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?]
>
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Received on Sun Mar 26 2017 - 18:00:03 PDT
