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train | JsLinkProvider.build_default_filepath | Called when 'filepath' is not defined in the settings | django_mako_plus/provider/link.py | def build_default_filepath(self):
'''Called when 'filepath' is not defined in the settings'''
return os.path.join(
self.app_config.name,
'scripts',
self.template_relpath + '.js',
) | def build_default_filepath(self):
'''Called when 'filepath' is not defined in the settings'''
return os.path.join(
self.app_config.name,
'scripts',
self.template_relpath + '.js',
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train | django_include | Mako tag to include a Django template withing the current DMP (Mako) template.
Since this is a Django template, it is search for using the Django search
algorithm (instead of the DMP app-based concept).
See https://docs.djangoproject.com/en/2.1/topics/templates/.
The current context is sent to the incl... | django_mako_plus/tags.py | def django_include(context, template_name, **kwargs):
'''
Mako tag to include a Django template withing the current DMP (Mako) template.
Since this is a Django template, it is search for using the Django search
algorithm (instead of the DMP app-based concept).
See https://docs.djangoproject.com/en/2... | def django_include(context, template_name, **kwargs):
'''
Mako tag to include a Django template withing the current DMP (Mako) template.
Since this is a Django template, it is search for using the Django search
algorithm (instead of the DMP app-based concept).
See https://docs.djangoproject.com/en/2... | [
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train | _toggle_autoescape | Internal method to toggle autoescaping on or off. This function
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Internal method to toggle autoescaping on or off. This function
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'''
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Internal method to toggle autoescaping on or off. This function
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'''
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train | pretty_relpath | Returns a relative path, but only if it doesn't start with a non-pretty parent directory ".." | django_mako_plus/management/commands/dmp_cleanup.py | def pretty_relpath(path, start):
'''
Returns a relative path, but only if it doesn't start with a non-pretty parent directory ".."
'''
relpath = os.path.relpath(path, start)
if relpath.startswith('..'):
return path
return relpath | def pretty_relpath(path, start):
'''
Returns a relative path, but only if it doesn't start with a non-pretty parent directory ".."
'''
relpath = os.path.relpath(path, start)
if relpath.startswith('..'):
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train | view_function.is_decorated | Returns True if the given function is decorated with @view_function | django_mako_plus/router/decorators.py | def is_decorated(cls, f):
'''Returns True if the given function is decorated with @view_function'''
real_func = inspect.unwrap(f)
return real_func in cls.DECORATED_FUNCTIONS | def is_decorated(cls, f):
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real_func = inspect.unwrap(f)
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train | ProviderRun.initialize_providers | Initializes the providers (called from dmp app ready()) | django_mako_plus/provider/runner.py | def initialize_providers(cls):
'''Initializes the providers (called from dmp app ready())'''
dmp = apps.get_app_config('django_mako_plus')
# regular content providers
cls.CONTENT_PROVIDERS = []
for provider_settings in dmp.options[cls.SETTINGS_KEY]:
# import the class... | def initialize_providers(cls):
'''Initializes the providers (called from dmp app ready())'''
dmp = apps.get_app_config('django_mako_plus')
# regular content providers
cls.CONTENT_PROVIDERS = []
for provider_settings in dmp.options[cls.SETTINGS_KEY]:
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train | ProviderRun.run | Performs the run through the templates and their providers | django_mako_plus/provider/runner.py | def run(self):
'''Performs the run through the templates and their providers'''
for tpl in self.templates:
for provider in tpl.providers:
provider.provide() | def run(self):
'''Performs the run through the templates and their providers'''
for tpl in self.templates:
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train | ProviderRun.write | Provider instances use this to write to the buffer | django_mako_plus/provider/runner.py | def write(self, content):
'''Provider instances use this to write to the buffer'''
self.buffer.write(content)
if settings.DEBUG:
self.buffer.write('\n') | def write(self, content):
'''Provider instances use this to write to the buffer'''
self.buffer.write(content)
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train | ConverterFunctionInfo.prepare_sort_key | Triggered by view_function._sort_converters when our sort key should be created.
This can't be called in the constructor because Django models might not be ready yet. | django_mako_plus/converter/info.py | def prepare_sort_key(self):
'''
Triggered by view_function._sort_converters when our sort key should be created.
This can't be called in the constructor because Django models might not be ready yet.
'''
if isinstance(self.convert_type, str):
try:
app_n... | def prepare_sort_key(self):
'''
Triggered by view_function._sort_converters when our sort key should be created.
This can't be called in the constructor because Django models might not be ready yet.
'''
if isinstance(self.convert_type, str):
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train | CompileProvider.build_command | Returns the command to run, as a list (see subprocess module) | django_mako_plus/provider/compile.py | def build_command(self):
'''Returns the command to run, as a list (see subprocess module)'''
# if defined in settings, run the function or return the string
if self.options['command']:
return self.options['command'](self) if callable(self.options['command']) else self.options['comman... | def build_command(self):
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train | CompileProvider.needs_compile | Returns True if self.sourcepath is newer than self.targetpath | django_mako_plus/provider/compile.py | def needs_compile(self):
'''Returns True if self.sourcepath is newer than self.targetpath'''
try:
source_mtime = os.stat(self.sourcepath).st_mtime
except OSError: # no source for this template, so just return
return False
try:
target_mtime = os.stat(s... | def needs_compile(self):
'''Returns True if self.sourcepath is newer than self.targetpath'''
try:
source_mtime = os.stat(self.sourcepath).st_mtime
except OSError: # no source for this template, so just return
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train | template_inheritance | Generator that iterates the template and its ancestors.
The order is from most specialized (furthest descendant) to
most general (furthest ancestor).
obj can be either:
1. Mako Template object
2. Mako `self` object (available within a rendering template) | django_mako_plus/template/util.py | def template_inheritance(obj):
'''
Generator that iterates the template and its ancestors.
