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Clinical-Genomics/trailblazer | trailblazer/mip/miplog.py | job_ids | def job_ids(log_stream):
"""Grep out all lines with scancel example."""
id_rows = [line for line in log_stream if 'scancel' in line]
jobs = [id_row.strip()[-7:-1] for id_row in id_rows]
return jobs | python | def job_ids(log_stream):
"""Grep out all lines with scancel example."""
id_rows = [line for line in log_stream if 'scancel' in line]
jobs = [id_row.strip()[-7:-1] for id_row in id_rows]
return jobs | [
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ARMmbed/autoversion | src/auto_version/config.py | get_or_create_config | def get_or_create_config(path, config):
"""Using TOML format, load config from given path, or write out example based on defaults"""
if os.path.isfile(path):
with open(path) as fh:
_LOG.debug("loading config from %s", os.path.abspath(path))
config._inflate(toml.load(fh))
else:
try:
os.makedirs(os.path.dirname(path))
except OSError:
pass
with open(path, "w") as fh:
toml.dump(config._deflate(), fh) | python | def get_or_create_config(path, config):
"""Using TOML format, load config from given path, or write out example based on defaults"""
if os.path.isfile(path):
with open(path) as fh:
_LOG.debug("loading config from %s", os.path.abspath(path))
config._inflate(toml.load(fh))
else:
try:
os.makedirs(os.path.dirname(path))
except OSError:
pass
with open(path, "w") as fh:
toml.dump(config._deflate(), fh) | [
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ARMmbed/autoversion | src/auto_version/config.py | AutoVersionConfig._deflate | def _deflate(cls):
"""Prepare for serialisation - returns a dictionary"""
data = {k: v for k, v in vars(cls).items() if not k.startswith("_")}
return {Constants.CONFIG_KEY: data} | python | def _deflate(cls):
"""Prepare for serialisation - returns a dictionary"""
data = {k: v for k, v in vars(cls).items() if not k.startswith("_")}
return {Constants.CONFIG_KEY: data} | [
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ARMmbed/autoversion | src/auto_version/config.py | AutoVersionConfig._inflate | def _inflate(cls, data):
"""Update config by deserialising input dictionary"""
for k, v in data[Constants.CONFIG_KEY].items():
setattr(cls, k, v)
return cls._deflate() | python | def _inflate(cls, data):
"""Update config by deserialising input dictionary"""
for k, v in data[Constants.CONFIG_KEY].items():
setattr(cls, k, v)
return cls._deflate() | [
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fudge-py/fudge | fudge/patcher.py | with_patched_object | def with_patched_object(obj, attr_name, patched_value):
"""Decorator that patches an object before the decorated method
is called and restores it afterwards.
This is a wrapper around :func:`fudge.patcher.patch_object`
Example::
>>> from fudge import with_patched_object
>>> class Session:
... state = 'clean'
...
>>> @with_patched_object(Session, "state", "dirty")
... def test():
... print Session.state
...
>>> test()
dirty
>>> print Session.state
clean
"""
def patcher(method):
@wraps(method)
def method_call(*m_args, **m_kw):
patched_obj = patch_object(obj, attr_name, patched_value)
try:
return method(*m_args, **m_kw)
finally:
patched_obj.restore()
return method_call
return patcher | python | def with_patched_object(obj, attr_name, patched_value):
"""Decorator that patches an object before the decorated method
is called and restores it afterwards.
This is a wrapper around :func:`fudge.patcher.patch_object`
Example::
>>> from fudge import with_patched_object
>>> class Session:
... state = 'clean'
...
>>> @with_patched_object(Session, "state", "dirty")
... def test():
... print Session.state
...
>>> test()
dirty
>>> print Session.state
clean
"""
def patcher(method):
@wraps(method)
def method_call(*m_args, **m_kw):
patched_obj = patch_object(obj, attr_name, patched_value)
try:
return method(*m_args, **m_kw)
finally:
patched_obj.restore()
return method_call
return patcher | [
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This is a wrapper around :func:`fudge.patcher.patch_object`
Example::
>>> from fudge import with_patched_object
>>> class Session:
... state = 'clean'
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fudge-py/fudge | fudge/patcher.py | PatchHandler.patch | def patch(self, patched_value):
"""Set a new value for the attribute of the object."""
try:
if self.getter:
setattr(self.getter_class, self.attr_name, patched_value)
else:
setattr(self.orig_object, self.attr_name, patched_value)
except TypeError:
# Workaround for patching builtin objects:
proxy_name = 'fudge_proxy_%s_%s_%s' % (
self.orig_object.__module__,
self.orig_object.__name__,
patched_value.__class__.__name__
)
self.proxy_object = type(proxy_name, (self.orig_object,),
{self.attr_name: patched_value})
mod = sys.modules[self.orig_object.__module__]
setattr(mod, self.orig_object.__name__, self.proxy_object) | python | def patch(self, patched_value):
"""Set a new value for the attribute of the object."""
try:
if self.getter:
setattr(self.getter_class, self.attr_name, patched_value)
else:
setattr(self.orig_object, self.attr_name, patched_value)
except TypeError:
# Workaround for patching builtin objects:
proxy_name = 'fudge_proxy_%s_%s_%s' % (
self.orig_object.__module__,
self.orig_object.__name__,
patched_value.__class__.__name__
)
self.proxy_object = type(proxy_name, (self.orig_object,),
{self.attr_name: patched_value})
mod = sys.modules[self.orig_object.__module__]
setattr(mod, self.orig_object.__name__, self.proxy_object) | [
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fudge-py/fudge | fudge/patcher.py | PatchHandler.restore | def restore(self):
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self.orig_object) | python | def restore(self):
"""Restore the saved value for the attribute of the object."""
if self.proxy_object is None:
if self.getter:
setattr(self.getter_class, self.attr_name, self.getter)
elif self.is_local:
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# Was not a local, safe to delete:
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setattr(sys.modules[self.orig_object.__module__],
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Clinical-Genomics/trailblazer | trailblazer/mip/files.py | parse_config | def parse_config(data: dict) -> dict:
"""Parse MIP config file.
Args:
data (dict): raw YAML input from MIP analysis config file
Returns:
dict: parsed data
"""
return {
'email': data.get('email'),
'family': data['family_id'],
'samples': [{
'id': sample_id,
'type': analysis_type,
} for sample_id, analysis_type in data['analysis_type'].items()],
'config_path': data['config_file_analysis'],
'is_dryrun': True if 'dry_run_all' in data else False,
'log_path': data['log_file'],
'out_dir': data['outdata_dir'],
'priority': data['slurm_quality_of_service'],
'sampleinfo_path': data['sample_info_file'],
} | python | def parse_config(data: dict) -> dict:
"""Parse MIP config file.
Args:
data (dict): raw YAML input from MIP analysis config file
Returns:
dict: parsed data
"""
return {
'email': data.get('email'),
'family': data['family_id'],
'samples': [{
'id': sample_id,
'type': analysis_type,
} for sample_id, analysis_type in data['analysis_type'].items()],
'config_path': data['config_file_analysis'],
'is_dryrun': True if 'dry_run_all' in data else False,
'log_path': data['log_file'],
'out_dir': data['outdata_dir'],
'priority': data['slurm_quality_of_service'],
'sampleinfo_path': data['sample_info_file'],
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Clinical-Genomics/trailblazer | trailblazer/mip/files.py | parse_sampleinfo | def parse_sampleinfo(data: dict) -> dict:
"""Parse MIP sample info file.
Args:
data (dict): raw YAML input from MIP qc sample info file
Returns:
dict: parsed data
"""
genome_build = data['human_genome_build']
genome_build_str = f"{genome_build['source']}{genome_build['version']}"
if 'svdb' in data['program']:
svdb_outpath = (f"{data['program']['svdb']['path']}")
else:
svdb_outpath = ''
outdata = {
'date': data['analysis_date'],
'family': data['family'],
'genome_build': genome_build_str,
'rank_model_version': data['program']['genmod']['rank_model']['version'],
'is_finished': True if data['analysisrunstatus'] == 'finished' else False,
'pedigree_path': data['pedigree_minimal'],
'peddy': {
'ped': (data['program']['peddy']['peddy']['path'] if
'peddy' in data['program'] else None),
'ped_check': (data['program']['peddy']['ped_check']['path'] if
'peddy' in data['program'] else None),
'sex_check': (data['program']['peddy']['sex_check']['path'] if
'peddy' in data['program'] else None),
},
'qcmetrics_path': data['program']['qccollect']['path'],
'samples': [],
'snv': {
'bcf': data['most_complete_bcf']['path'],
'clinical_vcf': data['vcf_binary_file']['clinical']['path'],
'gbcf': data['gbcf_file']['path'],
'research_vcf': data['vcf_binary_file']['research']['path'],
},
'svdb_outpath': svdb_outpath,
'sv': {
'bcf': data.get('sv_bcf_file', {}).get('path'),
'clinical_vcf': (data['sv_vcf_binary_file']['clinical']['path'] if
'sv_vcf_binary_file' in data else None),
'merged': svdb_outpath,
'research_vcf': (data['sv_vcf_binary_file']['research']['path'] if
'sv_vcf_binary_file' in data else None),
},
'version': data['mip_version'],
}
for sample_id, sample_data in data['sample'].items():
sample = {
'id': sample_id,
'bam': sample_data['most_complete_bam']['path'],
'sambamba': list(sample_data['program']['sambamba_depth'].values())[0]['path'],
'sex': sample_data['sex'],
# subsample mt is only for wgs data
'subsample_mt': (list(sample_data['program']['samtools_subsample_mt'].values())[0]['path'] if
'samtools_subsample_mt' in sample_data['program'] else None),
'vcf2cytosure': list(sample_data['program']['vcf2cytosure'].values())[0]['path'],
}
chanjo_sexcheck = list(sample_data['program']['chanjo_sexcheck'].values())[0]
sample['chanjo_sexcheck'] = chanjo_sexcheck['path']
outdata['samples'].append(sample)
return outdata | python | def parse_sampleinfo(data: dict) -> dict:
"""Parse MIP sample info file.
