scripts.config_generator.savu_config._open() - Code Metrics - Inspection of "Merge pull request #913 from DiamondLightSource/4_..." - DiamondLightSource/Savu - Measure and Improve Code Quality continuously with Scrutinizer

Test Failed

Push — master ( 26b3f2...a95b01 )

by Daniil

created 2022-06-16 15:39 UTC

scripts.config_generator.savu_config._open() A

↳ Parent: scripts.config_generator.savu_config

Complexity

Conditions

Size

Total Lines	8
Code Lines	7

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	7
nop	2
dl	0
loc	8
rs	10
c	0
b	0
f	0

# Copyright 2014 Diamond Light Source Ltd.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

"""
.. module:: savu_config
   :platform: Unix
   :synopsis: A command line tool for creating Savu plugin lists

.. moduleauthor:: Nicola Wadeson <[email protected]>

"""

import re
import sys
import logging
from pathlib import Path
from . import hdf_utils as hu

from colorama import Fore

logger = logging.getLogger('documentationLog')
logger_rst = logging.getLogger('documentationRst')

import warnings
with warnings.catch_warnings():
    warnings.simplefilter("ignore")
    from .content import Content
    from .completer import Completer
    from . import display_formatter
    from .display_formatter import ListDisplay, DispDisplay, \
        CiteDisplay
    from . import arg_parsers as parsers
    from savu.plugins import utils as pu
    from . import config_utils as utils
    from .config_utils import parse_args
    from .config_utils import error_catcher


def _help(content, args):
    """ Display the help information"""
    width = display_formatter.get_terminal_width()
    command_title = " Savu configurator commands "
    title_separator = "*"*((width-len(command_title))//2)
    print(f"{title_separator}{command_title}{title_separator}")
    for key in sorted(list(commands.keys()),  key=str.lower):
        doc = commands[key].__doc__
        if doc:
            print(Fore.GREEN + f"{key:>8}" + Fore.RESET
                  + f" : {commands[key].__doc__}")
    line_separator = "*" * width
    info_text = "* For more information about individual commands type " \
                "'<command> -h' *"
    title_separator = " "*((width-len(info_text))//2)
    print(f"\n{line_separator}")
    print(f"{title_separator}{info_text}{title_separator}")
    print(line_separator)
    return content


@parse_args
@error_catcher
def _open(content, args):
    """ Open an existing process list."""
    content.fopen(args.file, update=True, skip=args.skip)
    _disp(content, '-q')
    _ref(content, '* -n')
    return content


@parse_args
@error_catcher
def _disp(content, args):
    """ Display the plugins in the current list."""
    range_dict = content.split_plugin_string(args.start, args.stop,
                                             subelem_view=True)
    formatter = DispDisplay(content.plugin_list)
    verbosity = parsers._get_verbosity(args)
    level = 'advanced' if args.all else content.disp_level
    datasets = True if args.datasets else False
    content.display(formatter, current_level=level, verbose=verbosity,
                    datasets=datasets, disp_level=args.level, **range_dict)
    return content


@parse_args
@error_catcher
def _list(content, args):
    """ List the available plugins. """
    list_content = Content()
    # Instead of reloading all plugins, copy the list of failed plugins
    list_content.failed = content.failed
    utils._populate_plugin_list(list_content, pfilter=args.string)
    if not len(list_content.plugin_list.plugin_list):
        print("No result found.")
        return content

    # Sort the list of dictionaries.
    # Sort by the name of the plugin within each dictionary.
    list_content.plugin_list.plugin_list = \
        sorted(list_content.plugin_list.plugin_list,
                key=lambda i: i['name'])

    formatter = ListDisplay(list_content.plugin_list)
    verbosity = parsers._get_verbosity(args)
    list_content.display(formatter, verbose=verbosity)
    return content


@parse_args
@error_catcher
def _save(content, args):
    """ Save the current process list to file."""
    out_file = content.filename if args.input else args.filepath
    content.check_file(out_file)
    print()
    DispDisplay(content.plugin_list)._notices()
    content.save(out_file, check=input("Are you sure you want to save the "
                 "current data to %s [y/N]" % (out_file)),
                 template=args.template)
    return content