The order is from most specialized (furthest descendant) to
most general (furthest ancestor).
obj can be either:
1. Mako Template object
2. Mako `self` object (available within a rendering tem... | def template_inheritance(obj):
'''
Generator that iterates the template and its ancestors.
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train | get_template_debug | This structure is what Django wants when errors occur in templates.
It gives the user a nice stack trace in the error page during debug. | django_mako_plus/template/util.py | def get_template_debug(template_name, error):
'''
This structure is what Django wants when errors occur in templates.
It gives the user a nice stack trace in the error page during debug.
'''
# This is taken from mako.exceptions.html_error_template(), which has an issue
# in Py3 where files get l... | def get_template_debug(template_name, error):
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This structure is what Django wants when errors occur in templates.
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train | MakoTemplateAdapter.name | Returns the name of this template (if created from a file) or "string" if not | django_mako_plus/template/adapter.py | def name(self):
'''Returns the name of this template (if created from a file) or "string" if not'''
if self.mako_template.filename:
return os.path.basename(self.mako_template.filename)
return 'string' | def name(self):
'''Returns the name of this template (if created from a file) or "string" if not'''
if self.mako_template.filename:
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return 'string' | [
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train | MakoTemplateAdapter.render | Renders a template using the Mako system. This method signature conforms to
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@context A dictionary of name=value variables to send to the template page. This can be a real dictionary
or a Djang... | django_mako_plus/template/adapter.py | def render(self, context=None, request=None, def_name=None):
'''
Renders a template using the Mako system. This method signature conforms to
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@context A dictionary of name=value variables to send to t... | def render(self, context=None, request=None, def_name=None):
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Renders a template using the Mako system. This method signature conforms to
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train | MakoTemplateAdapter.render_to_response | Renders the template and returns an HttpRequest object containing its content.
This method returns a django.http.Http404 exception if the template is not found.
If the template raises a django_mako_plus.RedirectException, the browser is redirected to
the given page, and a new request from the b... | django_mako_plus/template/adapter.py | def render_to_response(self, context=None, request=None, def_name=None, content_type=None, status=None, charset=None):
'''
Renders the template and returns an HttpRequest object containing its content.
This method returns a django.http.Http404 exception if the template is not found.
If ... | def render_to_response(self, context=None, request=None, def_name=None, content_type=None, status=None, charset=None):
'''
Renders the template and returns an HttpRequest object containing its content.
This method returns a django.http.Http404 exception if the template is not found.
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train | DMPCommandMixIn.get_action_by_dest | Retrieves the given parser action object by its dest= attribute | django_mako_plus/management/mixins.py | def get_action_by_dest(self, parser, dest):
'''Retrieves the given parser action object by its dest= attribute'''
for action in parser._actions:
if action.dest == dest:
return action
return None | def get_action_by_dest(self, parser, dest):
'''Retrieves the given parser action object by its dest= attribute'''
for action in parser._actions:
if action.dest == dest:
return action
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train | DMPCommandMixIn.execute | Placing this in execute because then subclass handle() don't have to call super | django_mako_plus/management/mixins.py | def execute(self, *args, **options):
'''Placing this in execute because then subclass handle() don't have to call super'''
if options['verbose']:
options['verbosity'] = 3
if options['quiet']:
options['verbosity'] = 0
self.verbosity = options.get('verbosity', 1)
... | def execute(self, *args, **options):
'''Placing this in execute because then subclass handle() don't have to call super'''
if options['verbose']:
options['verbosity'] = 3
if options['quiet']:
options['verbosity'] = 0
self.verbosity = options.get('verbosity', 1)
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train | DMPCommandMixIn.message | Print a message to the console | django_mako_plus/management/mixins.py | def message(self, msg='', level=1, tab=0):
'''Print a message to the console'''
if self.verbosity >= level:
self.stdout.write('{}{}'.format(' ' * tab, msg)) | def message(self, msg='', level=1, tab=0):
'''Print a message to the console'''
if self.verbosity >= level:
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train | b58enc | Encodes a UID to an 11-length string, encoded using base58 url-safe alphabet | django_mako_plus/util/base58.py | def b58enc(uid):
'''Encodes a UID to an 11-length string, encoded using base58 url-safe alphabet'''
# note: i tested a buffer array too, but string concat was 2x faster
if not isinstance(uid, int):
raise ValueError('Invalid integer: {}'.format(uid))
if uid == 0:
return BASE58CHARS[0]
... | def b58enc(uid):
'''Encodes a UID to an 11-length string, encoded using base58 url-safe alphabet'''
# note: i tested a buffer array too, but string concat was 2x faster
if not isinstance(uid, int):
raise ValueError('Invalid integer: {}'.format(uid))
if uid == 0:
return BASE58CHARS[0]
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train | b58dec | Decodes a UID from base58, url-safe alphabet back to int. | django_mako_plus/util/base58.py | def b58dec(enc_uid):
'''Decodes a UID from base58, url-safe alphabet back to int.'''
if isinstance(enc_uid, str):
pass
elif isinstance(enc_uid, bytes):
enc_uid = enc_uid.decode('utf8')
else:
raise ValueError('Cannot decode this type: {}'.format(enc_uid))
uid = 0
try:
... | def b58dec(enc_uid):
'''Decodes a UID from base58, url-safe alphabet back to int.'''
