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inveniosoftware/invenio-access | invenio_access/models.py | get_action_cache_key | def get_action_cache_key(name, argument):
"""Get an action cache key string."""
tokens = [str(name)]
if argument:
tokens.append(str(argument))
return '::'.join(tokens) | python | def get_action_cache_key(name, argument):
"""Get an action cache key string."""
tokens = [str(name)]
if argument:
tokens.append(str(argument))
return '::'.join(tokens) | [
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inveniosoftware/invenio-access | invenio_access/models.py | removed_or_inserted_action | def removed_or_inserted_action(mapper, connection, target):
"""Remove the action from cache when an item is inserted or deleted."""
current_access.delete_action_cache(get_action_cache_key(target.action,
target.argument)) | python | def removed_or_inserted_action(mapper, connection, target):
"""Remove the action from cache when an item is inserted or deleted."""
current_access.delete_action_cache(get_action_cache_key(target.action,
target.argument)) | [
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inveniosoftware/invenio-access | invenio_access/models.py | changed_action | def changed_action(mapper, connection, target):
"""Remove the action from cache when an item is updated."""
action_history = get_history(target, 'action')
argument_history = get_history(target, 'argument')
owner_history = get_history(
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if action_history.has_changes() or argument_history.has_changes() \
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get_action_cache_key(target.action, target.argument))
current_access.delete_action_cache(
get_action_cache_key(
action_history.deleted[0] if action_history.deleted
else target.action,
argument_history.deleted[0] if argument_history.deleted
else target.argument)
) | python | def changed_action(mapper, connection, target):
"""Remove the action from cache when an item is updated."""
action_history = get_history(target, 'action')
argument_history = get_history(target, 'argument')
owner_history = get_history(
target,
'user' if isinstance(target, ActionUsers) else
'role' if isinstance(target, ActionRoles) else 'role_name')
if action_history.has_changes() or argument_history.has_changes() \
or owner_history.has_changes():
current_access.delete_action_cache(
get_action_cache_key(target.action, target.argument))
current_access.delete_action_cache(
get_action_cache_key(
action_history.deleted[0] if action_history.deleted
else target.action,
argument_history.deleted[0] if argument_history.deleted
else target.argument)
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inveniosoftware/invenio-access | invenio_access/models.py | ActionNeedMixin.allow | def allow(cls, action, **kwargs):
"""Allow the given action need.
:param action: The action to allow.
:returns: A :class:`invenio_access.models.ActionNeedMixin` instance.
"""
return cls.create(action, exclude=False, **kwargs) | python | def allow(cls, action, **kwargs):
"""Allow the given action need.
:param action: The action to allow.
:returns: A :class:`invenio_access.models.ActionNeedMixin` instance.
"""
return cls.create(action, exclude=False, **kwargs) | [
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inveniosoftware/invenio-access | invenio_access/models.py | ActionNeedMixin.deny | def deny(cls, action, **kwargs):
"""Deny the given action need.
:param action: The action to deny.
:returns: A :class:`invenio_access.models.ActionNeedMixin` instance.
"""
return cls.create(action, exclude=True, **kwargs) | python | def deny(cls, action, **kwargs):
"""Deny the given action need.
:param action: The action to deny.
:returns: A :class:`invenio_access.models.ActionNeedMixin` instance.
"""
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inveniosoftware/invenio-access | invenio_access/models.py | ActionNeedMixin.query_by_action | def query_by_action(cls, action, argument=None):
"""Prepare query object with filtered action.
:param action: The action to deny.
:param argument: The action argument. If it's ``None`` then, if exists,
the ``action.argument`` will be taken. In the worst case will be
set as ``None``. (Default: ``None``)
:returns: A query object.
"""
query = cls.query.filter_by(action=action.value)
argument = argument or getattr(action, 'argument', None)
if argument is not None:
query = query.filter(db.or_(
cls.argument == str(argument),
cls.argument.is_(None),
))
else:
query = query.filter(cls.argument.is_(None))
return query | python | def query_by_action(cls, action, argument=None):
"""Prepare query object with filtered action.
:param action: The action to deny.
:param argument: The action argument. If it's ``None`` then, if exists,
the ``action.argument`` will be taken. In the worst case will be
set as ``None``. (Default: ``None``)
:returns: A query object.
"""
query = cls.query.filter_by(action=action.value)
argument = argument or getattr(action, 'argument', None)
if argument is not None:
query = query.filter(db.or_(
cls.argument == str(argument),
cls.argument.is_(None),
))
else:
query = query.filter(cls.argument.is_(None))
return query | [
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BD2KGenomics/protect | src/protect/binding_prediction/mhci.py | predict_mhci_binding | def predict_mhci_binding(job, peptfile, allele, peplen, univ_options, mhci_options):
"""
Predict binding for each peptide in `peptfile` to `allele` using the IEDB mhci binding
prediction tool.
:param toil.fileStore.FileID peptfile: The input peptide fasta
:param str allele: Allele to predict binding against
:param str peplen: Length of peptides to process
:param dict univ_options: Dict of universal options used by almost all tools
:param dict mhci_options: Options specific to mhci binding prediction
:return: fsID for file containing the predictions
:rtype: toil.fileStore.FileID
"""
work_dir = os.getcwd()
input_files = {
'peptfile.faa': peptfile}
input_files = get_files_from_filestore(job, input_files, work_dir, docker=True)
peptides = read_peptide_file(os.path.join(os.getcwd(), 'peptfile.faa'))
if not peptides:
return job.fileStore.writeGlobalFile(job.fileStore.getLocalTempFile())
parameters = [mhci_options['pred'],
allele,
peplen,
input_files['peptfile.faa']]
with open('/'.join([work_dir, 'predictions.tsv']), 'w') as predfile:
docker_call(tool='mhci', tool_parameters=parameters, work_dir=work_dir,
dockerhub=univ_options['dockerhub'], outfile=predfile, interactive=True,
tool_version=mhci_options['version'])
output_file = job.fileStore.writeGlobalFile(predfile.name)
job.fileStore.logToMaster('Ran mhci on %s:%s:%s successfully'
% (univ_options['patient'], allele, peplen))
return output_file | python | def predict_mhci_binding(job, peptfile, allele, peplen, univ_options, mhci_options):
"""
Predict binding for each peptide in `peptfile` to `allele` using the IEDB mhci binding
prediction tool.
:param toil.fileStore.FileID peptfile: The input peptide fasta
:param str allele: Allele to predict binding against
:param str peplen: Length of peptides to process
:param dict univ_options: Dict of universal options used by almost all tools
:param dict mhci_options: Options specific to mhci binding prediction
:return: fsID for file containing the predictions
:rtype: toil.fileStore.FileID
"""
work_dir = os.getcwd()
input_files = {
'peptfile.faa': peptfile}
input_files = get_files_from_filestore(job, input_files, work_dir, docker=True)
peptides = read_peptide_file(os.path.join(os.getcwd(), 'peptfile.faa'))
if not peptides:
return job.fileStore.writeGlobalFile(job.fileStore.getLocalTempFile())
parameters = [mhci_options['pred'],
allele,
peplen,
input_files['peptfile.faa']]
with open('/'.join([work_dir, 'predictions.tsv']), 'w') as predfile:
docker_call(tool='mhci', tool_parameters=parameters, work_dir=work_dir,
dockerhub=univ_options['dockerhub'], outfile=predfile, interactive=True,
tool_version=mhci_options['version'])
output_file = job.fileStore.writeGlobalFile(predfile.name)
job.fileStore.logToMaster('Ran mhci on %s:%s:%s successfully'
% (univ_options['patient'], allele, peplen))
return output_file | [
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rmohr/static3 | static.py | iter_and_close | def iter_and_close(file_like, block_size):
"""Yield file contents by block then close the file."""
while 1:
try:
block = file_like.read(block_size)
if block:
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"""Yield file contents by block then close the file."""
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if block:
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rmohr/static3 | static.py | cling_wrap | def cling_wrap(package_name, dir_name, **kw):
"""Return a Cling that serves from the given package and dir_name.
This uses pkg_resources.resource_filename which is not the
recommended way, since it extracts the files.
I think this works fine unless you have some _very_ serious
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shouldn't be serving it through a WSGI app, IMHO. YMMV.
"""
resource = Requirement.parse(package_name)
return Cling(resource_filename(resource, dir_name), **kw) | python | def cling_wrap(package_name, dir_name, **kw):
"""Return a Cling that serves from the given package and dir_name.
This uses pkg_resources.resource_filename which is not the
recommended way, since it extracts the files.
I think this works fine unless you have some _very_ serious
requirements for static content, in which case you probably
shouldn't be serving it through a WSGI app, IMHO. YMMV.
"""
resource = Requirement.parse(package_name)
return Cling(resource_filename(resource, dir_name), **kw) | [
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rmohr/static3 | static.py | Cling._is_under_root | def _is_under_root(self, full_path):
"""Guard against arbitrary file retrieval."""
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return False | python | def _is_under_root(self, full_path):
"""Guard against arbitrary file retrieval."""
if (path.abspath(full_path) + path.sep)\
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rmohr/static3 | static.py | Shock._match_magic | def _match_magic(self, full_path):
"""Return the first magic that matches this path or None."""
for magic in self.magics:
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return magic | python | def _match_magic(self, full_path):
"""Return the first magic that matches this path or None."""
for magic in self.magics:
if magic.matches(full_path):
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rmohr/static3 | static.py | Shock._full_path | def _full_path(self, path_info):
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return full_path
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return magic.new_path(full_path)
else:
return full_path | python | def _full_path(self, path_info):
"""Return the full path from which to read."""
full_path = self.root + path_info
if path.exists(full_path):
return full_path
else:
for magic in self.magics:
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return magic.new_path(full_path)
else:
return full_path | [
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rmohr/static3 | static.py | Shock._guess_type | def _guess_type(self, full_path):
"""Guess the mime type magically or using the mimetypes module."""
magic = self._match_magic(full_path)
if magic is not None:
return (mimetypes.guess_type(magic.old_path(full_path))[0]
or 'text/plain')
else:
return mimetypes.guess_type(full_path)[0] or 'text/plain' | python | def _guess_type(self, full_path):
"""Guess the mime type magically or using the mimetypes module."""
magic = self._match_magic(full_path)
if magic is not None:
return (mimetypes.guess_type(magic.old_path(full_path))[0]
or 'text/plain')
else:
return mimetypes.guess_type(full_path)[0] or 'text/plain' | [
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rmohr/static3 | static.py | Shock._conditions | def _conditions(self, full_path, environ):
"""Return Etag and Last-Modified values defaults to now for both."""
magic = self._match_magic(full_path)
if magic is not None:
return magic.conditions(full_path, environ)
else:
mtime = stat(full_path).st_mtime
return str(mtime), rfc822.formatdate(mtime) | python | def _conditions(self, full_path, environ):
"""Return Etag and Last-Modified values defaults to now for both."""
magic = self._match_magic(full_path)
if magic is not None:
return magic.conditions(full_path, environ)
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mtime = stat(full_path).st_mtime
return str(mtime), rfc822.formatdate(mtime) | [
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rmohr/static3 | static.py | Shock._file_like | def _file_like(self, full_path):
"""Return the appropriate file object."""
magic = self._match_magic(full_path)
if magic is not None:
return magic.file_like(full_path, self.encoding)
else:
return open(full_path, 'rb') | python | def _file_like(self, full_path):
"""Return the appropriate file object."""
magic = self._match_magic(full_path)
if magic is not None:
return magic.file_like(full_path, self.encoding)
else:
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rmohr/static3 | static.py | BaseMagic.old_path | def old_path(self, full_path):
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"""Remove self.extension from path or raise MagicError."""
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rmohr/static3 | static.py | StringMagic.body | def body(self, environ, file_like):
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return [template.substitute(variables)] | python | def body(self, environ, file_like):
"""Pass environ and self.variables in to template.
self.variables overrides environ so that suprises in environ don't
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"""
variables = environ.copy()
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budacom/trading-bots | trading_bots/contrib/converters/base.py | Converter.get_rate_for | def get_rate_for(self, currency: str, to: str, reverse: bool=False) -> Number:
"""Get current market rate for currency"""
# Return 1 when currencies match
if currency.upper() == to.upper():
return self._format_number('1.0')
# Set base and quote currencies
base, quote = currency, to
if reverse:
base, quote = to, currency
try: # Get rate from source
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except Exception as e:
raise ConverterRateError(self.name) from e
# Convert rate to number
rate = self._format_number(rate)
try: # Validate rate value
assert isinstance(rate, (float, Decimal))
assert rate > 0
except AssertionError as e:
raise ConverterValidationError(self.name, rate) from e
# Return market rate
if reverse:
return self._format_number('1.0') / rate
return rate | python | def get_rate_for(self, currency: str, to: str, reverse: bool=False) -> Number:
"""Get current market rate for currency"""
# Return 1 when currencies match
if currency.upper() == to.upper():
return self._format_number('1.0')
# Set base and quote currencies
base, quote = currency, to
if reverse:
base, quote = to, currency
try: # Get rate from source
rate = self._get_rate(base, quote)
except Exception as e:
raise ConverterRateError(self.name) from e
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rate = self._format_number(rate)
try: # Validate rate value
assert isinstance(rate, (float, Decimal))
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# Return market rate
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budacom/trading-bots | trading_bots/contrib/converters/base.py | Converter.convert | def convert(self, amount: Number, currency: str, to: str, reverse: bool=False) -> Number:
"""Convert amount to another currency"""
rate = self.get_rate_for(currency, to, reverse)
if self.return_decimal:
amount = Decimal(amount)
return amount * rate | python | def convert(self, amount: Number, currency: str, to: str, reverse: bool=False) -> Number:
"""Convert amount to another currency"""
rate = self.get_rate_for(currency, to, reverse)
if self.return_decimal:
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budacom/trading-bots | trading_bots/contrib/converters/base.py | Converter.convert_money | def convert_money(self, money: Money, to: str, reverse: bool=False) -> Money:
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converted = self.convert(money.amount, money.currency, to, reverse)
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"""Convert money to another currency"""
converted = self.convert(money.amount, money.currency, to, reverse)
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jinglemansweep/lcdproc | lcdproc/screen.py | Screen.add_icon_widget | def add_icon_widget(self, ref, x=1, y=1, name="heart"):
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""" Add Icon Widget """
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jinglemansweep/lcdproc | lcdproc/screen.py | Screen.add_scroller_widget | def add_scroller_widget(self, ref, left=1, top=1, right=20, bottom=1, direction="h", speed=1, text="Message"):
""" Add Scroller Widget """
if ref not in self.widgets:
widget = ScrollerWidget(screen=self, ref=ref, left=left, top=top, right=right, bottom=bottom, direction=direction, speed=speed, text=text)
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return self.widgets[ref] | python | def add_scroller_widget(self, ref, left=1, top=1, right=20, bottom=1, direction="h", speed=1, text="Message"):
""" Add Scroller Widget """
if ref not in self.widgets:
widget = ScrollerWidget(screen=self, ref=ref, left=left, top=top, right=right, bottom=bottom, direction=direction, speed=speed, text=text)
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idlesign/steampak | steampak/libsteam/resources/apps.py | Application.install_dir | def install_dir(self):
"""Returns application installation path.
.. note::
If fails this falls back to a restricted interface, which can only be used by approved apps.
:rtype: str
"""
max_len = 500
directory = self._get_str(self._iface.get_install_dir, [self.app_id], max_len=max_len)
if not directory:
# Fallback to restricted interface (can only be used by approved apps).
directory = self._get_str(self._iface_list.get_install_dir, [self.app_id], max_len=max_len)
return directory | python | def install_dir(self):
"""Returns application installation path.
.. note::
If fails this falls back to a restricted interface, which can only be used by approved apps.
:rtype: str
"""
max_len = 500
directory = self._get_str(self._iface.get_install_dir, [self.app_id], max_len=max_len)
if not directory:
# Fallback to restricted interface (can only be used by approved apps).
directory = self._get_str(self._iface_list.get_install_dir, [self.app_id], max_len=max_len)
return directory | [
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idlesign/steampak | steampak/libsteam/resources/apps.py | Application.purchase_time | def purchase_time(self):
"""Date and time of app purchase.
