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harvard-nrg/yaxil | yaxil/bids/__init__.py | iterconfig | def iterconfig(config, scan_type):
'''
Iterate over BIDS configuration file
'''
if scan_type in config:
for modality,scans in iter(config[scan_type].items()):
for scan in scans:
scan.update({
'type': scan_type,
'modality': modality
})
yield scan | python | def iterconfig(config, scan_type):
'''
Iterate over BIDS configuration file
'''
if scan_type in config:
for modality,scans in iter(config[scan_type].items()):
for scan in scans:
scan.update({
'type': scan_type,
'modality': modality
})
yield scan | [
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harvard-nrg/yaxil | yaxil/bids/__init__.py | rename_fmapm | def rename_fmapm(bids_base, basename):
'''
Rename magnitude fieldmap file to BIDS specification
'''
files = dict()
for ext in ['nii.gz', 'json']:
for echo in [1, 2]:
fname = '{0}_e{1}.{2}'.format(basename, echo, ext)
src = os.path.join(bids_base, 'fmap', fname)
if os.path.exists(src):
dst = src.replace(
'magnitude_e{0}'.format(echo),
'magnitude{0}'.format(echo)
)
logger.debug('renaming %s to %s', src, dst)
os.rename(src, dst)
files[ext] = dst
return files | python | def rename_fmapm(bids_base, basename):
'''
Rename magnitude fieldmap file to BIDS specification
'''
files = dict()
for ext in ['nii.gz', 'json']:
for echo in [1, 2]:
fname = '{0}_e{1}.{2}'.format(basename, echo, ext)
src = os.path.join(bids_base, 'fmap', fname)
if os.path.exists(src):
dst = src.replace(
'magnitude_e{0}'.format(echo),
'magnitude{0}'.format(echo)
)
logger.debug('renaming %s to %s', src, dst)
os.rename(src, dst)
files[ext] = dst
return files | [
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harvard-nrg/yaxil | yaxil/bids/__init__.py | convert | def convert(input, output):
'''
Run dcm2niix on input file
'''
dirname = os.path.dirname(output)
if not os.path.exists(dirname):
os.makedirs(dirname)
basename = os.path.basename(output)
basename = re.sub('.nii(.gz)?', '', basename)
dcm2niix = commons.which('dcm2niix')
cmd = [
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'-z', 'y',
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'-o', dirname,
input
]
logger.debug(cmd)
sp.check_output(cmd) | python | def convert(input, output):
'''
Run dcm2niix on input file
'''
dirname = os.path.dirname(output)
if not os.path.exists(dirname):
os.makedirs(dirname)
basename = os.path.basename(output)
basename = re.sub('.nii(.gz)?', '', basename)
dcm2niix = commons.which('dcm2niix')
cmd = [
'dcm2niix',
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'-b', 'y',
'-z', 'y',
'-f', basename,
'-o', dirname,
input
]
logger.debug(cmd)
sp.check_output(cmd) | [
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Parsely/birding | src/birding/spout.py | DispatchSpout | def DispatchSpout(*a, **kw):
"""Factory to dispatch spout class based on config."""
spout_class_name = get_config()['Spout']
spout_class = import_name(spout_class_name, default_ns='birding.spout')
return spout_class(*a, **kw) | python | def DispatchSpout(*a, **kw):
"""Factory to dispatch spout class based on config."""
spout_class_name = get_config()['Spout']
spout_class = import_name(spout_class_name, default_ns='birding.spout')
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harvard-nrg/yaxil | yaxil/commons/__init__.py | which | def which(x):
'''
Same as which command on Linux
'''
for p in os.environ.get('PATH').split(os.pathsep):
p = os.path.join(p, x)
if os.path.exists(p):
return os.path.abspath(p)
return None | python | def which(x):
'''
Same as which command on Linux
'''
for p in os.environ.get('PATH').split(os.pathsep):
p = os.path.join(p, x)
if os.path.exists(p):
return os.path.abspath(p)
return None | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/tasks.py | serve | def serve(context: Context, port=8000, browsersync_port=3000, browsersync_ui_port=3030):
"""
Starts a development server with auto-building and live-reload
"""
try:
from watchdog.observers import Observer
except ImportError:
context.pip_command('install', 'watchdog>0.8,<0.9')
from watchdog.observers import Observer
from watchdog.events import PatternMatchingEventHandler
class RebuildHandler(PatternMatchingEventHandler):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._patterns = ['*.js', '*.scss', '*.html']
self._ignore_directories = True
self.builder = None
self.rebuild_javascript = threading.Event()
self.rebuild_stylesheets = threading.Event()
def on_any_event(self, event):
if self.builder:
self.builder.cancel()
extension = event.src_path.rsplit('.', 1)[-1].lower()
if extension == 'js':
self.rebuild_javascript.set()
elif extension == 'scss':
self.rebuild_stylesheets.set()
self.builder = threading.Timer(3, self.rebuild)
self.builder.start()
def rebuild(self):
if self.rebuild_javascript.is_set():
self.rebuild_javascript.clear()
context.debug('Triggering javascript build')
bundle_javascript(context)
if self.rebuild_stylesheets.is_set():
self.rebuild_stylesheets.clear()
context.debug('Triggering stylesheet build')
bundle_stylesheets(context)
context.debug('Reloading browsers')
context.node_tool('browser-sync', 'reload', '--port=%s' % browsersync_port)
context.info('Watching sources')
observer = Observer()
paths = [
context.app.common_asset_source_path,
context.app.asset_source_path,
context.app.common_templates_path,
context.app.templates_path,
]
handler = RebuildHandler()
for path in paths:
observer.schedule(handler, path, recursive=True)
observer.setDaemon(True)
observer.start()
context.info('Starting browser sync')
browsersync_args = ['start', '--host=localhost', '--no-open',
'--logLevel', {0: 'silent', 1: 'info', 2: 'debug'}[context.verbosity],
'--port=%s' % browsersync_port, '--proxy=localhost:%s' % port,
'--ui-port=%s' % browsersync_ui_port]
browsersync = functools.partial(context.node_tool, 'browser-sync', *browsersync_args)
threading.Thread(target=browsersync, daemon=True).start()
context.info('Starting web server')
return start(context, port=port) | python | def serve(context: Context, port=8000, browsersync_port=3000, browsersync_ui_port=3030):
"""
Starts a development server with auto-building and live-reload
"""
try:
from watchdog.observers import Observer
except ImportError:
context.pip_command('install', 'watchdog>0.8,<0.9')
from watchdog.observers import Observer
from watchdog.events import PatternMatchingEventHandler
class RebuildHandler(PatternMatchingEventHandler):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._patterns = ['*.js', '*.scss', '*.html']
self._ignore_directories = True
self.builder = None
self.rebuild_javascript = threading.Event()
self.rebuild_stylesheets = threading.Event()
def on_any_event(self, event):
if self.builder:
self.builder.cancel()
extension = event.src_path.rsplit('.', 1)[-1].lower()
if extension == 'js':
self.rebuild_javascript.set()
elif extension == 'scss':
self.rebuild_stylesheets.set()
self.builder = threading.Timer(3, self.rebuild)
self.builder.start()
def rebuild(self):
if self.rebuild_javascript.is_set():
self.rebuild_javascript.clear()
context.debug('Triggering javascript build')
bundle_javascript(context)
if self.rebuild_stylesheets.is_set():
self.rebuild_stylesheets.clear()
context.debug('Triggering stylesheet build')
bundle_stylesheets(context)
context.debug('Reloading browsers')
context.node_tool('browser-sync', 'reload', '--port=%s' % browsersync_port)
context.info('Watching sources')
observer = Observer()
paths = [
context.app.common_asset_source_path,
context.app.asset_source_path,
context.app.common_templates_path,
context.app.templates_path,
]
handler = RebuildHandler()
for path in paths:
observer.schedule(handler, path, recursive=True)
observer.setDaemon(True)
observer.start()
context.info('Starting browser sync')
browsersync_args = ['start', '--host=localhost', '--no-open',
'--logLevel', {0: 'silent', 1: 'info', 2: 'debug'}[context.verbosity],
'--port=%s' % browsersync_port, '--proxy=localhost:%s' % port,
'--ui-port=%s' % browsersync_ui_port]
browsersync = functools.partial(context.node_tool, 'browser-sync', *browsersync_args)
threading.Thread(target=browsersync, daemon=True).start()
context.info('Starting web server')
return start(context, port=port) | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/tasks.py | create_build_paths | def create_build_paths(context: Context):
"""
Creates directories needed for build outputs
"""
paths = [context.app.asset_build_path, context.app.screenshots_build_path, context.app.collected_assets_path]
for path in filter(None, paths):
os.makedirs(path, exist_ok=True) | python | def create_build_paths(context: Context):
"""
Creates directories needed for build outputs
"""
paths = [context.app.asset_build_path, context.app.screenshots_build_path, context.app.collected_assets_path]
for path in filter(None, paths):
os.makedirs(path, exist_ok=True) | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/tasks.py | node_dependencies | def node_dependencies(context: Context):
"""
Updates node.js dependencies
"""
args = ['--loglevel', {0: 'silent', 1: 'warn', 2: 'info'}[context.verbosity]]
if not context.use_colour:
args.append('--color false')
args.append('install')
return context.shell('npm', *args) | python | def node_dependencies(context: Context):
"""
Updates node.js dependencies
"""
args = ['--loglevel', {0: 'silent', 1: 'warn', 2: 'info'}[context.verbosity]]
if not context.use_colour:
args.append('--color false')
args.append('install')
return context.shell('npm', *args) | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/tasks.py | local_docker | def local_docker(context: Context):
"""
Runs the app in a docker container; for local development only!
Once performed, `docker-compose up` can be used directly
"""
output = io.StringIO()
with contextlib.redirect_stdout(output):
context.shell('docker-machine', 'ip', 'default')
host_machine_ip = output.getvalue().strip() or socket.gethostbyname(socket.gethostname())
args = ()
if context.verbosity > 1:
args += ('--verbose',)
args += ('up', '--build', '--remove-orphans')
if not context.use_colour:
args += ('--no-color',)
context.shell('docker-compose', *args, environment={'HOST_MACHINE_IP': host_machine_ip}) | python | def local_docker(context: Context):
"""
Runs the app in a docker container; for local development only!
Once performed, `docker-compose up` can be used directly
"""
output = io.StringIO()
with contextlib.redirect_stdout(output):
context.shell('docker-machine', 'ip', 'default')
host_machine_ip = output.getvalue().strip() or socket.gethostbyname(socket.gethostname())
args = ()
if context.verbosity > 1:
args += ('--verbose',)
args += ('up', '--build', '--remove-orphans')
if not context.use_colour:
args += ('--no-color',)
context.shell('docker-compose', *args, environment={'HOST_MACHINE_IP': host_machine_ip}) | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/tasks.py | lint_javascript | def lint_javascript(context: Context):
"""
Tests javascript for code and style errors
"""
args = [
'--config', os.path.join(context.app.common_templates_path, 'mtp_common', 'build_tasks', 'eslintrc.json'),
'--format', 'stylish',
]
if context.verbosity == 0:
args.append('--quiet')
if not context.use_colour:
args.append('--no-color')
args.append(context.app.javascript_source_path)
return context.node_tool('eslint', *args) | python | def lint_javascript(context: Context):
"""
Tests javascript for code and style errors
"""
args = [
'--config', os.path.join(context.app.common_templates_path, 'mtp_common', 'build_tasks', 'eslintrc.json'),
'--format', 'stylish',
]
if context.verbosity == 0:
args.append('--quiet')
if not context.use_colour:
args.append('--no-color')
args.append(context.app.javascript_source_path)
return context.node_tool('eslint', *args) | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/tasks.py | lint_stylesheets | def lint_stylesheets(context: Context):
"""
Tests stylesheets for code and style errors
"""
args = [
'--config', os.path.join(context.app.common_templates_path, 'mtp_common', 'build_tasks', 'sass-lint.yml'),
'--format', 'stylish',
'--syntax', 'scss',
]
if context.verbosity > 1:
args.append('--verbose')
args.append(os.path.join(context.app.scss_source_path, '**', '*.scss'))
return context.node_tool('sass-lint', *args) | python | def lint_stylesheets(context: Context):
"""
Tests stylesheets for code and style errors
"""
args = [
'--config', os.path.join(context.app.common_templates_path, 'mtp_common', 'build_tasks', 'sass-lint.yml'),
'--format', 'stylish',
'--syntax', 'scss',
]
if context.verbosity > 1:
args.append('--verbose')
args.append(os.path.join(context.app.scss_source_path, '**', '*.scss'))
return context.node_tool('sass-lint', *args) | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/tasks.py | govuk_template | def govuk_template(context: Context, version='0.23.0', replace_fonts=True):
"""
Installs GOV.UK template
"""
if FileSet(os.path.join(context.app.govuk_templates_path, 'base.html')):
# NB: check is only on main template and not the assets included
return
url = 'https://github.com/alphagov/govuk_template/releases' \
'/download/v{0}/django_govuk_template-{0}.tgz'.format(version)
try:
context.shell('curl --location %(silent)s --output govuk_template.tgz %(url)s' % {
'silent': '--silent' if context.verbosity == 0 else '',
'url': url,
})
context.shell('tar xzf govuk_template.tgz ./govuk_template')
rsync_flags = '-avz' if context.verbosity == 2 else '-az'
context.shell('rsync %s govuk_template/static/ %s/' % (rsync_flags, context.app.asset_build_path))
context.shell('rsync %s govuk_template/templates/ %s/' % (rsync_flags, context.app.templates_path))
finally:
context.shell('rm -rf govuk_template.tgz ./govuk_template')
if replace_fonts:
# govuk_template includes .eot font files for IE, but they load relative to current URL not the stylesheet
# this option removes these files so common's fonts-ie8.css override is used
context.shell('rm -rf %s/stylesheets/fonts-ie8.css'
' %s/stylesheets/fonts/' % (context.app.asset_build_path, context.app.asset_build_path)) | python | def govuk_template(context: Context, version='0.23.0', replace_fonts=True):
"""
Installs GOV.UK template
"""
if FileSet(os.path.join(context.app.govuk_templates_path, 'base.html')):
# NB: check is only on main template and not the assets included
return
url = 'https://github.com/alphagov/govuk_template/releases' \
'/download/v{0}/django_govuk_template-{0}.tgz'.format(version)
try:
context.shell('curl --location %(silent)s --output govuk_template.tgz %(url)s' % {
'silent': '--silent' if context.verbosity == 0 else '',
'url': url,
})
context.shell('tar xzf govuk_template.tgz ./govuk_template')
rsync_flags = '-avz' if context.verbosity == 2 else '-az'
context.shell('rsync %s govuk_template/static/ %s/' % (rsync_flags, context.app.asset_build_path))
context.shell('rsync %s govuk_template/templates/ %s/' % (rsync_flags, context.app.templates_path))
finally:
context.shell('rm -rf govuk_template.tgz ./govuk_template')
if replace_fonts:
# govuk_template includes .eot font files for IE, but they load relative to current URL not the stylesheet
# this option removes these files so common's fonts-ie8.css override is used
context.shell('rm -rf %s/stylesheets/fonts-ie8.css'
' %s/stylesheets/fonts/' % (context.app.asset_build_path, context.app.asset_build_path)) | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/tasks.py | additional_assets | def additional_assets(context: Context):
"""
Collects assets from GOV.UK frontend toolkit
"""
rsync_flags = '-avz' if context.verbosity == 2 else '-az'
for path in context.app.additional_asset_paths:
context.shell('rsync %s %s %s/' % (rsync_flags, path, context.app.asset_build_path)) | python | def additional_assets(context: Context):
"""
Collects assets from GOV.UK frontend toolkit
"""
rsync_flags = '-avz' if context.verbosity == 2 else '-az'
for path in context.app.additional_asset_paths:
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/tasks.py | precompile_python_code | def precompile_python_code(context: Context):
"""
Pre-compiles python modules
"""
from compileall import compile_dir
kwargs = {}
if context.verbosity < 2:
kwargs['quiet'] = True
compile_dir(context.app.django_app_name, **kwargs) | python | def precompile_python_code(context: Context):
"""
Pre-compiles python modules
"""
from compileall import compile_dir
kwargs = {}
if context.verbosity < 2:
kwargs['quiet'] = True
compile_dir(context.app.django_app_name, **kwargs) | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/tasks.py | make_messages | def make_messages(context: Context, javascript=False, fuzzy=False):
"""
Collects text into translation source files
"""
kwargs = {
'all': True,
'keep_pot': True,
'no_wrap': True,
}
if fuzzy:
kwargs['allow_fuzzy'] = True
if javascript:
kwargs.update(domain='djangojs', ignore_patterns=['*.bundle.js'])
with in_dir(context.app.django_app_name):
return context.management_command('makemessages', **kwargs) | python | def make_messages(context: Context, javascript=False, fuzzy=False):
"""
Collects text into translation source files
"""
kwargs = {
'all': True,
'keep_pot': True,
'no_wrap': True,
}
if fuzzy:
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if javascript:
kwargs.update(domain='djangojs', ignore_patterns=['*.bundle.js'])
with in_dir(context.app.django_app_name):
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koreyou/word_embedding_loader | word_embedding_loader/word_embedding.py | classify_format | def classify_format(f):
"""
Determine the format of word embedding file by their content. This operation
only looks at the first two lines and does not check the sanity of input
file.