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pass
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enc_uid = enc_uid.decode('utf8')
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uid = 0
try:
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train | minify | Minifies the source text (if needed) | django_mako_plus/management/commands/dmp_collectstatic.py | def minify(text, minifier):
'''Minifies the source text (if needed)'''
# there really isn't a good way to know if a file is already minified.
# our heuristic is if source is more than 50 bytes greater of dest OR
# if a hard return is found in the first 50 chars, we assume it is not minified.
minifie... | def minify(text, minifier):
'''Minifies the source text (if needed)'''
# there really isn't a good way to know if a file is already minified.
# our heuristic is if source is more than 50 bytes greater of dest OR
# if a hard return is found in the first 50 chars, we assume it is not minified.
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train | Rule.match | Returns the result score if the file matches this rule | django_mako_plus/management/commands/dmp_collectstatic.py | def match(self, fname, flevel, ftype):
'''Returns the result score if the file matches this rule'''
# if filetype is the same
# and level isn't set or level is the same
# and pattern matche the filename
if self.filetype == ftype and (self.level is None or self.level == flevel) an... | def match(self, fname, flevel, ftype):
'''Returns the result score if the file matches this rule'''
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train | Command.create_rules | Adds rules for the command line options | django_mako_plus/management/commands/dmp_collectstatic.py | def create_rules(self):
'''Adds rules for the command line options'''
dmp = apps.get_app_config('django_mako_plus')
# the default
rules = [
# files are included by default
Rule('*', level=None, filetype=TYPE_FILE, score=1),
... | def create_rules(self):
'''Adds rules for the command line options'''
dmp = apps.get_app_config('django_mako_plus')
# the default
rules = [
# files are included by default
Rule('*', level=None, filetype=TYPE_FILE, score=1),
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train | Command.copy_dir | Copies the static files from one directory to another. If this command is run, we assume the user wants to overwrite any existing files. | django_mako_plus/management/commands/dmp_collectstatic.py | def copy_dir(self, source, dest, level=0):
'''Copies the static files from one directory to another. If this command is run, we assume the user wants to overwrite any existing files.'''
encoding = settings.DEFAULT_CHARSET or 'utf8'
msglevel = 2 if level == 0 else 3
self.message('Directo... | def copy_dir(self, source, dest, level=0):
'''Copies the static files from one directory to another. If this command is run, we assume the user wants to overwrite any existing files.'''
encoding = settings.DEFAULT_CHARSET or 'utf8'
msglevel = 2 if level == 0 else 3
self.message('Directo... | [
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train | dmp_include | Includes a DMP (Mako) template into a normal django template.
context: automatically provided
template_name: specified as "app/template"
def_name: optional block to render within the template
Example:
{% load django_mako_plus %}
{% dmp_include "homepage/bsnav_dj.html" %}
... | django_mako_plus/templatetags/django_mako_plus.py | def dmp_include(context, template_name, def_name=None, **kwargs):
'''
Includes a DMP (Mako) template into a normal django template.
context: automatically provided
template_name: specified as "app/template"
def_name: optional block to render within the template
Example:
{... | def dmp_include(context, template_name, def_name=None, **kwargs):
'''
Includes a DMP (Mako) template into a normal django template.
context: automatically provided
template_name: specified as "app/template"
def_name: optional block to render within the template
Example:
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train | RoutingData.render | App-specific render function that renders templates in the *current app*, attached to the request for convenience | django_mako_plus/router/data.py | def render(self, template, context=None, def_name=None, subdir='templates', content_type=None, status=None, charset=None):
'''App-specific render function that renders templates in the *current app*, attached to the request for convenience'''
template_adapter = self.get_template_loader(subdir).get_templ... | def render(self, template, context=None, def_name=None, subdir='templates', content_type=None, status=None, charset=None):
'''App-specific render function that renders templates in the *current app*, attached to the request for convenience'''
template_adapter = self.get_template_loader(subdir).get_templ... | [
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train | RoutingData.render_to_string | App-specific render function that renders templates in the *current app*, attached to the request for convenience | django_mako_plus/router/data.py | def render_to_string(self, template, context=None, def_name=None, subdir='templates'):
'''App-specific render function that renders templates in the *current app*, attached to the request for convenience'''
template_adapter = self.get_template_loader(subdir).get_template(template)
return getattr... | def render_to_string(self, template, context=None, def_name=None, subdir='templates'):
'''App-specific render function that renders templates in the *current app*, attached to the request for convenience'''
template_adapter = self.get_template_loader(subdir).get_template(template)
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train | RoutingData.get_template_loader | App-specific function to get the current app's template loader | django_mako_plus/router/data.py | def get_template_loader(self, subdir='templates'):
'''App-specific function to get the current app's template loader'''
if self.request is None:
raise ValueError("this method can only be called after the view middleware is run. Check that `django_mako_plus.middleware` is in MIDDLEWARE.")
... | def get_template_loader(self, subdir='templates'):
'''App-specific function to get the current app's template loader'''
if self.request is None:
raise ValueError("this method can only be called after the view middleware is run. Check that `django_mako_plus.middleware` is in MIDDLEWARE.")
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train | Config.ready | Called by Django when the app is ready for use. | django_mako_plus/apps.py | def ready(self):
'''Called by Django when the app is ready for use.'''
# set up the options
self.options = {}
self.options.update(DEFAULT_OPTIONS)
for template_engine in settings.TEMPLATES:
if template_engine.get('BACKEND', '').startswith('django_mako_plus'):
... | def ready(self):
'''Called by Django when the app is ready for use.'''
# set up the options
self.options = {}
self.options.update(DEFAULT_OPTIONS)
for template_engine in settings.TEMPLATES:
if template_engine.get('BACKEND', '').startswith('django_mako_plus'):
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train | Config.is_registered_app | Returns true if the given app/app name is registered with DMP | django_mako_plus/apps.py | def is_registered_app(self, app):
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'''
Converts to int or float:
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Converts to int or float:
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train | convert_decimal | Converts to decimal.Decimal:
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'''
Converts to decimal.Decimal:
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Anything else uses Decimal constructor
'''
value = _check_default(value, parameter, ( '', '-', None ))
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Converts to decimal.Decimal:
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value = _check_default(value, parameter, ( '', '-', None ))
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train | convert_boolean | Converts to boolean (only the first char of the value is used):
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'''
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train | convert_datetime | Converts to datetime.datetime:
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Converts to datetime.datetime:
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Converts to datetime.datetime:
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train | convert_date | Converts to datetime.date:
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'''
value = _check_default(value, parameter, ( '', '-', None ))
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train | convert_id_to_model | Converts to a Model object.