@parse_args
@error_catcher
def _mod(content, args):
    """ Modify plugin parameters."""
    if args.globalpar:
        # deal with the global parameter
        command = 'global'
    else:
        pos_str, subelem, dims, command = \
            content.separate_plugin_subelem(args.param, False)
    if 'expand' in command:
        # Run the start stop step view for that dimension alone
        _expand(content, f"{pos_str} {dims} {True}")
    if 'global' in command:
        pos_list = content.get_positions()
        modified_list = False
        for pos_no in pos_list:
            valid_modification = content.modify_global(int(pos_no), args)
            if valid_modification:
                modified_list = True
        if modified_list:
            print("Parameter '{}' has been changed globally to '{}'".format(args.param, args.value[0]))
        else:
            print("Parameter '{}' has not been found in the process list".format(args.param))
    else:
        if not args.default:
            content.check_required_args(args.value, True)
        # Get the parameter name for the display later
        args.param = content.get_param_arg_str(pos_str, subelem)

        content_modified = content.modify(pos_str, subelem,
                                          ' '.join(args.value),
                                          default=args.default,
                                          dim=command)
        if content_modified:
            # Display the selected parameter only
            _disp(content, str(args.param))
    return content

@parse_args
@error_catcher
def _expand(content, args):
    """ Expand the plugin preview parameter. """
    content.set_preview_display(args.off, args.dim, args.dim_view,
                                args.plugin_pos)
    if content.expand_dim is not None:
        if content.expand_dim == "all" and args.dim is not None:
            check_str = f"Are you sure you want to alter the number of "\
                        f"dimensions to {args.dim}? [y/N]"
            is_modified = content.modify_dimensions(args.plugin_pos, args.dim,
                                                    check=input(check_str))
            if is_modified:
                _disp(content, f"{args.plugin_pos}.preview")
        else:
            _disp(content, f"{args.plugin_pos}.preview")
            #content.set_preview_display(args.off, "all")
    return content


@parse_args
@error_catcher
def _set(content, args):
    """ Set the status of the plugin to be on or off. """
    for pos in args.plugin_pos:
        content.on_and_off(pos, args.status.upper())
    _disp(content, '-q')
    return content


@parse_args
@error_catcher
def _add(content, args):
    """ Add a plugin to the list. """
    elems = content.get_positions()
    final = str(int(re.findall(r'\d+', elems[-1])[0])+1) if elems else 1
    content.add(args.name, args.pos if args.pos else str(final))
    content.check_iterative_loops([int(args.pos)] if args.pos else [int(final)], 1)
    _disp(content, '-q')
    return content


@parse_args
@error_catcher
def _iterate(content, args):
    """ Set a plugin (or group of plugins) to run iteratively. """
    # TODO: note the lack of use of _disp(); maybe will need this for
    # visually displaying the iterative loops in the terminal window?
    if args.remove is None and args.set is None:
        # display only the loops, not the rest of the process list
        content.display_iterative_loops()
    else:
        content.iterate(args)
        # display the process list with the visual markers of where iterative
        # loops are
        _disp(content, '-q')
    return content
    # TODO: the commented-out code below is associated with the TODO in
    # arg_parsers._iterate_arg_parser()
#    plugin_indices = args.indices
#    iterations = args.iterations
#
#    start = plugin_indices[0]
#    if len(plugin_indices) == 1:
#        # only the start index has been given, so there is only one element in
#        # the list
#        end = plugin_indices[0]
#    else:
#        # both the start and end index has been given, so there are two elements
#        # in the list
#        end = plugin_indices[1]
#
#    content.add_iterate_plugin_group(start, end, iterations[0])


@parse_args
@error_catcher
def _dupl(content, args):
    """ Duplicate a plugin in the list"""
    elems = content.get_positions()
    final = str(int(re.findall(r'\d+', elems[-1])[0])+1) if elems else 1
    content.duplicate(args.orig_pos, args.new_pos if args.new_pos else str(final))
    _disp(content, '-q')
    return content


