def __call__(self, parser, namespace, values, option_string=None):
# figure out what options are set
parse_files = hasattr(namespace, 'files')
parse_phil = hasattr(namespace, 'phil')
parse_dir = hasattr(namespace, 'dir')
# get previous values or define default
if ( parse_files and (getattr(namespace, 'files') is not None) ):
files = namespace.files
else:
files = list()
if ( parse_phil and (getattr(namespace, 'phil') is not None) ):
phil = namespace.phil
else:
phil = list()
if ( parse_dir and (getattr(namespace, 'dir') is not None) ):
directory = namespace.dir
else:
directory = list()
if ( hasattr(namespace, 'unknown') and
(getattr(namespace, 'unknown') is not None) ):
unknown = namespace.unknown
else:
unknown = list()
# separate values
for value in values:
if (os.path.isfile(value)):
files.append(value)
elif ( (isinstance(value, str)) and
('=' in value) ):
phil.append(value)
elif (os.path.isdir(value)):
directory.append(value)
else:
unknown.append(value)
# update options
if (parse_files):
setattr(namespace, 'files', files)
else:
unknown.extend(files)
if (parse_phil):
setattr(namespace, 'phil', phil)
else:
unknown.extend(phil)
if (parse_dir):
setattr(namespace, 'dir', directory)
else:
unknown.extend(directory)
# store unknown values for custom processing (if available)
setattr(namespace, 'unknown', unknown)
def process_phil(self, phil_list):
''''
Process PHIL arguments
Currently only handles command-line changes
Will add inclusion of PHIL files from data_manager first, then
command-line options
'''
print('Processing PHIL parameters:', file=self.logger)
print('-' * self.text_width, file=self.logger)
print('', file=self.logger)
printed_something = False
data_sources = list()
sources = list()
unused_phil = list()
# PHIL files are processed in order from command-line
if (self.data_manager.has_phils()):
phil_names = self.data_manager.get_phil_names()
phil = list()
print(' Adding PHIL files:', file=self.logger)
print(' ------------------', file=self.logger)
for name in phil_names:
# remove DataManager scope since input files are already loaded
phil_scope = self.data_manager.get_phil(name)
for phil_object in phil_scope.objects:
if (phil_object.name == 'data_manager'):
phil_scope.objects.remove(phil_object)
phil.append(phil_scope)
print(' %s' % name, file=self.logger)
data_sources.extend(phil)
print('', file=self.logger)
printed_something = True
# command-line PHIL arguments override any previous settings and are
# processed in given order
def custom_processor(arg):
unused_phil.append(arg)
return True
if (len(phil_list) > 0):
interpreter = self.master_phil.command_line_argument_interpreter(
home_scope='')
print(' Adding command-line PHIL:', file=self.logger)
print(' -------------------------', file=self.logger)
for phil in phil_list:
print(' %s' % phil, file=self.logger)
print('', file=self.logger)
printed_something = True
working = interpreter.process_args(
phil_list, custom_processor=custom_processor)
if (len(working) > 0):
sources.extend(working)
if (self.namespace.overwrite): # override overwrite if True
sources.append(iotbx.phil.parse('output.overwrite=True'))
if ((len(data_sources) + len(sources)) > 0):
self.working_phil, more_unused_phil = self.master_phil.fetch(
sources=data_sources + sources, track_unused_definitions=True)
unused_phil.extend(more_unused_phil)
else:
self.working_phil = self.master_phil
# show unrecognized parameters and abort
if (len(unused_phil) > 0):
print(' Unrecognized PHIL parameters:', file=self.logger)
print(' -----------------------------', file=self.logger)
for phil in unused_phil:
print(' %s' % phil, file=self.logger)
print('', file=self.logger)
error_message = 'Some PHIL parameters are not recognized by %s.\n' % \
self.prog
error_message += wordwrap(
'Please run this program with the --show-defaults option to see what parameters are available.',
max_chars=self.text_width) + '\n'
error_message += wordwrap(
'PHIL parameters in files should be fully specified (e.g. "output.overwrite" instead of just "overwrite")',
max_chars=self.text_width) + '\n'
raise Sorry(error_message)
if (not printed_something):
print(' No PHIL parameters found', file=self.logger)
print('', file=self.logger)
def process_phil(self, phil_list):
''''
Process PHIL arguments
Also checks PHIL arguments (command line and files) for parameters that
specify files (.type = path)
'''
print('Processing PHIL parameters:', file=self.logger)
print('-' * self.text_width, file=self.logger)
print('', file=self.logger)
printed_something = False
data_sources = list()
sources = list()
unused_phil = list()
# PHIL files are processed in order from command-line
if (self.data_manager.has_phils()):
phil_names = self.data_manager.get_phil_names()
phil = list()
print(' Adding PHIL files:', file=self.logger)
print(' ------------------', file=self.logger)
for name in phil_names:
# remove DataManager scope since input files are already loaded
phil_scope = self.data_manager.get_phil(name)
for phil_object in phil_scope.objects:
if (phil_object.name == 'data_manager'):
phil_scope.objects.remove(phil_object)
phil.append(phil_scope)
print(' %s' % name, file=self.logger)
data_sources.extend(phil)
print('', file=self.logger)
printed_something = True
# command-line PHIL arguments override any previous settings and are
# processed in given order
def custom_processor(arg):
unused_phil.append(arg)
return True
if (len(phil_list) > 0):
interpreter = self.master_phil.command_line_argument_interpreter(
home_scope='')
print(' Adding command-line PHIL:', file=self.logger)
print(' -------------------------', file=self.logger)
for phil in phil_list:
print(' %s' % phil, file=self.logger)
