Hi,
I pushed the fix. Thanks for the report,
scott
On Sun, Mar 26, 2017 at 08:56:48PM -0400, Hai Nguyen wrote:
> Hi Scott,
>
> is it good to test yet? I tried dummy command:
>
>
> MSE = loadmol2 MSE.mol2
>
> savepdb MSE MSE.pdb
>
> quit
>
>
> but still don't see expected behavior (stop when file not found?)
>
>
> output log
>
> ....
>
> Welcome to LEaP!
>
> (no leaprc in search path)
>
> Sourcing: ./test.in
>
> Could not open file MSE.mol2: not found
>
> savePdb: Argument #1 is type String must be of type: [unit]
>
> usage: savePdb <object> <filename>
>
> Quit
>
>
> Hai
>
>
>
> On Sun, Mar 26, 2017 at 6:48 PM, Scott Brozell <sbrozell.rci.rutgers.edu>
> wrote:
>
> > Hi,
> >
> > On branch tleap-f-abortonerror, I have added the basic functionality.
> > I recommend that we merge this into the master after the release and
> > give it a thorough test drive before releasing it. (We do not know
> > how much we are relying on the old behavior).
> >
> > Presently, there is no control switch - it is always on. It might be
> > useful to have a command line flag such as -a and/or a command such
> > as abortOnError. And currently, the only error that can cause an
> > abort is failing to open a file.
> >
> > Here are some details:
> >
> > fBasicsMyFopen aborts on error when commands are sourced from a file.
> > Presently this applies to commands inside a sourced file, ie inside bla for
> > -f bla, but it does not apply to the file itself, ie, if bla cannot be
> > opened
> > then there is no abort; nor does it apply to the default startup leaprc
> > file.
> >
> > The isatty approach does not work because leap is
> > always running interactively, ie, stdin is a tty even when files are
> > being sourced.
> >
> > scott
> >
> > On Tue, Feb 21, 2017 at 03:27:40AM -0500, Scott Brozell wrote:
> > > Ok, I'll investigate.
> > >
> > > On Mon, Feb 20, 2017 at 04:38:17PM -0500, Hai Nguyen wrote:
> > > > +1 for exiting right away if getting error since the final prmtop is
> > NOT ok
> > > > to use.
> > > >
> > > > On Mon, Feb 20, 2017 at 4:32 PM, Justin MacCallum <
> > justin.maccallum.me.com>
> > > > >
> > > > > We routinely use tleap non-interactively, and this behaviour bites us
> > > > > occasionally. It would be great if there was a mechanism to specify
> > that
> > > > > tleap should die with a suitable error code whenever ti would
> > otherwise
> > > > > print an error when called interactively.
> > >
> > > On Mon, Feb 20, 2017 at 11:48:10AM -0500, David Case wrote:
> > > > This is a long-standing behavior for tleap:
> > > >
> > > > > MSE = loadmol2 MSE.mol2
> > > > Could not open file MSE.mol2: not found
> > > >
> > > > ...soldier on, continue with the next command.
> > > >
> > > > The above behavior is appropriate for interactive use, to give the user
> > > > the chance to correct a typing mistake. But it mainly causes confusion
> > > > for non-interactive use, since the error message that almost
> > invevitably
> > > > will come often hides the true source of the error.
> > > >
> > > > Could we not use isatty() to make "not found" a fatal error for
> > > > non-interactive use? Can some kind soul with spare time try to do
> > this?
> > > >
> > > > [I know that there are some workflows that rely on the current
> > behavior,
> > > > e.g. they load files that may not exist but also may not be needed.
> > > > How much should we worry about breaking such behavior? Do we need a
> > > > command-line switch (or a new "global" variable) to control whether
> > > > "non-found" is fatal?]
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Mon Mar 27 2017 - 13:00:03 PDT
