Author: bugman
Date: Tue Sep 18 16:15:01 2012
New Revision: 17489
URL: http://svn.gna.org/viewcvs/relax?rev=17489&view=rev
Log:
Created the new generic_fns.result_files for standardising the handling of
results files.
This fixes the bug where results files are repetitively added to the list.
All of the code touching
cdp.result_files now uses this module instead.
Added:
trunk/generic_fns/result_files.py
Modified:
trunk/generic_fns/__init__.py
trunk/generic_fns/bmrb.py
trunk/generic_fns/grace.py
trunk/generic_fns/molmol.py
trunk/generic_fns/pymol_control.py
trunk/generic_fns/value.py
Modified: trunk/generic_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/__init__.py?rev=17489&r1=17488&r2=17489&view=diff
==============================================================================
--- trunk/generic_fns/__init__.py (original)
+++ trunk/generic_fns/__init__.py Tue Sep 18 16:15:01 2012
@@ -49,6 +49,7 @@
'relax_data',
'relax_re',
'reset',
+ 'result_files',
'results',
'script',
'selection',
Modified: trunk/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/bmrb.py?rev=17489&r1=17488&r2=17489&view=diff
==============================================================================
--- trunk/generic_fns/bmrb.py (original)
+++ trunk/generic_fns/bmrb.py Tue Sep 18 16:15:01 2012
@@ -33,6 +33,7 @@
from generic_fns import exp_info
from generic_fns.mol_res_spin import create_spin, generate_spin_id,
return_residue, return_spin, set_spin_element, set_spin_isotope
from generic_fns.pipes import cdp_name
+from generic_fns.result_files import add_result_file
from info import Info_box
from relax_errors import RelaxError, RelaxFileError,
RelaxFileOverwriteError, RelaxNoModuleInstallError, RelaxNoPipeError
from relax_io import get_file_path, mkdir_nofail
@@ -288,7 +289,4 @@
# Add the file to the results file list.
if isinstance(file, str):
- if not hasattr(cdp, 'result_files'):
- cdp.result_files = []
- cdp.result_files.append(['text', 'BMRB', file])
- status.observers.result_file.notify()
+ add_result_file(type='text', label='BMRB', file=file)
Modified: trunk/generic_fns/grace.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/grace.py?rev=17489&r1=17488&r2=17489&view=diff
==============================================================================
--- trunk/generic_fns/grace.py (original)
+++ trunk/generic_fns/grace.py Tue Sep 18 16:15:01 2012
@@ -31,6 +31,7 @@
import generic_fns
from generic_fns.mol_res_spin import count_molecules, count_residues,
count_spins, exists_mol_res_spin_data, generate_spin_id, spin_loop
from generic_fns import pipes
+from generic_fns.result_files import add_result_file
from relax_errors import RelaxError, RelaxNoSequenceError, RelaxNoSimError
from relax_io import get_file_path, open_write_file, test_binary
from relax_warnings import RelaxWarning
@@ -421,11 +422,7 @@
file.close()
# Add the file to the results file list.
- if not hasattr(cdp, 'result_files'):
- cdp.result_files = []
- cdp.result_files.append(['grace', 'Grace', file_path])
- status.observers.result_file.notify()
-
+ add_result_file(type='grace', label='Grace', file=file_path)
def write_xy_data(data, file=None, graph_type=None, norm=False):
Modified: trunk/generic_fns/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/molmol.py?rev=17489&r1=17488&r2=17489&view=diff
==============================================================================
--- trunk/generic_fns/molmol.py (original)
+++ trunk/generic_fns/molmol.py Tue Sep 18 16:15:01 2012
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2011 Edward d'Auvergne
#
+# Copyright (C) 2004-2012 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -31,6 +31,7 @@
# relax module imports.
from generic_fns.mol_res_spin import exists_mol_res_spin_data
from generic_fns import pipes
+from generic_fns.result_files import add_result_file
from relax_errors import RelaxError, RelaxNoSequenceError
from relax_io import get_file_path, open_read_file, open_write_file,
test_binary
from specific_fns.setup import get_specific_fn
@@ -338,10 +339,7 @@
file.close()