:rtype: datetime
"""
ts = self._iface.get_purchase_time(self.app_id)
return datetime.utcfromtimestamp(ts) | python | def purchase_time(self):
"""Date and time of app purchase.
:rtype: datetime
"""
ts = self._iface.get_purchase_time(self.app_id)
return datetime.utcfromtimestamp(ts) | [
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BD2KGenomics/protect | docker/pipelineWrapper.py | PipelineWrapperBuilder.get_args | def get_args(self):
"""
Use this context manager to add arguments to an argparse object with the add_argument
method. Arguments must be defined before the command is defined. Note that
no-clean and resume are added upon exit and should not be added in the context manager. For
more info about these default arguments see below.
"""
parser = argparse.ArgumentParser(description=self._desc,
formatter_class=MyUniversalHelpFormatter)
# default args
if self._no_clean:
parser.add_argument('--no-clean', action='store_true',
help='If this flag is used, temporary work directory is not '
'cleaned.')
if self._resume:
parser.add_argument('--resume', action='store_true',
help='If this flag is used, a previously uncleaned workflow in the'
' same directory will be resumed')
return parser | python | def get_args(self):
"""
Use this context manager to add arguments to an argparse object with the add_argument
method. Arguments must be defined before the command is defined. Note that
no-clean and resume are added upon exit and should not be added in the context manager. For
more info about these default arguments see below.
"""
parser = argparse.ArgumentParser(description=self._desc,
formatter_class=MyUniversalHelpFormatter)
# default args
if self._no_clean:
parser.add_argument('--no-clean', action='store_true',
help='If this flag is used, temporary work directory is not '
'cleaned.')
if self._resume:
parser.add_argument('--resume', action='store_true',
help='If this flag is used, a previously uncleaned workflow in the'
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return parser | [
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BD2KGenomics/protect | src/protect/rankboost.py | wrap_rankboost | def wrap_rankboost(job, rsem_files, merged_mhc_calls, transgene_out, univ_options,
rankboost_options):
"""
A wrapper for boost_ranks.
:param dict rsem_files: Dict of results from rsem
:param dict merged_mhc_calls: Dict of results from merging mhc peptide binding predictions
:param dict transgene_out: Dict of results from running Transgene
:param dict univ_options: Dict of universal options used by almost all tools
:param dict rankboost_options: Options specific to rankboost
:return: Dict of concise and detailed results for mhci and mhcii
output_files:
|- 'mhcii_rankboost_concise_results.tsv': fsID
|- 'mhcii_rankboost_detailed_results.txt': fsID
|- 'mhci_rankboost_concise_results.tsv': fsID
+- 'mhci_rankboost_detailed_results.txt': fsID
:rtype: dict
"""
rankboost = job.addChildJobFn(boost_ranks, rsem_files['rsem.isoforms.results'],
merged_mhc_calls, transgene_out, univ_options, rankboost_options)
return rankboost.rv() | python | def wrap_rankboost(job, rsem_files, merged_mhc_calls, transgene_out, univ_options,
rankboost_options):
"""
A wrapper for boost_ranks.
:param dict rsem_files: Dict of results from rsem
:param dict merged_mhc_calls: Dict of results from merging mhc peptide binding predictions
:param dict transgene_out: Dict of results from running Transgene
:param dict univ_options: Dict of universal options used by almost all tools
:param dict rankboost_options: Options specific to rankboost
:return: Dict of concise and detailed results for mhci and mhcii
output_files:
|- 'mhcii_rankboost_concise_results.tsv': fsID
|- 'mhcii_rankboost_detailed_results.txt': fsID
|- 'mhci_rankboost_concise_results.tsv': fsID
+- 'mhci_rankboost_detailed_results.txt': fsID
:rtype: dict
"""
rankboost = job.addChildJobFn(boost_ranks, rsem_files['rsem.isoforms.results'],
merged_mhc_calls, transgene_out, univ_options, rankboost_options)
return rankboost.rv() | [
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budacom/trading-bots | trading_bots/bots/registry.py | BotRegistry._path_from_module | def _path_from_module(module):
"""Attempt to determine bot's filesystem path from its module."""
# Convert paths to list because Python's _NamespacePath doesn't support
# indexing.
paths = list(getattr(module, '__path__', []))
if len(paths) != 1:
filename = getattr(module, '__file__', None)
if filename is not None:
paths = [os.path.dirname(filename)]
else:
# For unknown reasons, sometimes the list returned by __path__
# contains duplicates that must be removed.
paths = list(set(paths))
if len(paths) > 1:
raise ImproperlyConfigured(
"The bot module %r has multiple filesystem locations (%r); "
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elif not paths:
raise ImproperlyConfigured(
"The bot module %r has no filesystem location, "
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"with a 'path' class attribute." % (module,))
return paths[0] | python | def _path_from_module(module):
"""Attempt to determine bot's filesystem path from its module."""
# Convert paths to list because Python's _NamespacePath doesn't support
# indexing.
paths = list(getattr(module, '__path__', []))
if len(paths) != 1:
filename = getattr(module, '__file__', None)
if filename is not None:
paths = [os.path.dirname(filename)]
else:
# For unknown reasons, sometimes the list returned by __path__
# contains duplicates that must be removed.
paths = list(set(paths))
if len(paths) > 1:
raise ImproperlyConfigured(
"The bot module %r has multiple filesystem locations (%r); "
"you must configure this bot with an AppConfig subclass "
"with a 'path' class attribute." % (module, paths))
elif not paths:
raise ImproperlyConfigured(
"The bot module %r has no filesystem location, "
"you must configure this bot with an AppConfig subclass "
"with a 'path' class attribute." % (module,))
return paths[0] | [
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budacom/trading-bots | trading_bots/bots/registry.py | BotRegistry.create | def create(cls, entry):
"""
Factory that creates an bot config from an entry in INSTALLED_APPS.
"""
# trading_bots.example.bot.ExampleBot
try:
# If import_module succeeds, entry is a path to a bot module,
# which may specify a bot class with a default_bot attribute.
# Otherwise, entry is a path to a bot class or an error.
module = import_module(entry)
except ImportError:
# Track that importing as a bot module failed. If importing as a
# bot class fails too, we'll trigger the ImportError again.
module = None
mod_path, _, cls_name = entry.rpartition('.')
# Raise the original exception when entry cannot be a path to an
# bot config class.
if not mod_path:
raise
else:
try:
# If this works, the bot module specifies a bot class.
entry = module.default_bot
except AttributeError:
# Otherwise, it simply uses the default bot registry class.
return cls(f'{entry}.Bot', module)
else:
mod_path, _, cls_name = entry.rpartition('.')
# If we're reaching this point, we must attempt to load the bot
# class located at <mod_path>.<cls_name>
mod = import_module(mod_path)
try:
bot_cls = getattr(mod, cls_name)
except AttributeError:
if module is None:
# If importing as an bot module failed, that error probably
# contains the most informative traceback. Trigger it again.
import_module(entry)
raise
# Check for obvious errors. (This check prevents duck typing, but
# it could be removed if it became a problem in practice.)
if not issubclass(bot_cls, Bot):
raise ImproperlyConfigured(
"'%s' isn't a subclass of Bot." % entry)
# Entry is a path to an bot config class.
return cls(entry, mod, bot_cls.label) | python | def create(cls, entry):
"""
Factory that creates an bot config from an entry in INSTALLED_APPS.
"""
# trading_bots.example.bot.ExampleBot
try:
# If import_module succeeds, entry is a path to a bot module,
# which may specify a bot class with a default_bot attribute.
# Otherwise, entry is a path to a bot class or an error.
module = import_module(entry)
except ImportError:
# Track that importing as a bot module failed. If importing as a
# bot class fails too, we'll trigger the ImportError again.
module = None
mod_path, _, cls_name = entry.rpartition('.')
# Raise the original exception when entry cannot be a path to an
# bot config class.
if not mod_path:
raise
else:
try:
# If this works, the bot module specifies a bot class.
entry = module.default_bot
except AttributeError:
# Otherwise, it simply uses the default bot registry class.
return cls(f'{entry}.Bot', module)
else:
mod_path, _, cls_name = entry.rpartition('.')
# If we're reaching this point, we must attempt to load the bot
# class located at <mod_path>.<cls_name>
mod = import_module(mod_path)
try:
bot_cls = getattr(mod, cls_name)
except AttributeError:
if module is None:
# If importing as an bot module failed, that error probably
# contains the most informative traceback. Trigger it again.
import_module(entry)
raise
# Check for obvious errors. (This check prevents duck typing, but
# it could be removed if it became a problem in practice.)
if not issubclass(bot_cls, Bot):
raise ImproperlyConfigured(
"'%s' isn't a subclass of Bot." % entry)
# Entry is a path to an bot config class.
return cls(entry, mod, bot_cls.label) | [
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budacom/trading-bots | trading_bots/bots/registry.py | BotRegistry.get_config | def get_config(self, config_name, require_ready=True):
"""
Return the config with the given case-insensitive config_name.
Raise LookupError if no config exists with this name.
"""
if require_ready:
self.bots.check_configs_ready()
else:
self.bots.check_bots_ready()
return self.configs.get(config_name.lower(), {}) | python | def get_config(self, config_name, require_ready=True):
"""
Return the config with the given case-insensitive config_name.
Raise LookupError if no config exists with this name.
"""
if require_ready:
self.bots.check_configs_ready()
else:
self.bots.check_bots_ready()
return self.configs.get(config_name.lower(), {}) | [
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budacom/trading-bots | trading_bots/bots/registry.py | BotRegistry.get_configs | def get_configs(self):
"""
Return an iterable of models.
"""
self.bots.check_models_ready()
for config in self.configs.values():
yield config | python | def get_configs(self):
"""
Return an iterable of models.
"""
self.bots.check_models_ready()
for config in self.configs.values():
yield config | [
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budacom/trading-bots | trading_bots/bots/registry.py | Bots.populate | def populate(self, installed_bots=None):
"""
Load bots.
Import each bot module.
It is thread-safe and idempotent, but not re-entrant.
"""
if self.ready:
return
# populate() might be called by two threads in parallel on servers
# that create threads before initializing the WSGI callable.
with self._lock:
if self.ready:
return
# An RLock prevents other threads from entering this section. The
# compare and set operation below is atomic.
if self.loading:
# Prevent re-entrant calls to avoid running AppConfig.ready()
# methods twice.
raise RuntimeError("populate() isn't re-entrant")
self.loading = True
# Phase 1: Initialize bots
for entry in installed_bots or {}:
if isinstance(entry, Bot):
cls = entry
entry = '.'.join([cls.__module__, cls.__name__])
bot_reg = BotRegistry.create(entry)
if bot_reg.label in self.bots:
raise ImproperlyConfigured(
"Bot labels aren't unique, "
"duplicates: %s" % bot_reg.label)
self.bots[bot_reg.label] = bot_reg
bot_reg.bots = self
# Check for duplicate bot names.
counts = Counter(
bot_reg.name for bot_reg in self.bots.values())
duplicates = [
name for name, count in counts.most_common() if count > 1]
if duplicates:
raise ImproperlyConfigured(
"Bot names aren't unique, "
"duplicates: %s" % ", ".join(duplicates))
self.bots_ready = True
# Phase 2: import config files
for bot in self.bots.values():
bot.import_configs()
self.configs_ready = True
self.ready = True | python | def populate(self, installed_bots=None):
"""
Load bots.
Import each bot module.
It is thread-safe and idempotent, but not re-entrant.
"""
if self.ready:
return
# populate() might be called by two threads in parallel on servers
# that create threads before initializing the WSGI callable.
with self._lock:
if self.ready:
return
# An RLock prevents other threads from entering this section. The
# compare and set operation below is atomic.
if self.loading:
# Prevent re-entrant calls to avoid running AppConfig.ready()
# methods twice.
raise RuntimeError("populate() isn't re-entrant")
self.loading = True
# Phase 1: Initialize bots
for entry in installed_bots or {}:
if isinstance(entry, Bot):
cls = entry
entry = '.'.join([cls.__module__, cls.__name__])
bot_reg = BotRegistry.create(entry)
if bot_reg.label in self.bots:
raise ImproperlyConfigured(
"Bot labels aren't unique, "
"duplicates: %s" % bot_reg.label)
self.bots[bot_reg.label] = bot_reg
bot_reg.bots = self
# Check for duplicate bot names.
counts = Counter(
bot_reg.name for bot_reg in self.bots.values())
duplicates = [
name for name, count in counts.most_common() if count > 1]
if duplicates:
raise ImproperlyConfigured(
"Bot names aren't unique, "
"duplicates: %s" % ", ".join(duplicates))
self.bots_ready = True
# Phase 2: import config files
for bot in self.bots.values():
bot.import_configs()
self.configs_ready = True
self.ready = True | [
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budacom/trading-bots | trading_bots/bots/registry.py | Bots.get_bot | def get_bot(self, bot_label):
"""
Import all bots and returns a bot class for the given label.
Raise LookupError if no bot exists with this label.
"""
self.check_bots_ready()
try:
return self.bots[bot_label]
except KeyError:
message = "No installed bot with label '%s'." % bot_label
for bot_cls in self.get_bots():
if bot_cls.name == bot_label:
message += " Did you mean '%s'?" % bot_cls.label
break
raise LookupError(message) | python | def get_bot(self, bot_label):
"""
Import all bots and returns a bot class for the given label.
Raise LookupError if no bot exists with this label.
"""
self.check_bots_ready()
try:
return self.bots[bot_label]
except KeyError:
message = "No installed bot with label '%s'." % bot_label
for bot_cls in self.get_bots():
if bot_cls.name == bot_label:
message += " Did you mean '%s'?" % bot_cls.label
break
raise LookupError(message) | [
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budacom/trading-bots | trading_bots/bots/registry.py | Bots.get_configs | def get_configs(self):
"""
Return a list of all installed configs.
"""
self.check_configs_ready()
result = []
for bot in self.bots.values():
result.extend(list(bot.get_models()))
return result | python | def get_configs(self):
"""
Return a list of all installed configs.
"""
self.check_configs_ready()
result = []
for bot in self.bots.values():
result.extend(list(bot.get_models()))
return result | [
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budacom/trading-bots | trading_bots/bots/registry.py | Bots.get_config | def get_config(self, bot_label, config_name=None, require_ready=True):
"""
Return the config matching the given bot_label and config_name.
config_name is case-insensitive.
Raise LookupError if no bot exists with this label, or no config
exists with this name in the bot. Raise ValueError if called with a
single argument that doesn't contain exactly one dot.
"""
if require_ready:
self.check_configs_ready()
else:
self.check_bots_ready()
if config_name is None:
config_name = defaults.BOT_CONFIG
bot = self.get_bot(bot_label)
if not require_ready and bot.configs is None:
bot.import_configs()
return bot.get_config(config_name, require_ready=require_ready) | python | def get_config(self, bot_label, config_name=None, require_ready=True):
"""
Return the config matching the given bot_label and config_name.
config_name is case-insensitive.
Raise LookupError if no bot exists with this label, or no config
exists with this name in the bot. Raise ValueError if called with a
single argument that doesn't contain exactly one dot.
