Author: bugman
Date: Sat Feb 19 14:39:23 2011
New Revision: 12579
URL: http://svn.gna.org/viewcvs/relax?rev=12579&view=rev
Log:
Merged revisions 8153,8369-8388 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/bmrb
........
r8153 | bugman | 2008-12-05 20:44:46 +0100 (Fri, 05 Dec 2008) | 3 lines
Import fix!
........
r8369 | bugman | 2009-01-11 10:52:13 +0100 (Sun, 11 Jan 2009) | 11 lines
Added a directory for packaging the pystarlib STAR format reader/writer
library with relax.
The pystarlib project by Jurgen F. Doreleijers (jurgenfd att gmail dot com)
is located at
http://code.google.com/p/pystarlib/.
This packaging with relax is temporary until relax can fully use the
library to read and write STAR
files containing relaxation analysis results (model-free for now) for
submission to the BMRB. The
pystarlib library also needs to be packaged with distutils for easy
installation, prior to
reseparation.
........
r8370 | bugman | 2009-01-11 10:55:33 +0100 (Sun, 11 Jan 2009) | 6 lines
Added all the pystarlib code.
The original SVN repository path for this code is
http://pystarlib.googlecode.com/svn/trunk/src/STAR
and the code was copied at r15.
........
r8371 | bugman | 2009-01-11 12:20:07 +0100 (Sun, 11 Jan 2009) | 3 lines
Created a system test for the writing and reading of a BRMB STAR formatted
file.
........
r8372 | bugman | 2009-01-11 12:26:41 +0100 (Sun, 11 Jan 2009) | 3 lines
A few fixes for the BMRB system test.
........
r8373 | bugman | 2009-01-11 13:50:12 +0100 (Sun, 11 Jan 2009) | 3 lines
Added a missing import.
........
r8374 | bugman | 2009-01-11 13:54:24 +0100 (Sun, 11 Jan 2009) | 3 lines
Some more missing imports.
........
r8375 | bugman | 2009-01-11 13:57:26 +0100 (Sun, 11 Jan 2009) | 3 lines
A RelaxError is now raised if the specific_fns BMRB methods do not exist.
........
r8376 | bugman | 2009-01-11 14:01:28 +0100 (Sun, 11 Jan 2009) | 3 lines
Added a stub bmrb_write() model-free method.
........
r8377 | bugman | 2009-01-11 14:03:58 +0100 (Sun, 11 Jan 2009) | 3 lines
The bmrb_write() method is now in the model-free specific object.
........
r8378 | bugman | 2009-01-11 14:05:52 +0100 (Sun, 11 Jan 2009) | 3 lines
Activated the specific bmrb_write() methods.
........
r8379 | bugman | 2009-01-11 14:06:26 +0100 (Sun, 11 Jan 2009) | 3 lines
Activated the specific bmrb_read() methods.
........
r8380 | bugman | 2009-01-11 15:46:03 +0100 (Sun, 11 Jan 2009) | 5 lines
Import fixes for pystarlib, as they were all screwed up.
This allows the unit test framework to function and allows importing of the
code into relax.
........
r8381 | bugman | 2009-01-11 15:57:41 +0100 (Sun, 11 Jan 2009) | 5 lines
Removed the BMRB STAR file compression abilities from the user functions.
The pystarlib does not support this.
........
r8382 | bugman | 2009-01-11 16:28:13 +0100 (Sun, 11 Jan 2009) | 5 lines
Redesigned the generic BMRB write() function for the pystarlib.File.File
class object.
The open_write_file() function should not be used as pystarlib already
creates the file.
........
r8383 | bugman | 2009-01-11 16:30:33 +0100 (Sun, 11 Jan 2009) | 3 lines
Added a printout for the write() function.
........
r8384 | bugman | 2009-01-11 16:41:13 +0100 (Sun, 11 Jan 2009) | 5 lines
The pystarlib File object is now initialised and the write() method called.
This produces a relatively empty file.
........
r8385 | bugman | 2009-01-11 17:17:49 +0100 (Sun, 11 Jan 2009) | 5 lines
Fix for the test_rw_bmrb_model_free() system test.
The dir name was being set to the data pipe name!
........
r8386 | bugman | 2009-01-11 17:27:34 +0100 (Sun, 11 Jan 2009) | 3 lines
Fixes for the read() function.
........
r8387 | bugman | 2009-01-11 17:29:45 +0100 (Sun, 11 Jan 2009) | 3 lines
Fix for the write() function. The directory for placing the file into is
now created.
........
r8388 | bugman | 2009-01-11 17:33:47 +0100 (Sun, 11 Jan 2009) | 6 lines
Wrote a basic model-free bmrb_read() method.
This simply parses the STAR formatted file, but does not yet put the
contents into the relax data
store.
........
