public ArgParser(String[] args, boolean initsubstitutions,
BootstrapArgs bsa)
{
- // 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 --append/--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). )
+ /*
+ * 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 --append/--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) as
+ * that is not mutable. )
+ */
this(new ArrayList<>(Arrays.asList(args)), initsubstitutions, false,
bsa);
}
boolean allowPrivate)
{
this.substitutions = initsubstitutions;
- boolean openEachInitialFilenames = true;
- for (int i = 0; i < args.size(); i++)
- {
- String arg = args.get(i);
- // If the first arguments do not start with "--" or "-" or is not "open"
- // and` is a filename that exists it is probably a file/list of files to
- // open so we fake an Arg.OPEN argument and when adding files only add the
- // single arg[i] and increment the defaultLinkedIdCounter so that each of
- // these files is opened separately.
- if (openEachInitialFilenames && !arg.startsWith(DOUBLEDASH)
- && !arg.startsWith("-") && !arg.equals("open")
- && (new File(arg).exists()
- || HttpUtils.startsWithHttpOrHttps(arg)))
- {
- arg = Arg.OPEN.argString();
- }
- else
+ /*
+ * If the first argument does not start with "--" or "-" or is not "open",
+ * and is a filename that exists or a URL, it is probably a file/list of
+ * files to open so we insert an Arg.OPEN argument before it. This will
+ * mean the list of files at the start of the arguments are all opened
+ * separately.
+ */
+ if (args.size() > 0)
+ {
+ String arg0 = args.get(0);
+ if (arg0 != null
+ && (!arg0.startsWith(DOUBLEDASH) && !arg0.startsWith("-")
+ && !arg0.equals("open") && (new File(arg0).exists()
+ || HttpUtils.startsWithHttpOrHttps(arg0))))
{
- openEachInitialFilenames = false;
+ // insert "--open" at the start
+ args.add(0, Arg.OPEN.argString());
}
+ }
+
+ for (int i = 0; i < args.size(); i++)
+ {
+ String arg = args.get(i);
// look for double-dash, e.g. --arg
if (arg.startsWith(DOUBLEDASH))
{
// There is no "=" so value is next arg or args (possibly shell
// glob-expanded)
- if ((openEachInitialFilenames ? i : i + 1) >= args.size())
+ if (i + 1 >= args.size())
{
// no value to take for arg, which wants a value
Console.error("Argument '" + a.getName()
{
// if this is the first argument with a file list at the start of
// the args we add filenames from index i instead of i+1
- globVals = getShellGlobbedFilenameValues(a, args,
- openEachInitialFilenames ? i : i + 1);
+ globVals = getShellGlobbedFilenameValues(a, args, i + 1);
}
else
{
@Override
public void propertyChange(PropertyChangeEvent evt)
{
- // // jalview.bin.Console.outPrintln("Discoverer property change.");
+ // // jalview.bin.Console.outPrintln("Discoverer property
+ // change.");
// if (evt.getPropertyName().equals("services"))
{
SwingUtilities.invokeLater(new Runnable()
out.print(output);
out.flush();
- Console.trace("ALIGNFRAME about to close file");
- out.close();
- Console.trace("ALIGNFRAME closed file");
+ if (!stdout)
+ {
+ Console.trace("ALIGNFRAME about to close file");
+ out.close();
+ Console.trace("ALIGNFRAME closed file");
+ }
AlignFrame.this.setTitle(stdout ? "STDOUT" : file);
if (stdout)
{
{
try
{
- jalview.bin.Console.errPrintln("Waiting for building menu to finish.");
+ jalview.bin.Console
+ .errPrintln("Waiting for building menu to finish.");
Thread.sleep(10);
} catch (Exception e)
{
}
else
{
- jalview.bin.Console.errPrintln("Can't run Groovy script as console not found");
+ jalview.bin.Console
+ .errPrintln("Can't run Groovy script as console not found");
}
}
private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
int timeout)
{
+ return getJalviewDesktopRunner(withAwt, cmd, timeout, true);
+ }
+
+ private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
+ int timeout, boolean testoutput)
+ {
/*
boolean win = System.getProperty("os.name").indexOf("Win") >= 0;
String pwd = "";
Worker worker = null;
try
{
- cmd = " --testoutput " + cmd;
+ cmd = cmd + (testoutput ? " --testoutput " : "");
System.out.println("Running '" + _cmd + cmd + "'");
ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
} catch (Throwable e1)
{
String cmd = args;
File file = new File(comparisonFile);
- Worker worker = getJalviewDesktopRunner(true, cmd, timeout);
+ Worker worker = getJalviewDesktopRunner(true, cmd, timeout, false);
int b = -1;
StringBuilder sb = new StringBuilder();
try
// when running tests on build server, but we will keep this patch for now
// since it works.
// https://issues.jalview.org/browse/JAL-1889?focusedCommentId=21609&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-21609
- String workingDir = "test/jalview/bin/";
+ String workingDir = "test/jalview/bin";
return new Object[][] {
//
{ "--open=examples/uniref50.fa --output=-",
workingDir + "/uniref50-output.blc", TEST_TIMEOUT },
{ "--open examples/uniref50.fa --output - --format blc",
workingDir + "/uniref50-output.blc", TEST_TIMEOUT },
+ { "./examples/uniref50.fa --output=-",
+ workingDir + "/uniref50-output.fa", TEST_TIMEOUT },
+ { "./examples/uniref50.fa --output - --format blc",
+ workingDir + "/uniref50-output.blc", TEST_TIMEOUT },
+ // remember you can't use shell wildcards for filenames in a test
+ { "./test/jalview/bin/argparser/testfiles/test1.fa ./test/jalview/bin/argparser/testfiles/test2.fa ./test/jalview/bin/argparser/testfiles/test3.fa --all --output -",
+ workingDir + "/test1-3.fa", TEST_TIMEOUT },
+ // but you can use java wildcards when using an equals sign
+ { "--open=./test/jalview/bin/argparser/testfiles/test*.fa --all --output -",
+ workingDir + "/test1-3.fa", TEST_TIMEOUT },
//
};
}
git://source.jalview.org / jalview.git / commitdiff