"""
if require_ready:
self.check_configs_ready()
else:
self.check_bots_ready()
if config_name is None:
config_name = defaults.BOT_CONFIG
bot = self.get_bot(bot_label)
if not require_ready and bot.configs is None:
bot.import_configs()
return bot.get_config(config_name, require_ready=require_ready) | [
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mjj4791/python-buienradar | buienradar/buienradar_json.py | __to_float | def __to_float(val, digits):
"""Convert val into float with digits decimal."""
try:
return round(float(val), digits)
except (ValueError, TypeError):
return float(0) | python | def __to_float(val, digits):
"""Convert val into float with digits decimal."""
try:
return round(float(val), digits)
except (ValueError, TypeError):
return float(0) | [
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mjj4791/python-buienradar | buienradar/buienradar_json.py | get_json_data | def get_json_data(latitude=52.091579, longitude=5.119734):
"""Get buienradar json data and return results."""
final_result = {SUCCESS: False,
MESSAGE: None,
CONTENT: None,
RAINCONTENT: None}
log.info("Getting buienradar json data for latitude=%s, longitude=%s",
latitude, longitude)
result = __get_ws_data()
if result[SUCCESS]:
# store json data:
final_result[CONTENT] = result[CONTENT]
final_result[SUCCESS] = True
else:
if STATUS_CODE in result and MESSAGE in result:
msg = "Status: %d, Msg: %s" % (result[STATUS_CODE],
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elif MESSAGE in result:
msg = "Msg: %s" % (result[MESSAGE])
else:
msg = "Something went wrong (reason unknown)."
log.warning(msg)
final_result[MESSAGE] = msg
# load forecasted precipitation:
result = __get_precipfc_data(latitude,
longitude)
if result[SUCCESS]:
final_result[RAINCONTENT] = result[CONTENT]
else:
if STATUS_CODE in result and MESSAGE in result:
msg = "Status: %d, Msg: %s" % (result[STATUS_CODE],
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elif MESSAGE in result:
msg = "Msg: %s" % (result[MESSAGE])
else:
msg = "Something went wrong (reason unknown)."
log.warning(msg)
final_result[MESSAGE] = msg
return final_result | python | def get_json_data(latitude=52.091579, longitude=5.119734):
"""Get buienradar json data and return results."""
final_result = {SUCCESS: False,
MESSAGE: None,
CONTENT: None,
RAINCONTENT: None}
log.info("Getting buienradar json data for latitude=%s, longitude=%s",
latitude, longitude)
result = __get_ws_data()
if result[SUCCESS]:
# store json data:
final_result[CONTENT] = result[CONTENT]
final_result[SUCCESS] = True
else:
if STATUS_CODE in result and MESSAGE in result:
msg = "Status: %d, Msg: %s" % (result[STATUS_CODE],
result[MESSAGE])
elif MESSAGE in result:
msg = "Msg: %s" % (result[MESSAGE])
else:
msg = "Something went wrong (reason unknown)."
log.warning(msg)
final_result[MESSAGE] = msg
# load forecasted precipitation:
result = __get_precipfc_data(latitude,
longitude)
if result[SUCCESS]:
final_result[RAINCONTENT] = result[CONTENT]
else:
if STATUS_CODE in result and MESSAGE in result:
msg = "Status: %d, Msg: %s" % (result[STATUS_CODE],
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elif MESSAGE in result:
msg = "Msg: %s" % (result[MESSAGE])
else:
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final_result[MESSAGE] = msg
return final_result | [
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mjj4791/python-buienradar | buienradar/buienradar_json.py | __get_precipfc_data | def __get_precipfc_data(latitude, longitude):
"""Get buienradar forecasted precipitation."""
url = 'https://gpsgadget.buienradar.nl/data/raintext?lat={}&lon={}'
# rounding coordinates prevents unnecessary redirects/calls
url = url.format(
round(latitude, 2),
round(longitude, 2)
)
result = __get_url(url)
return result | python | def __get_precipfc_data(latitude, longitude):
"""Get buienradar forecasted precipitation."""
url = 'https://gpsgadget.buienradar.nl/data/raintext?lat={}&lon={}'
# rounding coordinates prevents unnecessary redirects/calls
url = url.format(
round(latitude, 2),
round(longitude, 2)
)
result = __get_url(url)
return result | [
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mjj4791/python-buienradar | buienradar/buienradar_json.py | __get_url | def __get_url(url):
"""Load json data from url and return result."""
log.info("Retrieving weather data (%s)...", url)
result = {SUCCESS: False, MESSAGE: None}
try:
r = requests.get(url)
result[STATUS_CODE] = r.status_code
result[HEADERS] = r.headers
result[CONTENT] = r.text
if (200 == r.status_code):
result[SUCCESS] = True
else:
result[MESSAGE] = "Got http statuscode: %d." % (r.status_code)
return result
except requests.RequestException as ose:
result[MESSAGE] = 'Error getting url data. %s' % ose
log.error(result[MESSAGE])
return result | python | def __get_url(url):
"""Load json data from url and return result."""
log.info("Retrieving weather data (%s)...", url)
result = {SUCCESS: False, MESSAGE: None}
try:
r = requests.get(url)
result[STATUS_CODE] = r.status_code
result[HEADERS] = r.headers
result[CONTENT] = r.text
if (200 == r.status_code):
result[SUCCESS] = True
else:
result[MESSAGE] = "Got http statuscode: %d." % (r.status_code)
return result
except requests.RequestException as ose:
result[MESSAGE] = 'Error getting url data. %s' % ose
log.error(result[MESSAGE])
return result | [
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mjj4791/python-buienradar | buienradar/buienradar_json.py | __parse_ws_data | def __parse_ws_data(jsondata, latitude=52.091579, longitude=5.119734):
"""Parse the buienradar json and rain data."""
log.info("Parse ws data: latitude: %s, longitude: %s", latitude, longitude)
result = {SUCCESS: False, MESSAGE: None, DATA: None}
# select the nearest weather station
loc_data = __select_nearest_ws(jsondata, latitude, longitude)
# process current weather data from selected weatherstation
if not loc_data:
result[MESSAGE] = 'No location selected.'
return result
if not __is_valid(loc_data):
result[MESSAGE] = 'Location data is invalid.'
return result
# add distance to weatherstation
log.debug("Raw location data: %s", loc_data)
result[DISTANCE] = __get_ws_distance(loc_data, latitude, longitude)
result = __parse_loc_data(loc_data, result)
# extract weather forecast
try:
fc_data = jsondata[__FORECAST][__FIVEDAYFORECAST]
except (json.JSONDecodeError, KeyError):
result[MESSAGE] = 'Unable to extract forecast data.'
log.exception(result[MESSAGE])
return result
if fc_data:
# result = __parse_fc_data(fc_data, result)
log.debug("Raw forecast data: %s", fc_data)
# pylint: disable=unsupported-assignment-operation
result[DATA][FORECAST] = __parse_fc_data(fc_data)
return result | python | def __parse_ws_data(jsondata, latitude=52.091579, longitude=5.119734):
"""Parse the buienradar json and rain data."""
log.info("Parse ws data: latitude: %s, longitude: %s", latitude, longitude)
result = {SUCCESS: False, MESSAGE: None, DATA: None}
# select the nearest weather station
loc_data = __select_nearest_ws(jsondata, latitude, longitude)
# process current weather data from selected weatherstation
if not loc_data:
result[MESSAGE] = 'No location selected.'
return result
if not __is_valid(loc_data):
result[MESSAGE] = 'Location data is invalid.'
return result
# add distance to weatherstation
log.debug("Raw location data: %s", loc_data)
result[DISTANCE] = __get_ws_distance(loc_data, latitude, longitude)
result = __parse_loc_data(loc_data, result)
# extract weather forecast
try:
fc_data = jsondata[__FORECAST][__FIVEDAYFORECAST]
except (json.JSONDecodeError, KeyError):
result[MESSAGE] = 'Unable to extract forecast data.'
log.exception(result[MESSAGE])
return result
if fc_data:
# result = __parse_fc_data(fc_data, result)
log.debug("Raw forecast data: %s", fc_data)
# pylint: disable=unsupported-assignment-operation
result[DATA][FORECAST] = __parse_fc_data(fc_data)
return result | [
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mjj4791/python-buienradar | buienradar/buienradar_json.py | __parse_loc_data | def __parse_loc_data(loc_data, result):
"""Parse the json data from selected weatherstation."""
result[DATA] = {ATTRIBUTION: ATTRIBUTION_INFO,
FORECAST: [],
PRECIPITATION_FORECAST: None}
for key, [value, func] in SENSOR_TYPES.items():
result[DATA][key] = None
try:
sens_data = loc_data[value]
if key == CONDITION:
# update weather symbol & status text
desc = loc_data[__WEATHERDESCRIPTION]
result[DATA][CONDITION] = __cond_from_desc(desc)
result[DATA][CONDITION][IMAGE] = loc_data[__ICONURL]
continue
if key == STATIONNAME:
result[DATA][key] = __getStationName(loc_data[__STATIONNAME],
loc_data[__STATIONID])
continue
# update all other data:
if func is not None:
result[DATA][key] = func(sens_data)
else:
result[DATA][key] = sens_data
except KeyError:
if result[MESSAGE] is None:
result[MESSAGE] = "Missing key(s) in br data: "
result[MESSAGE] += "%s " % value
log.warning("Data element with key='%s' "
"not loaded from br data!", key)
result[SUCCESS] = True
return result | python | def __parse_loc_data(loc_data, result):
"""Parse the json data from selected weatherstation."""
result[DATA] = {ATTRIBUTION: ATTRIBUTION_INFO,
FORECAST: [],
PRECIPITATION_FORECAST: None}
for key, [value, func] in SENSOR_TYPES.items():
result[DATA][key] = None
try:
sens_data = loc_data[value]
if key == CONDITION:
# update weather symbol & status text
desc = loc_data[__WEATHERDESCRIPTION]
result[DATA][CONDITION] = __cond_from_desc(desc)
result[DATA][CONDITION][IMAGE] = loc_data[__ICONURL]
continue
if key == STATIONNAME:
result[DATA][key] = __getStationName(loc_data[__STATIONNAME],
loc_data[__STATIONID])
continue
# update all other data:
if func is not None:
result[DATA][key] = func(sens_data)
else:
result[DATA][key] = sens_data
except KeyError:
if result[MESSAGE] is None:
result[MESSAGE] = "Missing key(s) in br data: "
result[MESSAGE] += "%s " % value
log.warning("Data element with key='%s' "
"not loaded from br data!", key)
result[SUCCESS] = True
return result | [
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mjj4791/python-buienradar | buienradar/buienradar_json.py | __parse_fc_data | def __parse_fc_data(fc_data):
"""Parse the forecast data from the json section."""
fc = []
for day in fc_data:
fcdata = {
CONDITION: __cond_from_desc(
__get_str(
day,
__WEATHERDESCRIPTION)
),
TEMPERATURE: __get_float(day, __MAXTEMPERATURE),
MIN_TEMP: __get_float(day, __MINTEMPERATURE),
MAX_TEMP: __get_float(day, __MAXTEMPERATURE),
SUN_CHANCE: __get_int(day, __SUNCHANCE),
RAIN_CHANCE: __get_int(day, __RAINCHANCE),
RAIN: __get_float(day, __MMRAINMAX),
MIN_RAIN: __get_float(day, __MMRAINMIN), # new
MAX_RAIN: __get_float(day, __MMRAINMAX), # new
SNOW: 0, # for compatibility
WINDFORCE: __get_int(day, __WIND),
WINDDIRECTION: __get_str(day, __WINDDIRECTION), # new
DATETIME: __to_localdatetime(__get_str(day, __DAY)),
}
fcdata[CONDITION][IMAGE] = day[__ICONURL]
fc.append(fcdata)
return fc | python | def __parse_fc_data(fc_data):
"""Parse the forecast data from the json section."""
fc = []
for day in fc_data:
fcdata = {
CONDITION: __cond_from_desc(
__get_str(
day,
__WEATHERDESCRIPTION)
),
TEMPERATURE: __get_float(day, __MAXTEMPERATURE),
MIN_TEMP: __get_float(day, __MINTEMPERATURE),
MAX_TEMP: __get_float(day, __MAXTEMPERATURE),
SUN_CHANCE: __get_int(day, __SUNCHANCE),
RAIN_CHANCE: __get_int(day, __RAINCHANCE),
RAIN: __get_float(day, __MMRAINMAX),
MIN_RAIN: __get_float(day, __MMRAINMIN), # new
MAX_RAIN: __get_float(day, __MMRAINMAX), # new
SNOW: 0, # for compatibility
WINDFORCE: __get_int(day, __WIND),
WINDDIRECTION: __get_str(day, __WINDDIRECTION), # new
DATETIME: __to_localdatetime(__get_str(day, __DAY)),
}
fcdata[CONDITION][IMAGE] = day[__ICONURL]
fc.append(fcdata)
return fc | [
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mjj4791/python-buienradar | buienradar/buienradar_json.py | __get_float | def __get_float(section, name):
"""Get the forecasted float from json section."""
try:
return float(section[name])
except (ValueError, TypeError, KeyError):
return float(0) | python | def __get_float(section, name):
"""Get the forecasted float from json section."""
try:
return float(section[name])
except (ValueError, TypeError, KeyError):
return float(0) | [
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mjj4791/python-buienradar | buienradar/buienradar_json.py | __parse_precipfc_data | def __parse_precipfc_data(data, timeframe):
"""Parse the forecasted precipitation data."""
result = {AVERAGE: None, TOTAL: None, TIMEFRAME: None}
log.debug("Precipitation data: %s", data)
lines = data.splitlines()
index = 1
totalrain = 0
numberoflines = 0
nrlines = min(len(lines), round(float(timeframe) / 5) + 1)
# looping through lines of forecasted precipitation data and
# not using the time data (HH:MM) int the data. This is to allow for
# correct data in case we are running in a different timezone.
while index < nrlines:
line = lines[index]
log.debug("__parse_precipfc_data: line: %s", line)
# pylint: disable=unused-variable
(val, key) = line.split("|")
# See buienradar documentation for this api, attribution
# https://www.buienradar.nl/overbuienradar/gratis-weerdata
#
# Op basis van de door u gewenste coordinaten (latitude en longitude)
# kunt u de neerslag tot twee uur vooruit ophalen in tekstvorm. De
# data wordt iedere 5 minuten geupdatet. Op deze pagina kunt u de
# neerslag in tekst vinden. De waarde 0 geeft geen neerslag aan (droog)
# de waarde 255 geeft zware neerslag aan. Gebruik de volgende formule
# voor het omrekenen naar de neerslagintensiteit in de eenheid
# millimeter per uur (mm/u):
#
# Neerslagintensiteit = 10^((waarde-109)/32)
#
# Ter controle: een waarde van 77 is gelijk aan een neerslagintensiteit
# van 0,1 mm/u.
mmu = 10**(float((int(val) - 109)) / 32)
totalrain = totalrain + float(mmu)
numberoflines = numberoflines + 1
index += 1
if numberoflines > 0:
result[AVERAGE] = round((totalrain / numberoflines), 2)
else:
result[AVERAGE] = 0
result[TOTAL] = round(totalrain / 12, 2)
result[TIMEFRAME] = timeframe
return result | python | def __parse_precipfc_data(data, timeframe):
"""Parse the forecasted precipitation data."""
result = {AVERAGE: None, TOTAL: None, TIMEFRAME: None}
log.debug("Precipitation data: %s", data)
lines = data.splitlines()
index = 1
totalrain = 0
numberoflines = 0
nrlines = min(len(lines), round(float(timeframe) / 5) + 1)
# looping through lines of forecasted precipitation data and
# not using the time data (HH:MM) int the data. This is to allow for
# correct data in case we are running in a different timezone.
while index < nrlines:
line = lines[index]
log.debug("__parse_precipfc_data: line: %s", line)
# pylint: disable=unused-variable
(val, key) = line.split("|")
# See buienradar documentation for this api, attribution
# https://www.buienradar.nl/overbuienradar/gratis-weerdata
#
# Op basis van de door u gewenste coordinaten (latitude en longitude)
# kunt u de neerslag tot twee uur vooruit ophalen in tekstvorm. De
# data wordt iedere 5 minuten geupdatet. Op deze pagina kunt u de
# neerslag in tekst vinden. De waarde 0 geeft geen neerslag aan (droog)
# de waarde 255 geeft zware neerslag aan. Gebruik de volgende formule
# voor het omrekenen naar de neerslagintensiteit in de eenheid
# millimeter per uur (mm/u):
#
# Neerslagintensiteit = 10^((waarde-109)/32)
#
# Ter controle: een waarde van 77 is gelijk aan een neerslagintensiteit
# van 0,1 mm/u.
mmu = 10**(float((int(val) - 109)) / 32)
totalrain = totalrain + float(mmu)
numberoflines = numberoflines + 1
index += 1
if numberoflines > 0:
result[AVERAGE] = round((totalrain / numberoflines), 2)
else:
result[AVERAGE] = 0
result[TOTAL] = round(totalrain / 12, 2)
result[TIMEFRAME] = timeframe
return result | [
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mjj4791/python-buienradar | buienradar/buienradar_json.py | __cond_from_desc | def __cond_from_desc(desc):
"""Get the condition name from the condition description."""