Args:
f (Filelike):
Returns:
class
"""
l0, l1 = _get_two_lines(f)
if loader.glove.check_valid(l0, l1):
return _glove
elif loader.word2vec_text.check_valid(l0, l1):
return _word2vec_text
elif loader.word2vec_bin.check_valid(l0, l1):
return _word2vec_bin
else:
raise OSError(b"Invalid format") | python | def classify_format(f):
"""
Determine the format of word embedding file by their content. This operation
only looks at the first two lines and does not check the sanity of input
file.
Args:
f (Filelike):
Returns:
class
"""
l0, l1 = _get_two_lines(f)
if loader.glove.check_valid(l0, l1):
return _glove
elif loader.word2vec_text.check_valid(l0, l1):
return _word2vec_text
elif loader.word2vec_bin.check_valid(l0, l1):
return _word2vec_bin
else:
raise OSError(b"Invalid format") | [
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koreyou/word_embedding_loader | word_embedding_loader/word_embedding.py | WordEmbedding.load | def load(cls, path, vocab=None, dtype=np.float32, max_vocab=None,
format=None, binary=False):
"""
Load pretrained word embedding from a file.
Args:
path (str): Path of file to load.
vocab (str or None): Path to vocabulary file created by word2vec
with ``-save-vocab <file>`` option. If vocab is given,
:py:attr:`~vectors` and :py:attr:`~vocab` is ordered in
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dtype (numpy.dtype): Element data type to use for the array.
max_vocab (int): Number of vocabulary to read.
format (str or None): Format of the file. ``'word2vec'`` for file
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`word2vec <https://code.google.com/archive/p/word2vec/>`_,
by Mikolov et al.. ``'glove'`` for file that was implemented in
`GloVe <https://nlp.stanford.edu/projects/glove/>`_, Global
Vectors for Word Representation, by Jeffrey Pennington,
Richard Socher, Christopher D. Manning from Stanford NLP group.
If ``None`` is given, the format is guessed from the content.
binary (bool): Load file as binary file as in word embedding file
created by
`word2vec <https://code.google.com/archive/p/word2vec/>`_ with
``-binary 1`` option. If ``format`` is ``'glove'`` or ``None``,
this argument is simply ignored
Returns:
:class:`~word_embedding_loader.word_embedding.WordEmbedding`
"""
freqs = None
if vocab is not None:
with open(vocab, mode='rb') as f:
freqs = loader.vocab.load_vocab(f)
# Create vocab from freqs
# [:None] gives all the list member
vocab = {k: i for i, (k, v) in enumerate(
sorted(six.iteritems(freqs),
key=lambda k_v: k_v[1], reverse=True)[:max_vocab])}
with open(path, mode='rb') as f:
if format is None:
mod = classify_format(f)
else:
mod = _select_module(format, binary)
with open(path, mode='rb') as f:
if vocab is not None:
arr = mod.loader.load_with_vocab(f, vocab, dtype=dtype)
v = vocab
else:
arr, v = mod.loader.load(f, max_vocab=max_vocab, dtype=dtype)
obj = cls(arr, v, freqs)
obj._load_cond = mod
return obj | python | def load(cls, path, vocab=None, dtype=np.float32, max_vocab=None,
format=None, binary=False):
"""
Load pretrained word embedding from a file.
Args:
path (str): Path of file to load.
vocab (str or None): Path to vocabulary file created by word2vec
with ``-save-vocab <file>`` option. If vocab is given,
:py:attr:`~vectors` and :py:attr:`~vocab` is ordered in
descending order of frequency.
dtype (numpy.dtype): Element data type to use for the array.
max_vocab (int): Number of vocabulary to read.
format (str or None): Format of the file. ``'word2vec'`` for file
that was implemented in
`word2vec <https://code.google.com/archive/p/word2vec/>`_,
by Mikolov et al.. ``'glove'`` for file that was implemented in
`GloVe <https://nlp.stanford.edu/projects/glove/>`_, Global
Vectors for Word Representation, by Jeffrey Pennington,
Richard Socher, Christopher D. Manning from Stanford NLP group.
If ``None`` is given, the format is guessed from the content.
binary (bool): Load file as binary file as in word embedding file
created by
`word2vec <https://code.google.com/archive/p/word2vec/>`_ with
``-binary 1`` option. If ``format`` is ``'glove'`` or ``None``,
this argument is simply ignored
Returns:
:class:`~word_embedding_loader.word_embedding.WordEmbedding`
"""
freqs = None
if vocab is not None:
with open(vocab, mode='rb') as f:
freqs = loader.vocab.load_vocab(f)
# Create vocab from freqs
# [:None] gives all the list member
vocab = {k: i for i, (k, v) in enumerate(
sorted(six.iteritems(freqs),
key=lambda k_v: k_v[1], reverse=True)[:max_vocab])}
with open(path, mode='rb') as f:
if format is None:
mod = classify_format(f)
else:
mod = _select_module(format, binary)
with open(path, mode='rb') as f:
if vocab is not None:
arr = mod.loader.load_with_vocab(f, vocab, dtype=dtype)
v = vocab
else:
arr, v = mod.loader.load(f, max_vocab=max_vocab, dtype=dtype)
obj = cls(arr, v, freqs)
obj._load_cond = mod
return obj | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/paths.py | paths_for_shell | def paths_for_shell(paths, separator=' '):
"""
Converts a list of paths for use in shell commands
"""
paths = filter(None, paths)
paths = map(shlex.quote, paths)
if separator is None:
return paths
return separator.join(paths) | python | def paths_for_shell(paths, separator=' '):
"""
Converts a list of paths for use in shell commands
"""
paths = filter(None, paths)
paths = map(shlex.quote, paths)
if separator is None:
return paths
return separator.join(paths) | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/executor.py | Tasks.register | def register(self, *dependencies, default=False, hidden=False, ignore_return_code=False):
"""
Decorates a callable to turn it into a task
"""
def outer(func):
task = Task(func, *dependencies, default=default, hidden=hidden, ignore_return_code=ignore_return_code)
overidden_task = self._tasks.pop(task.name, None)
if overidden_task:
self._overidden_tasks[task.name].append(overidden_task)
self[task.name] = task
return task
return outer | python | def register(self, *dependencies, default=False, hidden=False, ignore_return_code=False):
"""
Decorates a callable to turn it into a task
"""
def outer(func):
task = Task(func, *dependencies, default=default, hidden=hidden, ignore_return_code=ignore_return_code)
overidden_task = self._tasks.pop(task.name, None)
if overidden_task:
self._overidden_tasks[task.name].append(overidden_task)
self[task.name] = task
return task
return outer | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/executor.py | Tasks.lookup_task | def lookup_task(self, task):
"""
Looks up a task by name or by callable
"""
if isinstance(task, str):
try:
return self[task]
except KeyError:
pass
raise TaskError('Unknown task %s' % task) | python | def lookup_task(self, task):
"""
Looks up a task by name or by callable
"""
if isinstance(task, str):
try:
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except KeyError:
pass
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/executor.py | Tasks.get_default_task | def get_default_task(self):
"""
Returns the default task if there is only one
"""
default_tasks = list(filter(lambda task: task.default, self.values()))
if len(default_tasks) == 1:
return default_tasks[0] | python | def get_default_task(self):
"""
Returns the default task if there is only one
"""
default_tasks = list(filter(lambda task: task.default, self.values()))
if len(default_tasks) == 1:
return default_tasks[0] | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/executor.py | ParameterGroup.from_callable | def from_callable(cls, func, ignored_parameters=set()):
"""
Reads a function or method signature to produce a set of parameters
"""
group = cls()
signature = inspect.signature(func)
for parameter in signature.parameters.values():
if parameter.name.startswith('_') or parameter.name in ignored_parameters:
continue
parameter = Parameter.from_callable_parameter(parameter)
group[parameter.name] = parameter
return group | python | def from_callable(cls, func, ignored_parameters=set()):
"""
Reads a function or method signature to produce a set of parameters
"""
group = cls()
signature = inspect.signature(func)
for parameter in signature.parameters.values():
if parameter.name.startswith('_') or parameter.name in ignored_parameters:
continue
parameter = Parameter.from_callable_parameter(parameter)
group[parameter.name] = parameter
return group | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/executor.py | ParameterGroup.from_mapping | def from_mapping(cls, mapping):
"""
Produces a set of parameters from a mapping
"""
group = cls()
for name, value in mapping.items():
if name.startswith('_'):
continue
group[name] = Parameter(
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"""
Produces a set of parameters from a mapping
"""
group = cls()
for name, value in mapping.items():
if name.startswith('_'):
continue
group[name] = Parameter(
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/executor.py | ParameterGroup.to_dict | def to_dict(self):
"""
Converts the set of parameters into a dict
"""
return dict((parameter.name, parameter.value) for parameter in self.values()) | python | def to_dict(self):
"""
Converts the set of parameters into a dict
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return dict((parameter.name, parameter.value) for parameter in self.values()) | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/executor.py | ParameterGroup.consume_arguments | def consume_arguments(self, argument_list):
"""
Takes arguments from a list while there are parameters that can accept them
"""
while True:
argument_count = len(argument_list)
for parameter in self.values():
argument_list = parameter.consume_arguments(argument_list)
if len(argument_list) == argument_count:
return argument_list | python | def consume_arguments(self, argument_list):
"""
Takes arguments from a list while there are parameters that can accept them
"""
while True:
argument_count = len(argument_list)
for parameter in self.values():
argument_list = parameter.consume_arguments(argument_list)
if len(argument_list) == argument_count:
return argument_list | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/executor.py | ParameterGroup.update_from | def update_from(self, mapping):
"""
Updates the set of parameters from a mapping for keys that already exist
"""
for key, value in mapping.items():
if key in self:
if isinstance(value, Parameter):
value = value.value
self[key].value = value | python | def update_from(self, mapping):
"""
Updates the set of parameters from a mapping for keys that already exist
"""
for key, value in mapping.items():
if key in self:
if isinstance(value, Parameter):
value = value.value
self[key].value = value | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/executor.py | Parameter.from_callable_parameter | def from_callable_parameter(cls, parameter):
"""
Produces a parameter from a function or method
"""
if parameter.kind == parameter.KEYWORD_ONLY or \
parameter.kind == parameter.POSITIONAL_OR_KEYWORD and parameter.default is not parameter.empty:
if parameter.annotation is not parameter.empty:
constraint = parameter.annotation
else:
constraint = Parameter.constraint_from_type(parameter.default)
return cls(
name=parameter.name,
value=parameter.default,
constraint=constraint,
)
else:
raise ParameterError('Only keyword parameters are supported') | python | def from_callable_parameter(cls, parameter):
"""
Produces a parameter from a function or method
"""
if parameter.kind == parameter.KEYWORD_ONLY or \
parameter.kind == parameter.POSITIONAL_OR_KEYWORD and parameter.default is not parameter.empty:
if parameter.annotation is not parameter.empty:
constraint = parameter.annotation
else:
constraint = Parameter.constraint_from_type(parameter.default)
return cls(
name=parameter.name,
value=parameter.default,
constraint=constraint,
)
else:
raise ParameterError('Only keyword parameters are supported') | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/executor.py | Parameter.constraint_from_type | def constraint_from_type(cls, value):
"""
Returns the constraint callable given a value
"""
if value is None:
return None
value_type = type(value)
if value_type in (str, int, bool):
return value_type
raise ParameterError('Parameter type cannot be %s' % value_type) | python | def constraint_from_type(cls, value):
"""
Returns the constraint callable given a value
"""
if value is None:
return None
value_type = type(value)
if value_type in (str, int, bool):
return value_type
raise ParameterError('Parameter type cannot be %s' % value_type) | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/executor.py | Parameter.constraint_from_choices | def constraint_from_choices(cls, value_type: type, choices: collections.Sequence):
"""
Returns a constraint callable based on choices of a given type
"""
choices_str = ', '.join(map(str, choices))
def constraint(value):
value = value_type(value)
if value not in choices:
raise ParameterError('Argument must be one of %s' % choices_str)