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# not using a set here because it fails when value is unhashable
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train | parameter_converter | Decorator that denotes a function as a url parameter converter. | django_mako_plus/converter/decorators.py | def parameter_converter(*convert_types):
'''
Decorator that denotes a function as a url parameter converter.
'''
def inner(func):
for ct in convert_types:
ParameterConverter._register_converter(func, ct)
return func
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Decorator that denotes a function as a url parameter converter.
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train | protocol | Run all the stages in protocol
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handler : SystemHandler
Container of initial conditions of simulation
cfg : dict
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"""
Run all the stages in protocol
Parameters
----------
handler : SystemHandler
Container of initial conditions of simulation
cfg : dict
Imported YAML file.
"""
# Stages
if 'stages' not in cfg:
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Run all the stages in protocol
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handler : SystemHandler
Container of initial conditions of simulation
cfg : dict
Imported YAML file.
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positions, velocities : unit.Quantity([natoms, 3])
Position, velocity of each atom in the system
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Launch MD simulation, which may consist of:
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positions, velocities : unit.Quantity([natoms, 3])
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Launch MD simulation, which may consist of:
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train | Stage.minimize | Minimize energy of the system until meeting `tolerance` or
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"""
Minimize energy of the system until meeting `tolerance` or
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"""
if tolerance is None:
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train | Stage.simulate | Advance simulation n steps | ommprotocol/md.py | def simulate(self, steps=None):
"""
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"""
Advance simulation n steps
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Returns
-------
force : simtk.openmm.CustomExternalForce
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"""
Force that restrains atoms to fix their positions, while allowing
tiny movement to resolve severe clashes and so on.
Returns
-------
force : simtk.openmm.CustomExternalForce
A custom force to restrain... | def restraint_force(self, indices=None, strength=5.0):
"""
Force that restrains atoms to fix their positions, while allowing
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train | Stage.distance_restraint_force | Parameters
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atoms : tuple of tuple of int or str
Pair of atom indices to be restrained, with shape (n, 2),
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distances : tuple of float
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"""
Parameters
----------
atoms : tuple of tuple of int or str
Pair of atom indices to be restrained, with shape (n, 2),
like ((a1, a2), (a3, a4)). Items can be str compatible with MDTraj DSL.
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"""
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atoms : tuple of tuple of int or str
Pair of atom indices to be restrained, with shape (n, 2),
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"""
Returns a list of atom indices corresponding to a MDTraj DSL
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"""
if isinstance(selector, (list, tuple)):
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train | Stage.handle_exceptions | Handle Ctrl+C and accidental exceptions and attempt to save
the current state of the simulation | ommprotocol/md.py | def handle_exceptions(self, verbose=True):
"""
Handle Ctrl+C and accidental exceptions and attempt to save
the current state of the simulation
"""
try:
yield
except (KeyboardInterrupt, Exception) as ex:
if not self.attempt_rescue:
r... | def handle_exceptions(self, verbose=True):
"""
Handle Ctrl+C and accidental exceptions and attempt to save
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"""
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except (KeyboardInterrupt, Exception) as ex:
if not self.attempt_rescue:
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train | Stage.backup_simulation | Creates an emergency report run, .state included | ommprotocol/md.py | def backup_simulation(self):
"""
Creates an emergency report run, .state included
"""
path = self.new_filename(suffix='_emergency.state')
self.simulation.saveState(path)
uses_pbc = self.system.usesPeriodicBoundaryConditions()
state_kw = dict(getPositions=True, get... | def backup_simulation(self):
"""
Creates an emergency report run, .state included
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path = self.new_filename(suffix='_emergency.state')
self.simulation.saveState(path)
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train | prepare_input | Get, parse and prepare input file. | ommprotocol/io.py | def prepare_input(argv=None):
"""
Get, parse and prepare input file.
"""
p = ArgumentParser(description='InsiliChem Ommprotocol: '
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p.add_argument('input', metavar='INPUT FILE', type=extant_file,
help='YAML input file... | def prepare_input(argv=None):
"""
Get, parse and prepare input file.
"""
p = ArgumentParser(description='InsiliChem Ommprotocol: '
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train | prepare_handler | Load all files into single object. | ommprotocol/io.py | def prepare_handler(cfg):
"""
Load all files into single object.
"""
positions, velocities, box = None, None, None
_path = cfg.get('_path', './')
forcefield = cfg.pop('forcefield', None)
topology_args = sanitize_args_for_file(cfg.pop('topology'), _path)
if 'checkpoint' in cfg:
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train | prepare_system_options | Retrieve and delete (pop) system options from input configuration. | ommprotocol/io.py | def prepare_system_options(cfg, defaults=None):
"""
Retrieve and delete (pop) system options from input configuration.
"""
d = {} if defaults is None else defaults.copy()
if 'nonbondedMethod' in cfg:
d['nonbondedMethod'] = warned_getattr(openmm_app, cfg.pop('nonbondedMethod'), None)
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Retrieve and delete (pop) system options from input configuration.
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train | process_forcefield | Given a list of filenames, check which ones are `frcmods`. If so,
convert them to ffxml. Else, just return them. | ommprotocol/io.py | def process_forcefield(*forcefields):
"""
Given a list of filenames, check which ones are `frcmods`. If so,
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"""
for forcefield in forcefields:
if forcefield.endswith('.frcmod'):
gaffmol2 = os.path.splitext(forcefield)[0] + '.gaff.mol... | def process_forcefield(*forcefields):
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"""
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train | statexml2pdb | Given an OpenMM xml file containing the state of the simulation,
generate a PDB snapshot for easy visualization. | ommprotocol/io.py | def statexml2pdb(topology, state, output=None):
"""
Given an OpenMM xml file containing the state of the simulation,
generate a PDB snapshot for easy visualization.