# '{ 'code': 'conditon', 'detailed', 'exact', 'exact_nl'}
for code, [condition, detailed, exact, exact_nl] in __BRCONDITIONS.items():
if exact_nl == desc:
return {CONDCODE: code,
CONDITION: condition,
DETAILED: detailed,
EXACT: exact,
EXACTNL: exact_nl
}
return None | python | def __cond_from_desc(desc):
"""Get the condition name from the condition description."""
# '{ 'code': 'conditon', 'detailed', 'exact', 'exact_nl'}
for code, [condition, detailed, exact, exact_nl] in __BRCONDITIONS.items():
if exact_nl == desc:
return {CONDCODE: code,
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return None | [
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mjj4791/python-buienradar | buienradar/buienradar_json.py | __get_ws_distance | def __get_ws_distance(wstation, latitude, longitude):
"""Get the distance to the weatherstation from wstation section of json.
wstation: weerstation section of buienradar json (dict)
latitude: our latitude
longitude: our longitude
"""
if wstation:
try:
wslat = float(wstation[__LAT])
wslon = float(wstation[__LON])
dist = vincenty((latitude, longitude), (wslat, wslon))
log.debug("calc distance: %s (latitude: %s, longitude: "
"%s, wslat: %s, wslon: %s)", dist, latitude,
longitude, wslat, wslon)
return dist
except (ValueError, TypeError, KeyError):
# value does not exist, or is not a float
return None
else:
return None | python | def __get_ws_distance(wstation, latitude, longitude):
"""Get the distance to the weatherstation from wstation section of json.
wstation: weerstation section of buienradar json (dict)
latitude: our latitude
longitude: our longitude
"""
if wstation:
try:
wslat = float(wstation[__LAT])
wslon = float(wstation[__LON])
dist = vincenty((latitude, longitude), (wslat, wslon))
log.debug("calc distance: %s (latitude: %s, longitude: "
"%s, wslat: %s, wslon: %s)", dist, latitude,
longitude, wslat, wslon)
return dist
except (ValueError, TypeError, KeyError):
# value does not exist, or is not a float
return None
else:
return None | [
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mjj4791/python-buienradar | buienradar/buienradar_json.py | __getStationName | def __getStationName(name, id):
"""Construct a staiion name."""
name = name.replace("Meetstation", "")
name = name.strip()
name += " (%s)" % id
return name | python | def __getStationName(name, id):
"""Construct a staiion name."""
name = name.replace("Meetstation", "")
name = name.strip()
name += " (%s)" % id
return name | [
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stephrdev/django-formwizard | formwizard/views.py | WizardView.as_view | def as_view(cls, *args, **kwargs):
"""
This method is used within urls.py to create unique formwizard
instances for every request. We need to override this method because
we add some kwargs which are needed to make the formwizard usable.
"""
initkwargs = cls.get_initkwargs(*args, **kwargs)
return super(WizardView, cls).as_view(**initkwargs) | python | def as_view(cls, *args, **kwargs):
"""
This method is used within urls.py to create unique formwizard
instances for every request. We need to override this method because
we add some kwargs which are needed to make the formwizard usable.
"""
initkwargs = cls.get_initkwargs(*args, **kwargs)
return super(WizardView, cls).as_view(**initkwargs) | [
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stephrdev/django-formwizard | formwizard/views.py | WizardView.get_initkwargs | def get_initkwargs(cls, form_list, initial_dict=None,
instance_dict=None, condition_dict=None, *args, **kwargs):
"""
Creates a dict with all needed parameters for the form wizard instances.
* `form_list` - is a list of forms. The list entries can be single form
classes or tuples of (`step_name`, `form_class`). If you pass a list
of forms, the formwizard will convert the class list to
(`zero_based_counter`, `form_class`). This is needed to access the
form for a specific step.
* `initial_dict` - contains a dictionary of initial data dictionaries.
The key should be equal to the `step_name` in the `form_list` (or
the str of the zero based counter - if no step_names added in the
`form_list`)
* `instance_dict` - contains a dictionary of instance objects. This list
is only used when `ModelForm`s are used. The key should be equal to
the `step_name` in the `form_list`. Same rules as for `initial_dict`
apply.
* `condition_dict` - contains a dictionary of boolean values or
callables. If the value of for a specific `step_name` is callable it
will be called with the formwizard instance as the only argument.
If the return value is true, the step's form will be used.
"""
kwargs.update({
'initial_dict': initial_dict or {},
'instance_dict': instance_dict or {},
'condition_dict': condition_dict or {},
})
init_form_list = SortedDict()
assert len(form_list) > 0, 'at least one form is needed'
# walk through the passed form list
for i, form in enumerate(form_list):
if isinstance(form, (list, tuple)):
# if the element is a tuple, add the tuple to the new created
# sorted dictionary.
init_form_list[unicode(form[0])] = form[1]
else:
# if not, add the form with a zero based counter as unicode
init_form_list[unicode(i)] = form
# walk through the ne created list of forms
for form in init_form_list.itervalues():
if issubclass(form, formsets.BaseFormSet):
# if the element is based on BaseFormSet (FormSet/ModelFormSet)
# we need to override the form variable.
form = form.form
# check if any form contains a FileField, if yes, we need a
# file_storage added to the formwizard (by subclassing).
for field in form.base_fields.itervalues():
if (isinstance(field, forms.FileField) and
not hasattr(cls, 'file_storage')):
raise NoFileStorageConfigured
# build the kwargs for the formwizard instances
kwargs['form_list'] = init_form_list
return kwargs | python | def get_initkwargs(cls, form_list, initial_dict=None,
instance_dict=None, condition_dict=None, *args, **kwargs):
"""
Creates a dict with all needed parameters for the form wizard instances.
* `form_list` - is a list of forms. The list entries can be single form
classes or tuples of (`step_name`, `form_class`). If you pass a list
of forms, the formwizard will convert the class list to
(`zero_based_counter`, `form_class`). This is needed to access the
form for a specific step.
* `initial_dict` - contains a dictionary of initial data dictionaries.
The key should be equal to the `step_name` in the `form_list` (or
the str of the zero based counter - if no step_names added in the
`form_list`)
* `instance_dict` - contains a dictionary of instance objects. This list
is only used when `ModelForm`s are used. The key should be equal to
the `step_name` in the `form_list`. Same rules as for `initial_dict`
apply.
* `condition_dict` - contains a dictionary of boolean values or
callables. If the value of for a specific `step_name` is callable it
will be called with the formwizard instance as the only argument.
If the return value is true, the step's form will be used.
"""
kwargs.update({
'initial_dict': initial_dict or {},
'instance_dict': instance_dict or {},
'condition_dict': condition_dict or {},
})
init_form_list = SortedDict()
assert len(form_list) > 0, 'at least one form is needed'
# walk through the passed form list
for i, form in enumerate(form_list):
if isinstance(form, (list, tuple)):
# if the element is a tuple, add the tuple to the new created
# sorted dictionary.
init_form_list[unicode(form[0])] = form[1]
else:
# if not, add the form with a zero based counter as unicode
init_form_list[unicode(i)] = form
# walk through the ne created list of forms
for form in init_form_list.itervalues():
if issubclass(form, formsets.BaseFormSet):
# if the element is based on BaseFormSet (FormSet/ModelFormSet)
# we need to override the form variable.
form = form.form
# check if any form contains a FileField, if yes, we need a
# file_storage added to the formwizard (by subclassing).
for field in form.base_fields.itervalues():
if (isinstance(field, forms.FileField) and
not hasattr(cls, 'file_storage')):
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# build the kwargs for the formwizard instances
kwargs['form_list'] = init_form_list
return kwargs | [
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stephrdev/django-formwizard | formwizard/views.py | WizardView.dispatch | def dispatch(self, request, *args, **kwargs):
"""
This method gets called by the routing engine. The first argument is
`request` which contains a `HttpRequest` instance.
The request is stored in `self.request` for later use. The storage
instance is stored in `self.storage`.
After processing the request using the `dispatch` method, the
response gets updated by the storage engine (for example add cookies).
"""
# add the storage engine to the current formwizard instance
self.wizard_name = self.get_wizard_name()
self.prefix = self.get_prefix()
self.storage = get_storage(self.storage_name, self.prefix, request,
getattr(self, 'file_storage', None))
self.steps = StepsHelper(self)
response = super(WizardView, self).dispatch(request, *args, **kwargs)
# update the response (e.g. adding cookies)
self.storage.update_response(response)
return response | python | def dispatch(self, request, *args, **kwargs):
"""
This method gets called by the routing engine. The first argument is
`request` which contains a `HttpRequest` instance.
The request is stored in `self.request` for later use. The storage
instance is stored in `self.storage`.
After processing the request using the `dispatch` method, the
response gets updated by the storage engine (for example add cookies).
"""
# add the storage engine to the current formwizard instance
self.wizard_name = self.get_wizard_name()
self.prefix = self.get_prefix()
self.storage = get_storage(self.storage_name, self.prefix, request,
getattr(self, 'file_storage', None))
self.steps = StepsHelper(self)
response = super(WizardView, self).dispatch(request, *args, **kwargs)
# update the response (e.g. adding cookies)
self.storage.update_response(response)
return response | [
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stephrdev/django-formwizard | formwizard/views.py | WizardView.get | def get(self, request, *args, **kwargs):
"""
This method handles GET requests.
If a GET request reaches this point, the wizard assumes that the user
just starts at the first step or wants to restart the process.
The data of the wizard will be resetted before rendering the first step.
"""
self.storage.reset()
# reset the current step to the first step.
self.storage.current_step = self.steps.first
return self.render(self.get_form()) | python | def get(self, request, *args, **kwargs):
"""
This method handles GET requests.
If a GET request reaches this point, the wizard assumes that the user
just starts at the first step or wants to restart the process.
The data of the wizard will be resetted before rendering the first step.
"""
self.storage.reset()
# reset the current step to the first step.
self.storage.current_step = self.steps.first
return self.render(self.get_form()) | [
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stephrdev/django-formwizard | formwizard/views.py | WizardView.post | def post(self, *args, **kwargs):
"""
This method handles POST requests.
The wizard will render either the current step (if form validation
wasn't successful), the next step (if the current step was stored
successful) or the done view (if no more steps are available)
"""
# Look for a wizard_prev_step element in the posted data which
# contains a valid step name. If one was found, render the requested
# form. (This makes stepping back a lot easier).
wizard_prev_step = self.request.POST.get('wizard_prev_step', None)
if wizard_prev_step and wizard_prev_step in self.get_form_list():
self.storage.current_step = wizard_prev_step
form = self.get_form(
data=self.storage.get_step_data(self.steps.current),
files=self.storage.get_step_files(self.steps.current))
return self.render(form)
# Check if form was refreshed
management_form = ManagementForm(self.request.POST, prefix=self.prefix)
if not management_form.is_valid():
raise ValidationError(
'ManagementForm data is missing or has been tampered.')
form_current_step = management_form.cleaned_data['current_step']
if (form_current_step != self.steps.current and
self.storage.current_step is not None):
# form refreshed, change current step
self.storage.current_step = form_current_step
# get the form for the current step
form = self.get_form(data=self.request.POST, files=self.request.FILES)
# and try to validate
if form.is_valid():
# if the form is valid, store the cleaned data and files.
self.storage.set_step_data(self.steps.current, self.process_step(form))
self.storage.set_step_files(self.steps.current, self.process_step_files(form))
# check if the current step is the last step
if self.steps.current == self.steps.last:
# no more steps, render done view
return self.render_done(form, **kwargs)
else:
# proceed to the next step
return self.render_next_step(form)
return self.render(form) | python | def post(self, *args, **kwargs):
"""
This method handles POST requests.
The wizard will render either the current step (if form validation
wasn't successful), the next step (if the current step was stored
successful) or the done view (if no more steps are available)
"""
# Look for a wizard_prev_step element in the posted data which
# contains a valid step name. If one was found, render the requested
# form. (This makes stepping back a lot easier).
wizard_prev_step = self.request.POST.get('wizard_prev_step', None)
if wizard_prev_step and wizard_prev_step in self.get_form_list():
self.storage.current_step = wizard_prev_step
form = self.get_form(
data=self.storage.get_step_data(self.steps.current),
files=self.storage.get_step_files(self.steps.current))
return self.render(form)
# Check if form was refreshed
management_form = ManagementForm(self.request.POST, prefix=self.prefix)
if not management_form.is_valid():
raise ValidationError(
'ManagementForm data is missing or has been tampered.')
form_current_step = management_form.cleaned_data['current_step']
if (form_current_step != self.steps.current and
self.storage.current_step is not None):
# form refreshed, change current step
self.storage.current_step = form_current_step
# get the form for the current step
form = self.get_form(data=self.request.POST, files=self.request.FILES)
# and try to validate
if form.is_valid():
# if the form is valid, store the cleaned data and files.
self.storage.set_step_data(self.steps.current, self.process_step(form))
self.storage.set_step_files(self.steps.current, self.process_step_files(form))
# check if the current step is the last step
if self.steps.current == self.steps.last:
# no more steps, render done view
return self.render_done(form, **kwargs)
else:
# proceed to the next step
return self.render_next_step(form)
return self.render(form) | [
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stephrdev/django-formwizard | formwizard/views.py | WizardView.render_done | def render_done(self, form, **kwargs):
"""
This method gets called when all forms passed. The method should also
re-validate all steps to prevent manipulation. If any form don't
validate, `render_revalidation_failure` should get called.
If everything is fine call `done`.
"""
final_form_list = []
# walk through the form list and try to validate the data again.
for form_key in self.get_form_list():
form_obj = self.get_form(step=form_key,
data=self.storage.get_step_data(form_key),
files=self.storage.get_step_files(form_key))
if not form_obj.is_valid():
return self.render_revalidation_failure(form_key, form_obj, **kwargs)
final_form_list.append(form_obj)
# render the done view and reset the wizard before returning the
# response. This is needed to prevent from rendering done with the
# same data twice.
done_response = self.done(final_form_list, **kwargs)
self.storage.reset()
return done_response | python | def render_done(self, form, **kwargs):
"""
This method gets called when all forms passed. The method should also
re-validate all steps to prevent manipulation. If any form don't
validate, `render_revalidation_failure` should get called.
If everything is fine call `done`.
"""
final_form_list = []
# walk through the form list and try to validate the data again.
for form_key in self.get_form_list():
form_obj = self.get_form(step=form_key,
data=self.storage.get_step_data(form_key),
files=self.storage.get_step_files(form_key))
if not form_obj.is_valid():
return self.render_revalidation_failure(form_key, form_obj, **kwargs)
final_form_list.append(form_obj)
# render the done view and reset the wizard before returning the
# response. This is needed to prevent from rendering done with the
# same data twice.
done_response = self.done(final_form_list, **kwargs)
self.storage.reset()
return done_response | [
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stephrdev/django-formwizard | formwizard/views.py | WizardView.get_form_prefix | def get_form_prefix(self, step=None, form=None):
"""
Returns the prefix which will be used when calling the actual form for
the given step. `step` contains the step-name, `form` the form which
will be called with the returned prefix.
If no step is given, the form_prefix will determine the current step
automatically.
"""
if step is None:
step = self.steps.current
return str(step) | python | def get_form_prefix(self, step=None, form=None):
"""
Returns the prefix which will be used when calling the actual form for
the given step. `step` contains the step-name, `form` the form which
will be called with the returned prefix.
If no step is given, the form_prefix will determine the current step
automatically.