return value
constraint.__name__ = 'choices_%s' % value_type.__name__
constraint.__doc__ = 'choice of %s' % choices_str
return constraint | python | def constraint_from_choices(cls, value_type: type, choices: collections.Sequence):
"""
Returns a constraint callable based on choices of a given type
"""
choices_str = ', '.join(map(str, choices))
def constraint(value):
value = value_type(value)
if value not in choices:
raise ParameterError('Argument must be one of %s' % choices_str)
return value
constraint.__name__ = 'choices_%s' % value_type.__name__
constraint.__doc__ = 'choice of %s' % choices_str
return constraint | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/executor.py | Parameter.arg_name | def arg_name(self):
"""
Returns the name of the parameter as a command line flag
"""
if self.constraint is bool and self.value:
return '--no-%s' % self.name.replace('_', '-')
return '--%s' % self.name.replace('_', '-') | python | def arg_name(self):
"""
Returns the name of the parameter as a command line flag
"""
if self.constraint is bool and self.value:
return '--no-%s' % self.name.replace('_', '-')
return '--%s' % self.name.replace('_', '-') | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/executor.py | Parameter.consume_arguments | def consume_arguments(self, argument_list):
"""
Takes arguments from a list while this parameter can accept them
"""
if len(argument_list) == 0:
return []
if argument_list[0] == self.arg_name:
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try:
value = argument_list.pop(0)
except IndexError:
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self.value = value
return argument_list | python | def consume_arguments(self, argument_list):
"""
Takes arguments from a list while this parameter can accept them
"""
if len(argument_list) == 0:
return []
if argument_list[0] == self.arg_name:
argument_list = argument_list[1:]
if self.constraint is bool:
self.value = not self.value
else:
try:
value = argument_list.pop(0)
except IndexError:
raise ParameterError('Argument %s expects a value' % self.arg_name)
self.value = value
return argument_list | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/executor.py | Context.pip_command | def pip_command(self, command, *args):
"""
Runs a pip command
"""
try:
from pip._internal import main as pip_main
except ImportError:
from pip import main as pip_main
args = [command] + list(args)
if self.verbosity == 0:
args.insert(0, '--quiet')
elif self.verbosity == 2:
args.insert(0, '--verbose')
return pip_main(args) | python | def pip_command(self, command, *args):
"""
Runs a pip command
"""
try:
from pip._internal import main as pip_main
except ImportError:
from pip import main as pip_main
args = [command] + list(args)
if self.verbosity == 0:
args.insert(0, '--quiet')
elif self.verbosity == 2:
args.insert(0, '--verbose')
return pip_main(args) | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/executor.py | Context.shell | def shell(self, command, *args, environment=None):
"""
Runs a shell command
"""
command += ' ' + ' '.join(args)
command = command.strip()
self.debug(self.yellow_style('$ %s' % command))
env = self.env.copy()
env.update(environment or {})
return subprocess.call(command, shell=True, env=env) | python | def shell(self, command, *args, environment=None):
"""
Runs a shell command
"""
command += ' ' + ' '.join(args)
command = command.strip()
self.debug(self.yellow_style('$ %s' % command))
env = self.env.copy()
env.update(environment or {})
return subprocess.call(command, shell=True, env=env) | [
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ministryofjustice/money-to-prisoners-common | mtp_common/build_tasks/executor.py | Context.management_command | def management_command(self, command, *args, **kwargs):
"""
Runs a Django management command
"""
self.setup_django()
if 'verbosity' not in kwargs:
kwargs['verbosity'] = self.verbosity
if not self.use_colour:
kwargs['no_color'] = False
self.debug(self.yellow_style('$ manage.py %s' % command))
return call_command(command, *args, **kwargs) | python | def management_command(self, command, *args, **kwargs):
"""
Runs a Django management command
"""
self.setup_django()
if 'verbosity' not in kwargs:
kwargs['verbosity'] = self.verbosity
if not self.use_colour:
kwargs['no_color'] = False
self.debug(self.yellow_style('$ manage.py %s' % command))
return call_command(command, *args, **kwargs) | [
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ministryofjustice/money-to-prisoners-common | mtp_common/auth/__init__.py | login | def login(request, user):
"""
Persist a user id and a backend in the request. This way a user doesn't
have to reauthenticate on every request. Note that data set during
the anonymous session is retained when the user logs in.
"""
session_auth_hash = ''
if user is None:
user = request.user
if hasattr(user, 'get_session_auth_hash'):
session_auth_hash = user.get_session_auth_hash()
if SESSION_KEY in request.session:
session_key = request.session[SESSION_KEY]
if session_key != user.pk or (
session_auth_hash and
request.session.get(HASH_SESSION_KEY) != session_auth_hash):
# To avoid reusing another user's session, create a new, empty
# session if the existing session corresponds to a different
# authenticated user.
request.session.flush()
else:
request.session.cycle_key()
request.session[SESSION_KEY] = user.pk
request.session[BACKEND_SESSION_KEY] = user.backend
request.session[USER_DATA_SESSION_KEY] = user.user_data
request.session[HASH_SESSION_KEY] = session_auth_hash
update_token_in_session(request.session, user.token)
if hasattr(request, 'user'):
request.user = user
rotate_token(request)
user_logged_in.send(sender=user.__class__, request=request, user=user) | python | def login(request, user):
"""
Persist a user id and a backend in the request. This way a user doesn't
have to reauthenticate on every request. Note that data set during
the anonymous session is retained when the user logs in.
"""
session_auth_hash = ''
if user is None:
user = request.user
if hasattr(user, 'get_session_auth_hash'):
session_auth_hash = user.get_session_auth_hash()
if SESSION_KEY in request.session:
session_key = request.session[SESSION_KEY]
if session_key != user.pk or (
session_auth_hash and
request.session.get(HASH_SESSION_KEY) != session_auth_hash):
# To avoid reusing another user's session, create a new, empty
# session if the existing session corresponds to a different
# authenticated user.
request.session.flush()
else:
request.session.cycle_key()
request.session[SESSION_KEY] = user.pk
request.session[BACKEND_SESSION_KEY] = user.backend
request.session[USER_DATA_SESSION_KEY] = user.user_data
request.session[HASH_SESSION_KEY] = session_auth_hash
update_token_in_session(request.session, user.token)
if hasattr(request, 'user'):
request.user = user
rotate_token(request)
user_logged_in.send(sender=user.__class__, request=request, user=user) | [
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ministryofjustice/money-to-prisoners-common | mtp_common/auth/__init__.py | get_user | def get_user(request):
"""
Returns the user model instance associated with the given request session.
If no user is retrieved an instance of `MojAnonymousUser` is returned.
"""
user = None
try:
user_id = request.session[SESSION_KEY]
token = request.session[AUTH_TOKEN_SESSION_KEY]
user_data = request.session[USER_DATA_SESSION_KEY]
backend_path = request.session[BACKEND_SESSION_KEY]
except KeyError:
pass
else:
if backend_path in settings.AUTHENTICATION_BACKENDS:
backend = load_backend(backend_path)
user = backend.get_user(user_id, token, user_data)
# Verify the session
if hasattr(user, 'get_session_auth_hash'):
session_hash = request.session.get(HASH_SESSION_KEY)
session_hash_verified = session_hash and constant_time_compare(
session_hash,
user.get_session_auth_hash()
)
if not session_hash_verified:
request.session.flush()
user = None
return user or MojAnonymousUser() | python | def get_user(request):
"""
Returns the user model instance associated with the given request session.
If no user is retrieved an instance of `MojAnonymousUser` is returned.
"""
user = None
try:
user_id = request.session[SESSION_KEY]
token = request.session[AUTH_TOKEN_SESSION_KEY]
user_data = request.session[USER_DATA_SESSION_KEY]
backend_path = request.session[BACKEND_SESSION_KEY]
except KeyError:
pass
else:
if backend_path in settings.AUTHENTICATION_BACKENDS:
backend = load_backend(backend_path)
user = backend.get_user(user_id, token, user_data)
# Verify the session
if hasattr(user, 'get_session_auth_hash'):
session_hash = request.session.get(HASH_SESSION_KEY)
session_hash_verified = session_hash and constant_time_compare(
session_hash,
user.get_session_auth_hash()
)
if not session_hash_verified:
request.session.flush()
user = None
return user or MojAnonymousUser() | [
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ministryofjustice/money-to-prisoners-common | mtp_common/auth/__init__.py | logout | def logout(request):
"""
Removes the authenticated user's ID from the request and flushes their
session data.
"""
# Dispatch the signal before the user is logged out so the receivers have a
# chance to find out *who* logged out.
user = getattr(request, 'user', None)
if hasattr(user, 'is_authenticated') and not user.is_authenticated:
user = None
user_logged_out.send(sender=user.__class__, request=request, user=user)
# remember language choice saved to session
language = request.session.get(LANGUAGE_SESSION_KEY)
request.session.flush()
if language is not None:
request.session[LANGUAGE_SESSION_KEY] = language
if hasattr(request, 'user'):
request.user = MojAnonymousUser() | python | def logout(request):
"""
Removes the authenticated user's ID from the request and flushes their
session data.
"""
# Dispatch the signal before the user is logged out so the receivers have a
# chance to find out *who* logged out.
user = getattr(request, 'user', None)
if hasattr(user, 'is_authenticated') and not user.is_authenticated:
user = None
user_logged_out.send(sender=user.__class__, request=request, user=user)
# remember language choice saved to session
language = request.session.get(LANGUAGE_SESSION_KEY)
request.session.flush()
if language is not None:
request.session[LANGUAGE_SESSION_KEY] = language
if hasattr(request, 'user'):
request.user = MojAnonymousUser() | [
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Jaymon/prom | prom/model.py | Orm.fields | def fields(self):
"""
return all the fields and their raw values for this Orm instance. This
property returns a dict with the field names and their current values
if you want to control the values for outputting to an api, use .jsonable()
"""
return {k:getattr(self, k, None) for k in self.schema.fields} | python | def fields(self):
"""
return all the fields and their raw values for this Orm instance. This
property returns a dict with the field names and their current values
if you want to control the values for outputting to an api, use .jsonable()
"""
return {k:getattr(self, k, None) for k in self.schema.fields} | [
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Jaymon/prom | prom/model.py | Orm.create | def create(cls, fields=None, **fields_kwargs):
"""
create an instance of cls with the passed in fields and set it into the db
fields -- dict -- field_name keys, with their respective values
**fields_kwargs -- dict -- if you would rather pass in fields as name=val, that works also
"""
# NOTE -- you cannot use hydrate/populate here because populate alters modified fields
instance = cls(fields, **fields_kwargs)
instance.save()
return instance | python | def create(cls, fields=None, **fields_kwargs):
"""
create an instance of cls with the passed in fields and set it into the db
fields -- dict -- field_name keys, with their respective values
**fields_kwargs -- dict -- if you would rather pass in fields as name=val, that works also
"""
# NOTE -- you cannot use hydrate/populate here because populate alters modified fields
instance = cls(fields, **fields_kwargs)
instance.save()
return instance | [
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Jaymon/prom | prom/model.py | Orm.populate | def populate(self, fields=None, **fields_kwargs):
"""take the passed in fields, combine them with missing fields that should
be there and then run all those through appropriate methods to hydrate this
orm.
The method replaces cls.hydrate() since it was becoming hard to understand
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pop_fields = {}
fields = self.make_dict(fields, fields_kwargs)
for k in self.schema.fields.keys():
pop_fields[k] = fields.get(k, None)
self._populate(pop_fields) | python | def populate(self, fields=None, **fields_kwargs):
"""take the passed in fields, combine them with missing fields that should
be there and then run all those through appropriate methods to hydrate this
orm.
