Author: bugman
Date: Fri Sep 26 19:09:29 2014
New Revision: 26074
URL: http://svn.gna.org/viewcvs/relax?rev=26074&view=rev
Log:
Merged revisions 26044-26046,26048-26056 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26044 | bugman | 2014-09-26 09:52:37 +0200 (Fri, 26 Sep 2014) | 7 lines
Created the pipe_control.spectrometer.check_setup() function.
This follows the design on the wiki page
http://wiki.nmr-relax.com/Relax_source_design.
This is for checking if spectrometer information has been set up.
........
r26045 | bugman | 2014-09-26 09:55:10 +0200 (Fri, 26 Sep 2014) | 3 lines
Created the RelaxNoFrqWarning warning class for warning that no
spectrometer information is present.
........
r26046 | bugman | 2014-09-26 10:00:58 +0200 (Fri, 26 Sep 2014) | 5 lines
Renamed the pipe_control.spectrometer.check_setup() function to
check_spectrometer_setup().
This is so it can be used without confusion outside of the module.
........
r26048 | bugman | 2014-09-26 10:05:42 +0200 (Fri, 26 Sep 2014) | 3 lines
Fix for a broken elif block in the new
pipe_control.spectrometer.check_spectrometer_setup() function.
........
r26049 | bugman | 2014-09-26 10:06:58 +0200 (Fri, 26 Sep 2014) | 5 lines
The model-free bmrb_write() API method now checks for spectrometer
information.
This is via a call to the
pipe_control.spectrometer.check_spectrometer_setup() function.
........
r26050 | bugman | 2014-09-26 10:09:18 +0200 (Fri, 26 Sep 2014) | 3 lines
Modified the Bmrb.test_bug_22703_display_empty system/GUI test to catch the
RelaxNoFrqError.
........
r26051 | bugman | 2014-09-26 11:31:29 +0200 (Fri, 26 Sep 2014) | 6 lines
Created a special Check class based on the strategy design pattern.
This is in the new lib.checks module. The class will be used to simplify
and unify all of the
check_*() functions in the pipe_control and specific_analyses packages.
........
r26052 | bugman | 2014-09-26 11:43:15 +0200 (Fri, 26 Sep 2014) | 6 lines
Converted the pipe_control.spectrometer.check_*() functions to the strategy
design pattern.
These are now passed into the lib.checks.Check object, and the original
functions are now instances
of this class.
........
r26053 | bugman | 2014-09-26 11:44:00 +0200 (Fri, 26 Sep 2014) | 5 lines
Updated the Bmrb.test_bug_22703_display_empty system/GUI test.
The RelaxError type is now different.
........
r26054 | bugman | 2014-09-26 12:15:23 +0200 (Fri, 26 Sep 2014) | 3 lines
Alphabetical ordering of all functions in the pipe_control.pipes module.
........
r26055 | bugman | 2014-09-26 12:40:16 +0200 (Fri, 26 Sep 2014) | 9 lines
Changed the design of the Check object in lib.checks.
The design of the checking function to call has been modified - it should
now return either None if
the check passes or an instantiated RelaxError object if not. This is then
used to determine if the
__call__() method should return True (when None is received). Otherwise if
escalate is set to 1,
the text from the RelaxError object is sent into a RelaxWarning and False
is returned. And if
escalate is set to 2, then the error object is simply raised.
........
r26056 | bugman | 2014-09-26 12:41:06 +0200 (Fri, 26 Sep 2014) | 3 lines
Updated the pipe_control.spectrometer.check_*_func() functions to use the
new design.
........