"""
state = Restart.from_xml(state)
system = SystemHandler.load(topology, positions=state.positions)
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... | def statexml2pdb(topology, state, output=None):
"""
Given an OpenMM xml file containing the state of the simulation,
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"""
state = Restart.from_xml(state)
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train | export_frame_coordinates | Extract a single frame structure from a trajectory. | ommprotocol/io.py | def export_frame_coordinates(topology, trajectory, nframe, output=None):
"""
Extract a single frame structure from a trajectory.
"""
if output is None:
basename, ext = os.path.splitext(trajectory)
output = '{}.frame{}.inpcrd'.format(basename, nframe)
# ParmEd sometimes struggles wit... | def export_frame_coordinates(topology, trajectory, nframe, output=None):
"""
Extract a single frame structure from a trajectory.
"""
if output is None:
basename, ext = os.path.splitext(trajectory)
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train | YamlLoader.construct_include | Include file referenced at node. | ommprotocol/io.py | def construct_include(self, node):
"""Include file referenced at node."""
filename = os.path.join(self._root, self.construct_scalar(node))
filename = os.path.abspath(filename)
extension = os.path.splitext(filename)[1].lstrip('.')
with open(filename, 'r') as f:
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filename = os.path.join(self._root, self.construct_scalar(node))
filename = os.path.abspath(filename)
extension = os.path.splitext(filename)[1].lstrip('.')
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train | SystemHandler.from_pdb | Loads topology, positions and, potentially, velocities and vectors,
from a PDB or PDBx file
Parameters
----------
path : str
Path to PDB/PDBx file
forcefields : list of str
Paths to FFXML and/or FRCMOD forcefields. REQUIRED.
Returns
-----... | ommprotocol/io.py | def from_pdb(cls, path, forcefield=None, loader=PDBFile, strict=True, **kwargs):
"""
Loads topology, positions and, potentially, velocities and vectors,
from a PDB or PDBx file
Parameters
----------
path : str
Path to PDB/PDBx file
forcefields : list ... | def from_pdb(cls, path, forcefield=None, loader=PDBFile, strict=True, **kwargs):
"""
Loads topology, positions and, potentially, velocities and vectors,
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Parameters
----------
path : str
Path to PDB/PDBx file
forcefields : list ... | [
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train | SystemHandler.from_amber | Loads Amber Parm7 parameters and topology file
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path : str
Path to *.prmtop or *.top file
positions : simtk.unit.Quantity
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"""
Loads Amber Parm7 parameters and topology file
Parameters
----------
path : str
Path to *.prmtop or *.top file
positions : simtk.unit.Quantity
Atomic positions
Returns
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Loads Amber Parm7 parameters and topology file
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----------
path : str
Path to *.prmtop or *.top file
positions : simtk.unit.Quantity
Atomic positions
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path : str
Path to PSF file
forcefield : list of str
Paths to Charmm parameters files, such as *.par or *.str. REQUIRED
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"""
Loads PSF Charmm structure from `path`. Requires `charmm_parameters`.
Parameters
----------
path : str
Path to PSF file
forcefield : list of str
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Loads PSF Charmm structure from `path`. Requires `charmm_parameters`.
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path : str
Path to PSF file
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train | SystemHandler.from_desmond | Loads a topology from a Desmond DMS file located at `path`.
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train | SystemHandler.from_gromacs | Loads a topology from a Gromacs TOP file located at `path`.
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path : str
Path to a Gromacs TOP file
positions : simtk.unit.Quantity
Atomic positions
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"""
Loads a topology from a Gromacs TOP file located at `path`.
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Arguments
---------
path : str
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Loads a topology from a Gromacs TOP file located at `path`.
Additional root directory for parameters can be specified with `forcefield`.
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train | SystemHandler.from_parmed | Try to load a file automatically with ParmEd. Not guaranteed to work, but
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path : str
Path to file that ParmEd can load
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Path to file that ParmEd can load
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train | SystemHandler._pickle_load | Loads pickled topology. Careful with Python versions though! | ommprotocol/io.py | def _pickle_load(path):
"""
Loads pickled topology. Careful with Python versions though!
"""
_, ext = os.path.splitext(path)
topology = None
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Loads pickled topology. Careful with Python versions though!
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train | SystemHandler.create_system | Create an OpenMM system for every supported topology file with given system options | ommprotocol/io.py | def create_system(self, **system_options):
"""
Create an OpenMM system for every supported topology file with given system options
"""
if self.master is None:
raise ValueError('Handler {} is not able to create systems.'.format(self))
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Create an OpenMM system for every supported topology file with given system options
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train | SystemHandler.write_pdb | Outputs a PDB file with the current contents of the system | ommprotocol/io.py | def write_pdb(self, path):
"""
Outputs a PDB file with the current contents of the system
"""
if self.master is None and self.positions is None:
raise ValueError('Topology and positions are needed to write output files.')
with open(path, 'w') as f:
PDBFile... | def write_pdb(self, path):
"""
Outputs a PDB file with the current contents of the system
"""
if self.master is None and self.positions is None:
raise ValueError('Topology and positions are needed to write output files.')
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train | BoxVectors.from_xsc | Returns u.Quantity with box vectors from XSC file | ommprotocol/io.py | def from_xsc(cls, path):
""" Returns u.Quantity with box vectors from XSC file """
def parse(path):
"""
Open and parses an XSC file into its fields
Parameters
----------
path : str
Path to XSC file
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... | def from_xsc(cls, path):
""" Returns u.Quantity with box vectors from XSC file """
def parse(path):
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Open and parses an XSC file into its fields
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----------
path : str
Path to XSC file
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train | BoxVectors.from_csv | Get box vectors from comma-separated values in file `path`.
