JAL-629 extensive tests for ArgParser features

diff --git a/test/jalview/bin/ArgParserTest.java b/test/jalview/bin/ArgParserTest.java
deleted file mode 100644 (file)
index e93f36f..0000000
--- a/test/jalview/bin/ArgParserTest.java
+++ /dev/null
@@ -1,133 +0,0 @@
-package jalview.bin;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.List;
-import java.util.Properties;
-
-import org.testng.Assert;
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.DataProvider;
-import org.testng.annotations.Test;
-
-import jalview.bin.argparser.Arg;
-import jalview.bin.argparser.ArgParser;
-import jalview.bin.argparser.BootstrapArgs;
-
-@Test(singleThreaded = true)
-public class ArgParserTest
-{
-  @AfterClass(alwaysRun = true)
-  public static void resetProps()
-  {
-    Cache.loadProperties("test/jalview/testProps.jvprops");
-  }
-
-  @Test(groups = "Functional", dataProvider = "argLines")
-  public void parseArgsAndSubValsTest(String commandLineArgs, Arg a,
-          String other)
-  {
-    String[] args = commandLineArgs.split("\\s*");
-    ArgParser argparser = new ArgParser(args);
-  }
-
-  @Test(groups = "Functional", dataProvider = "argLines")
-  public void bootstrapArgsTest(String commandLineArgs, Arg a, String other)
-  {
-    String[] args = commandLineArgs.split("\\s+");
-    BootstrapArgs b = BootstrapArgs.getBootstrapArgs(args);
-
-    Assert.assertTrue(b.contains(a));
-    if (a == Arg.PROPS)
-    {
-      Properties bP = Cache.bootstrapProperties(b.get(Arg.PROPS));
-      Assert.assertTrue(other.equals(bP.get(Cache.BOOTSTRAP_TEST)));
-      Assert.assertFalse(bP.contains("NOT" + Cache.BOOTSTRAP_TEST));
-    }
-    else if (a == Arg.ARGFILE)
-    {
-      List<String> filenames = b.getList(a);
-      boolean found = false;
-      for (String s : filenames)
-      {
-        File f = new File(s);
-        File fo = new File(other);
-        try
-        {
-          if (fo.getCanonicalPath().equals(f.getCanonicalPath()))
-          {
-            found = true;
-            break;
-          }
-        } catch (IOException e)
-        {
-        }
-      }
-      Assert.assertTrue(found,
-              "File '" + other + "' not found in shell expanded glob '"
-                      + commandLineArgs + "'");
-    }
-
-  }
-
-  @Test(groups = "Functional", dataProvider = "argFiles")
-  public void argFilesTest(String commandLineArgs, Arg a, String other)
-  {
-    String[] args = commandLineArgs.split("\\s+");
-    BootstrapArgs b = BootstrapArgs.getBootstrapArgs(args);
-
-    Assert.assertTrue(b.contains(a));
-    Assert.assertFalse(b.contains(Arg.OPEN));
-    if (a == Arg.PROPS)
-    {
-      Properties bP = Cache.bootstrapProperties(b.get(Arg.PROPS));
-      Assert.assertTrue("true".equals(bP.get(Cache.BOOTSTRAP_TEST)));
-    }
-  }
-
-  @DataProvider(name = "argLinesNotworking")
-  public Object[][] argLinesTest()
-  {
-    return new Object[][] {
-        // can't use this one yet as it doesn't get shell glob expanded by the
-        // test
-        { "--argfile test/jalview/bin/argparser/argfile*.txt", Arg.ARGFILE,
-            "test/jalview/bin/argparser/argfile0.txt" }, };
-  }
-
-  @DataProvider(name = "argLines")
-  public Object[][] argLines()
-  {
-    return new Object[][] {
-        { "--debug --open=test/jalview/bin/argparser/test1.fa", Arg.DEBUG,
-            null },
-        { "--open=test/jalview/bin/argparser/test1.fa --headless",
-            Arg.HEADLESS, null },
-        { "--open=test/jalview/bin/argparser/test1.fa --props=test/jalview/bin/argparser/testProps.jvprops",
-            Arg.PROPS, "true" },
-        { "--argfile test/jalview/bin/argparser/argfile0.txt", Arg.ARGFILE,
-            "test/jalview/bin/argparser/argfile0.txt" },
-        // these next three are what a shell glob expansion would look like
-        { "--argfile test/jalview/bin/argparser/argfile0.txt test/jalview/bin/argparser/argfile1.txt test/jalview/bin/argparser/argfile2.txt",
-            Arg.ARGFILE, "test/jalview/bin/argparser/argfile0.txt" },
-        { "--argfile test/jalview/bin/argparser/argfile0.txt test/jalview/bin/argparser/argfile1.txt test/jalview/bin/argparser/argfile2.txt",
-            Arg.ARGFILE, "test/jalview/bin/argparser/argfile1.txt" },
-        { "--argfile test/jalview/bin/argparser/argfile0.txt test/jalview/bin/argparser/argfile1.txt test/jalview/bin/argparser/argfile2.txt",
-            Arg.ARGFILE, "test/jalview/bin/argparser/argfile2.txt" },
-        { "--argfile=test/jalview/bin/argparser/argfile*.txt", Arg.ARGFILE,
-            "test/jalview/bin/argparser/argfile0.txt" },
-        { "--argfile=test/jalview/bin/argparser/argfile*.txt", Arg.ARGFILE,
-            "test/jalview/bin/argparser/argfile1.txt" },
-        { "--argfile=test/jalview/bin/argparser/argfile*.txt", Arg.ARGFILE,
-            "test/jalview/bin/argparser/argfile2.txt" } };
-
-  }
-
-  @DataProvider(name = "argFiles")
-  public Object[][] argFiles()
-  {
-    return new Object[][] { {
-        "--argfile=test/jalview/bin/argparser/argfile0.txt --open=shouldntbeabootstrap",
-        Arg.ARGFILE, "test/jalview/bin/argfiles/test1.fa" } };
-  }
-}