Added:
branches/frame_order_cleanup/lib/checks.py
- copied unchanged from r26056, trunk/lib/checks.py
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/lib/__init__.py
branches/frame_order_cleanup/lib/warnings.py
branches/frame_order_cleanup/pipe_control/pipes.py
branches/frame_order_cleanup/pipe_control/spectrometer.py
branches/frame_order_cleanup/specific_analyses/model_free/api.py
branches/frame_order_cleanup/test_suite/system_tests/bmrb.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Sep 26 19:09:29 2014
@@ -1 +1 @@
-/trunk:1-26017,26043
+/trunk:1-26017,26043-26056
Modified: branches/frame_order_cleanup/lib/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/__init__.py?rev=26074&r1=26073&r2=26074&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/__init__.py (original)
+++ branches/frame_order_cleanup/lib/__init__.py Fri Sep 26 19:09:29
2014
@@ -29,6 +29,7 @@
'arg_check',
'auto_relaxation',
'check_types',
+ 'checks',
'chemical_shift',
'compat',
'curve_fit',
Modified: branches/frame_order_cleanup/lib/warnings.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/warnings.py?rev=26074&r1=26073&r2=26074&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/warnings.py (original)
+++ branches/frame_order_cleanup/lib/warnings.py Fri Sep 26 19:09:29
2014
@@ -188,3 +188,18 @@
class RelaxDeselectWarning(BaseWarning):
def __init__(self, spin_id, reason):
self.text = "The spin '%s' has been deselected because of %s." %
(spin_id, reason)
+
+
+# Spectrometer information warnings.
+####################################
+
+# No frequency information.
+class RelaxNoFrqWarning(BaseWarning):
+ def __init__(self, pipe_name=None, id=None):
+ self.text = "No spectrometer frequency information"
+ if id != None:
+ self.text += " for the '%s' experiment ID" % id
+ self.text += " is present"
+ if pipe_name != None:
+ self.text += " in the '%s' data pipe" % pipe_name
+ self.text += "."
Modified: branches/frame_order_cleanup/pipe_control/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/pipes.py?rev=26074&r1=26073&r2=26074&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/pipes.py (original)
+++ branches/frame_order_cleanup/pipe_control/pipes.py Fri Sep 26 19:09:29
2014
@@ -91,6 +91,16 @@
return list(ds.pipe_bundles.keys())
+def cdp_name():
+ """Return the name of the current data pipe.
+
+ @return: The name of the current data pipe.
+ @rtype: str
+ """
+
+ return ds.current_pipe
+
+
def change_type(pipe_type=None):
"""Change the type of the current data pipe.
@@ -112,6 +122,27 @@
# Change the type.
cdp.pipe_type = pipe_type
+
+
+def check_type(pipe_type):
+ """Check the validity of the given data pipe type.
+
+ @keyword pipe_type: The data pipe type to check.
+ @type pipe_type: str
+ @raises RelaxError: If the data pipe type is invalid or the required
Python modules are missing.
+ """
+
+ # Test if pipe_type is valid.
+ if not pipe_type in VALID_TYPES:
+ raise RelaxError("The data pipe type " + repr(pipe_type) + " is
invalid and must be one of the strings in the list " + repr(VALID_TYPES) +
".")
+
+ # Test that the C modules have been loaded.
+ if pipe_type == 'relax_fit' and not C_module_exp_fn:
+ raise RelaxError("Relaxation curve fitting is not available. Try
compiling the C modules on your platform.")
+
+ # Test that the scipy is installed for the frame order analysis.
+ if pipe_type == 'frame order' and not scipy_module:
+ raise RelaxError("The frame order analysis is not available. Please
install the scipy Python package.")
def copy(pipe_from=None, pipe_to=None, bundle_to=None):
@@ -197,37 +228,6 @@
status.pipe_lock.release(sys._getframe().f_code.co_name)
-def check_type(pipe_type):
- """Check the validity of the given data pipe type.
-
- @keyword pipe_type: The data pipe type to check.
- @type pipe_type: str
- @raises RelaxError: If the data pipe type is invalid or the required
Python modules are missing.
- """
-
- # Test if pipe_type is valid.
- if not pipe_type in VALID_TYPES:
- raise RelaxError("The data pipe type " + repr(pipe_type) + " is
invalid and must be one of the strings in the list " + repr(VALID_TYPES) +
".")
-
- # Test that the C modules have been loaded.
- if pipe_type == 'relax_fit' and not C_module_exp_fn:
- raise RelaxError("Relaxation curve fitting is not available. Try
compiling the C modules on your platform.")
-
- # Test that the scipy is installed for the frame order analysis.
- if pipe_type == 'frame order' and not scipy_module:
- raise RelaxError("The frame order analysis is not available. Please
install the scipy Python package.")
-
-
-def cdp_name():
- """Return the name of the current data pipe.
-
- @return: The name of the current data pipe.
- @rtype: str
- """
-
- return ds.current_pipe
-
-
def current():
"""Print the name of the current data pipe."""