The csv file must containt only one line, which in turn can contain
three values (orthogonal vectors) or nine values (triclinic box).
The values should be in nanometers.
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----------
path : str
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"""
Get box vectors from comma-separated values in file `path`.
The csv file must containt only one line, which in turn can contain
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Get box vectors from comma-separated values in file `path`.
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train | ProgressBarReporter.describeNextReport | Get information about the next report this object will generate.
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simulation : Simulation
The Simulation to generate a report for
Returns
-------
tuple
A five element tuple. The first element is the number of steps
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Parameters
----------
simulation : Simulation
The Simulation to generate a report for
Returns
-------
tuple
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simulation : Simulation
The Simulation to generate a report for
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train | ProgressBarReporter.report | Generate a report.
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simulation : Simulation
The Simulation to generate a report for
state : State
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"""Generate a report.
Parameters
----------
simulation : Simulation
The Simulation to generate a report for
state : State
The current state of the simulation
"""
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simulation : Simulation
The Simulation to generate a report for
state : State
The current state of the simulation
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train | SerializedReporter.report | Generate a report.
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simulation : Simulation
The Simulation to generate a report for
state : State
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exists, check if `file.1.txt` also exists. Repeat until we find
a non-existing version, such as `file.12.txt`.
Parameters
----------
path : str
Path to be chec... | ommprotocol/utils.py | def assert_not_exists(path, sep='.'):
"""
If path exists, modify to add a counter in the filename. Useful
for preventing accidental overrides. For example, if `file.txt`
exists, check if `file.1.txt` also exists. Repeat until we find
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Parameters
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If path exists, modify to add a counter in the filename. Useful
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train | assertinstance | Make sure object `obj` is of type `types`. Else, raise TypeError. | ommprotocol/utils.py | def assertinstance(obj, types):
"""
Make sure object `obj` is of type `types`. Else, raise TypeError.
"""
if isinstance(obj, types):
return obj
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train | extant_file | Check if file exists with argparse | ommprotocol/utils.py | def extant_file(path):
"""
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if not os.path.exists(path):
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return path | def extant_file(path):
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Check if file exists with argparse
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train | sort_key_for_numeric_suffixes | Sort files taking into account potentially absent suffixes like
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somefile.1000.dcd
somefile.2000.dcd
To be used with sorted(..., key=callable). | ommprotocol/utils.py | def sort_key_for_numeric_suffixes(path, sep='.', suffix_index=-2):
"""
Sort files taking into account potentially absent suffixes like
somefile.dcd
somefile.1000.dcd
somefile.2000.dcd
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"""
chunks = path.split(sep)
# Remove suffix... | def sort_key_for_numeric_suffixes(path, sep='.', suffix_index=-2):
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Sort files taking into account potentially absent suffixes like
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somefile.1000.dcd
somefile.2000.dcd
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train | json_response | Wrap a view in JSON.
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All errors are then packaged up with an appropriate Content-Type and a JSON
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is thrown it's encoded as a 500.
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train | import_by_path | Import a dotted module path and return the attribute/class designated by
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train | endpoint_loader | Load an AJAX endpoint.
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endpoint depending on what it finds. It first attempts to load ``model``
as if it were an ad-hoc endpoint. Alternatively, it will attempt to see if
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"""Load an AJAX endpoint.
This will load either an ad-hoc endpoint or it will load up a model
endpoint depending on what it finds. It first attempts to load ``model``
as if it were an ad-hoc endpoint. Alternatively, it will attempt to see if
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train | ModelEndpoint.list | List objects of a model. By default will show page 1 with 20 objects on it.
**Usage**::
params = {"items_per_page":10,"page":2} //all params are optional
$.post("/ajax/{app}/{model}/list.json"),params) | ajax/endpoints.py | def list(self, request):
"""
List objects of a model. By default will show page 1 with 20 objects on it.
**Usage**::
params = {"items_per_page":10,"page":2} //all params are optional
$.post("/ajax/{app}/{model}/list.json"),params)
"""
max_items_per_pag... | def list(self, request):
"""
List objects of a model. By default will show page 1 with 20 objects on it.
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params = {"items_per_page":10,"page":2} //all params are optional
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train | ModelEndpoint._extract_data | Extract data from POST.
Handles extracting a vanilla Python dict of values that are present
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will convert those to the appropriate object instances from the
database. In other words, it will see that user is a ``Foreig... | ajax/endpoints.py | def _extract_data(self, request):
"""Extract data from POST.
Handles extracting a vanilla Python dict of values that are present
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will convert those to the appropriate object instances from the
database. In oth... | def _extract_data(self, request):
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train | ModelEndpoint._extract_value | If the value is true/false/null replace with Python equivalent. | ajax/endpoints.py | def _extract_value(self, value):
"""If the value is true/false/null replace with Python equivalent."""
return ModelEndpoint._value_map.get(smart_str(value).lower(), value) | def _extract_value(self, value):
"""If the value is true/false/null replace with Python equivalent."""
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train | ModelEndpoint._get_record | Fetch a given record.
Handles fetching a record from the database along with throwing an
appropriate instance of ``AJAXError`. | ajax/endpoints.py | def _get_record(self):
"""Fetch a given record.
Handles fetching a record from the database along with throwing an
appropriate instance of ``AJAXError`.
"""
if not self.pk:
raise AJAXError(400, _('Invalid request for record.'))
try:
return self.m... | def _get_record(self):
"""Fetch a given record.
Handles fetching a record from the database along with throwing an
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"""
if not self.pk:
raise AJAXError(400, _('Invalid request for record.'))
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train | ModelEndpoint.authenticate | Authenticate the AJAX request.
By default any request to fetch a model is allowed for any user,
including anonymous users. All other methods minimally require that
the user is already logged in.