"""
if step is None:
step = self.steps.current
return str(step) | [
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stephrdev/django-formwizard | formwizard/views.py | WizardView.get_form | def get_form(self, step=None, data=None, files=None):
"""
Constructs the form for a given `step`. If no `step` is defined, the
current step will be determined automatically.
The form will be initialized using the `data` argument to prefill the
new form. If needed, instance or queryset (for `ModelForm` or
`ModelFormSet`) will be added too.
"""
if step is None:
step = self.steps.current
# prepare the kwargs for the form instance.
kwargs = self.get_form_kwargs(step)
kwargs.update({
'data': data,
'files': files,
'prefix': self.get_form_prefix(step, self.form_list[step]),
'initial': self.get_form_initial(step),
})
if issubclass(self.form_list[step], forms.ModelForm):
# If the form is based on ModelForm, add instance if available.
kwargs.update({'instance': self.get_form_instance(step)})
elif issubclass(self.form_list[step], forms.models.BaseModelFormSet):
# If the form is based on ModelFormSet, add queryset if available.
kwargs.update({'queryset': self.get_form_instance(step)})
return self.form_list[step](**kwargs) | python | def get_form(self, step=None, data=None, files=None):
"""
Constructs the form for a given `step`. If no `step` is defined, the
current step will be determined automatically.
The form will be initialized using the `data` argument to prefill the
new form. If needed, instance or queryset (for `ModelForm` or
`ModelFormSet`) will be added too.
"""
if step is None:
step = self.steps.current
# prepare the kwargs for the form instance.
kwargs = self.get_form_kwargs(step)
kwargs.update({
'data': data,
'files': files,
'prefix': self.get_form_prefix(step, self.form_list[step]),
'initial': self.get_form_initial(step),
})
if issubclass(self.form_list[step], forms.ModelForm):
# If the form is based on ModelForm, add instance if available.
kwargs.update({'instance': self.get_form_instance(step)})
elif issubclass(self.form_list[step], forms.models.BaseModelFormSet):
# If the form is based on ModelFormSet, add queryset if available.
kwargs.update({'queryset': self.get_form_instance(step)})
return self.form_list[step](**kwargs) | [
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stephrdev/django-formwizard | formwizard/views.py | WizardView.render_revalidation_failure | def render_revalidation_failure(self, step, form, **kwargs):
"""
Gets called when a form doesn't validate when rendering the done
view. By default, it changed the current step to failing forms step
and renders the form.
"""
self.storage.current_step = step
return self.render(form, **kwargs) | python | def render_revalidation_failure(self, step, form, **kwargs):
"""
Gets called when a form doesn't validate when rendering the done
view. By default, it changed the current step to failing forms step
and renders the form.
"""
self.storage.current_step = step
return self.render(form, **kwargs) | [
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stephrdev/django-formwizard | formwizard/views.py | WizardView.get_all_cleaned_data | def get_all_cleaned_data(self):
"""
Returns a merged dictionary of all step cleaned_data dictionaries.
If a step contains a `FormSet`, the key will be prefixed with formset
and contain a list of the formset' cleaned_data dictionaries.
"""
cleaned_data = {}
for form_key in self.get_form_list():
form_obj = self.get_form(
step=form_key,
data=self.storage.get_step_data(form_key),
files=self.storage.get_step_files(form_key)
)
if form_obj.is_valid():
if isinstance(form_obj.cleaned_data, (tuple, list)):
cleaned_data.update({
'formset-%s' % form_key: form_obj.cleaned_data
})
else:
cleaned_data.update(form_obj.cleaned_data)
return cleaned_data | python | def get_all_cleaned_data(self):
"""
Returns a merged dictionary of all step cleaned_data dictionaries.
If a step contains a `FormSet`, the key will be prefixed with formset
and contain a list of the formset' cleaned_data dictionaries.
"""
cleaned_data = {}
for form_key in self.get_form_list():
form_obj = self.get_form(
step=form_key,
data=self.storage.get_step_data(form_key),
files=self.storage.get_step_files(form_key)
)
if form_obj.is_valid():
if isinstance(form_obj.cleaned_data, (tuple, list)):
cleaned_data.update({
'formset-%s' % form_key: form_obj.cleaned_data
})
else:
cleaned_data.update(form_obj.cleaned_data)
return cleaned_data | [
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stephrdev/django-formwizard | formwizard/views.py | WizardView.get_cleaned_data_for_step | def get_cleaned_data_for_step(self, step):
"""
Returns the cleaned data for a given `step`. Before returning the
cleaned data, the stored values are being revalidated through the
form. If the data doesn't validate, None will be returned.
"""
if step in self.form_list:
form_obj = self.get_form(step=step,
data=self.storage.get_step_data(step),
files=self.storage.get_step_files(step))
if form_obj.is_valid():
return form_obj.cleaned_data
return None | python | def get_cleaned_data_for_step(self, step):
"""
Returns the cleaned data for a given `step`. Before returning the
cleaned data, the stored values are being revalidated through the
form. If the data doesn't validate, None will be returned.
"""
if step in self.form_list:
form_obj = self.get_form(step=step,
data=self.storage.get_step_data(step),
files=self.storage.get_step_files(step))
if form_obj.is_valid():
return form_obj.cleaned_data
return None | [
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stephrdev/django-formwizard | formwizard/views.py | WizardView.get_step_index | def get_step_index(self, step=None):
"""
Returns the index for the given `step` name. If no step is given,
the current step will be used to get the index.
"""
if step is None:
step = self.steps.current
return self.get_form_list().keyOrder.index(step) | python | def get_step_index(self, step=None):
"""
Returns the index for the given `step` name. If no step is given,
the current step will be used to get the index.
"""
if step is None:
step = self.steps.current
return self.get_form_list().keyOrder.index(step) | [
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stephrdev/django-formwizard | formwizard/views.py | WizardView.render | def render(self, form=None, **kwargs):
"""
Returns a ``HttpResponse`` containing a all needed context data.
"""
form = form or self.get_form()
context = self.get_context_data(form, **kwargs)
return self.render_to_response(context) | python | def render(self, form=None, **kwargs):
"""
Returns a ``HttpResponse`` containing a all needed context data.
"""
form = form or self.get_form()
context = self.get_context_data(form, **kwargs)
return self.render_to_response(context) | [
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stephrdev/django-formwizard | formwizard/views.py | NamedUrlWizardView.get_initkwargs | def get_initkwargs(cls, *args, **kwargs):
"""
We require a url_name to reverse URLs later. Additionally users can
pass a done_step_name to change the URL name of the "done" view.
"""
assert 'url_name' in kwargs, 'URL name is needed to resolve correct wizard URLs'
extra_kwargs = {
'done_step_name': kwargs.pop('done_step_name', 'done'),
'url_name': kwargs.pop('url_name'),
}
initkwargs = super(NamedUrlWizardView, cls).get_initkwargs(*args, **kwargs)
initkwargs.update(extra_kwargs)
assert initkwargs['done_step_name'] not in initkwargs['form_list'], \
'step name "%s" is reserved for "done" view' % initkwargs['done_step_name']
return initkwargs | python | def get_initkwargs(cls, *args, **kwargs):
"""
We require a url_name to reverse URLs later. Additionally users can
pass a done_step_name to change the URL name of the "done" view.
"""
assert 'url_name' in kwargs, 'URL name is needed to resolve correct wizard URLs'
extra_kwargs = {
'done_step_name': kwargs.pop('done_step_name', 'done'),
'url_name': kwargs.pop('url_name'),
}
initkwargs = super(NamedUrlWizardView, cls).get_initkwargs(*args, **kwargs)
initkwargs.update(extra_kwargs)
assert initkwargs['done_step_name'] not in initkwargs['form_list'], \
'step name "%s" is reserved for "done" view' % initkwargs['done_step_name']
return initkwargs | [
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stephrdev/django-formwizard | formwizard/views.py | NamedUrlWizardView.get | def get(self, *args, **kwargs):
"""
This renders the form or, if needed, does the http redirects.
"""
step_url = kwargs.get('step', None)
if step_url is None:
if 'reset' in self.request.GET:
self.storage.reset()
self.storage.current_step = self.steps.first
if self.request.GET:
query_string = "?%s" % self.request.GET.urlencode()
else:
query_string = ""
next_step_url = reverse(self.url_name, kwargs={
'step': self.steps.current,
}) + query_string
return redirect(next_step_url)
# is the current step the "done" name/view?
elif step_url == self.done_step_name:
last_step = self.steps.last
return self.render_done(self.get_form(step=last_step,
data=self.storage.get_step_data(last_step),
files=self.storage.get_step_files(last_step)
), **kwargs)
# is the url step name not equal to the step in the storage?
# if yes, change the step in the storage (if name exists)
elif step_url == self.steps.current:
# URL step name and storage step name are equal, render!
return self.render(self.get_form(
data=self.storage.current_step_data,
files=self.storage.current_step_data,
), **kwargs)
elif step_url in self.get_form_list():
self.storage.current_step = step_url
return self.render(self.get_form(
data=self.storage.current_step_data,
files=self.storage.current_step_data,
), **kwargs)
# invalid step name, reset to first and redirect.
else:
self.storage.current_step = self.steps.first
return redirect(self.url_name, step=self.steps.first) | python | def get(self, *args, **kwargs):
"""
This renders the form or, if needed, does the http redirects.
"""
step_url = kwargs.get('step', None)
if step_url is None:
if 'reset' in self.request.GET:
self.storage.reset()
self.storage.current_step = self.steps.first
if self.request.GET:
query_string = "?%s" % self.request.GET.urlencode()
else:
query_string = ""
next_step_url = reverse(self.url_name, kwargs={
'step': self.steps.current,
}) + query_string
return redirect(next_step_url)
# is the current step the "done" name/view?
elif step_url == self.done_step_name:
last_step = self.steps.last
return self.render_done(self.get_form(step=last_step,
data=self.storage.get_step_data(last_step),
files=self.storage.get_step_files(last_step)
), **kwargs)
# is the url step name not equal to the step in the storage?
# if yes, change the step in the storage (if name exists)
elif step_url == self.steps.current:
# URL step name and storage step name are equal, render!
return self.render(self.get_form(
data=self.storage.current_step_data,
files=self.storage.current_step_data,
), **kwargs)
elif step_url in self.get_form_list():
self.storage.current_step = step_url
return self.render(self.get_form(
data=self.storage.current_step_data,
files=self.storage.current_step_data,
), **kwargs)
# invalid step name, reset to first and redirect.
else:
self.storage.current_step = self.steps.first
return redirect(self.url_name, step=self.steps.first) | [
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stephrdev/django-formwizard | formwizard/views.py | NamedUrlWizardView.post | def post(self, *args, **kwargs):
"""
Do a redirect if user presses the prev. step button. The rest of this
is super'd from FormWizard.
"""
prev_step = self.request.POST.get('wizard_prev_step', None)
if prev_step and prev_step in self.get_form_list():
self.storage.current_step = prev_step
return redirect(self.url_name, step=prev_step)
return super(NamedUrlWizardView, self).post(*args, **kwargs) | python | def post(self, *args, **kwargs):
"""
Do a redirect if user presses the prev. step button. The rest of this
is super'd from FormWizard.
"""
prev_step = self.request.POST.get('wizard_prev_step', None)
if prev_step and prev_step in self.get_form_list():
self.storage.current_step = prev_step
return redirect(self.url_name, step=prev_step)
return super(NamedUrlWizardView, self).post(*args, **kwargs) | [
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stephrdev/django-formwizard | formwizard/views.py | NamedUrlWizardView.render_next_step | def render_next_step(self, form, **kwargs):
"""
When using the NamedUrlFormWizard, we have to redirect to update the
browser's URL to match the shown step.
"""
next_step = self.get_next_step()
self.storage.current_step = next_step
return redirect(self.url_name, step=next_step) | python | def render_next_step(self, form, **kwargs):
"""
When using the NamedUrlFormWizard, we have to redirect to update the
browser's URL to match the shown step.
"""
next_step = self.get_next_step()
self.storage.current_step = next_step
return redirect(self.url_name, step=next_step) | [
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stephrdev/django-formwizard | formwizard/views.py | NamedUrlWizardView.render_revalidation_failure | def render_revalidation_failure(self, failed_step, form, **kwargs):
"""
When a step fails, we have to redirect the user to the first failing
step.
"""
self.storage.current_step = failed_step
return redirect(self.url_name, step=failed_step) | python | def render_revalidation_failure(self, failed_step, form, **kwargs):
"""
When a step fails, we have to redirect the user to the first failing
step.
"""
self.storage.current_step = failed_step
return redirect(self.url_name, step=failed_step) | [
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budacom/trading-bots | trading_bots/core/storage.py | get_store | def get_store(logger: Logger=None) -> 'Store':
"""Get and configure the storage backend"""
from trading_bots.conf import settings
store_settings = settings.storage
store = store_settings.get('name', 'json')
if store == 'json':
store = 'trading_bots.core.storage.JSONStore'
elif store == 'redis':
store = 'trading_bots.core.storage.RedisStore'
store_cls = load_class_by_name(store)
kwargs = store_cls.configure(store_settings)
return store_cls(logger=logger, **kwargs) | python | def get_store(logger: Logger=None) -> 'Store':
"""Get and configure the storage backend"""
from trading_bots.conf import settings
store_settings = settings.storage
store = store_settings.get('name', 'json')
if store == 'json':
store = 'trading_bots.core.storage.JSONStore'
elif store == 'redis':
store = 'trading_bots.core.storage.RedisStore'
store_cls = load_class_by_name(store)
kwargs = store_cls.configure(store_settings)
return store_cls(logger=logger, **kwargs) | [
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coyo8/parinx | parinx/parser.py | parse_request_headers | def parse_request_headers(headers):
"""
convert headers in human readable format
:param headers:
:return:
"""
request_header_keys = set(headers.keys(lower=True))
request_meta_keys = set(XHEADERS_TO_ARGS_DICT.keys())
data_header_keys = request_header_keys.intersection(request_meta_keys)
return dict(([XHEADERS_TO_ARGS_DICT[key],
headers.get(key, None)] for key in data_header_keys)) | python | def parse_request_headers(headers):
"""
convert headers in human readable format
:param headers:
:return:
"""
request_header_keys = set(headers.keys(lower=True))
request_meta_keys = set(XHEADERS_TO_ARGS_DICT.keys())
data_header_keys = request_header_keys.intersection(request_meta_keys)
return dict(([XHEADERS_TO_ARGS_DICT[key],
headers.get(key, None)] for key in data_header_keys)) | [
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coyo8/parinx | parinx/parser.py | split_docstring | def split_docstring(docstring):
"""
Separates the method's description and paramter's
:return: Return description string and list of fields strings
"""
docstring_list = [line.strip() for line in docstring.splitlines()]
description_list = list(
takewhile(lambda line: not (line.startswith(':') or
line.startswith('@inherit')), docstring_list))
description = ' '.join(description_list).strip()
first_field_line_number = len(description_list)
fields = []
if first_field_line_number >= len(docstring_list):
return description, fields # only description, without any field
last_field_lines = [docstring_list[first_field_line_number]]
for line in docstring_list[first_field_line_number + 1:]:
if line.strip().startswith(':') or line.strip().startswith('@inherit'):
fields.append(' '.join(last_field_lines))
last_field_lines = [line]
else:
last_field_lines.append(line)
fields.append(' '.join(last_field_lines))
return description, fields | python | def split_docstring(docstring):
"""
Separates the method's description and paramter's
:return: Return description string and list of fields strings
"""
docstring_list = [line.strip() for line in docstring.splitlines()]
description_list = list(
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description = ' '.join(description_list).strip()
first_field_line_number = len(description_list)
fields = []
if first_field_line_number >= len(docstring_list):
return description, fields # only description, without any field
last_field_lines = [docstring_list[first_field_line_number]]
for line in docstring_list[first_field_line_number + 1:]:
if line.strip().startswith(':') or line.strip().startswith('@inherit'):
fields.append(' '.join(last_field_lines))
last_field_lines = [line]
else:
last_field_lines.append(line)
fields.append(' '.join(last_field_lines))
return description, fields | [
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coyo8/parinx | parinx/parser.py | get_method_docstring | def get_method_docstring(cls, method_name):
"""
return method docstring
if method docstring is empty we get docstring from parent
:param method:
:type method:
:return:
:rtype:
"""
method = getattr(cls, method_name, None)
if method is None:
return
docstrign = inspect.getdoc(method)
if docstrign is None:
for base in cls.__bases__:
docstrign = get_method_docstring(base, method_name)
if docstrign:
return docstrign
else:
return None
return docstrign | python | def get_method_docstring(cls, method_name):
"""
return method docstring
if method docstring is empty we get docstring from parent
:param method:
:type method:
:return:
:rtype:
"""
method = getattr(cls, method_name, None)
if method is None:
return
docstrign = inspect.getdoc(method)
if docstrign is None:
for base in cls.__bases__:
docstrign = get_method_docstring(base, method_name)
if docstrign:
return docstrign
else:
return None
return docstrign | [
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mjj4791/python-buienradar | buienradar/buienradar.py | condition_from_code | def condition_from_code(condcode):
"""Get the condition name from the condition code."""
if condcode in __BRCONDITIONS:
cond_data = __BRCONDITIONS[condcode]
return {CONDCODE: condcode,
CONDITION: cond_data[0],
DETAILED: cond_data[1],
EXACT: cond_data[2],
EXACTNL: cond_data[3],
}
return None | python | def condition_from_code(condcode):
"""Get the condition name from the condition code."""
if condcode in __BRCONDITIONS:
cond_data = __BRCONDITIONS[condcode]
return {CONDCODE: condcode,
CONDITION: cond_data[0],
DETAILED: cond_data[1],
EXACT: cond_data[2],
EXACTNL: cond_data[3],
}
return None | [
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HEPData/hepdata-validator | hepdata_validator/submission_file_validator.py | SubmissionFileValidator.validate | def validate(self, **kwargs):
"""
Validates a submission file
:param file_path: path to file to be loaded.