Args:
data (dict): raw YAML input from MIP qc sample info file
Returns:
dict: parsed data
"""
genome_build = data['human_genome_build']
genome_build_str = f"{genome_build['source']}{genome_build['version']}"
if 'svdb' in data['program']:
svdb_outpath = (f"{data['program']['svdb']['path']}")
else:
svdb_outpath = ''
outdata = {
'date': data['analysis_date'],
'family': data['family'],
'genome_build': genome_build_str,
'rank_model_version': data['program']['genmod']['rank_model']['version'],
'is_finished': True if data['analysisrunstatus'] == 'finished' else False,
'pedigree_path': data['pedigree_minimal'],
'peddy': {
'ped': (data['program']['peddy']['peddy']['path'] if
'peddy' in data['program'] else None),
'ped_check': (data['program']['peddy']['ped_check']['path'] if
'peddy' in data['program'] else None),
'sex_check': (data['program']['peddy']['sex_check']['path'] if
'peddy' in data['program'] else None),
},
'qcmetrics_path': data['program']['qccollect']['path'],
'samples': [],
'snv': {
'bcf': data['most_complete_bcf']['path'],
'clinical_vcf': data['vcf_binary_file']['clinical']['path'],
'gbcf': data['gbcf_file']['path'],
'research_vcf': data['vcf_binary_file']['research']['path'],
},
'svdb_outpath': svdb_outpath,
'sv': {
'bcf': data.get('sv_bcf_file', {}).get('path'),
'clinical_vcf': (data['sv_vcf_binary_file']['clinical']['path'] if
'sv_vcf_binary_file' in data else None),
'merged': svdb_outpath,
'research_vcf': (data['sv_vcf_binary_file']['research']['path'] if
'sv_vcf_binary_file' in data else None),
},
'version': data['mip_version'],
}
for sample_id, sample_data in data['sample'].items():
sample = {
'id': sample_id,
'bam': sample_data['most_complete_bam']['path'],
'sambamba': list(sample_data['program']['sambamba_depth'].values())[0]['path'],
'sex': sample_data['sex'],
# subsample mt is only for wgs data
'subsample_mt': (list(sample_data['program']['samtools_subsample_mt'].values())[0]['path'] if
'samtools_subsample_mt' in sample_data['program'] else None),
'vcf2cytosure': list(sample_data['program']['vcf2cytosure'].values())[0]['path'],
}
chanjo_sexcheck = list(sample_data['program']['chanjo_sexcheck'].values())[0]
sample['chanjo_sexcheck'] = chanjo_sexcheck['path']
outdata['samples'].append(sample)
return outdata | [
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Clinical-Genomics/trailblazer | trailblazer/mip/files.py | parse_peddy_sexcheck | def parse_peddy_sexcheck(handle: TextIO):
"""Parse Peddy sexcheck output."""
data = {}
samples = csv.DictReader(handle)
for sample in samples:
data[sample['sample_id']] = {
'predicted_sex': sample['predicted_sex'],
'het_ratio': float(sample['het_ratio']),
'error': True if sample['error'] == 'True' else False,
}
return data | python | def parse_peddy_sexcheck(handle: TextIO):
"""Parse Peddy sexcheck output."""
data = {}
samples = csv.DictReader(handle)
for sample in samples:
data[sample['sample_id']] = {
'predicted_sex': sample['predicted_sex'],
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return data | [
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Clinical-Genomics/trailblazer | trailblazer/mip/files.py | parse_chanjo_sexcheck | def parse_chanjo_sexcheck(handle: TextIO):
"""Parse Chanjo sex-check output."""
samples = csv.DictReader(handle, delimiter='\t')
for sample in samples:
return {
'predicted_sex': sample['sex'],
'x_coverage': float(sample['#X_coverage']),
'y_coverage': float(sample['Y_coverage']),
} | python | def parse_chanjo_sexcheck(handle: TextIO):
"""Parse Chanjo sex-check output."""
samples = csv.DictReader(handle, delimiter='\t')
for sample in samples:
return {
'predicted_sex': sample['sex'],
'x_coverage': float(sample['#X_coverage']),
'y_coverage': float(sample['Y_coverage']),
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ARMmbed/autoversion | src/auto_version/cli.py | get_cli | def get_cli():
"""Load cli options"""
parser = argparse.ArgumentParser(
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parser.add_argument(
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)
parser.add_argument(
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help="Locks the SemVer string. "
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)
parser.add_argument(
"--release",
action="store_true",
default=False,
help="Marks as a release build, which flags the build as released.",
)
parser.add_argument(
"--version",
action="store_true",
default=False,
help="Prints the version of auto_version itself (self-version).",
)
parser.add_argument("--config", help="Configuration file path.")
parser.add_argument(
"-v",
"--verbosity",
action="count",
default=0,
help="increase output verbosity. " "can be specified multiple times",
)
return parser.parse_known_args() | python | def get_cli():
"""Load cli options"""
parser = argparse.ArgumentParser(
prog="auto_version",
description="auto version v%s: a tool to control version numbers" % __version__,
)
parser.add_argument(
"--target",
action="append",
default=[],
help="Files containing version info. "
"Assumes unique variable names between files. (default: %s)."
% (config.targets,),
)
parser.add_argument(
"--bump",
choices=SemVerSigFig,
help="Bumps the specified part of SemVer string. "
"Use this locally to correctly modify the version file.",
)
parser.add_argument(
"--news",
"--file-triggers",
action="store_true",
dest="file_triggers",
help="Detects need to bump based on presence of files (as specified in config).",
)
parser.add_argument(
"--set",
help="Set the SemVer string. Use this locally to set the project version explicitly.",
)
parser.add_argument(
"--set-patch-count",
action="store_true",
help="Sets the patch number to the commit count.",
)
parser.add_argument(
"--lock",
action="store_true",
help="Locks the SemVer string. "
"Lock will remain for another call to autoversion before being cleared.",
)
parser.add_argument(
"--release",
action="store_true",
default=False,
help="Marks as a release build, which flags the build as released.",
)
parser.add_argument(
"--version",
action="store_true",
default=False,
help="Prints the version of auto_version itself (self-version).",
)
parser.add_argument("--config", help="Configuration file path.")
parser.add_argument(
"-v",
"--verbosity",
action="count",
default=0,
help="increase output verbosity. " "can be specified multiple times",
)
return parser.parse_known_args() | [
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bskinn/stdio-mgr | src/stdio_mgr/stdio_mgr.py | stdio_mgr | def stdio_mgr(in_str=""):
r"""Subsitute temporary text buffers for `stdio` in a managed context.
Context manager.
Substitutes empty :cls:`~io.StringIO`\ s for
:cls:`sys.stdout` and :cls:`sys.stderr`,
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"""
old_stdin = sys.stdin
old_stdout = sys.stdout
old_stderr = sys.stderr
new_stdout = StringIO()
new_stderr = StringIO()
new_stdin = TeeStdin(new_stdout, in_str)
sys.stdin = new_stdin
sys.stdout = new_stdout
sys.stderr = new_stderr
yield new_stdin, new_stdout, new_stderr
sys.stdin = old_stdin
sys.stdout = old_stdout
sys.stderr = old_stderr
new_stdin.close()
new_stdout.close()
new_stderr.close() | python | def stdio_mgr(in_str=""):
r"""Subsitute temporary text buffers for `stdio` in a managed context.
Context manager.
Substitutes empty :cls:`~io.StringIO`\ s for
:cls:`sys.stdout` and :cls:`sys.stderr`,
and a :cls:`TeeStdin` for :cls:`sys.stdin` within the managed context.
Upon exiting the context, the original stream objects are restored
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Parameters
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|str| *(optional)* -- Initialization text for
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Default is an empty string.
Yields
------
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:cls:`TeeStdin` -- Temporary stream for `stdin`.
out_
:cls:`~io.StringIO` -- Temporary stream for `stdout`,
initially empty.
err_
:cls:`~io.StringIO` -- Temporary stream for `stderr`,
initially empty.
