Author: bugman
Date: Thu Oct 16 18:18:54 2014
New Revision: 26298
URL: http://svn.gna.org/viewcvs/relax?rev=26298&view=rev
Log:
Merged revisions 26283-26285 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26283 | bugman | 2014-10-15 11:38:09 +0200 (Wed, 15 Oct 2014) | 13 lines
Added more checks to the determine_rnd() of the dauvergne_protocol
model-free auto-analysis.
This is to try to catch bizarre situations such as bug #22730
(https://gna.org/bugs/?22730),
model-free auto-analysis - relax stops and quits at the polate step.
The following additional fatal conditions are now checked for: A file with
the same name as the
base model directory already exists; The base model directory is not
readable; The base model
directory is not writable. The last two could be caused by file system
corruptions. In addition,
the presence of the base model directory is checked for using
os.path.isdir() rather than catching
errors coming out of the os.listdir() function. These changes should make
the analysis more robust
in the presence of 'strangeness'.
........
r26284 | bugman | 2014-10-15 11:42:25 +0200 (Wed, 15 Oct 2014) | 8 lines
Added an additional check to determine_rnd() of the dauvergne_protocol
model-free auto-analysis.
This is to try to catch bizarre situations such as bug #22730
(https://gna.org/bugs/?22730),
model-free auto-analysis - relax stops and quits at the polate step.
The additional check is that if the base model directory is not executable,
a RelaxError is raised.
........
r26285 | bugman | 2014-10-15 13:02:27 +0200 (Wed, 15 Oct 2014) | 7 lines
Added printouts to the determine_rnd() function of the dauvergne_protocol
model-free auto-analysis.
This is for better user feedback in the log files as to what is happening.
It may help in debugging
bug #22730 (https://gna.org/bugs/?22730): Model-free auto-analysis - relax
stops and quits at the
polate step.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/auto_analyses/dauvergne_protocol.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Oct 16 18:18:54 2014
@@ -1 +1 @@
-/trunk:1-26278
+/trunk:1-26278,26283-26285
Modified: branches/frame_order_cleanup/auto_analyses/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/auto_analyses/dauvergne_protocol.py?rev=26298&r1=26297&r2=26298&view=diff
==============================================================================
--- branches/frame_order_cleanup/auto_analyses/dauvergne_protocol.py
(original)
+++ branches/frame_order_cleanup/auto_analyses/dauvergne_protocol.py Thu
Oct 16 18:18:54 2014
@@ -21,9 +21,11 @@
# Python module imports.
from math import pi
-from os import F_OK, access, getcwd, listdir, sep
+from os import F_OK, R_OK, W_OK, X_OK, access, getcwd, listdir, sep
+from os.path import isdir
from re import search
from time import sleep
+import sys
# relax module imports.
from lib.float import floatAsByteArray
@@ -494,14 +496,35 @@
def determine_rnd(self, model=None):
"""Function for returning the name of next round of optimisation."""
- # Get a list of all files in the directory model. If no directory
exists, set the round to 'init' or 0.
- try:
- dir_list = listdir(self.results_dir+sep+model)
- except:
+ # The base model directory.
+ base_dir = self.results_dir+sep+model
+
+ # Printout.
+ sys.stdout.write("\n\nDetermining the next round of optimisation for
'%s': " % base_dir)
+
+ # Catch if a file exists with the name of the directory.
+ if not isdir(base_dir) and access(base_dir, F_OK):
+ raise RelaxError("The base model directory '%s' is not usable as
a file with the same name already exists." % base_dir)
+
+ # If no directory exists, set the round to 'init' or 0.
+ if not isdir(base_dir):
+ sys.stdout.write(" 0.\n\n")
return 0
+
+ # Is the directory readable, writable, and executable.
+ if not access(base_dir, R_OK):
+ raise RelaxError("The base model directory '%s' is not
readable." % base_dir)
+ if not access(base_dir, W_OK):
+ raise RelaxError("The base model directory '%s' is not
writable." % base_dir)
+ if not access(base_dir, X_OK):
+ raise RelaxError("The base model directory '%s' is not
executable." % base_dir)
+
+ # Get a list of all files in the directory model.
+ dir_list = listdir(base_dir)
# Set the round to 'init' or 0 if there is no directory called
'init'.
if 'init' not in dir_list:
+ sys.stdout.write(" 0.\n\n")
return 0
# Create a list of all files which begin with 'round_'.
@@ -521,6 +544,7 @@
# No directories beginning with 'round_' exist, set the round to 1.
if not len(numbers):
+ sys.stdout.write(" 1.\n\n")
return 1
# The highest number.
@@ -532,7 +556,7 @@
complete_round = i
# The file root.
- file_root = self.results_dir + sep + model + sep + "round_%i" %
i + sep + 'opt' + sep + 'results'
+ file_root = base_dir + sep + "round_%i" % i + sep + 'opt' + sep
+ 'results'
# Stop looping when the opt/results file is found.
if access(file_root + '.bz2', F_OK):
@@ -544,9 +568,11 @@
# No round, so assume the initial state.
if complete_round == 0:
+ sys.stdout.write(" 0.\n\n")
return 0
# Determine the number for the next round (add 1 to the highest
completed round).
+ sys.stdout.write(" %i.\n\n" % complete_round + 1)
return complete_round + 1
r26298 - in /branches/frame_order_cleanup: ./ auto_analyses/dauvergne_protocol.py