@parse_args
@error_catcher
def _ref(content, args):
    """ Refresh a plugin (update it). """
    positions = content.get_positions() if args.pos == ['*'] else args.pos
    for pos_str in positions:
        content.refresh(pos_str, defaults=args.defaults)
        if not args.nodisp:
            _disp(content, pos_str)
    return content


@parse_args
@error_catcher
def _cite(content, args):
    """ Display plugin citations."""
    range_dict = content.split_plugin_string(args.start, args.stop)
    formatter = CiteDisplay(content.plugin_list)
    content.display(formatter, **range_dict)
    return content


@parse_args
@error_catcher
def _rem(content, args):
    """ Remove plugin(s) from the list. """
    pos_sort = []
    for pos in args.pos:
        pos_sort.append(int(pos))
    pos_sort.sort()
    counter=0
    for pos in pos_sort:
        if ((counter>0 and pos>0)):
            pos-=counter
        content.remove(content.find_position(str(pos)))
        counter+=1
        content.check_iterative_loops([pos], -1)
    _disp(content, '-q')
    return content


@parse_args
@error_catcher
def _move(content, args):
    """ Move a plugin to a different position in the list."""
    content.move(args.orig_pos, args.new_pos)
    _disp(content, '-q')
    return content


@parse_args
@error_catcher
def _coll(content, arg):
    """ List all plugin collections. """
    colls = Completer([])._get_collections()
    print('\n')
    for c in colls:
        print('%s\n %s' % ('-'*40, c))
    print('-'*40, '\n')
    return content

@parse_args
@error_catcher
def _clear(content, arg):
    """ Clear the current plugin list."""
    content.clear(check=input("Are you sure you want to clear the current "
                  "plugin list? [y/N]"))
    return content

@parse_args
@error_catcher
def _exit(content, arg):
    """ Close the program."""
    content.set_finished(check=input("Are you sure? [y/N]"))
    return content

@parse_args
@error_catcher
def _level(content, args):
    """ Set a visibility level for the parameters."""
    content.level(args.level)
    return content

@parse_args
@error_catcher
def _history(content, arg):
    """ View the history of previous commands """
    hlen = utils.readline.get_current_history_length()
    for i in range(hlen):
        print("%5i : %s" % (i, utils.readline.get_history_item(i)))
    return content

@parse_args
@error_catcher
def _replace(content, args):
    """ Replace a plugin with another """
    content.replace(args.old, args.new_plugin)
    _disp(content, '-q')
    return content

commands = {'open': _open,
            'help': _help,
            'disp': _disp,
            'list': _list,
            'save': _save,
            'mod': _mod,
            'set': _set,
            'add': _add,
            'dupl': _dupl,
            'rem': _rem,
            'move': _move,
            'ref': _ref,
            'level': _level,
            'expand': _expand,
            'cite': _cite,
            'coll': _coll,
            'clear': _clear,
            'exit': _exit,
            'history': _history,
            'iterate': _iterate,
            'replace': _replace}

def get_description():
    """ For each command, enter the function and save the docstring to a
    dictionary
    """
    command_desc_dict = {command: function_name.__doc__
                         for command, function_name in commands.items()}
    return command_desc_dict

def main(test=False):
    """
    :param test: If test is True the last argument from sys.argv is removed,
                 as it contains the directory of the test scripts, which fails the
                 parsing of the arguments as it has an unexpected argument.

                 If test is False then nothing is touched.
    """

    # required for running the tests locally or on travis
    # drops the last argument from pytest which is the test file/module
    if test:
        try:
            # find where the /scripts argument is
            index_of_scripts_argument = ["scripts" in arg for arg in sys.argv].index(True)
            # remove it, including every arguments after it (e.g --cov)
            sys.argv = sys.argv[:index_of_scripts_argument]
        except ValueError:
            # scripts was not part of the arguments passed in by the test
            pass

    args = parsers._config_arg_parser(doc=False)
    if args.tree is not None:
        file_path = args.tree
        hu.get_hdf_tree(file_path, add_shape=True, display=True)
        sys.exit(0)
    if args.find is not None:
        vals = args.find
        file_path = vals[0][0]
        pattern = vals[0][1]
        hu.find_hdf_key(file_path, pattern, display=True)
        sys.exit(0)
    if args.check is not None:
        file_path = args.check
        hu.check_tomo_data(file_path)
        sys.exit(0)
    if args.name is not None:
        args.file = args.name

    if args.error:
        utils.error_level = 1

    print("Running the configurator")
    print("Starting Savu Config tool (please wait for prompt)")