"""
old_stdin = sys.stdin
old_stdout = sys.stdout
old_stderr = sys.stderr
new_stdout = StringIO()
new_stderr = StringIO()
new_stdin = TeeStdin(new_stdout, in_str)
sys.stdin = new_stdin
sys.stdout = new_stdout
sys.stderr = new_stderr
yield new_stdin, new_stdout, new_stderr
sys.stdin = old_stdin
sys.stdout = old_stdout
sys.stderr = old_stderr
new_stdin.close()
new_stdout.close()
new_stderr.close() | [
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andrewda/frc-livescore | livescore/simpleocr_utils/opencv_utils.py | draw_segments | def draw_segments(image, segments, color=(255, 0, 0), line_width=1):
"""draws segments on image"""
for segment in segments:
x, y, w, h = segment
cv2.rectangle(image, (x, y), (x + w, y + h), color, line_width) | python | def draw_segments(image, segments, color=(255, 0, 0), line_width=1):
"""draws segments on image"""
for segment in segments:
x, y, w, h = segment
cv2.rectangle(image, (x, y), (x + w, y + h), color, line_width) | [
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andrewda/frc-livescore | livescore/simpleocr_utils/opencv_utils.py | draw_lines | def draw_lines(image, ys, color=(255, 0, 0), line_width=1):
"""draws horizontal lines"""
for y in ys:
cv2.line(image, (0, y), (image.shape[1], y), color, line_width) | python | def draw_lines(image, ys, color=(255, 0, 0), line_width=1):
"""draws horizontal lines"""
for y in ys:
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Clinical-Genomics/trailblazer | trailblazer/mip/sacct.py | time_to_sec | def time_to_sec(time_str: str) -> int:
"""Convert time in string format to seconds.
Skipping seconds since sometimes the last column is truncated
for entries where >10 days.
"""
total_sec = 0
if '-' in time_str:
# parse out days
days, time_str = time_str.split('-')
total_sec += (int(days) * 24 * 60 * 60)
# parse out the hours and mins (skip seconds)
hours_min_raw = time_str.split(':')[:-1]
time_parts = [int(round(float(val))) for val in hours_min_raw]
total_sec += time_parts[-1] * 60 # minutes
if len(time_parts) > 1:
total_sec += time_parts[-2] * 60 * 60 # hours
return total_sec | python | def time_to_sec(time_str: str) -> int:
"""Convert time in string format to seconds.
Skipping seconds since sometimes the last column is truncated
for entries where >10 days.
"""
total_sec = 0
if '-' in time_str:
# parse out days
days, time_str = time_str.split('-')
total_sec += (int(days) * 24 * 60 * 60)
# parse out the hours and mins (skip seconds)
hours_min_raw = time_str.split(':')[:-1]
time_parts = [int(round(float(val))) for val in hours_min_raw]
total_sec += time_parts[-1] * 60 # minutes
if len(time_parts) > 1:
total_sec += time_parts[-2] * 60 * 60 # hours
return total_sec | [
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Clinical-Genomics/trailblazer | trailblazer/mip/sacct.py | convert_job | def convert_job(row: list) -> dict:
"""Convert sacct row to dict."""
state = row[-2]
start_time_raw = row[-4]
end_time_raw = row[-3]
if state not in ('PENDING', 'CANCELLED'):
start_time = datetime.strptime(start_time_raw, '%Y-%m-%dT%H:%M:%S')
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end_time = datetime.strptime(end_time_raw, '%Y-%m-%dT%H:%M:%S')
else:
end_time = None
else:
start_time = end_time = None
# parse name of job
job_name = row[1]
step_name, step_context = job_name.rstrip('_BOTH').rstrip('_SV').rsplit('_', 1)
return {
'id': int(row[0]),
'name': job_name,
'step': step_name,
'context': step_context,
'state': state,
'start': start_time,
'end': end_time,
'elapsed': time_to_sec(row[-5]),
'cpu': time_to_sec(row[-6]),
'is_completed': state == 'COMPLETED',
} | python | def convert_job(row: list) -> dict:
"""Convert sacct row to dict."""
state = row[-2]
start_time_raw = row[-4]
end_time_raw = row[-3]
if state not in ('PENDING', 'CANCELLED'):
start_time = datetime.strptime(start_time_raw, '%Y-%m-%dT%H:%M:%S')
if state != 'RUNNING':
end_time = datetime.strptime(end_time_raw, '%Y-%m-%dT%H:%M:%S')
else:
end_time = None
else:
start_time = end_time = None
# parse name of job
job_name = row[1]
step_name, step_context = job_name.rstrip('_BOTH').rstrip('_SV').rsplit('_', 1)
return {
'id': int(row[0]),
'name': job_name,
'step': step_name,
'context': step_context,
'state': state,
'start': start_time,
'end': end_time,
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'cpu': time_to_sec(row[-6]),
'is_completed': state == 'COMPLETED',
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Clinical-Genomics/trailblazer | trailblazer/mip/sacct.py | parse_sacct | def parse_sacct(sacct_stream):
"""Parse out information from sacct status output."""
rows = (line.split() for line in sacct_stream)
# filter rows that begin with a SLURM job id
relevant_rows = (row for row in rows if row[0].isdigit())
jobs = [convert_job(row) for row in relevant_rows]
return jobs | python | def parse_sacct(sacct_stream):
"""Parse out information from sacct status output."""
rows = (line.split() for line in sacct_stream)
# filter rows that begin with a SLURM job id
relevant_rows = (row for row in rows if row[0].isdigit())
jobs = [convert_job(row) for row in relevant_rows]
return jobs | [
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Clinical-Genomics/trailblazer | trailblazer/mip/sacct.py | filter_jobs | def filter_jobs(sacct_jobs, failed=True):
"""Filter jobs that have a FAILED etc. status."""
categories = FAILED_CATEGORIES if failed else NORMAL_CATEGORIES
filtered_jobs = [job for job in sacct_jobs if job['state'] in categories]
return filtered_jobs | python | def filter_jobs(sacct_jobs, failed=True):
"""Filter jobs that have a FAILED etc. status."""
categories = FAILED_CATEGORIES if failed else NORMAL_CATEGORIES
filtered_jobs = [job for job in sacct_jobs if job['state'] in categories]
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andrewda/frc-livescore | livescore/simpleocr_utils/segmentation_aux.py | guess_segments_lines | def guess_segments_lines(segments, lines, nearline_tolerance=5.0):
"""
given segments, outputs a array of line numbers, or -1 if it
doesn't belong to any
"""
ys = segments[:, 1]
closeness = numpy.abs(numpy.subtract.outer(ys, lines)) # each row a y, each collumn a distance to each line
line_of_y = numpy.argmin(closeness, axis=1)
distance = numpy.min(closeness, axis=1)
bad = distance > numpy.mean(distance) + nearline_tolerance * numpy.std(distance)
line_of_y[bad] = -1
return line_of_y | python | def guess_segments_lines(segments, lines, nearline_tolerance=5.0):
"""
given segments, outputs a array of line numbers, or -1 if it
doesn't belong to any
"""
ys = segments[:, 1]
closeness = numpy.abs(numpy.subtract.outer(ys, lines)) # each row a y, each collumn a distance to each line
line_of_y = numpy.argmin(closeness, axis=1)
distance = numpy.min(closeness, axis=1)
bad = distance > numpy.mean(distance) + nearline_tolerance * numpy.std(distance)
line_of_y[bad] = -1
return line_of_y | [
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andrewda/frc-livescore | livescore/simpleocr_utils/segmentation_aux.py | SegmentOrderer._process | def _process(self, segments):
"""sort segments in read order - left to right, up to down"""
# sort_f= lambda r: max_line_width*(r[1]/max_line_height)+r[0]
# segments= sorted(segments, key=sort_f)
# segments= segments_to_numpy( segments )
# return segments
mlh, mlw = self.max_line_height, self.max_line_width
s = segments.astype(numpy.uint32) # prevent overflows
order = mlw * (s[:, 1] // mlh) + s[:, 0]
sort_order = numpy.argsort(order)
return segments[sort_order] | python | def _process(self, segments):
"""sort segments in read order - left to right, up to down"""
# sort_f= lambda r: max_line_width*(r[1]/max_line_height)+r[0]
# segments= sorted(segments, key=sort_f)
# segments= segments_to_numpy( segments )
# return segments
mlh, mlw = self.max_line_height, self.max_line_width
s = segments.astype(numpy.uint32) # prevent overflows
order = mlw * (s[:, 1] // mlh) + s[:, 0]
sort_order = numpy.argsort(order)
return segments[sort_order] | [
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andrewda/frc-livescore | livescore/simpleocr_utils/segmentation_aux.py | LineFinder._guess_lines | def _guess_lines(ys, max_lines=50, confidence_minimum=0.0):
"""guesses and returns text inter-line distance, number of lines, y_position of first line"""
ys = ys.astype(numpy.float32)
compactness_list, means_list, diffs, deviations = [], [], [], []
start_n = 1
for k in range(start_n, min(len(ys), max_lines)):
compactness, classified_points, means = cv2.kmeans(data=ys, K=k, bestLabels=None, criteria=(
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means = numpy.sort(means, axis=0)
means_list.append(means)
compactness_list.append(compactness)
if k < 3:
tmp1 = [1, 2, 500, 550] # forge data for bad clusters
else:
