[AMBER-Developers] tleap error handling

From: Scott Brozell <sbrozell.rci.rutgers.edu>
Date: Thu, 25 Jan 2018 16:35:46 -0500


Read 1. 2 provides more context. 3 thru 4 are extra credit. :)

On Fri, Jan 19, 2018 at 09:53:05AM -0500, David A Case wrote:
> * Scott is doing the same thing with tleap, which is notorious for
> soldiering on even when it doesn't understand the input.
> Finding errors early is important: it gives users much better
> error messages than generic "prmtop was not created"-type messages later on.

I have just merged this tleap work into the master.
This may break your workflow/script/whatever.
If so, that is a good thing because we want to report problems early
and we want to survey the potential impact of this on users.

So please update to the current git master, rebuild leap, try it, and
report to me the types of problems and if nontrivial then how you
fixed them. Please include suggestions with respect
to additional improvements as well as complaints :)

2. A.
A bunch of existing leap messages have been rewrapped to clarify the
type of message: error, warning, informational(little rewrapping of
these has yet occurred).

2. B.
Error handling behavior depends on whether tLEaP is getting input
from standard input (note that input to tLEaP cannot be redirected)
or from an input file. The behavior upon error is to check for stdin:
emit "Error" and exit if not stdin else just emit and
keep going. The intention is to maintain tLEaP's very forgiving
behavior when used interactively, but to implement an immediate
reporting and failure behavior for scripted use.

The types of messages that were affected.

3. A.
Made fatal:

File i/o errors.

Type checking errors, eg:
Argument #1 is type Atom must be of type: [string]

'Improper number of arguments' errors.

All usage emissions for all commands except help.

Messages indicating something is illegal.

Messages indicating something is inconsistent.

Some things in the parser.

3. B.
Made warnings:

Messages indicating something is ignored.

The is-it-possible-to-neutralize checking in all 4 addIons commands.
This needs more work to fix poor coding in all 4 addIons commands.

For more detail, see bugs 349 and 352 as well as branch tleap-f-abortonerror
from am dev thread:
Subject: Re: [AMBER-Developers] having tleap fail when input files are not found


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Received on Thu Jan 25 2018 - 14:00:02 PST
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