diff --git a/test/jalview/bin/ArgsParserTest.java b/test/jalview/bin/ArgsParserTest.java
index a163a49..f36b45a 100644 (file)
--- a/test/jalview/bin/ArgsParserTest.java
+++ b/test/jalview/bin/ArgsParserTest.java
@@ -18,7 +18,7 @@
  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
-package jalview.bin.argparser;
+package jalview.bin;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;

diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index 41588e6..204714f 100644 (file)
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.java
@@ -85,8 +85,18 @@ public class CommandsTest
   @DataProvider(name = "cmdLines")
   public Object[][] cmdLines()
   {
-    return new Object[][] { { "--open=examples/uniref50.fa", "FER1_SPIOL" },
-        { "--argfile=test/jalview/bin/argparser/argfile0.txt", null } };
+    return new Object[][] {
+        { "--open=examples/uniref50.fa", "FER1_SPIOL" },
+        { "--argfile=test/jalview/bin/argparser/testfiles/argfile0.txt",
+            null } };
+  }
+
+  @DataProvider(name = "openingAlignments")
+  public Object[][] openingAlignments()
+  {
+    return new Object[][] {
+        { "--open=examples/uniref50.fa", 1 },
+        { "--argfile=test/jalview/bin/argparser/testfiles/argfile0.txt", } };
   }
 