# calculate the center of each cluster. Assuming lines are equally spaced...
tmp1 = numpy.diff(means, axis=0) # diff will be equal or very similar
tmp2 = numpy.std(tmp1) / numpy.mean(means) # so variance is minimal
tmp3 = numpy.sum((tmp1 - numpy.mean(tmp1)) ** 2) # root mean square deviation, more sensitive than std
diffs.append(tmp1)
deviations.append(tmp3)
compactness_list = numpy.diff(
numpy.log(numpy.array(compactness_list) + 0.01)) # sum small amount to avoid log(0)
deviations = numpy.array(deviations[1:])
deviations[0] = numpy.mean(deviations[1:])
compactness_list = (compactness_list - numpy.mean(compactness_list)) / numpy.std(compactness_list)
deviations = (deviations - numpy.mean(deviations)) / numpy.std(deviations)
aglomerated_metric = 0.1 * compactness_list + 0.9 * deviations
i = numpy.argmin(aglomerated_metric) + 1
lines = means_list[i]
# calculate confidence
betterness = numpy.sort(aglomerated_metric, axis=0)
confidence = (betterness[1] - betterness[0]) / (betterness[2] - betterness[1])
if confidence < confidence_minimum:
raise Exception("low confidence")
return lines | python | def _guess_lines(ys, max_lines=50, confidence_minimum=0.0):
"""guesses and returns text inter-line distance, number of lines, y_position of first line"""
ys = ys.astype(numpy.float32)
compactness_list, means_list, diffs, deviations = [], [], [], []
start_n = 1
for k in range(start_n, min(len(ys), max_lines)):
compactness, classified_points, means = cv2.kmeans(data=ys, K=k, bestLabels=None, criteria=(
cv2.TERM_CRITERIA_EPS | cv2.TERM_CRITERIA_MAX_ITER, 1, 10), attempts=2, flags=cv2.KMEANS_PP_CENTERS)
means = numpy.sort(means, axis=0)
means_list.append(means)
compactness_list.append(compactness)
if k < 3:
tmp1 = [1, 2, 500, 550] # forge data for bad clusters
else:
# calculate the center of each cluster. Assuming lines are equally spaced...
tmp1 = numpy.diff(means, axis=0) # diff will be equal or very similar
tmp2 = numpy.std(tmp1) / numpy.mean(means) # so variance is minimal
tmp3 = numpy.sum((tmp1 - numpy.mean(tmp1)) ** 2) # root mean square deviation, more sensitive than std
diffs.append(tmp1)
deviations.append(tmp3)
compactness_list = numpy.diff(
numpy.log(numpy.array(compactness_list) + 0.01)) # sum small amount to avoid log(0)
deviations = numpy.array(deviations[1:])
deviations[0] = numpy.mean(deviations[1:])
compactness_list = (compactness_list - numpy.mean(compactness_list)) / numpy.std(compactness_list)
deviations = (deviations - numpy.mean(deviations)) / numpy.std(deviations)
aglomerated_metric = 0.1 * compactness_list + 0.9 * deviations
i = numpy.argmin(aglomerated_metric) + 1
lines = means_list[i]
# calculate confidence
betterness = numpy.sort(aglomerated_metric, axis=0)
confidence = (betterness[1] - betterness[0]) / (betterness[2] - betterness[1])
if confidence < confidence_minimum:
raise Exception("low confidence")
return lines | [
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pytroll/posttroll | posttroll/message_broadcaster.py | MessageBroadcaster._run | def _run(self):
"""Broadcasts forever.
"""
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network_fail = False
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self._sender.close() | python | def _run(self):
"""Broadcasts forever.
"""
self._is_running = True
network_fail = False
try:
while self._do_run:
try:
if network_fail is True:
LOGGER.info("Network connection re-established!")
network_fail = False
self._sender(self._message)
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network_fail = True
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contentful-labs/contentful.py | contentful/cda/serialization.py | ResourceFactory.from_json | def from_json(self, json):
"""Create resource out of JSON data.
:param json: JSON dict.
:return: Resource with a type defined by the given JSON data.
"""
res_type = json['sys']['type']
if ResourceType.Array.value == res_type:
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"""Create resource out of JSON data.
:param json: JSON dict.
:return: Resource with a type defined by the given JSON data.
"""
res_type = json['sys']['type']
if ResourceType.Array.value == res_type:
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contentful-labs/contentful.py | contentful/cda/serialization.py | ResourceFactory.process_array_items | def process_array_items(self, array, json):
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:param array: Array resource.
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"""Iterate through all `items` and create a resource for each.
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:param array: Array resource.
:param json: Raw JSON dictionary.
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contentful-labs/contentful.py | contentful/cda/serialization.py | ResourceFactory.process_array_includes | def process_array_includes(self, array, json):
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:param array: Array resource.
:param json: Raw JSON dictionary.
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"""Iterate through all `includes` and create a resource for every item.
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:param array: Array resource.
:param json: Raw JSON dictionary.
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fudge-py/fudge | fudge/__init__.py | Registry.clear_calls | def clear_calls(self):
"""Clears out any calls that were made on previously
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"""
self.clear_actual_calls()
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call_order.reset_calls() | python | def clear_calls(self):
"""Clears out any calls that were made on previously
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"""
self.clear_actual_calls()
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"""Ensure all expected calls were called,
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You do not need to use this directly. Use fudge.verify()
"""
try:
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fudge-py/fudge | fudge/__init__.py | ExpectedCallOrder.assert_order_met | def assert_order_met(self, finalize=False):
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raise AssertionError(msg) | python | def assert_order_met(self, finalize=False):
"""assert that calls have been made in the right order."""
error = None
actual_call_len = len(self._actual_calls)
expected_call_len = len(self._call_order)
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fudge-py/fudge | fudge/__init__.py | Fake.expects_call | def expects_call(self):
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>>> fudge.clear_calls()
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...
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.. doctest::
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>>> fudge.clear_calls()
This is useful for when you stub out a function
as opposed to a class. For example::
>>> import fudge
>>> remove = fudge.Fake('os.remove').expects_call()
>>> fudge.verify()
Traceback (most recent call last):
...
AssertionError: fake:os.remove() was not called
.. doctest::
:hide:
>>> fudge.clear_expectations()
"""
self._callable = ExpectedCall(self, call_name=self._name,
callable=True)
return self | [
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.. doctest::
:hide:
>>> import fudge
>>> fudge.clear_expectations()
>>> fudge.clear_calls()
This is useful for when you stub out a function
as opposed to a class. For example::
>>> import fudge
>>> remove = fudge.Fake('os.remove').expects_call()
>>> fudge.verify()
Traceback (most recent call last):
...
AssertionError: fake:os.remove() was not called
.. doctest::
:hide:
>>> fudge.clear_expectations() | [
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fudge-py/fudge | fudge/__init__.py | Fake.is_callable | def is_callable(self):
"""The fake can be called.
This is useful for when you stub out a function
as opposed to a class. For example::
>>> import fudge
>>> remove = Fake('os.remove').is_callable()
>>> remove('some/path')
"""
self._callable = Call(self, call_name=self._name, callable=True)
return self | python | def is_callable(self):
"""The fake can be called.
This is useful for when you stub out a function
as opposed to a class. For example::
>>> import fudge
>>> remove = Fake('os.remove').is_callable()
>>> remove('some/path')
"""
self._callable = Call(self, call_name=self._name, callable=True)
return self | [
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This is useful for when you stub out a function
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>>> import fudge
>>> remove = Fake('os.remove').is_callable()
>>> remove('some/path') | [
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fudge-py/fudge | fudge/__init__.py | Fake.calls | def calls(self, call):
"""Redefine a call.
The fake method will execute your function. I.E.::
>>> f = Fake().provides('hello').calls(lambda: 'Why, hello there')
>>> f.hello()
'Why, hello there'
"""
exp = self._get_current_call()
exp.call_replacement = call
return self | python | def calls(self, call):
"""Redefine a call.
The fake method will execute your function. I.E.::
>>> f = Fake().provides('hello').calls(lambda: 'Why, hello there')
>>> f.hello()
'Why, hello there'
"""
exp = self._get_current_call()
exp.call_replacement = call
return self | [
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The fake method will execute your function. I.E.::
>>> f = Fake().provides('hello').calls(lambda: 'Why, hello there')
>>> f.hello()
'Why, hello there' | [
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fudge-py/fudge | fudge/__init__.py | Fake.expects | def expects(self, call_name):
"""Expect a call.
.. doctest::
:hide:
>>> import fudge
>>> fudge.clear_expectations()
>>> fudge.clear_calls()
If the method *call_name* is never called, then raise an error. I.E.::
>>> session = Fake('session').expects('open').expects('close')
>>> session.open()
>>> fudge.verify()
Traceback (most recent call last):
...