    _reduce_logging_level()

    content = Content(level="advanced" if args.disp_all else 'basic')

    with warnings.catch_warnings():
        warnings.simplefilter("ignore")
        # imports all the (working) plugin modules
        content.failed = utils.populate_plugins(error_mode=args.error,
                                                examples=args.examples)

    comp = Completer(commands=commands, plugin_list=pu.plugins)
    utils._set_readline(comp.complete)


    # if file flag is passed then open it here
    if args.file:
        commands['open'](content, args.file)

    print("\n*** Press Enter for a list of available commands. ***\n")

    utils.load_history_file(utils.histfile)
    accumulative_output = ''
    while True:
        try:
            name = f"{Path(content.filename).stem} " if content.filename else ""
            in_text = input(f"{name}>>> ").strip()
            in_list = in_text.split(' ', 1)
            _write_command_to_log(in_text)

        except KeyboardInterrupt:
            print()
            continue
        except EOFError:
            # makes possible exiting on CTRL + D (EOF, like Python interpreter)
            break

        command, arg = in_list if len(in_list) == 2 else in_list+['']
        command = command if command else 'help'
        if command not in commands:
            print("I'm sorry, that's not a command I recognise. Press Enter "
                  "for a list of available commands.")
        else:
            content = commands[command](content, arg)
            if logger.handlers:
                # Write the command output to a logger
                accumulative_output = _write_output_to_log(accumulative_output)

        if content.is_finished():
            break

    print("Thanks for using the application")


def _write_command_to_log(in_text):
    logger.debug("TEST COMMAND: " + in_text)
    logger_rst.debug(f".. dropdown:: >>> {in_text}\n\n" \
                     f"    .. code-block:: bash \n")


def _write_output_to_log(accumulative_output):
    """ Separate the current command output, format it correctly
    and write this to the restructured text log file.

    :param accumulative_output:
    :return: accumulative_output
    """
    current_output = sys.stdout.getvalue()

    # Find all previous command output
    length_Str = len(accumulative_output)
    if length_Str:
        # If there is previous output, then select only new lines from the
        # current command. This will demonstrate clearly the output of each
        # individual command
        current_output = current_output[length_Str:]

    # Characters used for command line colour
    unicode_chars = [u'\x1b[100m', u'\x1b[0m', u'\x1b[97m',
                     u'\x1b[49m', u'\x1b[46m', u'\x1b[39m',
                     u'\x1b[36m']
    # Remove unicode characters which cannot be displayed
    for code in unicode_chars:
        current_output = current_output.replace(code, '')

    # Indent the text for the rst file format
    indent_current_output = pu.indent_multi_line_str(current_output, 2)
    # Write to the rst log file
    logger_rst.debug(indent_current_output)
    return sys.stdout.getvalue()


def _reduce_logging_level():
    import logging
    logging.getLogger().setLevel(logging.CRITICAL)

if __name__ == '__main__':
    main()