Added:
1.3/pystarlib/
- copied from r8388, branches/bmrb/pystarlib/
1.3/specific_fns/model_free/bmrb.py
- copied unchanged from r8388,
branches/bmrb/specific_fns/model_free/bmrb.py
1.3/test_suite/system_tests/bmrb.py
- copied unchanged from r8388,
branches/bmrb/test_suite/system_tests/bmrb.py
Modified:
1.3/ (props changed)
1.3/generic_fns/bmrb.py
1.3/prompt/bmrb.py
1.3/prompt/interpreter.py
1.3/specific_fns/model_free/__init__.py
1.3/specific_fns/setup.py
1.3/test_suite/system_tests/__init__.py
Propchange: 1.3/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Sat Feb 19 14:39:23 2011
@@ -1,1 +1,1 @@
-/branches/bmrb:1-7041,7043-7046
+/branches/bmrb:1-7041,7043-7046,8153-8388
Modified: 1.3/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/bmrb.py?rev=12579&r1=12578&r2=12579&view=diff
==============================================================================
--- 1.3/generic_fns/bmrb.py (original)
+++ 1.3/generic_fns/bmrb.py Sat Feb 19 14:39:23 2011
@@ -23,9 +23,14 @@
# Module docstring.
"""Module for interfacing with the BMRB (http://www.bmrb.wisc.edu/) by
handling NMR-STAR v3.1 files."""
+# Python module imports.
+from os import F_OK, access
+
# relax module imports.
from data import Relax_data_store; ds = Relax_data_store()
-from relax_errors import RelaxError, RelaxNoPipeError
+from relax_errors import RelaxError, RelaxFileError,
RelaxFileOverwriteError, RelaxNoPipeError
+from relax_io import get_file_path, mkdir_nofail
+from specific_fns.setup import get_specific_fn
def display():
@@ -53,20 +58,21 @@
if not ds[ds.current_pipe].is_empty():
raise RelaxError, "The current data pipe is not empty."
- # Get the full file path, for later use.
+ # Get the full file path.
file_path = get_file_path(file_name=file, dir=directory)
- # Open the file.
- file = open_read_file(file_name=file, dir=directory)
+ # Fail if the file does not exist.
+ if not access(file_path, F_OK):
+ raise RelaxFileError, file_path
# Specific results reading function.
- read_function = get_specific_fn('bmrb_read',
ds[ds.current_pipe].pipe_type, raise_error=False)
+ read_function = get_specific_fn('bmrb_read',
ds[ds.current_pipe].pipe_type)
# Read the results.
- read_function(file)
+ read_function(file_path)
-def write(file=None, directory=None, force=False, compress_type=0,
verbosity=1):
+def write(file=None, directory=None, force=False):
"""Create a BMRB NMR-STAR v3.1 formatted file."""
# Test if the current data pipe exists.
@@ -78,13 +84,20 @@
directory = ds.current_pipe
# Specific results writing function.
- write_function = get_specific_fn('bmrb_write',
ds[ds.current_pipe].pipe_type, raise_error=False)
+ write_function = get_specific_fn('bmrb_write',
ds[ds.current_pipe].pipe_type)
- # Open the file for writing.
- results_file = open_write_file(file_name=file, dir=directory,
force=force, compress_type=compress_type, verbosity=verbosity)
+ # Get the full file path.
+ file_path = get_file_path(file, directory)
- # Write the results.
- write_function(results_file)
+ # Fail if the file already exists and the force flag is False.
+ if access(file_path, F_OK) and not force:
+ raise RelaxFileOverwriteError, (file_path, 'force flag')
- # Close the results file.
- results_file.close()
+ # Print out.
+ print "Opening the file '%s' for writing." % file_path
+
+ # Create the directories.
+ mkdir_nofail(directory, verbosity=0)
+
+ # Execute the specific BMRB writing code.
+ write_function(file_path)
Modified: 1.3/prompt/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/bmrb.py?rev=12579&r1=12578&r2=12579&view=diff
==============================================================================
--- 1.3/prompt/bmrb.py (original)
+++ 1.3/prompt/bmrb.py Sat Feb 19 14:39:23 2011
@@ -70,11 +70,6 @@
~~~~~~~~~~~
To search for the results file in the current working directory, set
dir to None.
-
- This function is able to handle uncompressed, bzip2 compressed
files, or gzip compressed
- files automatically. The full file name including extension can be
supplied, however, if
- the file cannot be found, this function will search for the file
name with '.bz2' appended
- followed by the file name with '.gz' appended.
"""
# Function intro text.
@@ -96,7 +91,7 @@
bmrb.read(file=file, directory=dir)
- def write(self, file=None, dir='pipe_name', force=False,
compress_type=0):
+ def write(self, file=None, dir='pipe_name', force=False):
"""Write the results to a BMRB NMR-STAR v3.1 formatted file.
Keyword Arguments
@@ -109,8 +104,6 @@
force: A flag which if True will cause the any pre-existing file to
be overwritten.