AssertionError: fake:session.close() was not called
.. note::
If you want to also verify the order these calls are made in,
use :func:`fudge.Fake.remember_order`. When using :func:`fudge.Fake.next_call`
after ``expects(...)``, each new call will be part of the expected order
Declaring ``expects()`` multiple times is the same as
declaring :func:`fudge.Fake.next_call`
"""
if call_name in self._declared_calls:
return self.next_call(for_method=call_name)
self._last_declared_call_name = call_name
c = ExpectedCall(self, call_name, call_order=self._expected_call_order)
self._declare_call(call_name, c)
return self | python | def expects(self, call_name):
"""Expect a call.
.. doctest::
:hide:
>>> import fudge
>>> fudge.clear_expectations()
>>> fudge.clear_calls()
If the method *call_name* is never called, then raise an error. I.E.::
>>> session = Fake('session').expects('open').expects('close')
>>> session.open()
>>> fudge.verify()
Traceback (most recent call last):
...
AssertionError: fake:session.close() was not called
.. note::
If you want to also verify the order these calls are made in,
use :func:`fudge.Fake.remember_order`. When using :func:`fudge.Fake.next_call`
after ``expects(...)``, each new call will be part of the expected order
Declaring ``expects()`` multiple times is the same as
declaring :func:`fudge.Fake.next_call`
"""
if call_name in self._declared_calls:
return self.next_call(for_method=call_name)
self._last_declared_call_name = call_name
c = ExpectedCall(self, call_name, call_order=self._expected_call_order)
self._declare_call(call_name, c)
return self | [
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.. doctest::
:hide:
>>> import fudge
>>> fudge.clear_expectations()
>>> fudge.clear_calls()
If the method *call_name* is never called, then raise an error. I.E.::
>>> session = Fake('session').expects('open').expects('close')
>>> session.open()
>>> fudge.verify()
Traceback (most recent call last):
...
AssertionError: fake:session.close() was not called
.. note::
If you want to also verify the order these calls are made in,
use :func:`fudge.Fake.remember_order`. When using :func:`fudge.Fake.next_call`
after ``expects(...)``, each new call will be part of the expected order
Declaring ``expects()`` multiple times is the same as
declaring :func:`fudge.Fake.next_call` | [
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fudge-py/fudge | fudge/__init__.py | Fake.next_call | def next_call(self, for_method=None):
"""Start expecting or providing multiple calls.
.. note:: next_call() cannot be used in combination with :func:`fudge.Fake.times_called`
Up until calling this method, calls are infinite.
For example, before next_call() ... ::
>>> from fudge import Fake
>>> f = Fake().provides('status').returns('Awake!')
>>> f.status()
'Awake!'
>>> f.status()
'Awake!'
After next_call() ... ::
>>> from fudge import Fake
>>> f = Fake().provides('status').returns('Awake!')
>>> f = f.next_call().returns('Asleep')
>>> f = f.next_call().returns('Dreaming')
>>> f.status()
'Awake!'
>>> f.status()
'Asleep'
>>> f.status()
'Dreaming'
>>> f.status()
Traceback (most recent call last):
...
AssertionError: This attribute of fake:unnamed can only be called 3 time(s). Call reset() if necessary or fudge.clear_calls().
If you need to affect the next call of something other than the last declared call,
use ``next_call(for_method="other_call")``. Here is an example using getters and setters
on a session object ::
>>> from fudge import Fake
>>> sess = Fake('session').provides('get_count').returns(1)
>>> sess = sess.provides('set_count').with_args(5)
Now go back and adjust return values for get_count() ::
>>> sess = sess.next_call(for_method='get_count').returns(5)
This allows these calls to be made ::
>>> sess.get_count()
1
>>> sess.set_count(5)
>>> sess.get_count()
5
When using :func:`fudge.Fake.remember_order` in combination with :func:`fudge.Fake.expects` and :func:`fudge.Fake.next_call` each new call will be part of the expected order.
"""
last_call_name = self._last_declared_call_name
if for_method:
if for_method not in self._declared_calls:
raise FakeDeclarationError(
"next_call(for_method=%r) is not possible; "
"declare expects(%r) or provides(%r) first" % (
for_method, for_method, for_method))
else:
# set this for the local function:
last_call_name = for_method
# reset this for subsequent methods:
self._last_declared_call_name = last_call_name
if last_call_name:
exp = self._declared_calls[last_call_name]
elif self._callable:
exp = self._callable
else:
raise FakeDeclarationError('next_call() must follow provides(), '
'expects() or is_callable()')
if getattr(exp, 'expected_times_called', None) is not None:
raise FakeDeclarationError("Cannot use next_call() in combination with times_called()")
if not isinstance(exp, CallStack):
# lazily create a stack with the last defined
# expected call as the first on the stack:
stack = CallStack(self, initial_calls=[exp],
expected=isinstance(exp, ExpectedCall),
call_name=exp.call_name)
# replace the old call obj using the same name:
if last_call_name:
self._declare_call(last_call_name, stack)
elif self._callable:
self._callable = stack
else:
stack = exp
# hmm, we need a copy here so that the last call
# falls off the stack.
if stack.expected:
next_call = ExpectedCall(self, call_name=exp.call_name, call_order=self._expected_call_order)
else:
next_call = Call(self, call_name=exp.call_name)
stack.add_call(next_call)
return self | python | def next_call(self, for_method=None):
"""Start expecting or providing multiple calls.
.. note:: next_call() cannot be used in combination with :func:`fudge.Fake.times_called`
Up until calling this method, calls are infinite.
For example, before next_call() ... ::
>>> from fudge import Fake
>>> f = Fake().provides('status').returns('Awake!')
>>> f.status()
'Awake!'
>>> f.status()
'Awake!'
After next_call() ... ::
>>> from fudge import Fake
>>> f = Fake().provides('status').returns('Awake!')
>>> f = f.next_call().returns('Asleep')
>>> f = f.next_call().returns('Dreaming')
>>> f.status()
'Awake!'
>>> f.status()
'Asleep'
>>> f.status()
'Dreaming'
>>> f.status()
Traceback (most recent call last):
...
AssertionError: This attribute of fake:unnamed can only be called 3 time(s). Call reset() if necessary or fudge.clear_calls().
If you need to affect the next call of something other than the last declared call,
use ``next_call(for_method="other_call")``. Here is an example using getters and setters
on a session object ::
>>> from fudge import Fake
>>> sess = Fake('session').provides('get_count').returns(1)
>>> sess = sess.provides('set_count').with_args(5)
Now go back and adjust return values for get_count() ::
>>> sess = sess.next_call(for_method='get_count').returns(5)
This allows these calls to be made ::
>>> sess.get_count()
1
>>> sess.set_count(5)
>>> sess.get_count()
5
When using :func:`fudge.Fake.remember_order` in combination with :func:`fudge.Fake.expects` and :func:`fudge.Fake.next_call` each new call will be part of the expected order.
"""
last_call_name = self._last_declared_call_name
if for_method:
if for_method not in self._declared_calls:
raise FakeDeclarationError(
"next_call(for_method=%r) is not possible; "
"declare expects(%r) or provides(%r) first" % (
for_method, for_method, for_method))
else:
# set this for the local function:
last_call_name = for_method
# reset this for subsequent methods:
self._last_declared_call_name = last_call_name
if last_call_name:
exp = self._declared_calls[last_call_name]
elif self._callable:
exp = self._callable
else:
raise FakeDeclarationError('next_call() must follow provides(), '
'expects() or is_callable()')
if getattr(exp, 'expected_times_called', None) is not None:
raise FakeDeclarationError("Cannot use next_call() in combination with times_called()")
if not isinstance(exp, CallStack):
# lazily create a stack with the last defined
# expected call as the first on the stack:
stack = CallStack(self, initial_calls=[exp],
expected=isinstance(exp, ExpectedCall),
call_name=exp.call_name)
# replace the old call obj using the same name:
if last_call_name:
self._declare_call(last_call_name, stack)
elif self._callable:
self._callable = stack
else:
stack = exp
# hmm, we need a copy here so that the last call
# falls off the stack.
if stack.expected:
next_call = ExpectedCall(self, call_name=exp.call_name, call_order=self._expected_call_order)
else:
next_call = Call(self, call_name=exp.call_name)
stack.add_call(next_call)
return self | [
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.. note:: next_call() cannot be used in combination with :func:`fudge.Fake.times_called`
Up until calling this method, calls are infinite.
For example, before next_call() ... ::
>>> from fudge import Fake
>>> f = Fake().provides('status').returns('Awake!')
>>> f.status()
'Awake!'
>>> f.status()
'Awake!'
After next_call() ... ::
>>> from fudge import Fake
>>> f = Fake().provides('status').returns('Awake!')
>>> f = f.next_call().returns('Asleep')
>>> f = f.next_call().returns('Dreaming')
>>> f.status()
'Awake!'
>>> f.status()
'Asleep'
>>> f.status()
'Dreaming'
>>> f.status()
Traceback (most recent call last):
...
AssertionError: This attribute of fake:unnamed can only be called 3 time(s). Call reset() if necessary or fudge.clear_calls().
