JAL-629 --initsubstitutions as a bootstrap arg, new tests

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 0870ecb..d0e76f2 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -432,12 +432,14 @@ public class Jalview
     // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
     if (bootstrapArgs.contains(Arg.ARGFILE))
     {
-      argparser = ArgParser
-              .parseArgFiles(bootstrapArgs.getList(Arg.ARGFILE));
+      argparser = ArgParser.parseArgFiles(
+              bootstrapArgs.getList(Arg.ARGFILE),
+              bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS));
     }
     else
     {
-      argparser = new ArgParser(args);
+      argparser = new ArgParser(args,
+              bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS));
     }
 
     if (!Platform.isJS())

diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index e658434..8207996 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -14,7 +14,7 @@ public enum Arg
   SSANNOTATION, NOTEMPFAC, TEMPFAC, TEMPFAC_LABEL, TEMPFAC_DESC,
   TEMPFAC_SHADING, TITLE, PAEMATRIX, WRAP, NOSTRUCTURE, STRUCTURE, IMAGE,
   QUIT, CLOSE, DEBUG("d"), QUIET("q"), ARGFILE, INCREMENT, NPP("n++"),
-  SUBSTITUTIONS, NIL, SPLASH, SETARGFILE, UNSETARGFILE;
+  SUBSTITUTIONS, INITSUBSTITUTIONS, NIL, SPLASH, SETARGFILE, UNSETARGFILE;
 
   protected static enum Opt
   {
@@ -86,6 +86,7 @@ public enum Arg
     INCREMENT.setOptions(Opt.UNARY, Opt.MULTI, Opt.NOACTION);
     NPP.setOptions(Opt.UNARY, Opt.MULTI, Opt.NOACTION);
     SUBSTITUTIONS.setOptions(Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION);
+    INITSUBSTITUTIONS.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP, Opt.NOACTION);
     NIL.setOptions(Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.NOACTION);
     SETARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
     UNSETARGFILE.setOptions(Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index c2568bb..7d4f187 100644 (file)
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -125,21 +125,27 @@ public class ArgParser
 
   public ArgParser(String[] args)
   {
+    this(args, false);
+  }
+
+  public ArgParser(String[] args, boolean initsubstitutions)
+  {
     // Make a mutable new ArrayList so that shell globbing parser works.
     // (When shell file globbing is used, there are a sequence of non-Arg
     // arguments (which are the expanded globbed filenames) that need to be
     // consumed by the --open/--argfile/etc Arg which is most easily done by
     // removing these filenames from the list one at a time. This can't be done
     // with an ArrayList made with only Arrays.asList(String[] args). )
-    this(new ArrayList<>(Arrays.asList(args)));
+    this(new ArrayList<>(Arrays.asList(args)), initsubstitutions);
   }
 
-  public ArgParser(List<String> args)
+  public ArgParser(List<String> args, boolean initsubstitutions)
   {
-    this(args, false);
+    this(args, initsubstitutions, false);
   }
 
-  public ArgParser(List<String> args, boolean allowPrivate)
+  public ArgParser(List<String> args, boolean initsubstitutions,
+          boolean allowPrivate)
   {
     // do nothing if there are no "--" args and some "-" args
     boolean d = false;
@@ -159,14 +165,16 @@ public class ArgParser
     if (d && !dd)
     {
       // leave it to the old style -- parse an empty list
-      parse(new ArrayList<String>(), allowPrivate);
+      parse(new ArrayList<String>(), false, false);
       return;
     }
-    parse(args, allowPrivate);
+    parse(args, initsubstitutions, allowPrivate);
   }
 
-  private void parse(List<String> args, boolean allowPrivate)
+  private void parse(List<String> args, boolean initsubstitutions,
+          boolean allowPrivate)
   {
+    this.substitutions = initsubstitutions;
     int argIndex = 0;
     boolean openEachInitialFilenames = true;
     for (int i = 0; i < args.size(); i++)
@@ -628,7 +636,8 @@ public class ArgParser
     return new SubVals(item);
   }
 
-  public static ArgParser parseArgFiles(List<String> argFilenameGlobs)
+  public static ArgParser parseArgFiles(List<String> argFilenameGlobs,
+          boolean initsubstitutions)
   {
     List<File> argFiles = new ArrayList<>();
 
@@ -638,10 +647,11 @@ public class ArgParser
       argFiles.addAll(FileUtils.getFilesFromGlob(pattern));
     }
 
-    return parseArgFileList(argFiles);
+    return parseArgFileList(argFiles, initsubstitutions);
   }
 
-  public static ArgParser parseArgFileList(List<File> argFiles)
+  public static ArgParser parseArgFileList(List<File> argFiles,
+          boolean initsubstitutions)
   {
     List<String> argsList = new ArrayList<>();
     for (File argFile : argFiles)
@@ -670,9 +680,9 @@ public class ArgParser
         Jalview.exit(message, 3);
       }
     }
-    // Second param "true" uses Opt.PRIVATE args --setargile=argfile and
+    // Third param "true" uses Opt.PRIVATE args --setargile=argfile and
     // --unsetargfile
-    return new ArgParser(argsList, true);
+    return new ArgParser(argsList, initsubstitutions, true);
   }
 