 }

diff --git a/test/jalview/bin/argparser/ArgParserTest.java b/test/jalview/bin/argparser/ArgParserTest.java
new file mode 100644 (file)
index 0000000..47d9e24
--- /dev/null
+++ b/test/jalview/bin/argparser/ArgParserTest.java
@@ -0,0 +1,229 @@
+package jalview.bin.argparser;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+import java.util.Properties;
+
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
+
+@Test(singleThreaded = true)
+public class ArgParserTest
+{
+  @AfterClass(alwaysRun = true)
+  public static void resetProps()
+  {
+    Cache.loadProperties("test/jalview/testProps.jvprops");
+  }
+
+  @Test(groups = "Functional", dataProvider = "argLines")
+  public void parseArgsTest(String commandLineArgs, Arg a, String other)
+  {
+    String[] args = commandLineArgs.split("\\s+");
+    ArgParser argparser = new ArgParser(args);
+  }
+
+  @Test(groups = "Functional", dataProvider = "argSubValsAndLinkedIds")
+  public void parseSubValsAndLinkedIdsTest(String commandLineArgs,
+          String linkedId, Arg a, String subvalKey, String value,
+          boolean trueOrFalse)
+  {
+    String[] args = commandLineArgs.split("\\s+");
+    ArgParser argparser = new ArgParser(args);
+    ArgValuesMap avm = argparser.linkedArgs(linkedId);
+    ArgValue av = avm.getArgValue(a);
+    SubVals sv = av.getSubVals();
+    String testString = null;
+    if (subvalKey.equals("GETINDEX"))
+    {
+      testString = String.valueOf(sv.getIndex());
+    }
+    else
+    {
+      testString = sv.get(subvalKey);
+    }
+    if (trueOrFalse)
+    {
+      Assert.assertEquals(testString, value);
+    }
+    else
+    {
+      Assert.assertNotEquals(testString, value);
+    }
+  }
+
+  @Test(
+    groups = "Functional",
+    dataProvider = "argAutoIndexAndSubstitutions")
+  public void parseAutoIndexAndSubstitutionsTest(String commandLineArgs,
+          String linkedId, Arg a, String filename)
+  {
+    // { "--open=filename0 --increment --open=filename1", "JALVIEW:1", Arg.OPEN,
+    // "filename1" },
+    String[] args = commandLineArgs.split("\\s+");
+    ArgParser argparser = new ArgParser(args);
+    ArgValuesMap avm = argparser.linkedArgs(linkedId);
+    ArgValue av = avm.getArgValue(a);
+    Assert.assertEquals(av.getValue(), filename);
+  }
+
+  @Test(groups = "Functional", dataProvider = "argLines")
+  public void bootstrapArgsTest(String commandLineArgs, Arg a, String other)
+  {
+    String[] args = commandLineArgs.split("\\s+");
+    BootstrapArgs b = BootstrapArgs.getBootstrapArgs(args);
+
+    Assert.assertTrue(b.contains(a));
+    if (a == Arg.PROPS)
+    {
+      Properties bP = Cache.bootstrapProperties(b.get(Arg.PROPS));
+      Assert.assertTrue(other.equals(bP.get(Cache.BOOTSTRAP_TEST)));
+      Assert.assertFalse(bP.contains("NOT" + Cache.BOOTSTRAP_TEST));
+    }
+    else if (a == Arg.ARGFILE)
+    {
+      List<String> filenames = b.getList(a);
+      boolean found = false;
+      for (String s : filenames)
+      {
+        File f = new File(s);
+        File fo = new File(other);
+        try
+        {
+          if (fo.getCanonicalPath().equals(f.getCanonicalPath()))
+          {
+            found = true;
+            break;
+          }
+        } catch (IOException e)
+        {
+        }
+      }
+      Assert.assertTrue(found,
+              "File '" + other + "' not found in shell expanded glob '"
+                      + commandLineArgs + "'");
+    }
+  }
+
+  @Test(groups = "Functional", dataProvider = "argFiles")
+  public void argFilesTest(String commandLineArgs, Arg a, String other)
+  {
+    String[] args = commandLineArgs.split("\\s+");
+    BootstrapArgs b = BootstrapArgs.getBootstrapArgs(args);
+
+    Assert.assertTrue(b.contains(a));
+    Assert.assertFalse(b.contains(Arg.OPEN));
+    if (a == Arg.PROPS)
+    {
+      Properties bP = Cache.bootstrapProperties(b.get(Arg.PROPS));
+      Assert.assertTrue("true".equals(bP.get(Cache.BOOTSTRAP_TEST)));
+    }
+  }
+
+  @DataProvider(name = "argLinesNotworking")
+  public Object[][] argLinesTest()
+  {
+    return new Object[][] {
+        // can't use this one yet as it doesn't get shell glob expanded by the
+        // test
+        { "--argfile test/jalview/bin/argparser/testfiles/argfile*.txt",
+            Arg.ARGFILE,
+            "test/jalview/bin/argparser/testfiles/argfile0.txt" }, };
+  }
+
+  @DataProvider(name = "argLines")
+  public Object[][] argLines()
+  {
+    return new Object[][] {
+        { "--debug --open=test/jalview/bin/argparser/testfiles/test1.fa",
+            Arg.DEBUG, null },
+        { "--open=test/jalview/bin/argparser/testfiles/test1.fa --headless",
+            Arg.HEADLESS, null },
+        { "--open=test/jalview/bin/argparser/testfiles/test1.fa --props=test/jalview/bin/argparser/testfiles/testProps.jvprops",
+            Arg.PROPS, "true" },
+        { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt",