If you need to affect the next call of something other than the last declared call,
use ``next_call(for_method="other_call")``. Here is an example using getters and setters
on a session object ::
>>> from fudge import Fake
>>> sess = Fake('session').provides('get_count').returns(1)
>>> sess = sess.provides('set_count').with_args(5)
Now go back and adjust return values for get_count() ::
>>> sess = sess.next_call(for_method='get_count').returns(5)
This allows these calls to be made ::
>>> sess.get_count()
1
>>> sess.set_count(5)
>>> sess.get_count()
5
When using :func:`fudge.Fake.remember_order` in combination with :func:`fudge.Fake.expects` and :func:`fudge.Fake.next_call` each new call will be part of the expected order. | [
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fudge-py/fudge | fudge/__init__.py | Fake.provides | def provides(self, call_name):
"""Provide a call.
The call acts as a stub -- no error is raised if it is not called.::
>>> session = Fake('session').provides('open').provides('close')
>>> import fudge
>>> fudge.clear_expectations() # from any previously declared fakes
>>> fudge.clear_calls()
>>> session.open()
>>> fudge.verify() # close() not called but no error
Declaring ``provides()`` multiple times is the same as
declaring :func:`fudge.Fake.next_call`
"""
if call_name in self._declared_calls:
return self.next_call(for_method=call_name)
self._last_declared_call_name = call_name
c = Call(self, call_name)
self._declare_call(call_name, c)
return self | python | def provides(self, call_name):
"""Provide a call.
The call acts as a stub -- no error is raised if it is not called.::
>>> session = Fake('session').provides('open').provides('close')
>>> import fudge
>>> fudge.clear_expectations() # from any previously declared fakes
>>> fudge.clear_calls()
>>> session.open()
>>> fudge.verify() # close() not called but no error
Declaring ``provides()`` multiple times is the same as
declaring :func:`fudge.Fake.next_call`
"""
if call_name in self._declared_calls:
return self.next_call(for_method=call_name)
self._last_declared_call_name = call_name
c = Call(self, call_name)
self._declare_call(call_name, c)
return self | [
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The call acts as a stub -- no error is raised if it is not called.::
>>> session = Fake('session').provides('open').provides('close')
>>> import fudge
>>> fudge.clear_expectations() # from any previously declared fakes
>>> fudge.clear_calls()
>>> session.open()
>>> fudge.verify() # close() not called but no error
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fudge-py/fudge | fudge/__init__.py | Fake.raises | def raises(self, exc):
"""Set last call to raise an exception class or instance.
For example::
>>> import fudge
>>> db = fudge.Fake('db').provides('insert').raises(ValueError("not enough parameters for insert"))
>>> db.insert()
Traceback (most recent call last):
...
ValueError: not enough parameters for insert
"""
exp = self._get_current_call()
exp.exception_to_raise = exc
return self | python | def raises(self, exc):
"""Set last call to raise an exception class or instance.
For example::
>>> import fudge
>>> db = fudge.Fake('db').provides('insert').raises(ValueError("not enough parameters for insert"))
>>> db.insert()
Traceback (most recent call last):
...
ValueError: not enough parameters for insert
"""
exp = self._get_current_call()
exp.exception_to_raise = exc
return self | [
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For example::
>>> import fudge
>>> db = fudge.Fake('db').provides('insert').raises(ValueError("not enough parameters for insert"))
>>> db.insert()
Traceback (most recent call last):
...
ValueError: not enough parameters for insert | [
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fudge-py/fudge | fudge/__init__.py | Fake.returns | def returns(self, val):
"""Set the last call to return a value.
Set a static value to return when a method is called. I.E.::
>>> f = Fake().provides('get_number').returns(64)
>>> f.get_number()
64
"""
exp = self._get_current_call()
exp.return_val = val
return self | python | def returns(self, val):
"""Set the last call to return a value.
Set a static value to return when a method is called. I.E.::
>>> f = Fake().provides('get_number').returns(64)
>>> f.get_number()
64
"""
exp = self._get_current_call()
exp.return_val = val
return self | [
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Set a static value to return when a method is called. I.E.::
>>> f = Fake().provides('get_number').returns(64)
>>> f.get_number()
64 | [
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fudge-py/fudge | fudge/__init__.py | Fake.times_called | def times_called(self, n):
"""Set the number of times an object can be called.
When working with provided calls, you'll only see an
error if the expected call count is exceeded ::
>>> auth = Fake('auth').provides('login').times_called(1)
>>> auth.login()
>>> auth.login()
Traceback (most recent call last):
...
AssertionError: fake:auth.login() was called 2 time(s). Expected 1.
When working with expected calls, you'll see an error if
the call count is never met ::
>>> import fudge
>>> auth = fudge.Fake('auth').expects('login').times_called(2)
>>> auth.login()
>>> fudge.verify()
Traceback (most recent call last):
...
AssertionError: fake:auth.login() was called 1 time(s). Expected 2.
.. note:: This cannot be used in combination with :func:`fudge.Fake.next_call`
"""
if self._last_declared_call_name:
actual_last_call = self._declared_calls[self._last_declared_call_name]
if isinstance(actual_last_call, CallStack):
raise FakeDeclarationError("Cannot use times_called() in combination with next_call()")
# else: # self._callable is in effect
exp = self._get_current_call()
exp.expected_times_called = n
return self | python | def times_called(self, n):
"""Set the number of times an object can be called.
When working with provided calls, you'll only see an
error if the expected call count is exceeded ::
>>> auth = Fake('auth').provides('login').times_called(1)
>>> auth.login()
>>> auth.login()
Traceback (most recent call last):
...
AssertionError: fake:auth.login() was called 2 time(s). Expected 1.
When working with expected calls, you'll see an error if
the call count is never met ::
>>> import fudge
>>> auth = fudge.Fake('auth').expects('login').times_called(2)
>>> auth.login()
>>> fudge.verify()
Traceback (most recent call last):
...
AssertionError: fake:auth.login() was called 1 time(s). Expected 2.
.. note:: This cannot be used in combination with :func:`fudge.Fake.next_call`
"""
if self._last_declared_call_name:
actual_last_call = self._declared_calls[self._last_declared_call_name]
if isinstance(actual_last_call, CallStack):
raise FakeDeclarationError("Cannot use times_called() in combination with next_call()")
# else: # self._callable is in effect
exp = self._get_current_call()
exp.expected_times_called = n
return self | [
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>>> auth = Fake('auth').provides('login').times_called(1)
>>> auth.login()
>>> auth.login()
Traceback (most recent call last):
...
AssertionError: fake:auth.login() was called 2 time(s). Expected 1.
When working with expected calls, you'll see an error if
the call count is never met ::
>>> import fudge
>>> auth = fudge.Fake('auth').expects('login').times_called(2)
>>> auth.login()
>>> fudge.verify()
Traceback (most recent call last):
...
AssertionError: fake:auth.login() was called 1 time(s). Expected 2.
.. note:: This cannot be used in combination with :func:`fudge.Fake.next_call` | [
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fudge-py/fudge | fudge/__init__.py | Fake.with_args | def with_args(self, *args, **kwargs):
"""Set the last call to expect specific argument values.
The app under test must send all declared arguments and keyword arguments
otherwise your test will raise an AssertionError. For example:
.. doctest::
>>> import fudge
>>> counter = fudge.Fake('counter').expects('increment').with_args(25, table='hits')
>>> counter.increment(24, table='clicks')
Traceback (most recent call last):
...
AssertionError: fake:counter.increment(25, table='hits') was called unexpectedly with args (24, table='clicks')
If you need to work with dynamic argument values
consider using :func:`fudge.Fake.with_matching_args` to make looser declarations.
You can also use :mod:`fudge.inspector` functions. Here is an example of providing
a more flexible ``with_args()`` declaration using inspectors:
.. doctest::
:hide:
>>> fudge.clear_expectations()
.. doctest::
>>> import fudge
>>> from fudge.inspector import arg
>>> counter = fudge.Fake('counter')
>>> counter = counter.expects('increment').with_args(
... arg.any(),
... table=arg.endswith("hits"))
...
The above declaration would allow you to call counter like this:
.. doctest::
>>> counter.increment(999, table="image_hits")
>>> fudge.verify()
.. doctest::
:hide:
>>> fudge.clear_calls()
Or like this:
.. doctest::
>>> counter.increment(22, table="user_profile_hits")
>>> fudge.verify()
.. doctest::
:hide:
>>> fudge.clear_expectations()
"""
exp = self._get_current_call()
if args:
exp.expected_args = args
if kwargs:
exp.expected_kwargs = kwargs
return self | python | def with_args(self, *args, **kwargs):
"""Set the last call to expect specific argument values.
The app under test must send all declared arguments and keyword arguments
otherwise your test will raise an AssertionError. For example:
.. doctest::
>>> import fudge
>>> counter = fudge.Fake('counter').expects('increment').with_args(25, table='hits')
>>> counter.increment(24, table='clicks')
Traceback (most recent call last):
...
AssertionError: fake:counter.increment(25, table='hits') was called unexpectedly with args (24, table='clicks')
If you need to work with dynamic argument values
consider using :func:`fudge.Fake.with_matching_args` to make looser declarations.