:param data: pre loaded YAML object (optional).
:return: Bool to indicate the validity of the file.
"""
try:
submission_file_schema = json.load(open(self.default_schema_file, 'r'))
additional_file_section_schema = json.load(open(self.additional_info_schema, 'r'))
# even though we are using the yaml package to load,
# it supports JSON and YAML
data = kwargs.pop("data", None)
file_path = kwargs.pop("file_path", None)
if file_path is None:
raise LookupError("file_path argument must be supplied")
if data is None:
data = yaml.load_all(open(file_path, 'r'), Loader=Loader)
for data_item_index, data_item in enumerate(data):
if data_item is None:
continue
try:
if not data_item_index and 'data_file' not in data_item:
validate(data_item, additional_file_section_schema)
else:
validate(data_item, submission_file_schema)
except ValidationError as ve:
self.add_validation_message(
ValidationMessage(file=file_path,
message=ve.message + ' in ' + str(ve.instance)))
if self.has_errors(file_path):
return False
else:
return True
except ScannerError as se: # pragma: no cover
self.add_validation_message( # pragma: no cover
ValidationMessage(file=file_path, message=
'There was a problem parsing the file. '
'This can be because you forgot spaces '
'after colons in your YAML file for instance. '
'Diagnostic information follows.\n' + str(se)))
return False
except Exception as e:
self.add_validation_message(ValidationMessage(file=file_path, message=e.__str__()))
return False | python | def validate(self, **kwargs):
"""
Validates a submission file
:param file_path: path to file to be loaded.
:param data: pre loaded YAML object (optional).
:return: Bool to indicate the validity of the file.
"""
try:
submission_file_schema = json.load(open(self.default_schema_file, 'r'))
additional_file_section_schema = json.load(open(self.additional_info_schema, 'r'))
# even though we are using the yaml package to load,
# it supports JSON and YAML
data = kwargs.pop("data", None)
file_path = kwargs.pop("file_path", None)
if file_path is None:
raise LookupError("file_path argument must be supplied")
if data is None:
data = yaml.load_all(open(file_path, 'r'), Loader=Loader)
for data_item_index, data_item in enumerate(data):
if data_item is None:
continue
try:
if not data_item_index and 'data_file' not in data_item:
validate(data_item, additional_file_section_schema)
else:
validate(data_item, submission_file_schema)
except ValidationError as ve:
self.add_validation_message(
ValidationMessage(file=file_path,
message=ve.message + ' in ' + str(ve.instance)))
if self.has_errors(file_path):
return False
else:
return True
except ScannerError as se: # pragma: no cover
self.add_validation_message( # pragma: no cover
ValidationMessage(file=file_path, message=
'There was a problem parsing the file. '
'This can be because you forgot spaces '
'after colons in your YAML file for instance. '
'Diagnostic information follows.\n' + str(se)))
return False
except Exception as e:
self.add_validation_message(ValidationMessage(file=file_path, message=e.__str__()))
return False | [
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budacom/trading-bots | trading_bots/core/utils.py | load_class_by_name | def load_class_by_name(name: str):
"""Given a dotted path, returns the class"""
mod_path, _, cls_name = name.rpartition('.')
mod = importlib.import_module(mod_path)
cls = getattr(mod, cls_name)
return cls | python | def load_class_by_name(name: str):
"""Given a dotted path, returns the class"""
mod_path, _, cls_name = name.rpartition('.')
mod = importlib.import_module(mod_path)
cls = getattr(mod, cls_name)
return cls | [
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BD2KGenomics/protect | src/protect/addons/assess_immunotherapy_resistance.py | run_itx_resistance_assessment | def run_itx_resistance_assessment(job, rsem_files, univ_options, reports_options):
"""
A wrapper for assess_itx_resistance.
:param dict rsem_files: Results from running rsem
:param dict univ_options: Dict of universal options used by almost all tools
:param dict reports_options: Options specific to reporting modules
:return: The results of running assess_itx_resistance
:rtype: toil.fileStore.FileID
"""
return job.addChildJobFn(assess_itx_resistance, rsem_files['rsem.genes.results'],
univ_options, reports_options).rv() | python | def run_itx_resistance_assessment(job, rsem_files, univ_options, reports_options):
"""
A wrapper for assess_itx_resistance.
:param dict rsem_files: Results from running rsem
:param dict univ_options: Dict of universal options used by almost all tools
:param dict reports_options: Options specific to reporting modules
:return: The results of running assess_itx_resistance
:rtype: toil.fileStore.FileID
"""
return job.addChildJobFn(assess_itx_resistance, rsem_files['rsem.genes.results'],
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APSL/django-kaio | kaio/mixins/celeryconf.py | CeleryMixin.CELERY_RESULT_BACKEND | def CELERY_RESULT_BACKEND(self):
"""Redis result backend config"""
# allow specify directly
configured = get('CELERY_RESULT_BACKEND', None)
if configured:
return configured
if not self._redis_available():
return None
host, port = self.REDIS_HOST, self.REDIS_PORT
if host and port:
default = "redis://{host}:{port}/{db}".format(
host=host, port=port,
db=self.CELERY_REDIS_RESULT_DB)
return default | python | def CELERY_RESULT_BACKEND(self):
"""Redis result backend config"""
# allow specify directly
configured = get('CELERY_RESULT_BACKEND', None)
if configured:
return configured
if not self._redis_available():
return None
host, port = self.REDIS_HOST, self.REDIS_PORT
if host and port:
default = "redis://{host}:{port}/{db}".format(
host=host, port=port,
db=self.CELERY_REDIS_RESULT_DB)
return default | [
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APSL/django-kaio | kaio/mixins/celeryconf.py | CeleryMixin.BROKER_TYPE | def BROKER_TYPE(self):
"""Custom setting allowing switch between rabbitmq, redis"""
broker_type = get('BROKER_TYPE', DEFAULT_BROKER_TYPE)
if broker_type not in SUPPORTED_BROKER_TYPES:
log.warn("Specified BROKER_TYPE {} not supported. Backing to default {}".format(
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return DEFAULT_BROKER_TYPE
else:
return broker_type | python | def BROKER_TYPE(self):
"""Custom setting allowing switch between rabbitmq, redis"""
broker_type = get('BROKER_TYPE', DEFAULT_BROKER_TYPE)
if broker_type not in SUPPORTED_BROKER_TYPES:
log.warn("Specified BROKER_TYPE {} not supported. Backing to default {}".format(
broker_type, DEFAULT_BROKER_TYPE))
return DEFAULT_BROKER_TYPE
else:
return broker_type | [
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APSL/django-kaio | kaio/mixins/celeryconf.py | CeleryMixin.BROKER_URL | def BROKER_URL(self):
"""Sets BROKER_URL depending on redis or rabbitmq settings"""
# also allow specify broker_url
broker_url = get('BROKER_URL', None)
if broker_url:
log.info("Using BROKER_URL setting: {}".format(broker_url))
return broker_url
redis_available = self._redis_available()
broker_type = self.BROKER_TYPE
if broker_type == 'redis' and not redis_available:
log.warn("Choosed broker type is redis, but redis not available. \
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if broker_type == 'redis' and redis_available:
return 'redis://{host}:{port}/{db}'.format(
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elif broker_type == 'rabbitmq':
return 'amqp://{user}:{passwd}@{host}:{port}/{vhost}'.format(
user=self.RABBITMQ_USER,
passwd=self.RABBITMQ_PASSWD,
host=self.RABBITMQ_HOST,
port=self.RABBITMQ_PORT,
vhost=self.RABBITMQ_VHOST)
else:
return DEFAULT_BROKER_URL | python | def BROKER_URL(self):
"""Sets BROKER_URL depending on redis or rabbitmq settings"""
# also allow specify broker_url
broker_url = get('BROKER_URL', None)
if broker_url:
log.info("Using BROKER_URL setting: {}".format(broker_url))
return broker_url
redis_available = self._redis_available()
broker_type = self.BROKER_TYPE
if broker_type == 'redis' and not redis_available:
log.warn("Choosed broker type is redis, but redis not available. \
Check redis package, and REDIS_HOST, REDIS_PORT settings")
if broker_type == 'redis' and redis_available:
return 'redis://{host}:{port}/{db}'.format(
host=self.REDIS_HOST,
port=self.REDIS_PORT,
db=self.CELERY_REDIS_BROKER_DB)
elif broker_type == 'rabbitmq':
return 'amqp://{user}:{passwd}@{host}:{port}/{vhost}'.format(
user=self.RABBITMQ_USER,
passwd=self.RABBITMQ_PASSWD,
host=self.RABBITMQ_HOST,
port=self.RABBITMQ_PORT,
vhost=self.RABBITMQ_VHOST)
else:
return DEFAULT_BROKER_URL | [
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idlesign/steampak | steampak/webapi/resources/user.py | User.traverse_inventory | def traverse_inventory(self, item_filter=None):
"""Generates market Item objects for each inventory item.
:param str item_filter: See `TAG_ITEM_CLASS_` contants from .market module.
"""
not self._intentory_raw and self._get_inventory_raw()
for item in self._intentory_raw['rgDescriptions'].values():
tags = item['tags']
for tag in tags:
internal_name = tag['internal_name']
if item_filter is None or internal_name == item_filter:
item_type = Item
if internal_name == TAG_ITEM_CLASS_CARD:
item_type = Card
appid = item['market_fee_app']
title = item['name']
yield item_type(appid, title) | python | def traverse_inventory(self, item_filter=None):
"""Generates market Item objects for each inventory item.
:param str item_filter: See `TAG_ITEM_CLASS_` contants from .market module.
"""
not self._intentory_raw and self._get_inventory_raw()
for item in self._intentory_raw['rgDescriptions'].values():
tags = item['tags']
for tag in tags:
internal_name = tag['internal_name']
if item_filter is None or internal_name == item_filter:
item_type = Item
if internal_name == TAG_ITEM_CLASS_CARD:
item_type = Card
appid = item['market_fee_app']
title = item['name']
yield item_type(appid, title) | [
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HEPData/hepdata-validator | hepdata_validator/data_file_validator.py | DataFileValidator.validate | def validate(self, **kwargs):
"""
Validates a data file
:param file_path: path to file to be loaded.
:param data: pre loaded YAML object (optional).
:return: Bool to indicate the validity of the file.
"""
default_data_schema = json.load(open(self.default_schema_file, 'r'))
# even though we are using the yaml package to load,
# it supports JSON and YAML
data = kwargs.pop("data", None)
file_path = kwargs.pop("file_path", None)
if file_path is None:
raise LookupError("file_path argument must be supplied")
if data is None:
try:
data = yaml.load(open(file_path, 'r'), Loader=Loader)
except Exception as e:
self.add_validation_message(ValidationMessage(file=file_path, message=
'There was a problem parsing the file.\n' + e.__str__()))
return False
try:
if 'type' in data:
custom_schema = self.load_custom_schema(data['type'])
json_validate(data, custom_schema)
else:
json_validate(data, default_data_schema)
except ValidationError as ve:
self.add_validation_message(
ValidationMessage(file=file_path,
message=ve.message + ' in ' + str(ve.instance)))
if self.has_errors(file_path):
return False
else:
return True | python | def validate(self, **kwargs):
"""
Validates a data file
:param file_path: path to file to be loaded.
:param data: pre loaded YAML object (optional).
:return: Bool to indicate the validity of the file.
"""
default_data_schema = json.load(open(self.default_schema_file, 'r'))
# even though we are using the yaml package to load,
# it supports JSON and YAML
data = kwargs.pop("data", None)
file_path = kwargs.pop("file_path", None)
if file_path is None:
raise LookupError("file_path argument must be supplied")
if data is None:
try:
data = yaml.load(open(file_path, 'r'), Loader=Loader)
except Exception as e:
self.add_validation_message(ValidationMessage(file=file_path, message=
'There was a problem parsing the file.\n' + e.__str__()))
return False
try:
if 'type' in data:
custom_schema = self.load_custom_schema(data['type'])
json_validate(data, custom_schema)
else:
json_validate(data, default_data_schema)
except ValidationError as ve:
self.add_validation_message(
ValidationMessage(file=file_path,
message=ve.message + ' in ' + str(ve.instance)))
if self.has_errors(file_path):
return False
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:param file_path: path to file to be loaded.
:param data: pre loaded YAML object (optional).