+            Arg.ARGFILE,
+            "test/jalview/bin/argparser/testfiles/argfile0.txt" },
+        // these next three are what a shell glob expansion would look like
+        { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
+            Arg.ARGFILE,
+            "test/jalview/bin/argparser/testfiles/argfile0.txt" },
+        { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
+            Arg.ARGFILE,
+            "test/jalview/bin/argparser/testfiles/argfile1.txt" },
+        { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt test/jalview/bin/argparser/testfiles/argfile1.txt test/jalview/bin/argparser/testfiles/argfile2.txt",
+            Arg.ARGFILE,
+            "test/jalview/bin/argparser/testfiles/argfile2.txt" },
+        { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
+            Arg.ARGFILE,
+            "test/jalview/bin/argparser/testfiles/argfile0.txt" },
+        { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
+            Arg.ARGFILE,
+            "test/jalview/bin/argparser/testfiles/argfile1.txt" },
+        { "--argfile=test/jalview/bin/argparser/testfiles/argfile*.txt",
+            Arg.ARGFILE,
+            "test/jalview/bin/argparser/testfiles/argfile2.txt" } };
+  }
+
+  @DataProvider(name = "argSubValsAndLinkedIds")
+  public Object[][] argSubValsAndLinkedIds()
+  {
+    return new Object[][] { {
+        "--debug --open=[hi]test/jalview/bin/argparser/testfiles/test1.fa",
+        "JALVIEW:0", Arg.OPEN, "hi", "true", true },
+        { "--open[linkedId1]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+            "linkedId1", Arg.OPEN, "new", "true", true },
+        { "--open[linkedId2]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+            "linkedId2", Arg.OPEN, "hello", "world", true },
+        { "--open[linkedId3]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+            "linkedId3", Arg.OPEN, "GETINDEX", "1", true },
+        { "--open[linkedId4]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --open[linkedId5]=[notnew;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+            "linkedId5", Arg.OPEN, "new", "true", false },
+        { "--open[linkedId5]=[new;hello=worlddomination;1]test/jalview/bin/argparser/testfiles/test1.fa --open[linkedId2]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+            "linkedId5", Arg.OPEN, "hello", "world", false },
+        { "--open[linkedId6]=[new;hello=world;0]test/jalview/bin/argparser/testfiles/test1.fa --open[linkedId7]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+            "linkedId7", Arg.OPEN, "GETINDEX", "0", false }, };
+  }
+
+  @DataProvider(name = "argAutoIndexAndSubstitutions")
+  public Object[][] argAutoIndexAndSubstitutions()
+  {
+    return new Object[][] { { "--open=filename0 --open=filename1",
+        "JALVIEW:0", Arg.OPEN, "filename0" },
+        { "--open=filename0 --increment --open=filename1", "JALVIEW:1",
+            Arg.OPEN, "filename1" },
+        { "--open=filename0 --increment --increment --open=filename2",
+            "JALVIEW:0", Arg.OPEN, "filename0" },
+        { "--open=filename0 --increment --increment --open=filename2",
+            "JALVIEW:2", Arg.OPEN, "filename2" },
+        { "--open[linkA-{n}]=filenameA0 --open[linkA-{++n}]=filenameA1",
+            "linkA-0", Arg.OPEN, "filenameA0" },
+        { "--open[linkB-{n}]=filenameB0 --open[linkB-{++n}]=filenameB1",
+            "linkB-1", Arg.OPEN, "filenameB1" },
+        { "--open[linkC-{n}]=filenameC0 --image[linkC-{n}]=outputC{n}.txt",
+            "linkC-0", Arg.IMAGE, "outputC{n}.txt" },
+        { "--open[linkD-{n}]=filenameD0 --substitutions --image[linkD-{n}]=outputD{n}.txt",
+            "linkD-0", Arg.IMAGE, "outputD0.txt" },
+        { "--open[linkE-{n}]=filenameE0 --substitutions --image[linkE-{n}]=output-E{n}.txt --nil[{++n}] --image[linkE-{n}]=outputE{n}.txt",
+            "linkE-0", Arg.IMAGE, "output-E0.txt" },
+        { "--open[linkF-{n}]=filenameF0 --substitutions --image[linkF-{n}]=output-F{n}.txt --nil[{++n}] --image[linkF-{n}]=outputF{n}.txt",
+            "linkF-1", Arg.IMAGE, "outputF1.txt" },
+        { "--open[linkG-{n}]=filenameG0 --substitutions --image[linkG-{n}]=output-G{n}.txt --nil[{++n}] --nosubstitutions --image[linkG-{n}]=outputG{n}.txt",
+            "linkG-1", Arg.IMAGE, "outputG{n}.txt" },
+        { "--open[linkH-{n}]=filenameH0 --substitutions --image[linkH-{n}]=output-H{n}.txt --nil[{++n}] --nosubstitutions --image[linkH-{n}]=outputH{n}.txt",
+            "linkH-0", Arg.IMAGE, "output-H0.txt" }, };
+  }
+
+  @DataProvider(name = "argFiles")
+  public Object[][] argFiles()
+  {
+    return new Object[][] { {
+        "--argfile=test/jalview/bin/argparser/testfiles/argfile0.txt --open=shouldntbeabootstrap",
+        Arg.ARGFILE, "test/jalview/bin/argfiles/testfiles/test1.fa" } };
+  }
+}