You can also use :mod:`fudge.inspector` functions. Here is an example of providing
a more flexible ``with_args()`` declaration using inspectors:
.. doctest::
:hide:
>>> fudge.clear_expectations()
.. doctest::
>>> import fudge
>>> from fudge.inspector import arg
>>> counter = fudge.Fake('counter')
>>> counter = counter.expects('increment').with_args(
... arg.any(),
... table=arg.endswith("hits"))
...
The above declaration would allow you to call counter like this:
.. doctest::
>>> counter.increment(999, table="image_hits")
>>> fudge.verify()
.. doctest::
:hide:
>>> fudge.clear_calls()
Or like this:
.. doctest::
>>> counter.increment(22, table="user_profile_hits")
>>> fudge.verify()
.. doctest::
:hide:
>>> fudge.clear_expectations()
"""
exp = self._get_current_call()
if args:
exp.expected_args = args
if kwargs:
exp.expected_kwargs = kwargs
return self | [
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The app under test must send all declared arguments and keyword arguments
otherwise your test will raise an AssertionError. For example:
.. doctest::
>>> import fudge
>>> counter = fudge.Fake('counter').expects('increment').with_args(25, table='hits')
>>> counter.increment(24, table='clicks')
Traceback (most recent call last):
...
AssertionError: fake:counter.increment(25, table='hits') was called unexpectedly with args (24, table='clicks')
If you need to work with dynamic argument values
consider using :func:`fudge.Fake.with_matching_args` to make looser declarations.
You can also use :mod:`fudge.inspector` functions. Here is an example of providing
a more flexible ``with_args()`` declaration using inspectors:
.. doctest::
:hide:
>>> fudge.clear_expectations()
.. doctest::
>>> import fudge
>>> from fudge.inspector import arg
>>> counter = fudge.Fake('counter')
>>> counter = counter.expects('increment').with_args(
... arg.any(),
... table=arg.endswith("hits"))
...
The above declaration would allow you to call counter like this:
.. doctest::
>>> counter.increment(999, table="image_hits")
>>> fudge.verify()
.. doctest::
:hide:
>>> fudge.clear_calls()
Or like this:
.. doctest::
>>> counter.increment(22, table="user_profile_hits")
>>> fudge.verify()
.. doctest::
:hide:
>>> fudge.clear_expectations() | [
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] | b283fbc1a41900f3f5845b10b8c2ef9136a67ebc | https://github.com/fudge-py/fudge/blob/b283fbc1a41900f3f5845b10b8c2ef9136a67ebc/fudge/__init__.py#L1178-L1243 | train | 49,838 |
fudge-py/fudge | fudge/__init__.py | Fake.with_matching_args | def with_matching_args(self, *args, **kwargs):
"""Set the last call to expect specific argument values if those arguments exist.
Unlike :func:`fudge.Fake.with_args` use this if you want to only declare
expectations about matching arguments. Any unknown keyword arguments
used by the app under test will be allowed.
For example, you can declare positional arguments but ignore keyword arguments:
.. doctest::
>>> import fudge
>>> db = fudge.Fake('db').expects('transaction').with_matching_args('insert')
With this declaration, any keyword argument is allowed:
.. doctest::
>>> db.transaction('insert', isolation_level='lock')
>>> db.transaction('insert', isolation_level='shared')
>>> db.transaction('insert', retry_on_error=True)
.. doctest::
:hide:
>>> fudge.clear_expectations()
.. note::
you may get more mileage out of :mod:`fudge.inspector` functions as
described in :func:`fudge.Fake.with_args`
"""
exp = self._get_current_call()
if args:
exp.expected_matching_args = args
if kwargs:
exp.expected_matching_kwargs = kwargs
return self | python | def with_matching_args(self, *args, **kwargs):
"""Set the last call to expect specific argument values if those arguments exist.
Unlike :func:`fudge.Fake.with_args` use this if you want to only declare
expectations about matching arguments. Any unknown keyword arguments
used by the app under test will be allowed.
For example, you can declare positional arguments but ignore keyword arguments:
.. doctest::
>>> import fudge
>>> db = fudge.Fake('db').expects('transaction').with_matching_args('insert')
With this declaration, any keyword argument is allowed:
.. doctest::
>>> db.transaction('insert', isolation_level='lock')
>>> db.transaction('insert', isolation_level='shared')
>>> db.transaction('insert', retry_on_error=True)
.. doctest::
:hide:
>>> fudge.clear_expectations()
.. note::
you may get more mileage out of :mod:`fudge.inspector` functions as
described in :func:`fudge.Fake.with_args`
"""
exp = self._get_current_call()
if args:
exp.expected_matching_args = args
if kwargs:
exp.expected_matching_kwargs = kwargs
return self | [
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expectations about matching arguments. Any unknown keyword arguments
used by the app under test will be allowed.
For example, you can declare positional arguments but ignore keyword arguments:
.. doctest::
>>> import fudge
>>> db = fudge.Fake('db').expects('transaction').with_matching_args('insert')
With this declaration, any keyword argument is allowed:
.. doctest::
>>> db.transaction('insert', isolation_level='lock')
>>> db.transaction('insert', isolation_level='shared')
>>> db.transaction('insert', retry_on_error=True)
.. doctest::
:hide:
>>> fudge.clear_expectations()
.. note::
you may get more mileage out of :mod:`fudge.inspector` functions as
described in :func:`fudge.Fake.with_args` | [
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fudge-py/fudge | fudge/__init__.py | Fake.without_args | def without_args(self, *args, **kwargs):
"""Set the last call to expect that certain arguments will not exist.
This is the opposite of :func:`fudge.Fake.with_matching_args`. It will
fail if any of the arguments are passed.
.. doctest::
>>> import fudge
>>> query = fudge.Fake('query').expects_call().without_args(
... 'http://example.com', name="Steve"
... )
>>> query('http://python.org', name="Joe")
>>> query('http://example.com')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with arg http://example.com
>>> query("Joe", "Frank", "Bartholomew", "Steve")
>>> query(name='Steve')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Steve
>>> query('http://python.org', name='Steve')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Steve
>>> query(city='Chicago', name='Steve')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Steve
>>> query.expects_call().without_args('http://example2.com')
fake:query
>>> query('foobar')
>>> query('foobar', 'http://example2.com')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with arg http://example2.com
>>> query.expects_call().without_args(name="Hieronymus")
fake:query
>>> query("Gottfried", "Hieronymus")
>>> query(name="Wexter", other_name="Hieronymus")
>>> query('asdf', name="Hieronymus")
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Hieronymus
>>> query(name="Hieronymus")
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Hieronymus
>>> query = fudge.Fake('query').expects_call().without_args(
... 'http://example.com', name="Steve"
... ).with_args('dog')
>>> query('dog')
>>> query('dog', 'http://example.com')
Traceback (most recent call last):
...
AssertionError: fake:query('dog') was called unexpectedly with args ('dog', 'http://example.com')
>>> query()
Traceback (most recent call last):
...
AssertionError: fake:query('dog') was called unexpectedly with args ()
"""
exp = self._get_current_call()
if args:
exp.unexpected_args = args
if kwargs:
exp.unexpected_kwargs = kwargs
return self | python | def without_args(self, *args, **kwargs):
"""Set the last call to expect that certain arguments will not exist.
This is the opposite of :func:`fudge.Fake.with_matching_args`. It will
fail if any of the arguments are passed.
.. doctest::
>>> import fudge
>>> query = fudge.Fake('query').expects_call().without_args(
... 'http://example.com', name="Steve"
... )
>>> query('http://python.org', name="Joe")
>>> query('http://example.com')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with arg http://example.com
>>> query("Joe", "Frank", "Bartholomew", "Steve")
>>> query(name='Steve')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Steve
>>> query('http://python.org', name='Steve')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Steve
>>> query(city='Chicago', name='Steve')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Steve
>>> query.expects_call().without_args('http://example2.com')
fake:query
>>> query('foobar')
>>> query('foobar', 'http://example2.com')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with arg http://example2.com
>>> query.expects_call().without_args(name="Hieronymus")
fake:query
>>> query("Gottfried", "Hieronymus")
>>> query(name="Wexter", other_name="Hieronymus")
>>> query('asdf', name="Hieronymus")
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Hieronymus
>>> query(name="Hieronymus")
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Hieronymus
>>> query = fudge.Fake('query').expects_call().without_args(
... 'http://example.com', name="Steve"
... ).with_args('dog')
>>> query('dog')
>>> query('dog', 'http://example.com')
Traceback (most recent call last):
...
AssertionError: fake:query('dog') was called unexpectedly with args ('dog', 'http://example.com')
>>> query()
Traceback (most recent call last):
...
AssertionError: fake:query('dog') was called unexpectedly with args ()
"""
exp = self._get_current_call()
if args:
exp.unexpected_args = args
if kwargs:
exp.unexpected_kwargs = kwargs
return self | [
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fail if any of the arguments are passed.