 }
\ No newline at end of file

diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index f7805fe..30c5e4e 100644 (file)
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.java
@@ -108,26 +108,53 @@ public class CommandsTest
             lookForSequenceName("THIS_SEQUENCE_ID_DOESN'T_EXIST"));
   }
 
-  @Test(groups = "Functional")
-  public void argFilesGlobAndSubstitutionsTest() throws IOException
+  @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
+  public void argFilesGlobAndSubstitutionsTest(String cmdLine,
+          String[] filenames) throws IOException
   {
-    cleanupArgfilesImages();
-    String cmdLine = "--argfile=" + testfiles + "/dir*/argfile.txt";
+    cleanupFiles(filenames);
     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();
+    Assert.assertNotNull(cmds);
+    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)
+        Assert.assertTrue(
+                Files.size(file.toPath()) > Files.size(lastFile.toPath()));
+    }
+    cleanupFiles(filenames);
+    tearDown();
+  }
+
+  @DataProvider(name = "argfileOutputFiles")
+  public Object[][] argfileOutputFiles()
+  {
+    return new Object[][] {
+        { "--argfile=" + testfiles + "/**/*.txt", new String[]
+        { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png",
+            testfiles + "/dir3/subdir/test0.png" } },
+        { "--argfile=" + testfiles + "/**/argfile.txt", new String[]
+        { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
+        { "--argfile=" + testfiles + "/dir*/argfile.txt", new String[]
+        { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
+        { "--initsubstitutions --open examples/uniref50.fa --image "
+                + testfiles + "/{basename}.png",
+            new String[]
+            { testfiles + "/uniref50.png" } },
+        { "--open examples/uniref50.fa --image " + testfiles
+                + "/{basename}.png",
+            new String[]
+            { testfiles + "/{basename}.png" } } };
   }
 
   @DataProvider(name = "cmdLines")
@@ -175,17 +202,15 @@ public class CommandsTest
     return false;
   }
 
-  public static void cleanupArgfilesImages()
+  public static void cleanupFiles(String[] filenames)
   {
-    File png1File = new File(png1);
-    File png2File = new File(png2);
-    if (png1File.exists())
-    {
-      png1File.delete();
-    }
-    if (png2File.exists())
+    for (String filename : filenames)
     {
-      png2File.delete();
+      File file = new File(filename);
+      if (file.exists())
+      {
+        file.delete();
+      }
     }
   }
 

diff --git a/test/jalview/bin/argparser/testfiles/dir3/subdir/subdirfile.txt b/test/jalview/bin/argparser/testfiles/dir3/subdir/subdirfile.txt
new file mode 100644 (file)
index 0000000..cd6b31b
--- /dev/null
+++ b/test/jalview/bin/argparser/testfiles/dir3/subdir/subdirfile.txt
@@ -0,0 +1,6 @@
+--substitutions
+--increment
+--open={argfiledirname}/*.fa
+--colour=gecos:flower
+--image={argfiledirname}/{basename}.png
+--close

diff --git a/test/jalview/bin/argparser/testfiles/dir3/subdir/test0.fa b/test/jalview/bin/argparser/testfiles/dir3/subdir/test0.fa
new file mode 100644 (file)
index 0000000..c9fae78
--- /dev/null
+++ b/test/jalview/bin/argparser/testfiles/dir3/subdir/test0.fa
@@ -0,0 +1,2 @@
+>TEST0
+AAAA

diff --git a/test/jalview/bin/argparser/testfiles/dir3/subdir/test1.fa b/test/jalview/bin/argparser/testfiles/dir3/subdir/test1.fa
new file mode 100644 (file)
index 0000000..c9e687f
--- /dev/null
+++ b/test/jalview/bin/argparser/testfiles/dir3/subdir/test1.fa
@@ -0,0 +1,2 @@
+>TEST1
+AAAA

diff --git a/test/jalview/bin/argparser/testfiles/dir3/subdir/test2.fa b/test/jalview/bin/argparser/testfiles/dir3/subdir/test2.fa
new file mode 100644 (file)
index 0000000..fbd15c3
--- /dev/null
+++ b/test/jalview/bin/argparser/testfiles/dir3/subdir/test2.fa
@@ -0,0 +1,2 @@
+>TEST2
+LLLL

diff --git a/test/jalview/bin/argparser/testfiles/dir3/subdir/test3.fa b/test/jalview/bin/argparser/testfiles/dir3/subdir/test3.fa
new file mode 100644 (file)
index 0000000..f9503d4
--- /dev/null
+++ b/test/jalview/bin/argparser/testfiles/dir3/subdir/test3.fa
@@ -0,0 +1,2 @@
+>TEST3
+AAARG