The method replaces cls.hydrate() since it was becoming hard to understand
what was going on with all these methods that did things just a little bit
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This is used to completely set all the fields of self. If you just want
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:param fields: dict, the fields in a dict
:param **fields_kwargs: dict, if you would like to pass the fields as key=val
this picks those up and combines them with fields
"""
# this will run all the fields of the Orm, not just the fields in fields
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pop_fields = {}
fields = self.make_dict(fields, fields_kwargs)
for k in self.schema.fields.keys():
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Jaymon/prom | prom/model.py | Orm._populate | def _populate(self, fields):
"""this runs all the fields through their iget methods to mimic them
freshly coming out of the db, then resets modified
:param fields: dict, the fields that were passed in
"""
schema = self.schema
for k, v in fields.items():
fields[k] = schema.fields[k].iget(self, v)
self.modify(fields)
self.reset_modified() | python | def _populate(self, fields):
"""this runs all the fields through their iget methods to mimic them
freshly coming out of the db, then resets modified
:param fields: dict, the fields that were passed in
"""
schema = self.schema
for k, v in fields.items():
fields[k] = schema.fields[k].iget(self, v)
self.modify(fields)
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Jaymon/prom | prom/model.py | Orm.depopulate | def depopulate(self, is_update):
"""Get all the fields that need to be saved
:param is_udpate: bool, True if update query, False if insert
:returns: dict, key is field_name and val is the field value to be saved
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fields[k] = v
if not is_update:
for field_name in schema.required_fields.keys():
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raise KeyError("Missing required field {}".format(field_name))
return fields | python | def depopulate(self, is_update):
"""Get all the fields that need to be saved
:param is_udpate: bool, True if update query, False if insert
:returns: dict, key is field_name and val is the field value to be saved
"""
fields = {}
schema = self.schema
for k, field in schema.fields.items():
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orig_v = getattr(self, k)
v = field.iset(
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is_update=is_update,
is_modified=is_modified
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if is_modified or v is not None:
if is_update and field.is_pk() and v == orig_v:
continue
else:
fields[k] = v
if not is_update:
for field_name in schema.required_fields.keys():
if field_name not in fields:
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return fields | [
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Jaymon/prom | prom/model.py | Orm.insert | def insert(self):
"""persist the field values of this orm"""
ret = True
schema = self.schema
fields = self.depopulate(False)
q = self.query
q.set_fields(fields)
pk = q.insert()
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fields[schema.pk.name] = pk
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return ret | python | def insert(self):
"""persist the field values of this orm"""
ret = True
schema = self.schema
fields = self.depopulate(False)
q = self.query
q.set_fields(fields)
pk = q.insert()
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Jaymon/prom | prom/model.py | Orm.update | def update(self):
"""re-persist the updated field values of this orm that has a primary key"""
ret = True
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q.set_fields(fields)
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"""re-persist the updated field values of this orm that has a primary key"""
ret = True
fields = self.depopulate(True)
q = self.query
q.set_fields(fields)
pk = self.pk
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Jaymon/prom | prom/model.py | Orm.save | def save(self):
"""
persist the fields in this object into the db, this will update if _id is set, otherwise
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see also -- .insert(), .update()
"""
ret = False
# we will only use the primary key if it hasn't been modified
pk = None
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return ret | python | def save(self):
"""
persist the fields in this object into the db, this will update if _id is set, otherwise
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see also -- .insert(), .update()
"""
ret = False
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Jaymon/prom | prom/model.py | Orm.delete | def delete(self):
"""delete the object from the db if pk is set"""
ret = False
q = self.query
pk = self.pk
if pk:
pk_name = self.schema.pk.name
self.query.is_field(pk_name, pk).delete()
setattr(self, pk_name, None)
# mark all the fields that still exist as modified
self.reset_modified()
for field_name in self.schema.fields:
if getattr(self, field_name, None) != None:
self.modified_fields.add(field_name)
ret = True
return ret | python | def delete(self):
"""delete the object from the db if pk is set"""
ret = False
q = self.query
pk = self.pk
if pk:
pk_name = self.schema.pk.name
self.query.is_field(pk_name, pk).delete()
setattr(self, pk_name, None)
# mark all the fields that still exist as modified
self.reset_modified()
for field_name in self.schema.fields:
if getattr(self, field_name, None) != None:
self.modified_fields.add(field_name)
ret = True
return ret | [
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Jaymon/prom | prom/model.py | Orm.reset_modified | def reset_modified(self):
"""
reset field modification tracking
this is handy for when you are loading a new Orm with the results from a query and
you don't want set() to do anything, you can Orm(**fields) and then orm.reset_modified() to
clear all the passed in fields from the modified list
"""
self.modified_fields = set()
# compensate for us not having knowledge of certain fields changing
for field_name, field in self.schema.normal_fields.items():
if isinstance(field, ObjectField):
self.modified_fields.add(field_name) | python | def reset_modified(self):
"""
reset field modification tracking
this is handy for when you are loading a new Orm with the results from a query and
you don't want set() to do anything, you can Orm(**fields) and then orm.reset_modified() to
clear all the passed in fields from the modified list
"""
self.modified_fields = set()
# compensate for us not having knowledge of certain fields changing
for field_name, field in self.schema.normal_fields.items():
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Jaymon/prom | prom/model.py | Orm.modify | def modify(self, fields=None, **fields_kwargs):
"""update the fields of this instance with the values in dict fields
this should rarely be messed with, if you would like to manipulate the
fields you should override _modify()
:param fields: dict, the fields in a dict
:param **fields_kwargs: dict, if you would like to pass the fields as key=val
this picks those up and combines them with fields
:returns: set, all the names of the fields that were modified
"""
modified_fields = set()
fields = self.make_dict(fields, fields_kwargs)
fields = self._modify(fields)
for field_name, field_val in fields.items():
in_schema = field_name in self.schema.fields
if in_schema:
setattr(self, field_name, field_val)
modified_fields.add(field_name)
return modified_fields | python | def modify(self, fields=None, **fields_kwargs):
"""update the fields of this instance with the values in dict fields
this should rarely be messed with, if you would like to manipulate the
fields you should override _modify()
:param fields: dict, the fields in a dict
:param **fields_kwargs: dict, if you would like to pass the fields as key=val
this picks those up and combines them with fields
:returns: set, all the names of the fields that were modified
"""
modified_fields = set()
fields = self.make_dict(fields, fields_kwargs)
fields = self._modify(fields)
for field_name, field_val in fields.items():
in_schema = field_name in self.schema.fields
if in_schema:
setattr(self, field_name, field_val)
modified_fields.add(field_name)
return modified_fields | [
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Jaymon/prom | prom/model.py | Orm.jsonable | def jsonable(self, *args, **options):
"""
return a public version of this instance that can be jsonified
Note that this does not return _id, _created, _updated, the reason why is
because lots of times you have a different name for _id (like if it is a
user object, then you might want to call it user_id instead of _id) and I
didn't want to make assumptions
note 2, I'm not crazy about the name, but I didn't like to_dict() and pretty
much any time I need to convert the object to a dict is for json, I kind of
like dictify() though, but I've already used this method in so many places
"""
d = {}
for field_name, field in self.schema.normal_fields.items():
field_val = getattr(self, field_name, None)
field_val = field.jsonable(self, field_val)
if field_val is not None:
d[field_name] = field_val
return d | python | def jsonable(self, *args, **options):
"""
return a public version of this instance that can be jsonified
Note that this does not return _id, _created, _updated, the reason why is
because lots of times you have a different name for _id (like if it is a
user object, then you might want to call it user_id instead of _id) and I
didn't want to make assumptions
note 2, I'm not crazy about the name, but I didn't like to_dict() and pretty
much any time I need to convert the object to a dict is for json, I kind of
like dictify() though, but I've already used this method in so many places
"""
d = {}
for field_name, field in self.schema.normal_fields.items():
field_val = getattr(self, field_name, None)
field_val = field.jsonable(self, field_val)
if field_val is not None:
d[field_name] = field_val
return d | [
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guaix-ucm/pyemir | emirdrp/tools/merge2images.py | merge2images | def merge2images(hdu1, hdu2, debugplot):
"""Merge 2 EMIR images, averaging the common region.
Parameters
----------
hdu1 : HDUList object
Input image #1.
hdu2 : HDUList object
Input image #2.
debugplot : int
Determines whether intermediate computations and/or plots
are displayed. The valid codes are defined in
numina.array.display.pause_debugplot.
Returns
-------
image_merged : HDUList object
Output image.
"""
# check image dimensions
image_header = hdu1[0].header
image_header_ = hdu2[0].header
#
naxis = image_header['naxis']
naxis_ = image_header_['naxis']
if naxis != naxis_:
raise ValueError('Incompatible NAXIS values: {}, {}'.format(
naxis, naxis_
))
naxis1 = image_header['naxis1']
naxis1_ = image_header_['naxis1']
if naxis1 != naxis1_:
raise ValueError('Incompatible NAXIS1 values: {}, {}'.format(
naxis1, naxis1_
))
if naxis == 1:
naxis2 = 1
elif naxis == 2:
naxis2 = image_header['naxis2']
naxis2_ = image_header_['naxis2']
if naxis2 != naxis2_:
raise ValueError('Incompatible NAXIS2 values: {}, {}'.format(
naxis2, naxis2_
))
else:
raise ValueError('Unexpected NAXIS value: {}'.format(naxis))
# initialize output array
image2d_merged = np.zeros((naxis2, naxis1))
# main loop
data1 = hdu1[0].data
data2 = hdu2[0].data
for i in range(naxis2):
sp1 = data1[i, :]
sp2 = data2[i, :]
jmin1, jmax1 = find_pix_borders(sp1, sought_value=0)
jmin2, jmax2 = find_pix_borders(sp2, sought_value=0)
image2d_merged[i, :] = sp1 + sp2
useful1 = (jmin1 != -1) and (jmax1 != naxis1)
useful2 = (jmin2 != -1) and (jmax2 != naxis1)
if useful1 and useful2:
jmineff = max(jmin1, jmin2)
jmaxeff = min(jmax1, jmax2)
image2d_merged[i, jmineff:(jmaxeff+1)] /= 2
# return result
image_merged = fits.PrimaryHDU(data=image2d_merged.astype(np.float32),
header=image_header)
return image_merged | python | def merge2images(hdu1, hdu2, debugplot):
"""Merge 2 EMIR images, averaging the common region.
Parameters
----------
hdu1 : HDUList object
Input image #1.
hdu2 : HDUList object
Input image #2.
debugplot : int
Determines whether intermediate computations and/or plots
are displayed. The valid codes are defined in
numina.array.display.pause_debugplot.
Returns
-------
image_merged : HDUList object
Output image.
"""
# check image dimensions
image_header = hdu1[0].header
image_header_ = hdu2[0].header
#
naxis = image_header['naxis']
naxis_ = image_header_['naxis']
if naxis != naxis_:
raise ValueError('Incompatible NAXIS values: {}, {}'.format(
naxis, naxis_
))
naxis1 = image_header['naxis1']
naxis1_ = image_header_['naxis1']
if naxis1 != naxis1_:
raise ValueError('Incompatible NAXIS1 values: {}, {}'.format(
naxis1, naxis1_
))
if naxis == 1:
naxis2 = 1
elif naxis == 2:
naxis2 = image_header['naxis2']
naxis2_ = image_header_['naxis2']
if naxis2 != naxis2_:
raise ValueError('Incompatible NAXIS2 values: {}, {}'.format(
naxis2, naxis2_
))
else:
raise ValueError('Unexpected NAXIS value: {}'.format(naxis))
# initialize output array
image2d_merged = np.zeros((naxis2, naxis1))
# main loop
data1 = hdu1[0].data
data2 = hdu2[0].data
for i in range(naxis2):
sp1 = data1[i, :]
sp2 = data2[i, :]
jmin1, jmax1 = find_pix_borders(sp1, sought_value=0)
jmin2, jmax2 = find_pix_borders(sp2, sought_value=0)
image2d_merged[i, :] = sp1 + sp2
useful1 = (jmin1 != -1) and (jmax1 != naxis1)
useful2 = (jmin2 != -1) and (jmax2 != naxis1)
if useful1 and useful2:
jmineff = max(jmin1, jmin2)
jmaxeff = min(jmax1, jmax2)
image2d_merged[i, jmineff:(jmaxeff+1)] /= 2
# return result
image_merged = fits.PrimaryHDU(data=image2d_merged.astype(np.float32),
header=image_header)
return image_merged | [
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hdu2 : HDUList object
Input image #2.
debugplot : int
Determines whether intermediate computations and/or plots
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Jaymon/prom | prom/interface/__init__.py | configure_environ | def configure_environ(dsn_env_name='PROM_DSN', connection_class=DsnConnection):
"""
configure interfaces based on environment variables
by default, when prom is imported, it will look for PROM_DSN, and PROM_DSN_N (where
N is 1 through infinity) in the environment, if it finds them, it will assume they
are dsn urls that prom understands and will configure db connections with them. If you
don't want this behavior (ie, you want to configure prom manually) then just make sure
you don't have any environment variables with matching names
The num checks (eg PROM_DSN_1, PROM_DSN_2) go in order, so you can't do PROM_DSN_1, PROM_DSN_3,
because it will fail on _2 and move on, so make sure your num dsns are in order (eg, 1, 2, 3, ...)
example --
export PROM_DSN_1=some.Interface://host:port/dbname#i1
export PROM_DSN_2=some.Interface://host2:port/dbname2#i2
$ python
>>> import prom
>>> print prom.interfaces # prints a dict with interfaces i1 and i2 keys
:param dsn_env_name: string, the name of the environment variables
"""
inters = []
cs = dsnparse.parse_environs(dsn_env_name, parse_class=connection_class)
for c in cs:
inter = c.interface
set_interface(inter, c.name)
inters.append(inter)
return inters | python | def configure_environ(dsn_env_name='PROM_DSN', connection_class=DsnConnection):
"""
configure interfaces based on environment variables
by default, when prom is imported, it will look for PROM_DSN, and PROM_DSN_N (where
N is 1 through infinity) in the environment, if it finds them, it will assume they
are dsn urls that prom understands and will configure db connections with them. If you
don't want this behavior (ie, you want to configure prom manually) then just make sure
you don't have any environment variables with matching names
The num checks (eg PROM_DSN_1, PROM_DSN_2) go in order, so you can't do PROM_DSN_1, PROM_DSN_3,
because it will fail on _2 and move on, so make sure your num dsns are in order (eg, 1, 2, 3, ...)