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proycon/python-timbl | timbl.py | b | def b(s):
"""Conversion to bytes"""
if sys.version < '3':
if isinstance(s, unicode): #pylint: disable=undefined-variable
return s.encode('utf-8')
else:
return s | python | def b(s):
"""Conversion to bytes"""
if sys.version < '3':
if isinstance(s, unicode): #pylint: disable=undefined-variable
return s.encode('utf-8')
else:
return s | [
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proycon/python-timbl | timbl.py | TimblClassifier.validatefeatures | def validatefeatures(self,features):
"""Returns features in validated form, or raises an Exception. Mostly for internal use"""
validatedfeatures = []
for feature in features:
if isinstance(feature, int) or isinstance(feature, float):
validatedfeatures.append( str(feature) )
elif self.delimiter in feature and not self.sklearn:
raise ValueError("Feature contains delimiter: " + feature)
elif self.sklearn and isinstance(feature, str): #then is sparse added together
validatedfeatures.append(feature)
else:
validatedfeatures.append(feature)
return validatedfeatures | python | def validatefeatures(self,features):
"""Returns features in validated form, or raises an Exception. Mostly for internal use"""
validatedfeatures = []
for feature in features:
if isinstance(feature, int) or isinstance(feature, float):
validatedfeatures.append( str(feature) )
elif self.delimiter in feature and not self.sklearn:
raise ValueError("Feature contains delimiter: " + feature)
elif self.sklearn and isinstance(feature, str): #then is sparse added together
validatedfeatures.append(feature)
else:
validatedfeatures.append(feature)
return validatedfeatures | [
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proycon/python-timbl | timbl.py | TimblClassifier.addinstance | def addinstance(self, testfile, features, classlabel="?"):
"""Adds an instance to a specific file. Especially suitable for generating test files"""
features = self.validatefeatures(features)
if self.delimiter in classlabel:
raise ValueError("Class label contains delimiter: " + self.delimiter)
f = io.open(testfile,'a', encoding=self.encoding)
f.write(self.delimiter.join(features) + self.delimiter + classlabel + "\n")
f.close() | python | def addinstance(self, testfile, features, classlabel="?"):
"""Adds an instance to a specific file. Especially suitable for generating test files"""
features = self.validatefeatures(features)
if self.delimiter in classlabel:
raise ValueError("Class label contains delimiter: " + self.delimiter)
f = io.open(testfile,'a', encoding=self.encoding)
f.write(self.delimiter.join(features) + self.delimiter + classlabel + "\n")
f.close() | [
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proycon/python-timbl | timbl.py | TimblClassifier.crossvalidate | def crossvalidate(self, foldsfile):
"""Train & Test using cross validation, testfile is a file that contains the filenames of all the folds!"""
options = "-F " + self.format + " " + self.timbloptions + " -t cross_validate"
print("Instantiating Timbl API : " + options,file=stderr)
if sys.version < '3':
self.api = timblapi.TimblAPI(b(options), b"")
else:
self.api = timblapi.TimblAPI(options, "")
if self.debug:
print("Enabling debug for timblapi",file=stderr)
self.api.enableDebug()
print("Calling Timbl Test : " + options,file=stderr)
if sys.version < '3':
self.api.test(b(foldsfile),b'',b'')
else:
self.api.test(u(foldsfile),'','')
a = self.api.getAccuracy()
del self.api
return a | python | def crossvalidate(self, foldsfile):
"""Train & Test using cross validation, testfile is a file that contains the filenames of all the folds!"""
options = "-F " + self.format + " " + self.timbloptions + " -t cross_validate"
print("Instantiating Timbl API : " + options,file=stderr)
if sys.version < '3':
self.api = timblapi.TimblAPI(b(options), b"")
else:
self.api = timblapi.TimblAPI(options, "")
if self.debug:
print("Enabling debug for timblapi",file=stderr)
self.api.enableDebug()
print("Calling Timbl Test : " + options,file=stderr)
if sys.version < '3':
self.api.test(b(foldsfile),b'',b'')
else:
self.api.test(u(foldsfile),'','')
a = self.api.getAccuracy()
del self.api
return a | [
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proycon/python-timbl | timbl.py | TimblClassifier.leaveoneout | def leaveoneout(self):
"""Train & Test using leave one out"""
traintestfile = self.fileprefix + '.train'
options = "-F " + self.format + " " + self.timbloptions + " -t leave_one_out"
if sys.version < '3':
self.api = timblapi.TimblAPI(b(options), b"")
else:
self.api = timblapi.TimblAPI(options, "")
if self.debug:
print("Enabling debug for timblapi",file=stderr)
self.api.enableDebug()
print("Calling Timbl API : " + options,file=stderr)
if sys.version < '3':
self.api.learn(b(traintestfile))
self.api.test(b(traintestfile), b(self.fileprefix + '.out'),b'')
else:
self.api.learn(u(traintestfile))
self.api.test(u(traintestfile), u(self.fileprefix + '.out'),'')
return self.api.getAccuracy() | python | def leaveoneout(self):
"""Train & Test using leave one out"""
traintestfile = self.fileprefix + '.train'
options = "-F " + self.format + " " + self.timbloptions + " -t leave_one_out"
if sys.version < '3':
self.api = timblapi.TimblAPI(b(options), b"")
else:
self.api = timblapi.TimblAPI(options, "")
if self.debug:
print("Enabling debug for timblapi",file=stderr)
self.api.enableDebug()
print("Calling Timbl API : " + options,file=stderr)
if sys.version < '3':
self.api.learn(b(traintestfile))
self.api.test(b(traintestfile), b(self.fileprefix + '.out'),b'')
else:
self.api.learn(u(traintestfile))
self.api.test(u(traintestfile), u(self.fileprefix + '.out'),'')
return self.api.getAccuracy() | [
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inveniosoftware/invenio-access | invenio_access/ext.py | _AccessState.set_action_cache | def set_action_cache(self, action_key, data):
"""Store action needs and excludes.
.. note:: The action is saved only if a cache system is defined.
:param action_key: The unique action name.
:param data: The action to be saved.
"""
if self.cache:
self.cache.set(
self.app.config['ACCESS_ACTION_CACHE_PREFIX'] +
action_key, data
) | python | def set_action_cache(self, action_key, data):
"""Store action needs and excludes.
.. note:: The action is saved only if a cache system is defined.
:param action_key: The unique action name.
:param data: The action to be saved.
"""
if self.cache:
self.cache.set(
self.app.config['ACCESS_ACTION_CACHE_PREFIX'] +
action_key, data
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inveniosoftware/invenio-access | invenio_access/ext.py | _AccessState.get_action_cache | def get_action_cache(self, action_key):
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:param action_key: The unique action name.
:returns: The action stored in cache or ``None``.
"""
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return data | python | def get_action_cache(self, action_key):
"""Get action needs and excludes from cache.
.. note:: It returns the action if a cache system is defined.
:param action_key: The unique action name.
:returns: The action stored in cache or ``None``.
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inveniosoftware/invenio-access | invenio_access/ext.py | _AccessState.delete_action_cache | def delete_action_cache(self, action_key):
"""Delete action needs and excludes from cache.
.. note:: It returns the action if a cache system is defined.
:param action_key: The unique action name.
"""
if self.cache:
self.cache.delete(
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) | python | def delete_action_cache(self, action_key):
"""Delete action needs and excludes from cache.
.. note:: It returns the action if a cache system is defined.
:param action_key: The unique action name.
"""
if self.cache:
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] | 3b033a4bdc110eb2f7e9f08f0744a780884bfc80 | https://github.com/inveniosoftware/invenio-access/blob/3b033a4bdc110eb2f7e9f08f0744a780884bfc80/invenio_access/ext.py#L82-L93 | train |
inveniosoftware/invenio-access | invenio_access/ext.py | _AccessState.register_action | def register_action(self, action):
"""Register an action to be showed in the actions list.
.. note:: A action can't be registered two times. If it happens, then
an assert exception will be raised.
:param action: The action to be registered.
"""
assert action.value not in self.actions
self.actions[action.value] = action | python | def register_action(self, action):
"""Register an action to be showed in the actions list.
.. note:: A action can't be registered two times. If it happens, then
an assert exception will be raised.
:param action: The action to be registered.
"""
assert action.value not in self.actions
self.actions[action.value] = action | [
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.. note:: A action can't be registered two times. If it happens, then
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inveniosoftware/invenio-access | invenio_access/ext.py | _AccessState.register_system_role | def register_system_role(self, system_role):
"""Register a system role.
.. note:: A system role can't be registered two times. If it happens,
then an assert exception will be raised.
:param system_role: The system role to be registered.
"""
assert system_role.value not in self.system_roles
self.system_roles[system_role.value] = system_role | python | def register_system_role(self, system_role):
"""Register a system role.
.. note:: A system role can't be registered two times. If it happens,
then an assert exception will be raised.
:param system_role: The system role to be registered.
"""
assert system_role.value not in self.system_roles
self.system_roles[system_role.value] = system_role | [
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.. note:: A system role can't be registered two times. If it happens,
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inveniosoftware/invenio-access | invenio_access/ext.py | _AccessState.load_entry_point_system_roles | def load_entry_point_system_roles(self, entry_point_group):
"""Load system roles from an entry point group.
:param entry_point_group: The entrypoint for extensions.
"""
for ep in pkg_resources.iter_entry_points(group=entry_point_group):
self.register_system_role(ep.load()) | python | def load_entry_point_system_roles(self, entry_point_group):
"""Load system roles from an entry point group.
:param entry_point_group: The entrypoint for extensions.
"""
for ep in pkg_resources.iter_entry_points(group=entry_point_group):
self.register_system_role(ep.load()) | [
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mjj4791/python-buienradar | buienradar/__main__.py | main | def main(argv=sys.argv[1:]):
"""Parse argument and start main program."""
args = docopt(__doc__, argv=argv,
version=pkg_resources.require('buienradar')[0].version)
level = logging.ERROR
if args['-v']:
level = logging.INFO
if args['-v'] == 2:
level = logging.DEBUG
logging.basicConfig(level=level)
log = logging.getLogger(__name__)
log.info("Start...")
latitude = float(args['--latitude'])
longitude = float(args['--longitude'])
timeframe = int(args['--timeframe'])
usexml = False
if args['--usexml']:
usexml = True
result = get_data(latitude, longitude, usexml)
if result[SUCCESS]:
log.debug("Retrieved data:\n%s", result)
result = parse_data(result[CONTENT], result[RAINCONTENT],
latitude, longitude, timeframe, usexml)
log.info("result: %s", result)
print(result)
else:
log.error("Retrieving weather data was not successfull (%s)",
result[MESSAGE]) | python | def main(argv=sys.argv[1:]):
"""Parse argument and start main program."""
args = docopt(__doc__, argv=argv,
version=pkg_resources.require('buienradar')[0].version)
level = logging.ERROR
if args['-v']:
level = logging.INFO
if args['-v'] == 2:
level = logging.DEBUG
logging.basicConfig(level=level)
log = logging.getLogger(__name__)
log.info("Start...")
latitude = float(args['--latitude'])
longitude = float(args['--longitude'])
timeframe = int(args['--timeframe'])
usexml = False
if args['--usexml']:
usexml = True
result = get_data(latitude, longitude, usexml)
if result[SUCCESS]:
log.debug("Retrieved data:\n%s", result)
result = parse_data(result[CONTENT], result[RAINCONTENT],
latitude, longitude, timeframe, usexml)
log.info("result: %s", result)
print(result)
else:
log.error("Retrieving weather data was not successfull (%s)",
result[MESSAGE]) | [
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idlesign/steampak | steampak/libsteam/resources/stats.py | Achievement.global_unlock_percent | def global_unlock_percent(self):
"""Global achievement unlock percent.
:rtype: float
"""
percent = CRef.cfloat()
result = self._iface.get_ach_progress(self.name, percent)
if not result:
return 0.0
return float(percent) | python | def global_unlock_percent(self):
"""Global achievement unlock percent.
:rtype: float
"""
percent = CRef.cfloat()
result = self._iface.get_ach_progress(self.name, percent)
if not result:
return 0.0
return float(percent) | [
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idlesign/steampak | steampak/libsteam/resources/stats.py | Achievement.unlocked | def unlocked(self):
"""``True`` if achievement is unlocked.
:rtype: bool
"""
achieved = CRef.cbool()
result = self._iface.get_ach(self.name, achieved)
if not result:
return False
return bool(achieved) | python | def unlocked(self):
"""``True`` if achievement is unlocked.
:rtype: bool
"""
achieved = CRef.cbool()
result = self._iface.get_ach(self.name, achieved)
if not result:
return False
return bool(achieved) | [
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idlesign/steampak | steampak/libsteam/resources/stats.py | Achievement.unlock | def unlock(self, store=True):
"""Unlocks the achievement.
:param bool store: Whether to send data to server immediately (as to get overlay notification).
:rtype: bool
"""
result = self._iface.ach_unlock(self.name)
result and store and self._store()
return result | python | def unlock(self, store=True):
"""Unlocks the achievement.
:param bool store: Whether to send data to server immediately (as to get overlay notification).
:rtype: bool
"""
result = self._iface.ach_unlock(self.name)
result and store and self._store()
return result | [
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:param bool store: Whether to send data to server immediately (as to get overlay notification).
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mjj4791/python-buienradar | buienradar/buienradar_xml.py | __parse_ws_data | def __parse_ws_data(content, latitude=52.091579, longitude=5.119734):
"""Parse the buienradar xml and rain data."""
log.info("Parse ws data: latitude: %s, longitude: %s", latitude, longitude)
result = {SUCCESS: False, MESSAGE: None, DATA: None}
# convert the xml data into a dictionary:
try:
xmldata = xmltodict.parse(content)[__BRROOT]
except (xmltodict.expat.ExpatError, KeyError):
result[MESSAGE] = "Unable to parse content as xml."
log.exception(result[MESSAGE])
return result
# select the nearest weather station
loc_data = __select_nearest_ws(xmldata, latitude, longitude)
# process current weather data from selected weatherstation
if not loc_data:
result[MESSAGE] = 'No location selected.'
return result
if not __is_valid(loc_data):
result[MESSAGE] = 'Location data is invalid.'
return result
# add distance to weatherstation
log.debug("Raw location data: %s", loc_data)
result[DISTANCE] = __get_ws_distance(loc_data, latitude, longitude)
result = __parse_loc_data(loc_data, result)
# extract weather forecast
try:
fc_data = xmldata[__BRWEERGEGEVENS][__BRVERWACHTING]
except (xmltodict.expat.ExpatError, KeyError):
result[MESSAGE] = 'Unable to extract forecast data.'
log.exception(result[MESSAGE])
return result
if fc_data:
# result = __parse_fc_data(fc_data, result)
log.debug("Raw forecast data: %s", fc_data)
# pylint: disable=unsupported-assignment-operation
result[DATA][FORECAST] = __parse_fc_data(fc_data)
return result | python | def __parse_ws_data(content, latitude=52.091579, longitude=5.119734):
"""Parse the buienradar xml and rain data."""
log.info("Parse ws data: latitude: %s, longitude: %s", latitude, longitude)
result = {SUCCESS: False, MESSAGE: None, DATA: None}
# convert the xml data into a dictionary:
try:
xmldata = xmltodict.parse(content)[__BRROOT]
except (xmltodict.expat.ExpatError, KeyError):
result[MESSAGE] = "Unable to parse content as xml."
log.exception(result[MESSAGE])
return result
# select the nearest weather station
loc_data = __select_nearest_ws(xmldata, latitude, longitude)
# process current weather data from selected weatherstation
if not loc_data:
result[MESSAGE] = 'No location selected.'
return result
if not __is_valid(loc_data):
result[MESSAGE] = 'Location data is invalid.'
return result
# add distance to weatherstation
log.debug("Raw location data: %s", loc_data)
result[DISTANCE] = __get_ws_distance(loc_data, latitude, longitude)
result = __parse_loc_data(loc_data, result)
# extract weather forecast
try:
fc_data = xmldata[__BRWEERGEGEVENS][__BRVERWACHTING]
except (xmltodict.expat.ExpatError, KeyError):
result[MESSAGE] = 'Unable to extract forecast data.'
log.exception(result[MESSAGE])
return result
if fc_data:
# result = __parse_fc_data(fc_data, result)
log.debug("Raw forecast data: %s", fc_data)
# pylint: disable=unsupported-assignment-operation
result[DATA][FORECAST] = __parse_fc_data(fc_data)
return result | [
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mjj4791/python-buienradar | buienradar/buienradar_xml.py | __parse_loc_data | def __parse_loc_data(loc_data, result):
"""Parse the xml data from selected weatherstation."""
result[DATA] = {ATTRIBUTION: ATTRIBUTION_INFO,
FORECAST: [],
PRECIPITATION_FORECAST: None}
for key, [value, func] in SENSOR_TYPES.items():
result[DATA][key] = None
try:
from buienradar.buienradar import condition_from_code
sens_data = loc_data[value]
if key == CONDITION:
# update weather symbol & status text
code = sens_data[__BRID][:1]
result[DATA][CONDITION] = condition_from_code(code)
result[DATA][CONDITION][IMAGE] = sens_data[__BRTEXT]
else:
if key == STATIONNAME:
name = sens_data[__BRTEXT].replace("Meetstation", "")
name = name.strip()
name += " (%s)" % loc_data[__BRSTATIONCODE]
result[DATA][key] = name
else:
# update all other data
if func is not None:
result[DATA][key] = func(sens_data)
else:
result[DATA][key] = sens_data
except KeyError:
if result[MESSAGE] is None:
result[MESSAGE] = "Missing key(s) in br data: "
result[MESSAGE] += "%s " % value
log.warning("Data element with key='%s' "
"not loaded from br data!", key)
result[SUCCESS] = True
return result | python | def __parse_loc_data(loc_data, result):
"""Parse the xml data from selected weatherstation."""