1			# Copyright 2014 Diamond Light Source Ltd.
2			#
3			# Licensed under the Apache License, Version 2.0 (the "License");
4			# you may not use this file except in compliance with the License.
5			# You may obtain a copy of the License at
6			#
7			# http://www.apache.org/licenses/LICENSE-2.0
8			#
9			# Unless required by applicable law or agreed to in writing, software
10			# distributed under the License is distributed on an "AS IS" BASIS,
11			# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12			# See the License for the specific language governing permissions and
13			# limitations under the License.
14
15			"""
16			.. module:: savu_config
17			:platform: Unix
18			:synopsis: A command line tool for creating Savu plugin lists
19
20			.. moduleauthor:: Nicola Wadeson <[email protected]>
21
22			"""
23
24			import re
25			import sys
26			import logging
27			from pathlib import Path
28			from . import hdf_utils as hu
29
30			from colorama import Fore
31
32			logger = logging.getLogger('documentationLog')
33			logger_rst = logging.getLogger('documentationRst')
34
35			import warnings
36			with warnings.catch_warnings():
37			warnings.simplefilter("ignore")
38			from .content import Content
39			from .completer import Completer
40			from . import display_formatter
41			from .display_formatter import ListDisplay, DispDisplay, \
42			CiteDisplay
43			from . import arg_parsers as parsers
44			from savu.plugins import utils as pu
45			from . import config_utils as utils
46			from .config_utils import parse_args
47			from .config_utils import error_catcher
48
49
50			def _help(content, args):
51			""" Display the help information"""
52			width = display_formatter.get_terminal_width()
53			command_title = " Savu configurator commands "
54			title_separator = ""((width-len(command_title))//2)
55			print(f"{title_separator}{command_title}{title_separator}")
56			for key in sorted(list(commands.keys()), key=str.lower):
57			doc = commands[key].__doc__
58			if doc:
59			print(Fore.GREEN + f"{key:>8}" + Fore.RESET
60			+ f" : {commands[key].__doc__}")
61			line_separator = "" width
62			info_text = "* For more information about individual commands type " \
63			"'<command> -h' *"
64			title_separator = " "*((width-len(info_text))//2)
65			print(f"\n{line_separator}")
66			print(f"{title_separator}{info_text}{title_separator}")
67			print(line_separator)
68			return content
69
70
71			@parse_args
72			@error_catcher
73			def _open(content, args):
74			""" Open an existing process list."""
75			content.fopen(args.file, update=True, skip=args.skip)
76			_disp(content, '-q')
77			_ref(content, '* -n')
78			return content
79
80
81			@parse_args
82			@error_catcher
83			def _disp(content, args):
84			""" Display the plugins in the current list."""
85			range_dict = content.split_plugin_string(args.start, args.stop,
86			subelem_view=True)
87			formatter = DispDisplay(content.plugin_list)
88			verbosity = parsers._get_verbosity(args)
89			level = 'advanced' if args.all else content.disp_level
90			datasets = True if args.datasets else False
91			content.display(formatter, current_level=level, verbose=verbosity,
92			datasets=datasets, disp_level=args.level, **range_dict)
93			return content
94
95
96			@parse_args
97			@error_catcher
98			def _list(content, args):
99			""" List the available plugins. """
100			list_content = Content()
101			# Instead of reloading all plugins, copy the list of failed plugins
102			list_content.failed = content.failed
103			utils._populate_plugin_list(list_content, pfilter=args.string)
104			if not len(list_content.plugin_list.plugin_list):
105			print("No result found.")
106			return content
107
108			# Sort the list of dictionaries.
109			# Sort by the name of the plugin within each dictionary.
110			list_content.plugin_list.plugin_list = \
111			sorted(list_content.plugin_list.plugin_list,
112			key=lambda i: i['name'])
113
114			formatter = ListDisplay(list_content.plugin_list)
115			verbosity = parsers._get_verbosity(args)
116			list_content.display(formatter, verbose=verbosity)
117			return content
118
119
120			@parse_args
121			@error_catcher
122			def _save(content, args):
123			""" Save the current process list to file."""
124			out_file = content.filename if args.input else args.filepath
125			content.check_file(out_file)
126			print()
127			DispDisplay(content.plugin_list)._notices()
128			content.save(out_file, check=input("Are you sure you want to save the "