example --
export PROM_DSN_1=some.Interface://host:port/dbname#i1
export PROM_DSN_2=some.Interface://host2:port/dbname2#i2
$ python
>>> import prom
>>> print prom.interfaces # prints a dict with interfaces i1 and i2 keys
:param dsn_env_name: string, the name of the environment variables
"""
inters = []
cs = dsnparse.parse_environs(dsn_env_name, parse_class=connection_class)
for c in cs:
inter = c.interface
set_interface(inter, c.name)
inters.append(inter)
return inters | [
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export PROM_DSN_2=some.Interface://host2:port/dbname2#i2
$ python
>>> import prom
>>> print prom.interfaces # prints a dict with interfaces i1 and i2 keys
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Jaymon/prom | prom/interface/__init__.py | configure | def configure(dsn, connection_class=DsnConnection):
"""
configure an interface to be used to query a backend
you use this function to configure an Interface using a dsn, then you can get
that interface using the get_interface() method
dsn -- string -- a properly formatted prom dsn, see DsnConnection for how to format the dsn
"""
c = dsnparse.parse(dsn, parse_class=connection_class)
inter = c.interface
set_interface(inter, c.name)
return inter | python | def configure(dsn, connection_class=DsnConnection):
"""
configure an interface to be used to query a backend
you use this function to configure an Interface using a dsn, then you can get
that interface using the get_interface() method
dsn -- string -- a properly formatted prom dsn, see DsnConnection for how to format the dsn
"""
c = dsnparse.parse(dsn, parse_class=connection_class)
inter = c.interface
set_interface(inter, c.name)
return inter | [
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Jaymon/prom | prom/interface/__init__.py | set_interface | def set_interface(interface, name=''):
"""
don't want to bother with a dsn? Use this method to make an interface available
"""
global interfaces
if not interface: raise ValueError('interface is empty')
# close down the interface before we discard it
if name in interfaces:
interfaces[name].close()
interfaces[name] = interface | python | def set_interface(interface, name=''):
"""
don't want to bother with a dsn? Use this method to make an interface available
"""
global interfaces
if not interface: raise ValueError('interface is empty')
# close down the interface before we discard it
if name in interfaces:
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Fuyukai/asyncwebsockets | asyncwebsockets/server.py | open_websocket_server | async def open_websocket_server(sock, filter=None): # pylint: disable=W0622
"""
A context manager which serves this websocket.
:param filter: an async callback which accepts the connection request
and returns a bool, or an explicit Accept/Reject message.
"""
ws = await create_websocket_server(sock, filter=filter)
try:
yield ws
finally:
await ws.close() | python | async def open_websocket_server(sock, filter=None): # pylint: disable=W0622
"""
A context manager which serves this websocket.
:param filter: an async callback which accepts the connection request
and returns a bool, or an explicit Accept/Reject message.
"""
ws = await create_websocket_server(sock, filter=filter)
try:
yield ws
finally:
await ws.close() | [
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Fuyukai/asyncwebsockets | asyncwebsockets/server.py | create_websocket_server | async def create_websocket_server(sock, filter=None): # pylint: disable=W0622
"""
A more low-level form of open_websocket_server.
You are responsible for closing this websocket.
"""
ws = Websocket()
await ws.start_server(sock, filter=filter)
return ws | python | async def create_websocket_server(sock, filter=None): # pylint: disable=W0622
"""
A more low-level form of open_websocket_server.
You are responsible for closing this websocket.
"""
ws = Websocket()
await ws.start_server(sock, filter=filter)
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Jaymon/prom | prom/config.py | Schema.magic_fields | def magic_fields(self):
"""the magic fields for the schema"""
return {f:v for f, v in self.fields.items() if f.startswith('_')} | python | def magic_fields(self):
"""the magic fields for the schema"""
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Jaymon/prom | prom/config.py | Schema.set_index | def set_index(self, index_name, index):
"""
add an index to the schema
for the most part, you will use the __getattr__ method of adding indexes for a more fluid interface,
but you can use this if you want to get closer to the bare metal
index_name -- string -- the name of the index
index -- Index() -- an Index instance
"""
if not index_name:
raise ValueError("index_name must have a value")
if index_name in self.indexes:
raise ValueError("index_name {} has already been defined on {}".format(
index_name, str(self.indexes[index_name].fields)
))
if not isinstance(index, Index): raise ValueError("{} is not an Index instance".format(type(index)))
index.name = index_name
self.indexes[index_name] = index
return self | python | def set_index(self, index_name, index):
"""
add an index to the schema
for the most part, you will use the __getattr__ method of adding indexes for a more fluid interface,
but you can use this if you want to get closer to the bare metal
index_name -- string -- the name of the index
index -- Index() -- an Index instance
"""
if not index_name:
raise ValueError("index_name must have a value")
if index_name in self.indexes:
raise ValueError("index_name {} has already been defined on {}".format(
index_name, str(self.indexes[index_name].fields)
))
if not isinstance(index, Index): raise ValueError("{} is not an Index instance".format(type(index)))
index.name = index_name
self.indexes[index_name] = index
return self | [
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Jaymon/prom | prom/config.py | Field.schema | def schema(self):
"""return the schema instance if this is reference to another table"""
if not hasattr(self, "_schema"):
ret = None
o = self._type
if isinstance(o, type):
ret = getattr(o, "schema", None)
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ret = o
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ret = klass.schema
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"""return the schema instance if this is reference to another table"""
if not hasattr(self, "_schema"):
ret = None
o = self._type
if isinstance(o, type):
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Jaymon/prom | prom/config.py | Field.fval | def fval(self, instance):
"""return the raw value that this property is holding internally for instance"""
try:
val = instance.__dict__[self.instance_field_name]
except KeyError as e:
#raise AttributeError(str(e))
val = None
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openmicroanalysis/pyxray | pyxray/base.py | _Database.set_default_reference | def set_default_reference(self, method, reference):
"""
Set the default reference for a method.
:arg method: name of a method
:type method: :class:`str`
{reference}
"""
if method not in self._available_methods:
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Set the default reference for a method.
:arg method: name of a method
:type method: :class:`str`
{reference}
"""
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openmicroanalysis/pyxray | pyxray/base.py | _Database.get_default_reference | def get_default_reference(self, method):
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"""
Returns the default reference for a method.
:arg method: name of a method
:type method: :class:`str`
:return: reference
:rtype: :class:`Reference <pyxray.descriptor.Reference>` or :class:`str`
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openmicroanalysis/pyxray | pyxray/base.py | _Database.print_element_xray_transitions | def print_element_xray_transitions(self, element, file=sys.stdout, tabulate_kwargs=None):
"""
Prints all x-ray transitions for an element, with their different
notations and energy.
{element}
:arg file: file for output, default to standard out
"""
header = ['IUPAC', 'Siegbahn', 'Energy (eV)', 'Probability']
rows = []
for xraytransition in self.element_xray_transitions(element):
try:
iupac = self.xray_transition_notation(xraytransition, 'iupac')
except:
iupac = ''
try:
siegbahn = self.xray_transition_notation(xraytransition, 'siegbahn')
except:
siegbahn = ''
try:
energy_eV = self.xray_transition_energy_eV(element, xraytransition)
except:
energy_eV = ''
try:
probability = self.xray_transition_probability(element, xraytransition)
except:
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rows.append([iupac, siegbahn, energy_eV, probability])
rows.sort(key=operator.itemgetter(2))
if tabulate_kwargs is None:
tabulate_kwargs = {}
file.write(tabulate.tabulate(rows, header, **tabulate_kwargs)) | python | def print_element_xray_transitions(self, element, file=sys.stdout, tabulate_kwargs=None):
"""
Prints all x-ray transitions for an element, with their different
notations and energy.
{element}
:arg file: file for output, default to standard out
"""
header = ['IUPAC', 'Siegbahn', 'Energy (eV)', 'Probability']
rows = []
for xraytransition in self.element_xray_transitions(element):
try:
iupac = self.xray_transition_notation(xraytransition, 'iupac')
except:
iupac = ''
try:
siegbahn = self.xray_transition_notation(xraytransition, 'siegbahn')
except:
siegbahn = ''
try:
energy_eV = self.xray_transition_energy_eV(element, xraytransition)
except:
energy_eV = ''
try:
probability = self.xray_transition_probability(element, xraytransition)
except:
probability = ''
rows.append([iupac, siegbahn, energy_eV, probability])
rows.sort(key=operator.itemgetter(2))
if tabulate_kwargs is None:
tabulate_kwargs = {}
file.write(tabulate.tabulate(rows, header, **tabulate_kwargs)) | [
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Jaymon/prom | prom/cli/dump.py | get_subclasses | def get_subclasses(modulepath, parent_class):
"""given a module return all the parent_class subclasses that are found in
that module and any submodules.
:param modulepath: string, a path like foo.bar.che
:param parent_class: object, the class whose children you are looking for
:returns: set, all the found child classes in modulepath of parent_class
"""
if isinstance(modulepath, ModuleType):
modules = get_modules(modulepath.__name__)
else:
modules = get_modules(modulepath)
ret = set()
for m in modules:
cs = inspect.getmembers(m, lambda v: inspect.isclass(v) and issubclass(v, parent_class))
for class_name, klass in cs:
ret.add(klass)
return ret | python | def get_subclasses(modulepath, parent_class):
"""given a module return all the parent_class subclasses that are found in
that module and any submodules.
:param modulepath: string, a path like foo.bar.che
:param parent_class: object, the class whose children you are looking for
:returns: set, all the found child classes in modulepath of parent_class
"""
if isinstance(modulepath, ModuleType):
modules = get_modules(modulepath.__name__)
else:
modules = get_modules(modulepath)
ret = set()
for m in modules:
cs = inspect.getmembers(m, lambda v: inspect.isclass(v) and issubclass(v, parent_class))
for class_name, klass in cs:
ret.add(klass)
return ret | [
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Jaymon/prom | prom/cli/dump.py | build_dump_order | def build_dump_order(orm_class, orm_classes):
"""pass in an array, when you encounter a ref, call this method again with the array
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orm_classes.append(orm_class) | python | def build_dump_order(orm_class, orm_classes):
"""pass in an array, when you encounter a ref, call this method again with the array
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build_dump_order(field_val.schema.orm_class, orm_classes)
if orm_class not in orm_classes:
orm_classes.append(orm_class) | [
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Jaymon/prom | prom/cli/dump.py | main_dump | def main_dump(paths, directory, dry_run):
"""dump all or part of the prom data, currently only works on Postgres databases
basically just a wrapper around `dump backup` https://github.com/Jaymon/dump
"""
table_map = get_table_map(paths)
for conn_name, conn_info in table_map.items():
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conn = inter.connection_config
table_names = conn_info["table_names"]
cmd = get_base_cmd("backup", inter, directory)
cmd.extend(table_names)
if dry_run:
echo.out(" ".join(cmd))
else:
run_cmd(cmd) | python | def main_dump(paths, directory, dry_run):
"""dump all or part of the prom data, currently only works on Postgres databases
basically just a wrapper around `dump backup` https://github.com/Jaymon/dump
"""
table_map = get_table_map(paths)
for conn_name, conn_info in table_map.items():
inter = conn_info["interface"]
conn = inter.connection_config
table_names = conn_info["table_names"]
cmd = get_base_cmd("backup", inter, directory)
cmd.extend(table_names)
if dry_run:
echo.out(" ".join(cmd))
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run_cmd(cmd) | [
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Jaymon/prom | prom/cli/dump.py | main_restore | def main_restore(directory, conn_name):
"""Restore your database dumped with the dump command
just a wrapper around `dump restore` https://github.com/Jaymon/dump
"""
inter = get_interface(conn_name)
conn = inter.connection_config
cmd = get_base_cmd("restore", inter, directory)
run_cmd(cmd) | python | def main_restore(directory, conn_name):
"""Restore your database dumped with the dump command
just a wrapper around `dump restore` https://github.com/Jaymon/dump
"""
inter = get_interface(conn_name)
conn = inter.connection_config
cmd = get_base_cmd("restore", inter, directory)
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just a wrapper around `dump restore` https://github.com/Jaymon/dump | [
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Jaymon/prom | prom/interface/postgres.py | PostgreSQL._get_fields | def _get_fields(self, table_name, **kwargs):
"""return all the fields for the given schema"""
ret = {}
query_str = []
query_args = ['f', table_name]
# I had to brush up on my join knowledge while writing this query
# https://en.wikipedia.org/wiki/Join_(SQL)
#
# other helpful links
# https://wiki.postgresql.org/wiki/Retrieve_primary_key_columns
# https://www.postgresql.org/docs/9.4/static/catalog-pg-attribute.html
# https://www.postgresql.org/docs/9.3/static/catalog-pg-type.html
#
# another approach
# http://dba.stackexchange.com/questions/22362/how-do-i-list-all-columns-for-a-specified-table
# http://gis.stackexchange.com/questions/94049/how-to-get-the-data-type-of-each-column-from-a-postgis-table
query_str.append('SELECT')