Most likely you will want to lock down who can edit and delete various
models. To d... | ajax/endpoints.py | def authenticate(self, request, application, method):
"""Authenticate the AJAX request.
By default any request to fetch a model is allowed for any user,
including anonymous users. All other methods minimally require that
the user is already logged in.
Most likely you will want ... | def authenticate(self, request, application, method):
"""Authenticate the AJAX request.
By default any request to fetch a model is allowed for any user,
including anonymous users. All other methods minimally require that
the user is already logged in.
Most likely you will want ... | [
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train | EntriesProxy.all | Gets all entries of a space. | contentful_management/entries_proxy.py | def all(self, query=None):
"""
Gets all entries of a space.
"""
if query is None:
query = {}
if self.content_type_id is not None:
query['content_type'] = self.content_type_id
normalize_select(query)
return super(EntriesProxy, self).all(... | def all(self, query=None):
"""
Gets all entries of a space.
"""
if query is None:
query = {}
if self.content_type_id is not None:
query['content_type'] = self.content_type_id
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train | EntriesProxy.find | Gets a single entry by ID. | contentful_management/entries_proxy.py | def find(self, entry_id, query=None):
"""
Gets a single entry by ID.
"""
if query is None:
query = {}
if self.content_type_id is not None:
query['content_type'] = self.content_type_id
normalize_select(query)
return super(EntriesProxy, s... | def find(self, entry_id, query=None):
"""
Gets a single entry by ID.
"""
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query = {}
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train | EntriesProxy.create | Creates an entry with a given ID (optional) and attributes. | contentful_management/entries_proxy.py | def create(self, resource_id=None, attributes=None, **kwargs):
"""
Creates an entry with a given ID (optional) and attributes.
"""
if self.content_type_id is not None:
if attributes is None:
attributes = {}
attributes['content_type_id'] = self.con... | def create(self, resource_id=None, attributes=None, **kwargs):
"""
Creates an entry with a given ID (optional) and attributes.
"""
if self.content_type_id is not None:
if attributes is None:
attributes = {}
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train | WebhooksProxy.create | Creates a webhook with given attributes. | contentful_management/webhooks_proxy.py | def create(self, attributes=None, **kwargs):
"""
Creates a webhook with given attributes.
"""
return super(WebhooksProxy, self).create(resource_id=None, attributes=attributes) | def create(self, attributes=None, **kwargs):
"""
Creates a webhook with given attributes.
"""
return super(WebhooksProxy, self).create(resource_id=None, attributes=attributes) | [
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train | camel_case | Returns a camel-cased version of a string.
:param a_string: any :class:`str` object.
Usage:
>>> camel_case('foo_bar')
"fooBar" | contentful_management/utils.py | def camel_case(snake_str):
"""
Returns a camel-cased version of a string.
:param a_string: any :class:`str` object.
Usage:
>>> camel_case('foo_bar')
"fooBar"
"""
components = snake_str.split('_')
# We capitalize the first letter of each component except the first one
#... | def camel_case(snake_str):
"""
Returns a camel-cased version of a string.
:param a_string: any :class:`str` object.
Usage:
>>> camel_case('foo_bar')
"fooBar"
"""
components = snake_str.split('_')
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train | normalize_select | If the query contains the :select operator, we enforce :sys properties.
The SDK requires sys.type to function properly, but as other of our
SDKs require more parts of the :sys properties, we decided that every
SDK should include the complete :sys block to provide consistency
accross our SDKs. | contentful_management/utils.py | def normalize_select(query):
"""
If the query contains the :select operator, we enforce :sys properties.
The SDK requires sys.type to function properly, but as other of our
SDKs require more parts of the :sys properties, we decided that every
SDK should include the complete :sys block to provide con... | def normalize_select(query):
"""
If the query contains the :select operator, we enforce :sys properties.
The SDK requires sys.type to function properly, but as other of our
SDKs require more parts of the :sys properties, we decided that every
SDK should include the complete :sys block to provide con... | [
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train | Environment.to_json | Returns the JSON representation of the environment. | contentful_management/environment.py | def to_json(self):
"""
Returns the JSON representation of the environment.
"""
result = super(Environment, self).to_json()
result.update({
'name': self.name
})
return result | def to_json(self):
"""
Returns the JSON representation of the environment.
"""
result = super(Environment, self).to_json()
result.update({
'name': self.name
})
return result | [
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train | Environment.content_types | Provides access to content type management methods for content types of an environment.
API reference: https://www.contentful.com/developers/docs/references/content-management-api/#/reference/content-types
:return: :class:`EnvironmentContentTypesProxy <contentful_management.space_content_types_proxy.E... | contentful_management/environment.py | def content_types(self):
"""
Provides access to content type management methods for content types of an environment.
API reference: https://www.contentful.com/developers/docs/references/content-management-api/#/reference/content-types
:return: :class:`EnvironmentContentTypesProxy <cont... | def content_types(self):
"""
Provides access to content type management methods for content types of an environment.
API reference: https://www.contentful.com/developers/docs/references/content-management-api/#/reference/content-types
:return: :class:`EnvironmentContentTypesProxy <cont... | [
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train | Environment.entries | Provides access to entry management methods.
API reference: https://www.contentful.com/developers/docs/references/content-management-api/#/reference/entries
:return: :class:`EnvironmentEntriesProxy <contentful_management.environment_entries_proxy.EnvironmentEntriesProxy>` object.
:rtype: conte... | contentful_management/environment.py | def entries(self):
"""
Provides access to entry management methods.
API reference: https://www.contentful.com/developers/docs/references/content-management-api/#/reference/entries
:return: :class:`EnvironmentEntriesProxy <contentful_management.environment_entries_proxy.EnvironmentEntri... | def entries(self):
"""
Provides access to entry management methods.
API reference: https://www.contentful.com/developers/docs/references/content-management-api/#/reference/entries
:return: :class:`EnvironmentEntriesProxy <contentful_management.environment_entries_proxy.EnvironmentEntri... | [
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train | Environment.assets | Provides access to asset management methods.