129			"current data to %s [y/N]" % (out_file)),
130			template=args.template)
131			return content
132
133
134			@parse_args
135			@error_catcher
136			def _mod(content, args):
137			""" Modify plugin parameters."""
138			if args.globalpar:
139			# deal with the global parameter
140			command = 'global'
141			else:
142			pos_str, subelem, dims, command = \
143			content.separate_plugin_subelem(args.param, False)
144			if 'expand' in command:
145			# Run the start stop step view for that dimension alone
146			_expand(content, f"{pos_str} {dims} {True}")
147			if 'global' in command:
148			pos_list = content.get_positions()
149			modified_list = False
150			for pos_no in pos_list:
151			valid_modification = content.modify_global(int(pos_no), args)
152			if valid_modification:
153			modified_list = True
154			if modified_list:
155			print("Parameter '{}' has been changed globally to '{}'".format(args.param, args.value[0]))
156			else:
157			print("Parameter '{}' has not been found in the process list".format(args.param))
158			else:
159			if not args.default:
160			content.check_required_args(args.value, True)
161			# Get the parameter name for the display later
162			args.param = content.get_param_arg_str(pos_str, subelem)
			0 ignored issues – show introduced 2022-06-15 14:24 UTC by Report Bug Copy Issue Report The variable `subelem` does not seem to be defined for all execution paths. Loading history... introduced 2022-06-15 14:24 UTC by Report Bug Copy Issue Report The variable `pos_str` does not seem to be defined for all execution paths. Loading history...
163			content_modified = content.modify(pos_str, subelem,
164			' '.join(args.value),
165			default=args.default,
166			dim=command)
167			if content_modified:
168			# Display the selected parameter only
169			_disp(content, str(args.param))
170			return content
171
172			@parse_args
173			@error_catcher
174			def _expand(content, args):
175			""" Expand the plugin preview parameter. """
176			content.set_preview_display(args.off, args.dim, args.dim_view,
177			args.plugin_pos)
178			if content.expand_dim is not None:
179			if content.expand_dim == "all" and args.dim is not None:
180			check_str = f"Are you sure you want to alter the number of "\
181			f"dimensions to {args.dim}? [y/N]"
182			is_modified = content.modify_dimensions(args.plugin_pos, args.dim,
183			check=input(check_str))
184			if is_modified:
185			_disp(content, f"{args.plugin_pos}.preview")
186			else:
187			_disp(content, f"{args.plugin_pos}.preview")
188			#content.set_preview_display(args.off, "all")
189			return content
190
191
192			@parse_args
193			@error_catcher
194			def _set(content, args):
195			""" Set the status of the plugin to be on or off. """
196			for pos in args.plugin_pos:
197			content.on_and_off(pos, args.status.upper())
198			_disp(content, '-q')
199			return content
200
201
202			@parse_args
203			@error_catcher
204			def _add(content, args):
205			""" Add a plugin to the list. """
206			elems = content.get_positions()
207			final = str(int(re.findall(r'\d+', elems[-1])[0])+1) if elems else 1
208			content.add(args.name, args.pos if args.pos else str(final))
209			content.check_iterative_loops([int(args.pos)] if args.pos else [int(final)], 1)
210			_disp(content, '-q')
211			return content
212
213
214			@parse_args
215			@error_catcher
216			def _iterate(content, args):
217			""" Set a plugin (or group of plugins) to run iteratively. """
218			# TODO: note the lack of use of _disp(); maybe will need this for
219			# visually displaying the iterative loops in the terminal window?
220			if args.remove is None and args.set is None:
221			# display only the loops, not the rest of the process list
222			content.display_iterative_loops()
223			else:
224			content.iterate(args)
225			# display the process list with the visual markers of where iterative
226			# loops are
227			_disp(content, '-q')
228			return content
229			# TODO: the commented-out code below is associated with the TODO in
230			# arg_parsers._iterate_arg_parser()
231			# plugin_indices = args.indices
232			# iterations = args.iterations
233			#
234			# start = plugin_indices[0]
235			# if len(plugin_indices) == 1:
236			# # only the start index has been given, so there is only one element in
237			# # the list
238			# end = plugin_indices[0]
239			# else:
240			# # both the start and end index has been given, so there are two elements
241			# # in the list
242			# end = plugin_indices[1]