query_str.append(', '.join([
'a.attnum',
'a.attname',
'a.attnotnull',
't.typname',
'i.indisprimary',
#'s.conname',
#'pg_get_constraintdef(s.oid, true) as condef',
'c.relname AS confrelname',
]))
query_str.append('FROM')
query_str.append(' pg_attribute a')
query_str.append('JOIN pg_type t ON a.atttypid = t.oid')
query_str.append('LEFT JOIN pg_index i ON a.attrelid = i.indrelid')
query_str.append(' AND a.attnum = any(i.indkey)')
query_str.append('LEFT JOIN pg_constraint s ON a.attrelid = s.conrelid')
query_str.append(' AND s.contype = {} AND a.attnum = any(s.conkey)'.format(self.val_placeholder))
query_str.append('LEFT JOIN pg_class c ON s.confrelid = c.oid')
query_str.append('WHERE')
query_str.append(' a.attrelid = {}::regclass'.format(self.val_placeholder))
query_str.append(' AND a.attisdropped = False')
query_str.append(' AND a.attnum > 0')
query_str.append('ORDER BY a.attnum ASC')
query_str = os.linesep.join(query_str)
fields = self.query(query_str, *query_args, **kwargs)
pg_types = {
"float8": float,
"timestamp": datetime.datetime,
"int2": int,
"int4": int,
"int8": long,
"numeric": decimal.Decimal,
"text": str,
"bpchar": str,
"varchar": str,
"bool": bool,
"date": datetime.date,
"blob": bytearray,
}
# the rows we can set: field_type, name, field_required, min_size, max_size,
# size, unique, pk, <foreign key info>
# These keys will roughly correspond with schema.Field
for row in fields:
field = {
"name": row["attname"],
"field_type": pg_types[row["typname"]],
"field_required": row["attnotnull"],
"pk": bool(row["indisprimary"]),
}
if row["confrelname"]:
# TODO -- I can't decide which name I like
field["schema_table_name"] = row["confrelname"]
field["ref_table_name"] = row["confrelname"]
ret[field["name"]] = field
return ret | python | def _get_fields(self, table_name, **kwargs):
"""return all the fields for the given schema"""
ret = {}
query_str = []
query_args = ['f', table_name]
# I had to brush up on my join knowledge while writing this query
# https://en.wikipedia.org/wiki/Join_(SQL)
#
# other helpful links
# https://wiki.postgresql.org/wiki/Retrieve_primary_key_columns
# https://www.postgresql.org/docs/9.4/static/catalog-pg-attribute.html
# https://www.postgresql.org/docs/9.3/static/catalog-pg-type.html
#
# another approach
# http://dba.stackexchange.com/questions/22362/how-do-i-list-all-columns-for-a-specified-table
# http://gis.stackexchange.com/questions/94049/how-to-get-the-data-type-of-each-column-from-a-postgis-table
query_str.append('SELECT')
query_str.append(', '.join([
'a.attnum',
'a.attname',
'a.attnotnull',
't.typname',
'i.indisprimary',
#'s.conname',
#'pg_get_constraintdef(s.oid, true) as condef',
'c.relname AS confrelname',
]))
query_str.append('FROM')
query_str.append(' pg_attribute a')
query_str.append('JOIN pg_type t ON a.atttypid = t.oid')
query_str.append('LEFT JOIN pg_index i ON a.attrelid = i.indrelid')
query_str.append(' AND a.attnum = any(i.indkey)')
query_str.append('LEFT JOIN pg_constraint s ON a.attrelid = s.conrelid')
query_str.append(' AND s.contype = {} AND a.attnum = any(s.conkey)'.format(self.val_placeholder))
query_str.append('LEFT JOIN pg_class c ON s.confrelid = c.oid')
query_str.append('WHERE')
query_str.append(' a.attrelid = {}::regclass'.format(self.val_placeholder))
query_str.append(' AND a.attisdropped = False')
query_str.append(' AND a.attnum > 0')
query_str.append('ORDER BY a.attnum ASC')
query_str = os.linesep.join(query_str)
fields = self.query(query_str, *query_args, **kwargs)
pg_types = {
"float8": float,
"timestamp": datetime.datetime,
"int2": int,
"int4": int,
"int8": long,
"numeric": decimal.Decimal,
"text": str,
"bpchar": str,
"varchar": str,
"bool": bool,
"date": datetime.date,
"blob": bytearray,
}
# the rows we can set: field_type, name, field_required, min_size, max_size,
# size, unique, pk, <foreign key info>
# These keys will roughly correspond with schema.Field
for row in fields:
field = {
"name": row["attname"],
"field_type": pg_types[row["typname"]],
"field_required": row["attnotnull"],
"pk": bool(row["indisprimary"]),
}
if row["confrelname"]:
# TODO -- I can't decide which name I like
field["schema_table_name"] = row["confrelname"]
field["ref_table_name"] = row["confrelname"]
ret[field["name"]] = field
return ret | [
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IdentityPython/oidcendpoint | src/oidcendpoint/oidc/token.py | AccessToken.client_authentication | def client_authentication(self, request, auth=None, **kwargs):
"""
Deal with client authentication
:param request: The refresh access token request
:param auth: Client authentication information
:param kwargs: Extra keyword arguments
:return: dictionary containing client id, client authentication method
and possibly access token.
"""
try:
auth_info = verify_client(self.endpoint_context, request, auth)
except Exception as err:
msg = "Failed to verify client due to: {}".format(err)
logger.error(msg)
return self.error_cls(error="unauthorized_client",
error_description=msg)
else:
if 'client_id' not in auth_info:
logger.error('No client_id, authentication failed')
return self.error_cls(error="unauthorized_client",
error_description='unknown client')
return auth_info | python | def client_authentication(self, request, auth=None, **kwargs):
"""
Deal with client authentication
:param request: The refresh access token request
:param auth: Client authentication information
:param kwargs: Extra keyword arguments
:return: dictionary containing client id, client authentication method
and possibly access token.
"""
try:
auth_info = verify_client(self.endpoint_context, request, auth)
except Exception as err:
msg = "Failed to verify client due to: {}".format(err)
logger.error(msg)
return self.error_cls(error="unauthorized_client",
error_description=msg)
else:
if 'client_id' not in auth_info:
logger.error('No client_id, authentication failed')
return self.error_cls(error="unauthorized_client",
error_description='unknown client')
return auth_info | [
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IdentityPython/oidcendpoint | src/oidcendpoint/oidc/token.py | AccessToken._post_parse_request | def _post_parse_request(self, request, client_id='', **kwargs):
"""
This is where clients come to get their access tokens
:param request: The request
:param authn: Authentication info, comes from HTTP header
:returns:
"""
if 'state' in request:
try:
sinfo = self.endpoint_context.sdb[request['code']]
except KeyError:
logger.error('Code not present in SessionDB')
return self.error_cls(error="unauthorized_client")
else:
state = sinfo['authn_req']['state']
if state != request['state']:
logger.error('State value mismatch')
return self.error_cls(error="unauthorized_client")
if "client_id" not in request: # Optional for access token request
request["client_id"] = client_id
logger.debug("%s: %s" % (request.__class__.__name__, sanitize(request)))
return request | python | def _post_parse_request(self, request, client_id='', **kwargs):
"""
This is where clients come to get their access tokens
:param request: The request
:param authn: Authentication info, comes from HTTP header
:returns:
"""
if 'state' in request:
try:
sinfo = self.endpoint_context.sdb[request['code']]
except KeyError:
logger.error('Code not present in SessionDB')
return self.error_cls(error="unauthorized_client")
else:
state = sinfo['authn_req']['state']
if state != request['state']:
logger.error('State value mismatch')
return self.error_cls(error="unauthorized_client")
if "client_id" not in request: # Optional for access token request
request["client_id"] = client_id
logger.debug("%s: %s" % (request.__class__.__name__, sanitize(request)))
return request | [
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BreakingBytes/simkit | simkit/core/outputs.py | OutputRegistry.register | def register(self, new_outputs, *args, **kwargs):
"""
Register outputs and metadata.
* ``initial_value`` - used in dynamic calculations
* ``size`` - number of elements per timestep
* ``uncertainty`` - in percent of nominal value
* ``variance`` - dictionary of covariances, diagonal is square of
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* ``jacobian`` - dictionary of sensitivities dxi/dfj
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* ``isproperty`` - ``True`` if output stays at last value during
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* ``timeseries`` - name of corresponding time series output, ``None`` if
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* ``output_source`` - name
:param new_outputs: new outputs to register.
"""
kwargs.update(zip(self.meta_names, args))
# call super method
super(OutputRegistry, self).register(new_outputs, **kwargs) | python | def register(self, new_outputs, *args, **kwargs):
"""
Register outputs and metadata.
* ``initial_value`` - used in dynamic calculations
* ``size`` - number of elements per timestep
* ``uncertainty`` - in percent of nominal value
* ``variance`` - dictionary of covariances, diagonal is square of
uncertianties, no units
* ``jacobian`` - dictionary of sensitivities dxi/dfj
* ``isconstant`` - ``True`` if constant, ``False`` if periodic
* ``isproperty`` - ``True`` if output stays at last value during
thresholds, ``False`` if reverts to initial value
* ``timeseries`` - name of corresponding time series output, ``None`` if
no time series
* ``output_source`` - name
:param new_outputs: new outputs to register.
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kwargs.update(zip(self.meta_names, args))
# call super method
super(OutputRegistry, self).register(new_outputs, **kwargs) | [
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guaix-ucm/pyemir | emirdrp/recipes/image/dither.py | FullDitheredImagesRecipe.initial_classification | def initial_classification(self, obresult, target_is_sky=False):
"""Classify input frames, """
# lists of targets and sky frames
with obresult.frames[0].open() as baseimg:
# Initial checks
has_bpm_ext = 'BPM' in baseimg
self.logger.debug('images have BPM extension: %s', has_bpm_ext)
images_info = []
for f in obresult.frames:
with f.open() as img:
# Getting some metadata from FITS header
hdr = img[0].header
iinfo = ImageInfo(f)
finfo = {}
iinfo.metadata = finfo
finfo['uuid'] = hdr['UUID']
finfo['exposure'] = hdr['EXPTIME']
# frame.baseshape = get_image_shape(hdr)
finfo['airmass'] = hdr['airmass']
finfo['mjd'] = hdr['tstamp']
iinfo.label = 'result_image_{}'.format(finfo['uuid'])
iinfo.mask = nfcom.Extension("BPM")
# Insert pixel offsets between frames
iinfo.objmask_data = None
iinfo.valid_target = False
iinfo.valid_sky = False
# FIXME: hardcode itype for the moment
iinfo.itype = 'TARGET'
if iinfo.itype == 'TARGET':
iinfo.valid_target = True
#targetframes.append(iinfo)
if target_is_sky:
iinfo.valid_sky = True
#skyframes.append(iinfo)
if iinfo.itype == 'SKY':
iinfo.valid_sky = True
#skyframes.append(iinfo)
images_info.append(iinfo)
return images_info | python | def initial_classification(self, obresult, target_is_sky=False):
"""Classify input frames, """
# lists of targets and sky frames
with obresult.frames[0].open() as baseimg:
# Initial checks
has_bpm_ext = 'BPM' in baseimg
self.logger.debug('images have BPM extension: %s', has_bpm_ext)
images_info = []
for f in obresult.frames:
with f.open() as img:
# Getting some metadata from FITS header
hdr = img[0].header
iinfo = ImageInfo(f)
finfo = {}
iinfo.metadata = finfo
finfo['uuid'] = hdr['UUID']
finfo['exposure'] = hdr['EXPTIME']
# frame.baseshape = get_image_shape(hdr)
finfo['airmass'] = hdr['airmass']
finfo['mjd'] = hdr['tstamp']
iinfo.label = 'result_image_{}'.format(finfo['uuid'])
iinfo.mask = nfcom.Extension("BPM")
# Insert pixel offsets between frames
iinfo.objmask_data = None
iinfo.valid_target = False
iinfo.valid_sky = False
# FIXME: hardcode itype for the moment
iinfo.itype = 'TARGET'
if iinfo.itype == 'TARGET':
iinfo.valid_target = True
#targetframes.append(iinfo)
if target_is_sky:
iinfo.valid_sky = True
#skyframes.append(iinfo)
if iinfo.itype == 'SKY':
iinfo.valid_sky = True
#skyframes.append(iinfo)
images_info.append(iinfo)
return images_info | [
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thorgate/tg-utils | tg_utils/managers.py | NotifyPostChangeQuerySet.update_or_create | def update_or_create(self, *args, **kwargs):
""" Only sent when not created, since default implementation will
call `self.create` when creating which triggers our signal
already.
"""
obj, created = super().update_or_create(*args, **kwargs)
if not created:
return self.with_signal(result=(obj, created))
return obj, created | python | def update_or_create(self, *args, **kwargs):
""" Only sent when not created, since default implementation will
call `self.create` when creating which triggers our signal
already.
"""
obj, created = super().update_or_create(*args, **kwargs)
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Yelp/uwsgi_metrics | uwsgi_metrics/timer.py | Timer.update | def update(self, duration):
"""Add a recorded duration."""
if duration >= 0:
self.histogram.update(duration)
self.meter.mark() | python | def update(self, duration):
"""Add a recorded duration."""
if duration >= 0:
self.histogram.update(duration)
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BeyondTheClouds/enoslib | enoslib/infra/enos_vmong5k/provider.py | _build_g5k_conf | def _build_g5k_conf(vmong5k_conf):
"""Build the conf of the g5k provider from the vmong5k conf."""
clusters = [m.cluster for m in vmong5k_conf.machines]
sites = g5k_api_utils.get_clusters_sites(clusters)
site_names = set(sites.values())
if len(site_names) > 1:
raise Exception("Multisite deployment not supported yet")
site = site_names.pop()
return _do_build_g5k_conf(vmong5k_conf, site) | python | def _build_g5k_conf(vmong5k_conf):
"""Build the conf of the g5k provider from the vmong5k conf."""
clusters = [m.cluster for m in vmong5k_conf.machines]
sites = g5k_api_utils.get_clusters_sites(clusters)
site_names = set(sites.values())
if len(site_names) > 1:
raise Exception("Multisite deployment not supported yet")
site = site_names.pop()
return _do_build_g5k_conf(vmong5k_conf, site) | [
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BreakingBytes/simkit | simkit/contrib/readers.py | copy_model_instance | def copy_model_instance(obj):
"""
Copy Django model instance as a dictionary excluding automatically created
fields like an auto-generated sequence as a primary key or an auto-created
many-to-one reverse relation.