API reference: https://www.contentful.com/developers/docs/references/content-management-api/#/reference/assets
:return: :class:`EnvironmentAssetsProxy <contentful_management.environment_assets_proxy.EnvironmentAssetsProxy>` object.
:rtype: contentfu... | contentful_management/environment.py | def assets(self):
"""
Provides access to asset management methods.
API reference: https://www.contentful.com/developers/docs/references/content-management-api/#/reference/assets
:return: :class:`EnvironmentAssetsProxy <contentful_management.environment_assets_proxy.EnvironmentAssetsPro... | def assets(self):
"""
Provides access to asset management methods.
API reference: https://www.contentful.com/developers/docs/references/content-management-api/#/reference/assets
:return: :class:`EnvironmentAssetsProxy <contentful_management.environment_assets_proxy.EnvironmentAssetsPro... | [
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train | Environment.locales | Provides access to locale management methods.
API reference: https://www.contentful.com/developers/docs/references/content-management-api/#/reference/locales
:return: :class:`EnvironmentLocalesProxy <contentful_management.environment_locales_proxy.EnvironmentLocalesProxy>` object.
:rtype: cont... | contentful_management/environment.py | def locales(self):
"""
Provides access to locale management methods.
API reference: https://www.contentful.com/developers/docs/references/content-management-api/#/reference/locales
:return: :class:`EnvironmentLocalesProxy <contentful_management.environment_locales_proxy.EnvironmentLoca... | def locales(self):
"""
Provides access to locale management methods.
API reference: https://www.contentful.com/developers/docs/references/content-management-api/#/reference/locales
:return: :class:`EnvironmentLocalesProxy <contentful_management.environment_locales_proxy.EnvironmentLoca... | [
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] | contentful/contentful-management.py | python | https://github.com/contentful/contentful-management.py/blob/707dd30883b98a10c7ff0f7f5bdb8edbdc1d8df0/contentful_management/environment.py#L119-L134 | [
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train | Environment.ui_extensions | Provides access to UI extensions management methods.
API reference: https://www.contentful.com/developers/docs/references/content-management-api/#/reference/ui-extensions
:return: :class:`EnvironmentUIExtensionsProxy <contentful_management.ui_extensions_proxy.EnvironmentUIExtensionsProxy>` object.
... | contentful_management/environment.py | def ui_extensions(self):
"""
Provides access to UI extensions management methods.
API reference: https://www.contentful.com/developers/docs/references/content-management-api/#/reference/ui-extensions
:return: :class:`EnvironmentUIExtensionsProxy <contentful_management.ui_extensions_pro... | def ui_extensions(self):
"""
Provides access to UI extensions management methods.
API reference: https://www.contentful.com/developers/docs/references/content-management-api/#/reference/ui-extensions
:return: :class:`EnvironmentUIExtensionsProxy <contentful_management.ui_extensions_pro... | [
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train | PersonalAccessTokensProxy.delete | Revokes a personal access token. | contentful_management/personal_access_tokens_proxy.py | def delete(self, token_id, *args, **kwargs):
"""
Revokes a personal access token.
"""
return self.client._put(
"{0}/revoked".format(
self._url(token_id)
),
None,
*args,
**kwargs
) | def delete(self, token_id, *args, **kwargs):
"""
Revokes a personal access token.
"""
return self.client._put(
"{0}/revoked".format(
self._url(token_id)
),
None,
*args,
**kwargs
) | [
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] | contentful/contentful-management.py | python | https://github.com/contentful/contentful-management.py/blob/707dd30883b98a10c7ff0f7f5bdb8edbdc1d8df0/contentful_management/personal_access_tokens_proxy.py#L39-L51 | [
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train | PersonalAccessTokensProxy.revoke | Revokes a personal access token. | contentful_management/personal_access_tokens_proxy.py | def revoke(self, token_id, *args, **kwargs):
"""
Revokes a personal access token.
"""
return self.delete(token_id, *args, **kwargs) | def revoke(self, token_id, *args, **kwargs):
"""
Revokes a personal access token.
"""
return self.delete(token_id, *args, **kwargs) | [
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train | Resource.base_url | Returns the URI for the resource. | contentful_management/resource.py | def base_url(klass, space_id='', resource_id=None, environment_id=None, **kwargs):
"""
Returns the URI for the resource.
"""
url = "spaces/{0}".format(
space_id)
if environment_id is not None:
url = url = "{0}/environments/{1}".format(url, environment_id... | def base_url(klass, space_id='', resource_id=None, environment_id=None, **kwargs):
"""
Returns the URI for the resource.
"""
url = "spaces/{0}".format(
space_id)
if environment_id is not None:
url = url = "{0}/environments/{1}".format(url, environment_id... | [
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] | contentful/contentful-management.py | python | https://github.com/contentful/contentful-management.py/blob/707dd30883b98a10c7ff0f7f5bdb8edbdc1d8df0/contentful_management/resource.py#L37-L56 | [
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train | Resource.create_attributes | Attributes for resource creation. | contentful_management/resource.py | def create_attributes(klass, attributes, previous_object=None):
"""
Attributes for resource creation.
"""
result = {}
if previous_object is not None:
result = {k: v for k, v in previous_object.to_json().items() if k != 'sys'}
result.update(attributes)
... | def create_attributes(klass, attributes, previous_object=None):
"""
Attributes for resource creation.
"""
result = {}
if previous_object is not None:
result = {k: v for k, v in previous_object.to_json().items() if k != 'sys'}
result.update(attributes)
... | [
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] | contentful/contentful-management.py | python | https://github.com/contentful/contentful-management.py/blob/707dd30883b98a10c7ff0f7f5bdb8edbdc1d8df0/contentful_management/resource.py#L59-L71 | [
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