Modified: branches/frame_order_cleanup/pipe_control/spectrometer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/spectrometer.py?rev=26074&r1=26073&r2=26074&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/spectrometer.py (original)
+++ branches/frame_order_cleanup/pipe_control/spectrometer.py Fri Sep 26
19:09:29 2014
@@ -27,22 +27,47 @@
from warnings import warn
# relax module imports.
+from lib.checks import Check
from lib.errors import RelaxError, RelaxNoFrqError
from lib.periodic_table import periodic_table
-from lib.warnings import RelaxWarning
+from lib.warnings import RelaxWarning, RelaxNoFrqWarning
from pipe_control import pipes
-def check_frequency(id=None):
+def check_frequency_func(self, id=None):
"""Check that the frequency for the given ID has been set.
- @param id: The experiment ID string.
- @type id: str
+ @keyword id: The experiment ID string.
+ @type id: str
+ @return: The initialised RelaxError object or nothing.
+ @rtype: None or RelaxError instance
"""
# Check for the ID.
- if not hasattr(cdp, 'spectrometer_frq') or id not in
cdp.spectrometer_frq.keys():
- raise RelaxNoFrqError(id=id)
+ if not hasattr(cdp, 'spectrometer_frq') and id not in
cdp.spectrometer_frq.keys():
+ return RelaxNoFrqError(id=id)
+
+# Create the checking object.
+check_frequency = Check(check_frequency_func)
+
+
+def check_spectrometer_setup_func(self):
+ """Check that spectrometer frequencies have been set up.
+
+ @return: The initialised RelaxError object or nothing.
+ @rtype: None or RelaxError instance
+ """
+
+ # No data structure.
+ if not hasattr(cdp, 'spectrometer_frq'):
+ return RelaxNoFrqError()
+
+ # An empty list.
+ if not len(cdp.spectrometer_frq):
+ return RelaxNoFrqError()
+
+# Create the checking object.
+check_spectrometer_setup = Check(check_spectrometer_setup_func)
def copy_frequencies(pipe_from=None, pipe_to=None, id=None):
Modified: branches/frame_order_cleanup/specific_analyses/model_free/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/model_free/api.py?rev=26074&r1=26073&r2=26074&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/model_free/api.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/model_free/api.py Fri
Sep 26 19:09:29 2014
@@ -51,6 +51,7 @@
from pipe_control.exp_info import bmrb_write_citations, bmrb_write_methods,
bmrb_write_software
from pipe_control.interatomic import return_interatom_list
from pipe_control.mol_res_spin import count_spins, exists_mol_res_spin_data,
find_index, get_molecule_names, return_spin, return_spin_from_index,
return_spin_indices, spin_loop
+from pipe_control.spectrometer import check_spectrometer_setup
from specific_analyses.api_base import API_base
from specific_analyses.api_common import API_common
from specific_analyses.model_free.bmrb import sf_csa_read,
sf_model_free_read, to_bmrb_model
@@ -180,6 +181,9 @@
@keyword version: The BMRB NMR-STAR dictionary format to output to.
@type version: str
"""
+
+ # Checks.
+ check_spectrometer_setup(escalate=2)
# Alias the current data pipe.
cdp = pipes.get_pipe()
Modified: branches/frame_order_cleanup/test_suite/system_tests/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/bmrb.py?rev=26074&r1=26073&r2=26074&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/system_tests/bmrb.py
(original)
+++ branches/frame_order_cleanup/test_suite/system_tests/bmrb.py Fri
Sep 26 19:09:29 2014
@@ -260,14 +260,14 @@
self.interpreter.pipe.create('test', 'mf')
# Display.
- self.interpreter.bmrb.display(version='3.1')
+ self.assertRaises(RelaxError, self.interpreter.bmrb.display,
version='3.1')
# Reset and create a new data pipe.
self.interpreter.reset()
self.interpreter.pipe.create('test2', 'mf')
# Display again to show a GUI breakage.
- self.interpreter.bmrb.display(version='3.1')
+ self.assertRaises(RelaxError, self.interpreter.bmrb.display,
version='3.1')
def test_rw_bmrb_3_0_model_free(self):
r26074 - in /branches/frame_order_cleanup: ./ lib/ pipe_control/ specific_analyses/model_free/ test_suite/system_tests/