:param obj: Django model object
:return: copy of model instance as dictionary
"""
meta = getattr(obj, '_meta') # make pycharm happy
# dictionary of model values excluding auto created and related fields
return {f.name: getattr(obj, f.name)
for f in meta.get_fields(include_parents=False)
if not f.auto_created} | python | def copy_model_instance(obj):
"""
Copy Django model instance as a dictionary excluding automatically created
fields like an auto-generated sequence as a primary key or an auto-created
many-to-one reverse relation.
:param obj: Django model object
:return: copy of model instance as dictionary
"""
meta = getattr(obj, '_meta') # make pycharm happy
# dictionary of model values excluding auto created and related fields
return {f.name: getattr(obj, f.name)
for f in meta.get_fields(include_parents=False)
if not f.auto_created} | [
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BreakingBytes/simkit | simkit/contrib/readers.py | ArgumentReader.load_data | def load_data(self, *args, **kwargs):
"""
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:return: data
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# get positional argument names from parameters and apply them to args
# update data with additional kwargs
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data = dict(
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return self.apply_units_to_cache(data) | python | def load_data(self, *args, **kwargs):
"""
Collects positional and keyword arguments into `data` and applies units.
:return: data
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# get positional argument names from parameters and apply them to args
# update data with additional kwargs
argpos = {
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BeyondTheClouds/enoslib | enoslib/infra/enos_g5k/g5k_api_utils.py | grid_reload_from_name | def grid_reload_from_name(job_name):
"""Reload all running or pending jobs of Grid'5000 with a given name.
By default all the sites will be searched for jobs with the name
``job_name``. Using EnOSlib there can be only one job per site with name
``job_name``.
Note that it honors the ``exluded_sites`` attribute of the client so the
scan can be reduced.
Args:
job_name (str): the job name
Returns:
The list of the python-grid5000 jobs retrieved.
Raises:
EnosG5kDuplicateJobsError: if there's several jobs with the same name
on a site.
"""
gk = get_api_client()
sites = get_all_sites_obj()
jobs = []
for site in [s for s in sites if s.uid not in gk.excluded_site]:
logger.info("Reloading %s from %s" % (job_name, site.uid))
_jobs = site.jobs.list(name=job_name,
state="waiting,launching,running")
if len(_jobs) == 1:
logger.info("Reloading %s from %s" % (_jobs[0].uid, site.uid))
jobs.append(_jobs[0])
elif len(_jobs) > 1:
raise EnosG5kDuplicateJobsError(site, job_name)
return jobs | python | def grid_reload_from_name(job_name):
"""Reload all running or pending jobs of Grid'5000 with a given name.
By default all the sites will be searched for jobs with the name
``job_name``. Using EnOSlib there can be only one job per site with name
``job_name``.
Note that it honors the ``exluded_sites`` attribute of the client so the
scan can be reduced.
Args:
job_name (str): the job name
Returns:
The list of the python-grid5000 jobs retrieved.
Raises:
EnosG5kDuplicateJobsError: if there's several jobs with the same name
on a site.
"""
gk = get_api_client()
sites = get_all_sites_obj()
jobs = []
for site in [s for s in sites if s.uid not in gk.excluded_site]:
logger.info("Reloading %s from %s" % (job_name, site.uid))
_jobs = site.jobs.list(name=job_name,
state="waiting,launching,running")
if len(_jobs) == 1:
logger.info("Reloading %s from %s" % (_jobs[0].uid, site.uid))
jobs.append(_jobs[0])
elif len(_jobs) > 1:
raise EnosG5kDuplicateJobsError(site, job_name)
return jobs | [
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BeyondTheClouds/enoslib | enoslib/infra/enos_g5k/g5k_api_utils.py | grid_reload_from_ids | def grid_reload_from_ids(oargrid_jobids):
"""Reload all running or pending jobs of Grid'5000 from their ids
Args:
oargrid_jobids (list): list of ``(site, oar_jobid)`` identifying the
jobs on each site
Returns:
The list of python-grid5000 jobs retrieved
"""
gk = get_api_client()
jobs = []
for site, job_id in oargrid_jobids:
jobs.append(gk.sites[site].jobs[job_id])
return jobs | python | def grid_reload_from_ids(oargrid_jobids):
"""Reload all running or pending jobs of Grid'5000 from their ids
Args:
oargrid_jobids (list): list of ``(site, oar_jobid)`` identifying the
jobs on each site
Returns:
The list of python-grid5000 jobs retrieved
"""
gk = get_api_client()
jobs = []
for site, job_id in oargrid_jobids:
jobs.append(gk.sites[site].jobs[job_id])
return jobs | [
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BeyondTheClouds/enoslib | enoslib/infra/enos_g5k/g5k_api_utils.py | grid_destroy_from_name | def grid_destroy_from_name(job_name):
"""Destroy all the jobs with a given name.
Args:
job_name (str): the job name
"""
jobs = grid_reload_from_name(job_name)
for job in jobs:
job.delete()
logger.info("Killing the job (%s, %s)" % (job.site, job.uid)) | python | def grid_destroy_from_name(job_name):
"""Destroy all the jobs with a given name.
Args:
job_name (str): the job name
"""
jobs = grid_reload_from_name(job_name)
for job in jobs:
job.delete()
logger.info("Killing the job (%s, %s)" % (job.site, job.uid)) | [
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BeyondTheClouds/enoslib | enoslib/infra/enos_g5k/g5k_api_utils.py | grid_destroy_from_ids | def grid_destroy_from_ids(oargrid_jobids):
"""Destroy all the jobs with corresponding ids
Args:
oargrid_jobids (list): the ``(site, oar_job_id)`` list of tuple
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jobs = grid_reload_from_ids(oargrid_jobids)
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logger.info("Killing the jobs %s" % oargrid_jobids) | python | def grid_destroy_from_ids(oargrid_jobids):
"""Destroy all the jobs with corresponding ids
Args:
oargrid_jobids (list): the ``(site, oar_job_id)`` list of tuple
identifying the jobs for each site. """
jobs = grid_reload_from_ids(oargrid_jobids)
for job in jobs:
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BeyondTheClouds/enoslib | enoslib/infra/enos_g5k/g5k_api_utils.py | wait_for_jobs | def wait_for_jobs(jobs):
"""Waits for all the jobs to be runnning.
Args:
jobs(list): list of the python-grid5000 jobs to wait for
Raises:
Exception: if one of the job gets in error state.
"""
all_running = False
while not all_running:
all_running = True
time.sleep(5)
for job in jobs:
job.refresh()
scheduled = getattr(job, "scheduled_at", None)
if scheduled is not None:
logger.info("Waiting for %s on %s [%s]" % (job.uid,
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_date2h(scheduled)))
all_running = all_running and job.state == "running"
if job.state == "error":
raise Exception("The job %s is in error state" % job)
logger.info("All jobs are Running !") | python | def wait_for_jobs(jobs):
"""Waits for all the jobs to be runnning.
Args:
jobs(list): list of the python-grid5000 jobs to wait for
Raises:
Exception: if one of the job gets in error state.
"""
all_running = False
while not all_running:
all_running = True
time.sleep(5)
for job in jobs:
job.refresh()
scheduled = getattr(job, "scheduled_at", None)
if scheduled is not None:
logger.info("Waiting for %s on %s [%s]" % (job.uid,
job.site,
_date2h(scheduled)))
all_running = all_running and job.state == "running"
if job.state == "error":
raise Exception("The job %s is in error state" % job)
logger.info("All jobs are Running !") | [
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BeyondTheClouds/enoslib | enoslib/infra/enos_g5k/g5k_api_utils.py | grid_deploy | def grid_deploy(site, nodes, options):
"""Deploy and wait for the deployment to be finished.
Args:
site(str): the site
nodes(list): list of nodes (str) to depoy
options(dict): option of the deployment (refer to the Grid'5000 API
Specifications)
Returns:
tuple of deployed(list), undeployed(list) nodes.
"""
gk = get_api_client()
environment = options.pop("env_name")
options.update(environment=environment)
options.update(nodes=nodes)
key_path = DEFAULT_SSH_KEYFILE
options.update(key=key_path.read_text())
logger.info("Deploying %s with options %s" % (nodes, options))
deployment = gk.sites[site].deployments.create(options)
while deployment.status not in ["terminated", "error"]:
deployment.refresh()
print("Waiting for the end of deployment [%s]" % deployment.uid)
time.sleep(10)
deploy = []
undeploy = []
if deployment.status == "terminated":
deploy = [node for node, v in deployment.result.items()
if v["state"] == "OK"]
undeploy = [node for node, v in deployment.result.items()
if v["state"] == "KO"]
elif deployment.status == "error":
undeploy = nodes
return deploy, undeploy | python | def grid_deploy(site, nodes, options):
"""Deploy and wait for the deployment to be finished.
Args:
site(str): the site
nodes(list): list of nodes (str) to depoy
options(dict): option of the deployment (refer to the Grid'5000 API
Specifications)
Returns:
tuple of deployed(list), undeployed(list) nodes.
"""
gk = get_api_client()
environment = options.pop("env_name")
options.update(environment=environment)
options.update(nodes=nodes)
key_path = DEFAULT_SSH_KEYFILE
options.update(key=key_path.read_text())
logger.info("Deploying %s with options %s" % (nodes, options))
deployment = gk.sites[site].deployments.create(options)
while deployment.status not in ["terminated", "error"]:
deployment.refresh()
print("Waiting for the end of deployment [%s]" % deployment.uid)
time.sleep(10)
deploy = []
undeploy = []
if deployment.status == "terminated":
deploy = [node for node, v in deployment.result.items()
if v["state"] == "OK"]
undeploy = [node for node, v in deployment.result.items()
if v["state"] == "KO"]
elif deployment.status == "error":
undeploy = nodes
return deploy, undeploy | [
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BeyondTheClouds/enoslib | enoslib/infra/enos_g5k/g5k_api_utils.py | set_nodes_vlan | def set_nodes_vlan(site, nodes, interface, vlan_id):
"""Set the interface of the nodes in a specific vlan.
It is assumed that the same interface name is available on the node.
Args:
site(str): site to consider
nodes(list): nodes to consider
interface(str): the network interface to put in the vlan
vlan_id(str): the id of the vlan
"""
def _to_network_address(host):
"""Translate a host to a network address
e.g:
paranoia-20.rennes.grid5000.fr -> paranoia-20-eth2.rennes.grid5000.fr
"""
splitted = host.split('.')
splitted[0] = splitted[0] + "-" + interface
return ".".join(splitted)
gk = get_api_client()
network_addresses = [_to_network_address(n) for n in nodes]
gk.sites[site].vlans[str(vlan_id)].submit({"nodes": network_addresses}) | python | def set_nodes_vlan(site, nodes, interface, vlan_id):
"""Set the interface of the nodes in a specific vlan.
It is assumed that the same interface name is available on the node.
Args:
site(str): site to consider
nodes(list): nodes to consider
interface(str): the network interface to put in the vlan
vlan_id(str): the id of the vlan
"""
def _to_network_address(host):
"""Translate a host to a network address
e.g:
paranoia-20.rennes.grid5000.fr -> paranoia-20-eth2.rennes.grid5000.fr
"""
splitted = host.split('.')
splitted[0] = splitted[0] + "-" + interface
return ".".join(splitted)
gk = get_api_client()
network_addresses = [_to_network_address(n) for n in nodes]
gk.sites[site].vlans[str(vlan_id)].submit({"nodes": network_addresses}) | [
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BeyondTheClouds/enoslib | enoslib/infra/enos_g5k/g5k_api_utils.py | clusters_sites_obj | def clusters_sites_obj(clusters):
"""Get all the corresponding sites of the passed clusters.
Args:
clusters(list): list of string uid of sites (e.g 'rennes')
Return:
dict corresponding to the mapping cluster uid to python-grid5000 site
"""
result = {}
all_clusters = get_all_clusters_sites()
clusters_sites = {c: s for (c, s) in all_clusters.items()
if c in clusters}
for cluster, site in clusters_sites.items():
# here we want the site python-grid5000 site object
result.update({cluster: get_site_obj(site)})
return result | python | def clusters_sites_obj(clusters):
"""Get all the corresponding sites of the passed clusters.
Args:
clusters(list): list of string uid of sites (e.g 'rennes')
Return:
dict corresponding to the mapping cluster uid to python-grid5000 site
"""
result = {}
all_clusters = get_all_clusters_sites()
clusters_sites = {c: s for (c, s) in all_clusters.items()
if c in clusters}
for cluster, site in clusters_sites.items():
# here we want the site python-grid5000 site object
result.update({cluster: get_site_obj(site)})
return result | [
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BeyondTheClouds/enoslib | enoslib/infra/enos_g5k/g5k_api_utils.py | get_all_clusters_sites | def get_all_clusters_sites():
"""Get all the cluster of all the sites.
Returns:
dict corresponding to the mapping cluster uid to python-grid5000 site
"""
result = {}
gk = get_api_client()
sites = gk.sites.list()
for site in sites:
clusters = site.clusters.list()
result.update({c.uid: site.uid for c in clusters})
return result | python | def get_all_clusters_sites():
"""Get all the cluster of all the sites.
Returns:
dict corresponding to the mapping cluster uid to python-grid5000 site
"""
result = {}
gk = get_api_client()
sites = gk.sites.list()
for site in sites:
clusters = site.clusters.list()
result.update({c.uid: site.uid for c in clusters})
return result | [
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BeyondTheClouds/enoslib | enoslib/infra/enos_g5k/g5k_api_utils.py | get_nodes | def get_nodes(cluster):
"""Get all the nodes of a given cluster.
Args:
cluster(string): uid of the cluster (e.g 'rennes')
"""
gk = get_api_client()
site = get_cluster_site(cluster)
return gk.sites[site].clusters[cluster].nodes.list() | python | def get_nodes(cluster):
"""Get all the nodes of a given cluster.