result[DATA] = {ATTRIBUTION: ATTRIBUTION_INFO,
FORECAST: [],
PRECIPITATION_FORECAST: None}
for key, [value, func] in SENSOR_TYPES.items():
result[DATA][key] = None
try:
from buienradar.buienradar import condition_from_code
sens_data = loc_data[value]
if key == CONDITION:
# update weather symbol & status text
code = sens_data[__BRID][:1]
result[DATA][CONDITION] = condition_from_code(code)
result[DATA][CONDITION][IMAGE] = sens_data[__BRTEXT]
else:
if key == STATIONNAME:
name = sens_data[__BRTEXT].replace("Meetstation", "")
name = name.strip()
name += " (%s)" % loc_data[__BRSTATIONCODE]
result[DATA][key] = name
else:
# update all other data
if func is not None:
result[DATA][key] = func(sens_data)
else:
result[DATA][key] = sens_data
except KeyError:
if result[MESSAGE] is None:
result[MESSAGE] = "Missing key(s) in br data: "
result[MESSAGE] += "%s " % value
log.warning("Data element with key='%s' "
"not loaded from br data!", key)
result[SUCCESS] = True
return result | [
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mjj4791/python-buienradar | buienradar/buienradar_xml.py | __parse_fc_data | def __parse_fc_data(fc_data):
"""Parse the forecast data from the xml section."""
from buienradar.buienradar import condition_from_code
fc = []
for daycnt in range(1, 6):
daysection = __BRDAYFC % daycnt
if daysection in fc_data:
tmpsect = fc_data[daysection]
fcdatetime = datetime.now(pytz.timezone(__TIMEZONE))
fcdatetime = fcdatetime.replace(hour=12,
minute=0,
second=0,
microsecond=0)
# add daycnt days
fcdatetime = fcdatetime + timedelta(days=daycnt)
code = tmpsect.get(__BRICOON, []).get(__BRID)
fcdata = {
CONDITION: condition_from_code(code),
TEMPERATURE: __get_float(tmpsect, __BRMAXTEMP),
MIN_TEMP: __get_float(tmpsect, __BRMINTEMP),
MAX_TEMP: __get_float(tmpsect, __BRMAXTEMP),
SUN_CHANCE: __get_int(tmpsect, __BRKANSZON),
RAIN_CHANCE: __get_int(tmpsect, __BRKANSREGEN),
RAIN: __get_float(tmpsect, __BRMAXMMREGEN),
SNOW: __get_float(tmpsect, __BRSNEEUWCMS),
WINDFORCE: __get_int(tmpsect, __BRWINDKRACHT),
DATETIME: fcdatetime,
}
fcdata[CONDITION][IMAGE] = tmpsect.get(__BRICOON, []).get(__BRTEXT)
fc.append(fcdata)
return fc | python | def __parse_fc_data(fc_data):
"""Parse the forecast data from the xml section."""
from buienradar.buienradar import condition_from_code
fc = []
for daycnt in range(1, 6):
daysection = __BRDAYFC % daycnt
if daysection in fc_data:
tmpsect = fc_data[daysection]
fcdatetime = datetime.now(pytz.timezone(__TIMEZONE))
fcdatetime = fcdatetime.replace(hour=12,
minute=0,
second=0,
microsecond=0)
# add daycnt days
fcdatetime = fcdatetime + timedelta(days=daycnt)
code = tmpsect.get(__BRICOON, []).get(__BRID)
fcdata = {
CONDITION: condition_from_code(code),
TEMPERATURE: __get_float(tmpsect, __BRMAXTEMP),
MIN_TEMP: __get_float(tmpsect, __BRMINTEMP),
MAX_TEMP: __get_float(tmpsect, __BRMAXTEMP),
SUN_CHANCE: __get_int(tmpsect, __BRKANSZON),
RAIN_CHANCE: __get_int(tmpsect, __BRKANSREGEN),
RAIN: __get_float(tmpsect, __BRMAXMMREGEN),
SNOW: __get_float(tmpsect, __BRSNEEUWCMS),
WINDFORCE: __get_int(tmpsect, __BRWINDKRACHT),
DATETIME: fcdatetime,
}
fcdata[CONDITION][IMAGE] = tmpsect.get(__BRICOON, []).get(__BRTEXT)
fc.append(fcdata)
return fc | [
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mjj4791/python-buienradar | buienradar/buienradar_xml.py | __get_ws_distance | def __get_ws_distance(wstation, latitude, longitude):
"""Get the distance to the weatherstation from wstation section of xml.
wstation: weerstation section of buienradar xml (dict)
latitude: our latitude
longitude: our longitude
"""
if wstation:
try:
wslat = float(wstation[__BRLAT])
wslon = float(wstation[__BRLON])
dist = vincenty((latitude, longitude), (wslat, wslon))
log.debug("calc distance: %s (latitude: %s, longitude: "
"%s, wslat: %s, wslon: %s)", dist, latitude,
longitude, wslat, wslon)
return dist
except (ValueError, TypeError, KeyError):
# value does not exist, or is not a float
return None
else:
return None | python | def __get_ws_distance(wstation, latitude, longitude):
"""Get the distance to the weatherstation from wstation section of xml.
wstation: weerstation section of buienradar xml (dict)
latitude: our latitude
longitude: our longitude
"""
if wstation:
try:
wslat = float(wstation[__BRLAT])
wslon = float(wstation[__BRLON])
dist = vincenty((latitude, longitude), (wslat, wslon))
log.debug("calc distance: %s (latitude: %s, longitude: "
"%s, wslat: %s, wslon: %s)", dist, latitude,
longitude, wslat, wslon)
return dist
except (ValueError, TypeError, KeyError):
# value does not exist, or is not a float
return None
else:
return None | [
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BD2KGenomics/protect | src/protect/binding_prediction/mhcii.py | predict_mhcii_binding | def predict_mhcii_binding(job, peptfile, allele, univ_options, mhcii_options):
"""
Predict binding for each peptide in `peptfile` to `allele` using the IEDB mhcii binding
prediction tool.
:param toil.fileStore.FileID peptfile: The input peptide fasta
:param str allele: Allele to predict binding against
:param dict univ_options: Dict of universal options used by almost all tools
:param dict mhcii_options: Options specific to mhcii binding prediction
:return: tuple of fsID for file containing the predictions and the predictor used
:rtype: tuple(toil.fileStore.FileID, str|None)
"""
work_dir = os.getcwd()
input_files = {
'peptfile.faa': peptfile}
input_files = get_files_from_filestore(job, input_files, work_dir, docker=True)
peptides = read_peptide_file(os.path.join(os.getcwd(), 'peptfile.faa'))
parameters = [mhcii_options['pred'],
allele,
input_files['peptfile.faa']]
if not peptides:
return job.fileStore.writeGlobalFile(job.fileStore.getLocalTempFile()), None
with open('/'.join([work_dir, 'predictions.tsv']), 'w') as predfile:
docker_call(tool='mhcii', tool_parameters=parameters, work_dir=work_dir,
dockerhub=univ_options['dockerhub'], outfile=predfile, interactive=True,
tool_version=mhcii_options['version'])
run_netmhciipan = True
predictor = None
with open(predfile.name, 'r') as predfile:
for line in predfile:
if not line.startswith('HLA'):
continue
if line.strip().split('\t')[5] == 'NetMHCIIpan':
break
# If the predictor type is sturniolo then it needs to be processed differently
elif line.strip().split('\t')[5] == 'Sturniolo':
predictor = 'Sturniolo'
else:
predictor = 'Consensus'
run_netmhciipan = False
break
if run_netmhciipan:
netmhciipan = job.addChildJobFn(predict_netmhcii_binding, peptfile, allele, univ_options,
mhcii_options['netmhciipan'], disk='100M', memory='100M',
cores=1)
job.fileStore.logToMaster('Ran mhcii on %s:%s successfully'
% (univ_options['patient'], allele))
return netmhciipan.rv()
else:
output_file = job.fileStore.writeGlobalFile(predfile.name)
job.fileStore.logToMaster('Ran mhcii on %s:%s successfully'
% (univ_options['patient'], allele))
return output_file, predictor | python | def predict_mhcii_binding(job, peptfile, allele, univ_options, mhcii_options):
"""
Predict binding for each peptide in `peptfile` to `allele` using the IEDB mhcii binding
prediction tool.
:param toil.fileStore.FileID peptfile: The input peptide fasta
:param str allele: Allele to predict binding against
:param dict univ_options: Dict of universal options used by almost all tools
:param dict mhcii_options: Options specific to mhcii binding prediction
:return: tuple of fsID for file containing the predictions and the predictor used
:rtype: tuple(toil.fileStore.FileID, str|None)
"""
work_dir = os.getcwd()
input_files = {
'peptfile.faa': peptfile}
input_files = get_files_from_filestore(job, input_files, work_dir, docker=True)
peptides = read_peptide_file(os.path.join(os.getcwd(), 'peptfile.faa'))
parameters = [mhcii_options['pred'],
allele,
input_files['peptfile.faa']]
if not peptides:
return job.fileStore.writeGlobalFile(job.fileStore.getLocalTempFile()), None
with open('/'.join([work_dir, 'predictions.tsv']), 'w') as predfile:
docker_call(tool='mhcii', tool_parameters=parameters, work_dir=work_dir,
dockerhub=univ_options['dockerhub'], outfile=predfile, interactive=True,
tool_version=mhcii_options['version'])
run_netmhciipan = True
predictor = None
with open(predfile.name, 'r') as predfile:
for line in predfile:
if not line.startswith('HLA'):
continue
if line.strip().split('\t')[5] == 'NetMHCIIpan':
break
# If the predictor type is sturniolo then it needs to be processed differently
elif line.strip().split('\t')[5] == 'Sturniolo':
predictor = 'Sturniolo'
else:
predictor = 'Consensus'
run_netmhciipan = False
break
if run_netmhciipan:
netmhciipan = job.addChildJobFn(predict_netmhcii_binding, peptfile, allele, univ_options,
mhcii_options['netmhciipan'], disk='100M', memory='100M',
cores=1)
job.fileStore.logToMaster('Ran mhcii on %s:%s successfully'
% (univ_options['patient'], allele))
return netmhciipan.rv()
else:
output_file = job.fileStore.writeGlobalFile(predfile.name)
job.fileStore.logToMaster('Ran mhcii on %s:%s successfully'
% (univ_options['patient'], allele))
return output_file, predictor | [
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:param toil.fileStore.FileID peptfile: The input peptide fasta
:param str allele: Allele to predict binding against
:param dict univ_options: Dict of universal options used by almost all tools
:param dict mhcii_options: Options specific to mhcii binding prediction
:return: tuple of fsID for file containing the predictions and the predictor used
:rtype: tuple(toil.fileStore.FileID, str|None) | [
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BD2KGenomics/protect | src/protect/binding_prediction/mhcii.py | predict_netmhcii_binding | def predict_netmhcii_binding(job, peptfile, allele, univ_options, netmhciipan_options):
"""
Predict binding for each peptide in `peptfile` to `allele` using netMHCIIpan.
:param toil.fileStore.FileID peptfile: The input peptide fasta
:param str allele: Allele to predict binding against
:param dict univ_options: Dict of universal options used by almost all tools
:param dict netmhciipan_options: Options specific to netmhciipan binding prediction
:return: tuple of fsID for file containing the predictions and the predictor used (netMHCIIpan)
:rtype: tuple(toil.fileStore.FileID, str)
"""
work_dir = os.getcwd()
input_files = {
'peptfile.faa': peptfile}
input_files = get_files_from_filestore(job, input_files, work_dir, docker=True)
peptides = read_peptide_file(os.path.join(os.getcwd(), 'peptfile.faa'))
if not peptides:
return job.fileStore.writeGlobalFile(job.fileStore.getLocalTempFile()), None
# netMHCIIpan accepts differently formatted alleles so we need to modify the input alleles
if allele.startswith('HLA-DQA') or allele.startswith('HLA-DPA'):
allele = re.sub(r'[*:]', '', allele)
allele = re.sub(r'/', '-', allele)
elif allele.startswith('HLA-DRB'):
allele = re.sub(r':', '', allele)
allele = re.sub(r'\*', '_', allele)
allele = allele.lstrip('HLA-')
else:
raise RuntimeError('Unknown allele seen')
parameters = ['-a', allele,
'-xls', '1',
'-xlsfile', 'predictions.tsv',
'-f', input_files['peptfile.faa']]
# netMHC writes a lot of useless stuff to sys.stdout so we open /dev/null and dump output there.
with open(os.devnull, 'w') as output_catcher:
docker_call(tool='netmhciipan', tool_parameters=parameters, work_dir=work_dir,
dockerhub=univ_options['dockerhub'], outfile=output_catcher,
tool_version=netmhciipan_options['version'])
output_file = job.fileStore.writeGlobalFile('/'.join([work_dir, 'predictions.tsv']))
job.fileStore.logToMaster('Ran netmhciipan on %s successfully' % allele)
return output_file, 'netMHCIIpan' | python | def predict_netmhcii_binding(job, peptfile, allele, univ_options, netmhciipan_options):
"""
Predict binding for each peptide in `peptfile` to `allele` using netMHCIIpan.
:param toil.fileStore.FileID peptfile: The input peptide fasta
:param str allele: Allele to predict binding against
:param dict univ_options: Dict of universal options used by almost all tools
:param dict netmhciipan_options: Options specific to netmhciipan binding prediction
:return: tuple of fsID for file containing the predictions and the predictor used (netMHCIIpan)
:rtype: tuple(toil.fileStore.FileID, str)
"""
work_dir = os.getcwd()
input_files = {
'peptfile.faa': peptfile}
input_files = get_files_from_filestore(job, input_files, work_dir, docker=True)
peptides = read_peptide_file(os.path.join(os.getcwd(), 'peptfile.faa'))
if not peptides:
return job.fileStore.writeGlobalFile(job.fileStore.getLocalTempFile()), None
# netMHCIIpan accepts differently formatted alleles so we need to modify the input alleles
if allele.startswith('HLA-DQA') or allele.startswith('HLA-DPA'):
allele = re.sub(r'[*:]', '', allele)
allele = re.sub(r'/', '-', allele)
elif allele.startswith('HLA-DRB'):
allele = re.sub(r':', '', allele)
allele = re.sub(r'\*', '_', allele)
allele = allele.lstrip('HLA-')
else:
raise RuntimeError('Unknown allele seen')
parameters = ['-a', allele,
'-xls', '1',
'-xlsfile', 'predictions.tsv',
'-f', input_files['peptfile.faa']]
# netMHC writes a lot of useless stuff to sys.stdout so we open /dev/null and dump output there.
with open(os.devnull, 'w') as output_catcher:
docker_call(tool='netmhciipan', tool_parameters=parameters, work_dir=work_dir,
dockerhub=univ_options['dockerhub'], outfile=output_catcher,
tool_version=netmhciipan_options['version'])
output_file = job.fileStore.writeGlobalFile('/'.join([work_dir, 'predictions.tsv']))
job.fileStore.logToMaster('Ran netmhciipan on %s successfully' % allele)
return output_file, 'netMHCIIpan' | [
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:param toil.fileStore.FileID peptfile: The input peptide fasta
:param str allele: Allele to predict binding against
:param dict univ_options: Dict of universal options used by almost all tools
:param dict netmhciipan_options: Options specific to netmhciipan binding prediction
:return: tuple of fsID for file containing the predictions and the predictor used (netMHCIIpan)
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] | 06310682c50dcf8917b912c8e551299ff7ee41ce | https://github.com/BD2KGenomics/protect/blob/06310682c50dcf8917b912c8e551299ff7ee41ce/src/protect/binding_prediction/mhcii.py#L79-L118 | train |
inveniosoftware/invenio-access | invenio_access/permissions.py | _P.update | def update(self, permission):
"""In-place update of permissions."""
self.needs.update(permission.needs)
self.excludes.update(permission.excludes) | python | def update(self, permission):
"""In-place update of permissions."""
self.needs.update(permission.needs)
self.excludes.update(permission.excludes) | [
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