfile=" + testfiles + "/dir*/argfile.txt";
+    String[] args = cmdLine.split("\\s+");
+    Jalview.main(args);
+    Commands cmds = Jalview.getInstance().getCommands();
+    File file1 = new File(png1);
+    File file2 = new File(png2);
+    Assert.assertTrue(file1.exists(),
+            "Did not make file " + png1 + " from argfile");
+    Assert.assertTrue(file2.exists(),
+            "Did not make file " + png2 + " from argfile");
+    long size1 = Files.size(file1.toPath());
+    long size2 = Files.size(file2.toPath());
+    Assert.assertTrue(file1.isFile() && size1 > 0);
+    Assert.assertTrue(file2.isFile() && size2 > 0);
+    Assert.assertTrue(size2 > size1); // png2 has three sequences, png1 has 2
+    cleanupArgfilesImages();
+  }
+
   @DataProvider(name = "cmdLines")
   public Object[][] cmdLines()
   {
@@ -104,16 +148,15 @@ public class CommandsTest
         { "--open=[new]examples/uniref50*.fa", true, 2, someUniref50Seqs },
         { "--opennew=examples/uniref50*.fa", true, 2, someUniref50Seqs },
         { "examples/uniref50.fa", true, 1, someUniref50Seqs },
-        { "examples/uniref50.fa test/jalview/bin/argparser/testfiles/test1.fa",
-            true, 2, ArrayUtils.concatArrays(someUniref50Seqs, t1) },
-        { "examples/uniref50.fa test/jalview/bin/argparser/testfiles/test1.fa",
-            true, 2, t1 },
-        { "--argfile=test/jalview/bin/argparser/testfiles/argfile0.txt",
-            true, 1, ArrayUtils.concatArrays(t1, t3) },
-        { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
-            true, 4, ArrayUtils.concatArrays(t1, t2, t3) },
-        { "--argfile=test/jalview/bin/argparser/testfiles/argfile.autocounter",
-            true, 3, ArrayUtils.concatArrays(t1, t2) } };
+        { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
+            ArrayUtils.concatArrays(someUniref50Seqs, t1) },
+        { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
+        { "--argfile=" + testfiles + "/argfile0.txt", true, 1,
+            ArrayUtils.concatArrays(t1, t3) },
+        { "--argfile=" + testfiles + "/argfile*.txt", true, 4,
+            ArrayUtils.concatArrays(t1, t2, t3) },
+        { "--argfile=" + testfiles + "/argfile.autocounter", true, 3,
+            ArrayUtils.concatArrays(t1, t2) } };
   }
 
   public static boolean lookForSequenceName(String sequenceName)
@@ -132,4 +175,18 @@ public class CommandsTest
     return false;
   }
 
+  public static void cleanupArgfilesImages()
+  {
+    File png1File = new File(png1);
+    File png2File = new File(png2);
+    if (png1File.exists())
+    {
+      png1File.delete();
+    }
+    if (png2File.exists())
+    {
+      png2File.delete();
+    }
+  }
+
 }