Args:
cluster(string): uid of the cluster (e.g 'rennes')
"""
gk = get_api_client()
site = get_cluster_site(cluster)
return gk.sites[site].clusters[cluster].nodes.list() | [
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BeyondTheClouds/enoslib | enoslib/infra/enos_g5k/g5k_api_utils.py | get_cluster_interfaces | def get_cluster_interfaces(cluster, extra_cond=lambda nic: True):
"""Get the network interfaces names corresponding to a criteria.
Note that the cluster is passed (not the individual node names), thus it is
assumed that all nodes in a cluster have the same interface names same
configuration. In addition to ``extra_cond``, only the mountable and
Ehernet interfaces are returned.
Args:
cluster(str): the cluster to consider
extra_cond(lambda): boolean lambda that takes the nic(dict) as
parameter
"""
nics = get_nics(cluster)
# NOTE(msimonin): Since 05/18 nics on g5k nodes have predictable names but
# the api description keep the legacy name (device key) and the new
# predictable name (key name). The legacy names is still used for api
# request to the vlan endpoint This should be fixed in
# https://intranet.grid5000.fr/bugzilla/show_bug.cgi?id=9272
# When its fixed we should be able to only use the new predictable name.
nics = [(nic['device'], nic['name']) for nic in nics
if nic['mountable']
and nic['interface'] == 'Ethernet'
and not nic['management']
and extra_cond(nic)]
nics = sorted(nics)
return nics | python | def get_cluster_interfaces(cluster, extra_cond=lambda nic: True):
"""Get the network interfaces names corresponding to a criteria.
Note that the cluster is passed (not the individual node names), thus it is
assumed that all nodes in a cluster have the same interface names same
configuration. In addition to ``extra_cond``, only the mountable and
Ehernet interfaces are returned.
Args:
cluster(str): the cluster to consider
extra_cond(lambda): boolean lambda that takes the nic(dict) as
parameter
"""
nics = get_nics(cluster)
# NOTE(msimonin): Since 05/18 nics on g5k nodes have predictable names but
# the api description keep the legacy name (device key) and the new
# predictable name (key name). The legacy names is still used for api
# request to the vlan endpoint This should be fixed in
# https://intranet.grid5000.fr/bugzilla/show_bug.cgi?id=9272
# When its fixed we should be able to only use the new predictable name.
nics = [(nic['device'], nic['name']) for nic in nics
if nic['mountable']
and nic['interface'] == 'Ethernet'
and not nic['management']
and extra_cond(nic)]
nics = sorted(nics)
return nics | [
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BeyondTheClouds/enoslib | enoslib/infra/enos_g5k/g5k_api_utils.py | get_clusters_interfaces | def get_clusters_interfaces(clusters, extra_cond=lambda nic: True):
""" Returns for each cluster the available cluster interfaces
Args:
clusters (str): list of the clusters
extra_cond (lambda): extra predicate to filter network card retrieved
from the API. E.g lambda nic: not nic['mounted'] will retrieve all the
usable network cards that are not mounted by default.
Returns:
dict of cluster with their associated nic names
Examples:
.. code-block:: python
# pseudo code
actual = get_clusters_interfaces(["paravance"])
expected = {"paravance": ["eth0", "eth1"]}
assertDictEquals(expected, actual)
"""
interfaces = {}
for cluster in clusters:
nics = get_cluster_interfaces(cluster, extra_cond=extra_cond)
interfaces.setdefault(cluster, nics)
return interfaces | python | def get_clusters_interfaces(clusters, extra_cond=lambda nic: True):
""" Returns for each cluster the available cluster interfaces
Args:
clusters (str): list of the clusters
extra_cond (lambda): extra predicate to filter network card retrieved
from the API. E.g lambda nic: not nic['mounted'] will retrieve all the
usable network cards that are not mounted by default.
Returns:
dict of cluster with their associated nic names
Examples:
.. code-block:: python
# pseudo code
actual = get_clusters_interfaces(["paravance"])
expected = {"paravance": ["eth0", "eth1"]}
assertDictEquals(expected, actual)
"""
interfaces = {}
for cluster in clusters:
nics = get_cluster_interfaces(cluster, extra_cond=extra_cond)
interfaces.setdefault(cluster, nics)
return interfaces | [
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BeyondTheClouds/enoslib | enoslib/infra/enos_g5k/g5k_api_utils.py | _do_synchronise_jobs | def _do_synchronise_jobs(walltime, machines):
""" This returns a common reservation date for all the jobs.
This reservation date is really only a hint and will be supplied to each
oar server. Without this *common* reservation_date, one oar server can
decide to postpone the start of the job while the other are already
running. But this doens't prevent the start of a job on one site to drift
(e.g because the machines need to be restarted.) But this shouldn't exceed
few minutes.
"""
offset = SYNCHRONISATION_OFFSET
start = time.time() + offset
_t = time.strptime(walltime, "%H:%M:%S")
_walltime = _t.tm_hour * 3600 + _t.tm_min * 60 + _t.tm_sec
# Compute the demand for each cluster
demands = defaultdict(int)
for machine in machines:
cluster = machine["cluster"]
demands[cluster] += machine["nodes"]
# Early leave if only one cluster is there
if len(list(demands.keys())) <= 1:
logger.debug("Only one cluster detected: no synchronisation needed")
return None
clusters = clusters_sites_obj(list(demands.keys()))
# Early leave if only one site is concerned
sites = set(list(clusters.values()))
if len(sites) <= 1:
logger.debug("Only one site detected: no synchronisation needed")
return None
# Test the proposed reservation_date
ok = True
for cluster, nodes in demands.items():
cluster_status = clusters[cluster].status.list()
ok = ok and can_start_on_cluster(cluster_status.nodes,
nodes,
start,
_walltime)
if not ok:
break
if ok:
# The proposed reservation_date fits
logger.info("Reservation_date=%s (%s)" % (_date2h(start), sites))
return start
if start is None:
raise EnosG5kSynchronisationError(sites) | python | def _do_synchronise_jobs(walltime, machines):
""" This returns a common reservation date for all the jobs.
This reservation date is really only a hint and will be supplied to each
oar server. Without this *common* reservation_date, one oar server can
decide to postpone the start of the job while the other are already
running. But this doens't prevent the start of a job on one site to drift
(e.g because the machines need to be restarted.) But this shouldn't exceed
few minutes.
"""
offset = SYNCHRONISATION_OFFSET
start = time.time() + offset
_t = time.strptime(walltime, "%H:%M:%S")
_walltime = _t.tm_hour * 3600 + _t.tm_min * 60 + _t.tm_sec
# Compute the demand for each cluster
demands = defaultdict(int)
for machine in machines:
cluster = machine["cluster"]
demands[cluster] += machine["nodes"]
# Early leave if only one cluster is there
if len(list(demands.keys())) <= 1:
logger.debug("Only one cluster detected: no synchronisation needed")
return None
clusters = clusters_sites_obj(list(demands.keys()))
# Early leave if only one site is concerned
sites = set(list(clusters.values()))
if len(sites) <= 1:
logger.debug("Only one site detected: no synchronisation needed")
return None
# Test the proposed reservation_date
ok = True
for cluster, nodes in demands.items():
cluster_status = clusters[cluster].status.list()
ok = ok and can_start_on_cluster(cluster_status.nodes,
nodes,
start,
_walltime)
if not ok:
break
if ok:
# The proposed reservation_date fits
logger.info("Reservation_date=%s (%s)" % (_date2h(start), sites))
return start
if start is None:
raise EnosG5kSynchronisationError(sites) | [
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volafiled/python-volapi | volapi/handler.py | Handler.add_data | def add_data(self, rawdata):
"""Add data to given room's state"""
for data in rawdata:
try:
item = data[0]
if item[0] == 2:
# Flush messages but we got nothing to flush
continue
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except IndexError:
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try:
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method(data)
except AttributeError:
self._handle_unhandled(target, data)
except IndexError:
LOGGER.warning("Wrongly constructed message received: %r", data)
self.conn.process_queues() | python | def add_data(self, rawdata):
"""Add data to given room's state"""
for data in rawdata:
try:
item = data[0]
if item[0] == 2:
# Flush messages but we got nothing to flush
continue
if item[0] != 0:
warnings.warn(f"Unknown message type '{item[0]}'", Warning)
continue
item = item[1]
# convert target to string because error codes are ints
target = str(item[0])
try:
data = item[1]
except IndexError:
data = dict()
try:
method = getattr(self, self.__head + target)
method(data)
except AttributeError:
self._handle_unhandled(target, data)
except IndexError:
LOGGER.warning("Wrongly constructed message received: %r", data)
self.conn.process_queues() | [
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volafiled/python-volapi | volapi/handler.py | Handler.register_callback | def register_callback(self):
"""Register callback that we will have to wait for"""
cid = str(self.__cid)
self.__cid += 1
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self.__callbacks[cid] = event
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"""Register callback that we will have to wait for"""
cid = str(self.__cid)
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self.__callbacks[cid] = event
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"""Handle lain's callback. Only used with getFileinfo so far"""
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volafiled/python-volapi | volapi/handler.py | Handler._handle_userCount | def _handle_userCount(self, data):
"""Handle user count changes"""
self.room.user_count = data
self.conn.enqueue_data("user_count", self.room.user_count) | python | def _handle_userCount(self, data):
"""Handle user count changes"""
self.room.user_count = data
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volafiled/python-volapi | volapi/handler.py | Handler._handle_userInfo | def _handle_userInfo(self, data):
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self.conn.enqueue_data("user_info", self.room.user_info) | python | def _handle_userInfo(self, data):
"""Handle user information"""
for k, v in data.items():
if k == "nick":
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volafiled/python-volapi | volapi/handler.py | Handler._handle_config | def _handle_config(self, data):
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self.room.config.update(data)
self.conn.enqueue_data("config", data) | python | def _handle_config(self, data):
"""Handle initial config push and config changes"""
self.room.config.update(data)
self.conn.enqueue_data("config", data) | [
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volafiled/python-volapi | volapi/handler.py | Handler._handle_files | def _handle_files(self, data):
"""Handle new files being uploaded"""
initial = data.get("set", False)
files = data["files"]
for f in files:
try:
fobj = File(
self.room,
self.conn,
f[0],
f[1],
type=f[2],
size=f[3],
expire_time=int(f[4]) / 1000,
uploader=f[6].get("nick") or f[6].get("user"),
)
self.room.filedict = fobj.fid, fobj
if not initial:
self.conn.enqueue_data("file", fobj)
except Exception:
import pprint
LOGGER.exception("bad file")
pprint.pprint(f)
if initial:
self.conn.enqueue_data("initial_files", self.room.files) | python | def _handle_files(self, data):
"""Handle new files being uploaded"""
initial = data.get("set", False)
files = data["files"]
for f in files:
try:
fobj = File(
self.room,
self.conn,
f[0],
f[1],
type=f[2],
size=f[3],
expire_time=int(f[4]) / 1000,
uploader=f[6].get("nick") or f[6].get("user"),
)
self.room.filedict = fobj.fid, fobj
if not initial:
self.conn.enqueue_data("file", fobj)
except Exception:
import pprint
LOGGER.exception("bad file")
pprint.pprint(f)
if initial:
self.conn.enqueue_data("initial_files", self.room.files) | [
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volafiled/python-volapi | volapi/handler.py | Handler._handle_delete_file | def _handle_delete_file(self, data):
"""Handle files being removed"""
file = self.room.filedict.get(data)
if file:
self.room.filedict = data, None
self.conn.enqueue_data("delete_file", file) | python | def _handle_delete_file(self, data):
"""Handle files being removed"""
file = self.room.filedict.get(data)
if file:
self.room.filedict = data, None
self.conn.enqueue_data("delete_file", file) | [
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volafiled/python-volapi | volapi/handler.py | Handler._handle_chat | def _handle_chat(self, data):
"""Handle chat messages"""
self.conn.enqueue_data(
"chat", ChatMessage.from_data(self.room, self.conn, data)
) | python | def _handle_chat(self, data):
"""Handle chat messages"""
self.conn.enqueue_data(
"chat", ChatMessage.from_data(self.room, self.conn, data)
) | [
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] | 5f0bc03dbde703264ac6ed494e2050761f688a3e | https://github.com/volafiled/python-volapi/blob/5f0bc03dbde703264ac6ed494e2050761f688a3e/volapi/handler.py#L187-L192 | train | 49,197 |
volafiled/python-volapi | volapi/handler.py | Handler._handle_changed_config | def _handle_changed_config(self, change):
"""Handle configuration changes"""
key, value = change.get("key"), change.get("value")
self.room.config.update({key: value})
self.conn.enqueue_data("config", self.room.config) | python | def _handle_changed_config(self, change):
"""Handle configuration changes"""
key, value = change.get("key"), change.get("value")
self.room.config.update({key: value})
self.conn.enqueue_data("config", self.room.config) | [
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] | 5f0bc03dbde703264ac6ed494e2050761f688a3e | https://github.com/volafiled/python-volapi/blob/5f0bc03dbde703264ac6ed494e2050761f688a3e/volapi/handler.py#L194-L199 | train | 49,198 |
volafiled/python-volapi | volapi/handler.py | Handler._handle_chat_name | def _handle_chat_name(self, data):
"""Handle user name changes"""
self.room.user.nick = data
self.conn.enqueue_data("user", self.room.user) | python | def _handle_chat_name(self, data):
"""Handle user name changes"""
self.room.user.nick = data
self.conn.enqueue_data("user", self.room.user) | [
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] | 5f0bc03dbde703264ac6ed494e2050761f688a3e | https://github.com/volafiled/python-volapi/blob/5f0bc03dbde703264ac6ed494e2050761f688a3e/volapi/handler.py#L201-L205 | train | 49,199 |
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