243			#
244			# content.add_iterate_plugin_group(start, end, iterations[0])
245
246
247			@parse_args
248			@error_catcher
249			def _dupl(content, args):
250			""" Duplicate a plugin in the list"""
251			elems = content.get_positions()
252			final = str(int(re.findall(r'\d+', elems[-1])[0])+1) if elems else 1
253			content.duplicate(args.orig_pos, args.new_pos if args.new_pos else str(final))
254			_disp(content, '-q')
255			return content
256
257
258			@parse_args
259			@error_catcher
260			def _ref(content, args):
261			""" Refresh a plugin (update it). """
262			positions = content.get_positions() if args.pos == ['*'] else args.pos
263			for pos_str in positions:
264			content.refresh(pos_str, defaults=args.defaults)
265			if not args.nodisp:
266			_disp(content, pos_str)
267			return content
268
269
270			@parse_args
271			@error_catcher
272			def _cite(content, args):
273			""" Display plugin citations."""
274			range_dict = content.split_plugin_string(args.start, args.stop)
275			formatter = CiteDisplay(content.plugin_list)
276			content.display(formatter, **range_dict)
277			return content
278
279
280			@parse_args
281			@error_catcher
282			def _rem(content, args):
283			""" Remove plugin(s) from the list. """
284			pos_sort = []
285			for pos in args.pos:
286			pos_sort.append(int(pos))
287			pos_sort.sort()
288			counter=0
289			for pos in pos_sort:
290			if ((counter>0 and pos>0)):
291			pos-=counter
292			content.remove(content.find_position(str(pos)))
293			counter+=1
294			content.check_iterative_loops([pos], -1)
295			_disp(content, '-q')
296			return content
297
298
299			@parse_args
300			@error_catcher
301			def _move(content, args):
302			""" Move a plugin to a different position in the list."""
303			content.move(args.orig_pos, args.new_pos)
304			_disp(content, '-q')
305			return content
306
307
308			@parse_args
309			@error_catcher
310			def _coll(content, arg):
311			""" List all plugin collections. """
312			colls = Completer([])._get_collections()
313			print('\n')
314			for c in colls:
315			print('%s\n %s' % ('-'*40, c))
316			print('-'*40, '\n')
317			return content
318
319			@parse_args
320			@error_catcher
321			def _clear(content, arg):
322			""" Clear the current plugin list."""
323			content.clear(check=input("Are you sure you want to clear the current "
324			"plugin list? [y/N]"))
325			return content
326
327			@parse_args
328			@error_catcher
329			def _exit(content, arg):
330			""" Close the program."""
331			content.set_finished(check=input("Are you sure? [y/N]"))
332			return content
333
334			@parse_args
335			@error_catcher
336			def _level(content, args):
337			""" Set a visibility level for the parameters."""
338			content.level(args.level)
339			return content
340
341			@parse_args
342			@error_catcher
343			def _history(content, arg):
344			""" View the history of previous commands """
345			hlen = utils.readline.get_current_history_length()
346			for i in range(hlen):
347			print("%5i : %s" % (i, utils.readline.get_history_item(i)))
348			return content
349
350			@parse_args
351			@error_catcher
352			def _replace(content, args):
353			""" Replace a plugin with another """
354			content.replace(args.old, args.new_plugin)
355			_disp(content, '-q')
356			return content
357
358			commands = {'open': _open,
359			'help': _help,
360			'disp': _disp,
361			'list': _list,
362			'save': _save,
363			'mod': _mod,
364			'set': _set,
365			'add': _add,
366			'dupl': _dupl,
367			'rem': _rem,
368			'move': _move,
369			'ref': _ref,
370			'level': _level,
371			'expand': _expand,
372			'cite': _cite,
373			'coll': _coll,
374			'clear': _clear,
375			'exit': _exit,
376			'history': _history,
377			'iterate': _iterate,
378			'replace': _replace}
379
380			def get_description():
381			""" For each command, enter the function and save the docstring to a
382			dictionary
383			"""
384			command_desc_dict = {command: function_name.__doc__
385			for command, function_name in commands.items()}
386			return command_desc_dict
387
388			def main(test=False):
389			"""
390			:param test: If test is True the last argument from sys.argv is removed,
391			as it contains the directory of the test scripts, which fails the
392			parsing of the arguments as it has an unexpected argument.
393
394			If test is False then nothing is touched.
395			"""
396
397			# required for running the tests locally or on travis
398			# drops the last argument from pytest which is the test file/module