diff --git a/test/jalview/bin/argparser/argfile.autocounter b/test/jalview/bin/argparser/testfiles/argfile.autocounter
similarity index 100%
rename from test/jalview/bin/argparser/argfile.autocounter
rename to test/jalview/bin/argparser/testfiles/argfile.autocounter

diff --git a/test/jalview/bin/argparser/argfile0.txt b/test/jalview/bin/argparser/testfiles/argfile0.txt
similarity index 100%
rename from test/jalview/bin/argparser/argfile0.txt
rename to test/jalview/bin/argparser/testfiles/argfile0.txt

diff --git a/test/jalview/bin/argparser/argfile1.txt b/test/jalview/bin/argparser/testfiles/argfile1.txt
similarity index 100%
rename from test/jalview/bin/argparser/argfile1.txt
rename to test/jalview/bin/argparser/testfiles/argfile1.txt

diff --git a/test/jalview/bin/argparser/argfile2.txt b/test/jalview/bin/argparser/testfiles/argfile2.txt
similarity index 100%
rename from test/jalview/bin/argparser/argfile2.txt
rename to test/jalview/bin/argparser/testfiles/argfile2.txt

diff --git a/test/jalview/bin/argparser/test1.fa b/test/jalview/bin/argparser/testfiles/test1.fa
similarity index 100%
rename from test/jalview/bin/argparser/test1.fa
rename to test/jalview/bin/argparser/testfiles/test1.fa

diff --git a/test/jalview/bin/argparser/test2.fa b/test/jalview/bin/argparser/testfiles/test2.fa
similarity index 100%
rename from test/jalview/bin/argparser/test2.fa
rename to test/jalview/bin/argparser/testfiles/test2.fa

diff --git a/test/jalview/bin/argparser/test3.fa b/test/jalview/bin/argparser/testfiles/test3.fa
similarity index 100%
rename from test/jalview/bin/argparser/test3.fa
rename to test/jalview/bin/argparser/testfiles/test3.fa

diff --git a/test/jalview/bin/argparser/testProps.jvprops b/test/jalview/bin/argparser/testfiles/testProps.jvprops
similarity index 100%
rename from test/jalview/bin/argparser/testProps.jvprops
rename to test/jalview/bin/argparser/testfiles/testProps.jvprops