print('', file=self.logger)
printed_something = True
working = interpreter.process_args(
phil_list, custom_processor=custom_processor)
if (len(working) > 0):
sources.extend(working)
if (self.namespace.overwrite): # override overwrite if True
sources.append(iotbx.phil.parse('output.overwrite=True'))
if ((len(data_sources) + len(sources)) > 0):
self.working_phil, more_unused_phil = self.master_phil.fetch(
sources=data_sources + sources, track_unused_definitions=True)
unused_phil.extend(more_unused_phil)
else:
self.working_phil = self.master_phil.fetch()
# show unrecognized parameters and abort
if (len(unused_phil) > 0):
print(' Unrecognized PHIL parameters:', file=self.logger)
print(' -----------------------------', file=self.logger)
for phil in unused_phil:
print(' %s' % phil, file=self.logger)
print('', file=self.logger)
error_message = 'Some PHIL parameters are not recognized by %s.\n' % \
self.prog
error_message += wordwrap(
'Please run this program with the --show-defaults option to see what parameters are available.',
max_chars=self.text_width) + '\n'
error_message += wordwrap(
'PHIL parameters in files should be fully specified (e.g. "output.overwrite" instead of just "overwrite")',
max_chars=self.text_width) + '\n'
raise Sorry(error_message)
# process input phil for file/directory defintions and add to DataManager
# Note: if a PHIL file is input as a PHIL parameter, the contents of the
# file will NOT be parsed and validated. The PHIL file should be provided
# as a command-line argument. This is mostly for finding data files
# defined by PHIL parameters that should be added to the DataManager
diff_phil = self.master_phil.fetch_diff(self.working_phil)
paths = self.check_phil_for_paths(diff_phil)
if (len(paths) > 0):
files = list()
dirs = list()
for path in paths:
if (path is not None):
if (os.path.isfile(path)):
files.append(path)
elif (os.path.isdir(path)):
dirs.append(path)
if (self.parse_files):
self.process_files(files,
message='Processing files from PHIL:')
if (self.parse_dir):
self.process_dir(dirs,
message='Processing directories from PHIL:')
if (not printed_something):
print(' No PHIL parameters found', file=self.logger)
print('', file=self.logger)
def process_phil(self, phil_list):
''''
Process PHIL arguments
Currently only handles command-line changes
Will add inclusion of PHIL files from data_manager first, then
command-line options
'''
print('Processing PHIL parameters:', file=self.logger)
print('-' * 79, file=self.logger)
print('', file=self.logger)
printed_something = False
data_sources = list()
sources = list()
unused_phil = list()
# PHIL files are processed in order from command-line
if (self.data_manager.has_phils()):
phil_names = self.data_manager.get_phil_names()
phil = list()
for name in phil_names:
phil.append(self.data_manager.get_phil(name))
data_sources.extend(phil)
# command-line PHIL arguments override any previous settings
def custom_processor(arg):
unused_phil.append(arg)
return True
interpreter = self.master_phil.command_line_argument_interpreter(
home_scope='')
working = interpreter.process_args(phil_list,
custom_processor=custom_processor)
if (len(working) > 0):
sources.extend(working)
if (self.namespace.overwrite): # override overwrite if True
sources.append(iotbx.phil.parse('output.overwrite=True'))
self.working_phil, more_unused_phil = self.master_phil.fetch(
sources=data_sources + sources, track_unused_definitions=True)
unused_phil.extend(more_unused_phil)
try:
phil_diff = self.master_phil.fetch_diff(self.working_phil)
except RuntimeError as err:
raise Sorry(err)
is_different = (len(phil_diff.as_str()) > 0)
# show differences
if (is_different):
print(' Non-default PHIL parameters:', file=self.logger)
print(' ----------------------------', file=self.logger)
phil_diff.show(prefix=' ', out=self.logger)
printed_something = True
# write differences
if (self.namespace.write_modified):
if (is_different):
self.data_manager.write_phil_file(
self.modified_filename,
phil_diff.as_str(),
overwrite=self.namespace.overwrite)
else:
print(' No PHIL modifications to write', file=self.logger)
printed_something = True
# show unrecognized parameters and abort
if (len(unused_phil) > 0):
print('', file=self.logger)
print(' Unrecognized PHIL parameters:', file=self.logger)
print(' -----------------------------', file=self.logger)
for phil in unused_phil:
print(' %s' % phil, file=self.logger)
print('', file=self.logger)
error_message = 'Some PHIL parameters are not recognized by %s.\n' % \
self.prog
error_message += 'Please run this program with the --show-defaults option to see what parameters are available.\n'
error_message += 'PHIL parameters in files should be fully specified (e.g. "output.overwrite" instead of just "overwrite")'
raise Sorry(error_message)
if (not printed_something):
print(' No PHIL parameters found', file=self.logger)
print('', file=self.logger)
# show final processed phil scope
try:
data_diff = self.data_manager.master_phil.fetch_diff(
self.data_manager.export_phil_scope())
except RuntimeError as err:
raise Sorry(err)
is_different = ((len(data_diff.as_str()) + len(phil_diff.as_str())) >
0)
if (is_different):
print('Final processed PHIL parameters:')
print('-' * 79, file=self.logger)
data_diff.show(prefix=' ', out=self.logger)
phil_diff.show(prefix=' ', out=self.logger)
# write all parameters (DataManager + Program)
if (self.namespace.write_all):
all_phil = self.data_manager.export_phil_scope().as_str()
all_phil += self.working_phil.as_str(expert_level=3)
self.data_manager.write_phil_file(
self.all_filename,
all_phil,
overwrite=self.namespace.overwrite)
print('', file=self.logger)