399			if test:
400			try:
401			# find where the /scripts argument is
402			index_of_scripts_argument = ["scripts" in arg for arg in sys.argv].index(True)
403			# remove it, including every arguments after it (e.g --cov)
404			sys.argv = sys.argv[:index_of_scripts_argument]
405			except ValueError:
406			# scripts was not part of the arguments passed in by the test
407			pass
408
409			args = parsers._config_arg_parser(doc=False)
410			if args.tree is not None:
411			file_path = args.tree
412			hu.get_hdf_tree(file_path, add_shape=True, display=True)
413			sys.exit(0)
414			if args.find is not None:
415			vals = args.find
416			file_path = vals[0][0]
417			pattern = vals[0][1]
418			hu.find_hdf_key(file_path, pattern, display=True)
419			sys.exit(0)
420			if args.check is not None:
421			file_path = args.check
422			hu.check_tomo_data(file_path)
423			sys.exit(0)
424			if args.name is not None:
425			args.file = args.name
426
427			if args.error:
428			utils.error_level = 1
429
430			print("Running the configurator")
431			print("Starting Savu Config tool (please wait for prompt)")
432
433			_reduce_logging_level()
434
435			content = Content(level="advanced" if args.disp_all else 'basic')
436
437			with warnings.catch_warnings():
438			warnings.simplefilter("ignore")
439			# imports all the (working) plugin modules
440			content.failed = utils.populate_plugins(error_mode=args.error,
441			examples=args.examples)
442
443			comp = Completer(commands=commands, plugin_list=pu.plugins)
444			utils._set_readline(comp.complete)
445
446
447			# if file flag is passed then open it here
448			if args.file:
449			commands['open'](content, args.file)
450
451			print("\n* Press Enter for a list of available commands. *\n")
452
453			utils.load_history_file(utils.histfile)
454			accumulative_output = ''
455			while True:
456			try:
457			name = f"{Path(content.filename).stem} " if content.filename else ""
458			in_text = input(f"{name}>>> ").strip()
459			in_list = in_text.split(' ', 1)
460			_write_command_to_log(in_text)
461
462			except KeyboardInterrupt:
463			print()
464			continue
465			except EOFError:
466			# makes possible exiting on CTRL + D (EOF, like Python interpreter)
467			break
468
469			command, arg = in_list if len(in_list) == 2 else in_list+['']
470			command = command if command else 'help'
471			if command not in commands:
472			print("I'm sorry, that's not a command I recognise. Press Enter "
473			"for a list of available commands.")
474			else:
475			content = commands[command](content, arg)
476			if logger.handlers:
477			# Write the command output to a logger
478			accumulative_output = _write_output_to_log(accumulative_output)
479
480			if content.is_finished():
481			break
482
483			print("Thanks for using the application")
484
485
486			def _write_command_to_log(in_text):
487			logger.debug("TEST COMMAND: " + in_text)
488			logger_rst.debug(f".. dropdown:: >>> {in_text}\n\n" \
489			f" .. code-block:: bash \n")
490
491
492			def _write_output_to_log(accumulative_output):
493			""" Separate the current command output, format it correctly
494			and write this to the restructured text log file.
495
496			:param accumulative_output:
497			:return: accumulative_output
498			"""
499			current_output = sys.stdout.getvalue()
500
501			# Find all previous command output
502			length_Str = len(accumulative_output)
503			if length_Str:
504			# If there is previous output, then select only new lines from the
505			# current command. This will demonstrate clearly the output of each
506			# individual command
507			current_output = current_output[length_Str:]
508
509			# Characters used for command line colour
510			unicode_chars = [u'\x1b[100m', u'\x1b[0m', u'\x1b[97m',
511			u'\x1b[49m', u'\x1b[46m', u'\x1b[39m',
512			u'\x1b[36m']
513			# Remove unicode characters which cannot be displayed
514			for code in unicode_chars:
515			current_output = current_output.replace(code, '')
516
517			# Indent the text for the rst file format
518			indent_current_output = pu.indent_multi_line_str(current_output, 2)
519			# Write to the rst log file
520			logger_rst.debug(indent_current_output)
521			return sys.stdout.getvalue()
522
523
524			def _reduce_logging_level():
525			import logging
526			logging.getLogger().setLevel(logging.CRITICAL)
527
528			if __name__ == '__main__':
529			main()
530

DiamondLightSource / Savu

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