- compress_type: The type of compression to use when creating the
file.
-
Description
~~~~~~~~~~~
@@ -118,16 +111,6 @@
To place the BMRB file in the current working directory, set dir to
None. If dir is set
to the special name 'pipe_name', then the results file will be
placed into a directory with
the same name as the current data pipe.
-
- The default behaviour of this function is to create an uncompressed
BMRB file. The file can
- however be saved in compressed format. This is controlled by the
compress_type argument
- which can be set to one of:
-
- 0: No compression (no file extension),
- 1: bzip2 compression ('.bz2' file extension),
- 2: gzip compression ('.gz' file extension).
-
- The complementary read function will automatically handle the
compressed files.
"""
# Function intro text.
@@ -135,8 +118,7 @@
text = sys.ps3 + "bmrb.write("
text = text + "file=" + `file`
text = text + ", dir=" + `dir`
- text = text + ", force=" + `force`
- text = text + ", compress_type=" + `compress_type` + ")"
+ text = text + ", force=" + `force` + ")"
print text
# File.
@@ -151,9 +133,5 @@
if type(force) != bool:
raise RelaxBoolError, ('force flag', force)
- # Compression type.
- if type(compress_type) != int:
- raise RelaxIntError, ('compression type', compress_type)
-
# Execute the functional code.
- bmrb.write(file=file, directory=dir, force=force,
compress_type=compress_type)
+ bmrb.write(file=file, directory=dir, force=force)
Modified: 1.3/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/interpreter.py?rev=12579&r1=12578&r2=12579&view=diff
==============================================================================
--- 1.3/prompt/interpreter.py (original)
+++ 1.3/prompt/interpreter.py Sat Feb 19 14:39:23 2011
@@ -63,7 +63,7 @@
from temperature import Temp
# User classes.
-from bmrb import Align_tensor
+from align_tensor import Align_tensor
from bmrb import BMRB
from consistency_tests import Consistency_tests
from dasha import Dasha
Modified: 1.3/specific_fns/model_free/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/__init__.py?rev=12579&r1=12578&r2=12579&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/__init__.py (original)
+++ 1.3/specific_fns/model_free/__init__.py Sat Feb 19 14:39:23 2011
@@ -31,6 +31,7 @@
'results']
# relax module imports.
+from bmrb import Bmrb
from main import Model_free_main
from mf_minimise import Mf_minimise
from molmol import Molmol
@@ -39,7 +40,7 @@
from specific_fns.api_common import API_common
-class Model_free(Model_free_main, Mf_minimise, Molmol, Results, API_base,
API_common):
+class Model_free(Model_free_main, Mf_minimise, Molmol, Results, Bmrb,
API_base, API_common):
"""Parent class containing all the model-free specific functions."""
def __init__(self):
Modified: 1.3/specific_fns/setup.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/setup.py?rev=12579&r1=12578&r2=12579&view=diff
==============================================================================
--- 1.3/specific_fns/setup.py (original)
+++ 1.3/specific_fns/setup.py Sat Feb 19 14:39:23 2011
@@ -65,6 +65,14 @@
if eqi == 'base_data_loop':
function = inst.base_data_loop
+ # BMRB NMR-STAR v3.1 reading function.
+ if eqi == 'bmrb_read':
+ function = inst.bmrb_read
+
+ # BMRB NMR-STAR v3.1 writing function.
+ if eqi == 'bmrb_write':
+ function = inst.bmrb_write
+
# Calculate function.
if eqi == 'calculate':
function = inst.calculate
Modified: 1.3/test_suite/system_tests/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/__init__.py?rev=12579&r1=12578&r2=12579&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/__init__.py (original)
+++ 1.3/test_suite/system_tests/__init__.py Sat Feb 19 14:39:23 2011
@@ -34,6 +34,7 @@
# relax system/functional test module imports.
from align_tensor import Align_tensor
from angles import Angles
+from bmrb import Bmrb
from consistency_tests import Ct
from dasha import Dasha
from diffusion_tensor import Diffusion_tensor
@@ -62,6 +63,7 @@
__all__ = ['align_tensor',
'angles',
+ 'brmb',
'consistency_tests',
'dasha'
'diffusion_tensor',
@@ -124,6 +126,7 @@
# All tests.
if not tests:
suite_array.append(TestLoader().loadTestsFromTestCase(Align_tensor))
+ suite_array.append(TestLoader().loadTestsFromTestCase(Bmrb))
suite_array.append(TestLoader().loadTestsFromTestCase(Angles))
suite_array.append(TestLoader().loadTestsFromTestCase(Ct))
suite_array.append(TestLoader().loadTestsFromTestCase(Dasha))
r12579 - in /1.3: ./ generic_fns/ prompt/ pystarlib/ specific_fns/ specific_fns/model_free/ test_suite/system_tests/