Author: bugman
Date: Sun Oct 11 15:59:38 2009
New Revision: 9722
URL: http://svn.gna.org/viewcvs/relax?rev=9722&view=rev
Log:
Shifted the software() and software_select() functions into their own module,
'generic_fns.exp_info'.
Added:
branches/bmrb/generic_fns/exp_info.py
- copied, changed from r9721, branches/bmrb/generic_fns/bmrb.py
Modified:
branches/bmrb/generic_fns/bmrb.py
branches/bmrb/prompt/bmrb.py
Modified: branches/bmrb/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/bmrb.py?rev=9722&r1=9721&r2=9722&view=diff
==============================================================================
--- branches/bmrb/generic_fns/bmrb.py (original)
+++ branches/bmrb/generic_fns/bmrb.py Sun Oct 11 15:59:38 2009
@@ -73,62 +73,6 @@
read_function(file_path, version=version)
-def software(name=None, version=None, url=None, vendor_name=None, cite=None,
tasks=None):
- """Select by name the software used in the analysis.
-
- @param name: The name of the software program.
- @type name: str
- @keyword version: The program version.
- @type version: None or str
- @keyword url: The program's URL.
- @type url: None or str
- @keyword vendor_name: The name of the company or person behind the
program.
- @type vendor_name: str
- @keyword cite: The literature citation.
- @type cite: None or str
- @keyword tasks: The tasks performed by the program.
- @type tasks: list of str
- """
-
- # Set up the experimental info data container, if needed.
- if not hasattr(cdp, 'exp_info'):
- cdp.exp_info = ExpInfo()
-
- # Place the data in the container.
- cdp.exp_info.software_setup(name=name, version=version, url=url,
vendor_name=vendor_name, cite=cite, tasks=tasks)
-
-
-def software_select(name, version=None):
- """Select by name the software used in the analysis.
-
- @param name: The name of the software program.
- @type name: str
- @keyword version: The program version.
- @type version: None or str
- """
-
- # Unknown program.
- if name not in ['NMRPipe', 'Sparky']:
- raise RelaxError("The software '%s' is unknown. Please use the user
function for manually specifying software details instead." % name)
-
- # Set up the experimental info data container, if needed.
- if not hasattr(cdp, 'exp_info'):
- cdp.exp_info = ExpInfo()
-
- # NMRPipe.
- if name == 'NMRPipe':
- cdp.exp_info.software_setup('NMRPipe', version=version,
url="http://spin.niddk.nih.gov/NMRPipe/";, vendor_name="Delaglio, F.",
cite="Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and
Bax, A. (1995). NMRPipe: a multidimensional spectral processing system based
on UNIX pipes. J. Biomol. NMR. 6, 277-293.", tasks=["processing"])
-
- # Sparky.
- elif name == 'Sparky':
- # Check if the version information has been supplied.
- if not version:
- raise RelaxError("The Sparky version number has not been
supplied.")
-
- # Add the data.
- cdp.exp_info.software_setup('Sparky', version=version,
url="http://www.cgl.ucsf.edu/home/sparky/";, vendor_name="Goddard, T. D.",
cite="Goddard, T. D. and Kneller, D. G., SPARKY 3, University of California,
San Francisco.", tasks=["spectral analysis"])
-
-
def write(file=None, directory=None, version='3.1', force=False):
"""Create a BMRB NMR-STAR formatted file."""
Copied: branches/bmrb/generic_fns/exp_info.py (from r9721,
branches/bmrb/generic_fns/bmrb.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/exp_info.py?p2=branches/bmrb/generic_fns/exp_info.py&p1=branches/bmrb/generic_fns/bmrb.py&r1=9721&r2=9722&rev=9722&view=diff
==============================================================================
--- branches/bmrb/generic_fns/bmrb.py (original)
+++ branches/bmrb/generic_fns/exp_info.py Sun Oct 11 15:59:38 2009
@@ -21,56 +21,11 @@
###############################################################################
# Module docstring.
-"""Module containing functions for BMRB support."""
-
-# Python module imports.
-from os import F_OK, access
+"""Module containing functions for specifying the experimental details."""
# relax module imports.
-from data import Relax_data_store; ds = Relax_data_store()
from data.exp_info import ExpInfo
-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(version='3.1'):
- """Display the results in the BMRB NMR-STAR format."""
-
- # Test if the current data pipe exists.
- if not ds.current_pipe:
- raise RelaxNoPipeError
-
- # Specific results writing function.
- write_function = get_specific_fn('bmrb_write',
ds[ds.current_pipe].pipe_type, raise_error=False)
-
- # Write the results.
- write_function(sys.stdout, version=version)
-
-
-def read(file=None, directory=None, version='3.1'):
- """Read the contents of a BMRB NMR-STAR formatted file."""
-
- # Test if the current data pipe exists.
- if not ds.current_pipe:
- raise RelaxNoPipeError
-
- # Make sure that the data pipe is empty.
- if not ds[ds.current_pipe].is_empty():
- raise RelaxError("The current data pipe is not empty.")
-
- # Get the full file path.
- file_path = get_file_path(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)
-
- # Read the results.
- read_function(file_path, version=version)
+from relax_errors import RelaxError
def software(name=None, version=None, url=None, vendor_name=None, cite=None,
tasks=None):
@@ -127,34 +82,3 @@
# Add the data.
cdp.exp_info.software_setup('Sparky', version=version,
url="http://www.cgl.ucsf.edu/home/sparky/";, vendor_name="Goddard, T. D.",
cite="Goddard, T. D. and Kneller, D. G., SPARKY 3, University of California,
San Francisco.", tasks=["spectral analysis"])
-
-
-def write(file=None, directory=None, version='3.1', force=False):
- """Create a BMRB NMR-STAR formatted file."""
-
- # Test if the current data pipe exists.
- if not ds.current_pipe:
- raise RelaxNoPipeError
-
- # The special data pipe name directory.
- if directory == 'pipe_name':
- directory = ds.current_pipe
-
- # Specific results writing function.
- write_function = get_specific_fn('bmrb_write',
ds[ds.current_pipe].pipe_type)
-
- # Get the full file path.
- file_path = get_file_path(file, directory)
-
- # 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')
-
- # 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, version=version)
Modified: branches/bmrb/prompt/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/bmrb.py?rev=9722&r1=9721&r2=9722&view=diff
==============================================================================
--- branches/bmrb/prompt/bmrb.py (original)
+++ branches/bmrb/prompt/bmrb.py Sun Oct 11 15:59:38 2009
@@ -30,7 +30,7 @@
# relax module imports.
from base_class import User_fn_class
import check
-from generic_fns import bmrb
+from generic_fns import bmrb, exp_info
from relax_errors import RelaxBoolError, RelaxIntError, RelaxNoneStrError,
RelaxStrError, RelaxStrFileError
@@ -153,7 +153,7 @@
check.is_str_list(tasks, 'tasks', can_be_none=True)
# Execute the functional code.
- bmrb.software(name=name, version=version, url=url,
vendor_name=vendor_name, cite=cite, tasks=tasks)
+ exp_info.software(name=name, version=version, url=url,
vendor_name=vendor_name, cite=cite, tasks=tasks)
def software_select(self, name=None, version=None):
@@ -203,7 +203,7 @@
check.is_str(version, 'version', can_be_none=True)
# Execute the functional code.
- bmrb.software_select(name=name, version=version)
+ exp_info.software_select(name=name, version=version)
def write(self, file=None, dir='pipe_name', version='3.1', force=False):
r9722 - in /branches/bmrb: generic_fns/bmrb.py generic_fns/exp_info.py prompt/bmrb.py