# Add the file to the results file list.
- if not hasattr(cdp, 'result_files'):
- cdp.result_files = []
- cdp.result_files.append(['molmol', 'Molmol', file_path])
- status.observers.result_file.notify()
+ add_result_file(type='molmol', label='Molmol', file=file_path)
def ribbon():
Modified: trunk/generic_fns/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/pymol_control.py?rev=17489&r1=17488&r2=17489&view=diff
==============================================================================
--- trunk/generic_fns/pymol_control.py (original)
+++ trunk/generic_fns/pymol_control.py Tue Sep 18 16:15:01 2012
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2006-2011 Edward d'Auvergne
#
+# Copyright (C) 2006-2012 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -38,6 +38,7 @@
# relax module imports.
from generic_fns.mol_res_spin import exists_mol_res_spin_data
from generic_fns import pipes
+from generic_fns.result_files import add_result_file
from maths_fns.rotation_matrix import euler_to_R_zyz, R_to_axis_angle
from relax_errors import RelaxError, RelaxNoPdbError, RelaxNoSequenceError
from relax_io import delete, file_root, get_file_path, open_read_file,
open_write_file, test_binary
@@ -512,10 +513,7 @@
file.close()
# Add the file to the results file list.
- if not hasattr(cdp, 'result_files'):
- cdp.result_files = []
- cdp.result_files.append(['pymol', 'PyMOL', file_path])
- status.observers.result_file.notify()
+ add_result_file(type='pymol', label='PyMOL', file=file_path)
def tensor_pdb(file=None):
Added: trunk/generic_fns/result_files.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/result_files.py?rev=17489&view=auto
==============================================================================
--- trunk/generic_fns/result_files.py (added)
+++ trunk/generic_fns/result_files.py Tue Sep 18 16:15:01 2012
@@ -1,0 +1,58 @@
+###############################################################################
+#
#
+# Copyright (C) 2012 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax (http://www.nmr-relax.com).
#
+#
#
+# This program is free software: you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation, either version 3 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# This program is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
+#
#
+###############################################################################
+
+# Module docstring.
+"""Module for handling result files."""
+
+# relax module imports.
+from status import Status; status = Status()
+
+
+def add_result_file(type=None, label=None, file=None):
+ """Add a results file to the current data pipe.
+
+ @keyword type: The mimetype of the result file, for example 'text',
'grace', 'molmol' or 'pymol'.
+ @type type: str
+ @keyword label: The label to attach to the file. For example a BMRB
file can have the label 'BMRB' and type 'text'.
+ @type label: str
+ @keyword file: The path of the file.
+ @type file: str
+ """
+
+ # First check if the structure exists, creating it if needed.
+ if not hasattr(cdp, 'result_files'):
+ cdp.result_files = []
+
+ # Check if the file already exists.
+ for i in range(len(cdp.result_files)):
+ if cdp.result_files[i][2] == file:
+ # Overwrite the settings.
+ cdp.result_files[i][0] = type
+ cdp.result_files[i][1] = label
+
+ # Nothing left to do.
+ return True
+
+ # Add the file.
+ cdp.result_files.append([type, label, file])
+
+ # Notify all observers.
+ status.observers.result_file.notify()
Modified: trunk/generic_fns/value.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/value.py?rev=17489&r1=17488&r2=17489&view=diff
==============================================================================
--- trunk/generic_fns/value.py (original)
+++ trunk/generic_fns/value.py Tue Sep 18 16:15:01 2012
@@ -29,6 +29,7 @@
# relax module imports.
from generic_fns import minimise, pipes
from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id, generate_spin_id_data_array, return_spin, spin_loop
+from generic_fns.result_files import add_result_file
from relax_errors import RelaxError, RelaxNoSequenceError, RelaxNoSpinError,
RelaxParamSetError, RelaxValueError
from relax_io import get_file_path, open_write_file, read_spin_data,
write_spin_data
import specific_fns
@@ -462,10 +463,7 @@
file.close()
# Add the file to the results file list.
- if not hasattr(cdp, 'result_files'):
- cdp.result_files = []
- cdp.result_files.append(['text', 'Text', file_path])
- status.observers.result_file.notify()
+ add_result_file(type='text', label='Text', file=file_path)
def write_data(param=None, file=None, bc=False, return_value=None):
r17489 - in /trunk/generic_fns: __init__.py bmrb.py grace.py molmol.py pymol_control.py result_files.py value.py