.. doctest::
>>> import fudge
>>> query = fudge.Fake('query').expects_call().without_args(
... 'http://example.com', name="Steve"
... )
>>> query('http://python.org', name="Joe")
>>> query('http://example.com')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with arg http://example.com
>>> query("Joe", "Frank", "Bartholomew", "Steve")
>>> query(name='Steve')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Steve
>>> query('http://python.org', name='Steve')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Steve
>>> query(city='Chicago', name='Steve')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Steve
>>> query.expects_call().without_args('http://example2.com')
fake:query
>>> query('foobar')
>>> query('foobar', 'http://example2.com')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with arg http://example2.com
>>> query.expects_call().without_args(name="Hieronymus")
fake:query
>>> query("Gottfried", "Hieronymus")
>>> query(name="Wexter", other_name="Hieronymus")
>>> query('asdf', name="Hieronymus")
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Hieronymus
>>> query(name="Hieronymus")
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Hieronymus
>>> query = fudge.Fake('query').expects_call().without_args(
... 'http://example.com', name="Steve"
... ).with_args('dog')
>>> query('dog')
>>> query('dog', 'http://example.com')
Traceback (most recent call last):
...
AssertionError: fake:query('dog') was called unexpectedly with args ('dog', 'http://example.com')
>>> query()
Traceback (most recent call last):
...
AssertionError: fake:query('dog') was called unexpectedly with args () | [
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fudge-py/fudge | fudge/__init__.py | Fake.with_arg_count | def with_arg_count(self, count):
"""Set the last call to expect an exact argument count.
I.E.::
>>> auth = Fake('auth').provides('login').with_arg_count(2)
>>> auth.login('joe_user') # forgot password
Traceback (most recent call last):
...
AssertionError: fake:auth.login() was called with 1 arg(s) but expected 2
"""
exp = self._get_current_call()
exp.expected_arg_count = count
return self | python | def with_arg_count(self, count):
"""Set the last call to expect an exact argument count.
I.E.::
>>> auth = Fake('auth').provides('login').with_arg_count(2)
>>> auth.login('joe_user') # forgot password
Traceback (most recent call last):
...
AssertionError: fake:auth.login() was called with 1 arg(s) but expected 2
"""
exp = self._get_current_call()
exp.expected_arg_count = count
return self | [
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I.E.::
>>> auth = Fake('auth').provides('login').with_arg_count(2)
>>> auth.login('joe_user') # forgot password
Traceback (most recent call last):
...
AssertionError: fake:auth.login() was called with 1 arg(s) but expected 2 | [
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] | b283fbc1a41900f3f5845b10b8c2ef9136a67ebc | https://github.com/fudge-py/fudge/blob/b283fbc1a41900f3f5845b10b8c2ef9136a67ebc/fudge/__init__.py#L1359-L1373 | train | 49,841 |
fudge-py/fudge | fudge/__init__.py | Fake.with_kwarg_count | def with_kwarg_count(self, count):
"""Set the last call to expect an exact count of keyword arguments.
I.E.::
>>> auth = Fake('auth').provides('login').with_kwarg_count(2)
>>> auth.login(username='joe') # forgot password=
Traceback (most recent call last):
...
AssertionError: fake:auth.login() was called with 1 keyword arg(s) but expected 2
"""
exp = self._get_current_call()
exp.expected_kwarg_count = count
return self | python | def with_kwarg_count(self, count):
"""Set the last call to expect an exact count of keyword arguments.
I.E.::
>>> auth = Fake('auth').provides('login').with_kwarg_count(2)
>>> auth.login(username='joe') # forgot password=
Traceback (most recent call last):
...
AssertionError: fake:auth.login() was called with 1 keyword arg(s) but expected 2
"""
exp = self._get_current_call()
exp.expected_kwarg_count = count
return self | [
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>>> auth.login(username='joe') # forgot password=
Traceback (most recent call last):
...
AssertionError: fake:auth.login() was called with 1 keyword arg(s) but expected 2 | [
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thespacedoctor/sherlock | sherlock/database.py | database.connect | def connect(self):
"""connect to the various databases, the credientals and settings of which are found in the sherlock settings file
**Return:**
- ``transientsDbConn`` -- the database hosting the transient source data
- ``cataloguesDbConn`` -- connection to the database hosting the contextual catalogues the transients are to be crossmatched against
- ``pmDbConn`` -- connection to the PESSTO Marshall database
See the class docstring for usage
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``get`` method')
transientSettings = self.settings[
"database settings"]["transients"]
catalogueSettings = self.settings[
"database settings"]["static catalogues"]
if "pessto marshall" in self.settings[
"database settings"]:
marshallSettings = self.settings[
"database settings"]["pessto marshall"]
else:
marshallSettings = False
dbConns = []
for dbSettings in [transientSettings, catalogueSettings, marshallSettings]:
port = False
if dbSettings and dbSettings["tunnel"]:
port = self._setup_tunnel(
tunnelParameters=dbSettings["tunnel"]
)
if dbSettings:
# SETUP A DATABASE CONNECTION FOR THE STATIC CATALOGUES
host = dbSettings["host"]
user = dbSettings["user"]
passwd = dbSettings["password"]
dbName = dbSettings["db"]
thisConn = ms.connect(
host=host,
user=user,
passwd=passwd,
db=dbName,
port=port,
use_unicode=True,
charset='utf8',
client_flag=ms.constants.CLIENT.MULTI_STATEMENTS,
connect_timeout=3600
)
thisConn.autocommit(True)
dbConns.append(thisConn)
else:
dbConns.append(None)
# CREATE A DICTIONARY OF DATABASES
dbConns = {
"transients": dbConns[0],
"catalogues": dbConns[1],
"marshall": dbConns[2]
}
dbVersions = {}
for k, v in dbConns.iteritems():
if v:
sqlQuery = u"""
SELECT VERSION() as v;
""" % locals()
rows = readquery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=v,
quiet=False
)
version = rows[0]['v']
dbVersions[k] = version
else:
dbVersions[k] = None
self.log.debug('completed the ``get`` method')
return dbConns, dbVersions | python | def connect(self):
"""connect to the various databases, the credientals and settings of which are found in the sherlock settings file
**Return:**
- ``transientsDbConn`` -- the database hosting the transient source data
- ``cataloguesDbConn`` -- connection to the database hosting the contextual catalogues the transients are to be crossmatched against
- ``pmDbConn`` -- connection to the PESSTO Marshall database
See the class docstring for usage
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``get`` method')
transientSettings = self.settings[
"database settings"]["transients"]
catalogueSettings = self.settings[
"database settings"]["static catalogues"]
if "pessto marshall" in self.settings[
"database settings"]:
marshallSettings = self.settings[
"database settings"]["pessto marshall"]
else:
marshallSettings = False
dbConns = []
for dbSettings in [transientSettings, catalogueSettings, marshallSettings]:
port = False
if dbSettings and dbSettings["tunnel"]:
port = self._setup_tunnel(
tunnelParameters=dbSettings["tunnel"]
)
if dbSettings:
# SETUP A DATABASE CONNECTION FOR THE STATIC CATALOGUES
host = dbSettings["host"]
user = dbSettings["user"]
passwd = dbSettings["password"]
dbName = dbSettings["db"]
thisConn = ms.connect(
host=host,
user=user,
passwd=passwd,
db=dbName,
port=port,
use_unicode=True,
charset='utf8',
client_flag=ms.constants.CLIENT.MULTI_STATEMENTS,
connect_timeout=3600
)
thisConn.autocommit(True)
dbConns.append(thisConn)
else:
dbConns.append(None)
# CREATE A DICTIONARY OF DATABASES
dbConns = {
"transients": dbConns[0],
"catalogues": dbConns[1],
"marshall": dbConns[2]
}
dbVersions = {}
for k, v in dbConns.iteritems():
if v:
sqlQuery = u"""
SELECT VERSION() as v;
""" % locals()
rows = readquery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=v,
quiet=False
)
version = rows[0]['v']
dbVersions[k] = version
else:
dbVersions[k] = None
self.log.debug('completed the ``get`` method')
return dbConns, dbVersions | [
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- ``cataloguesDbConn`` -- connection to the database hosting the contextual catalogues the transients are to be crossmatched against
- ``pmDbConn`` -- connection to the PESSTO Marshall database
See the class docstring for usage
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring | [
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ozgurgunes/django-manifest | manifest/accounts/forms.py | RegistrationForm.clean_username | def clean_username(self):
"""
Validate that the username is unique and not listed
in ``defaults.ACCOUNTS_FORBIDDEN_USERNAMES`` list.
"""
try:
user = get_user_model().objects.get(username=self.cleaned_data["username"])
except get_user_model().DoesNotExist:
pass
else:
raise forms.ValidationError(
self.error_messages['duplicate_username'])
if self.cleaned_data['username'].lower() \
in defaults.ACCOUNTS_FORBIDDEN_USERNAMES:
raise forms.ValidationError(_(u'This username is not allowed.'))
return self.cleaned_data['username'] | python | def clean_username(self):
"""
Validate that the username is unique and not listed
in ``defaults.ACCOUNTS_FORBIDDEN_USERNAMES`` list.
"""
try:
user = get_user_model().objects.get(username=self.cleaned_data["username"])
except get_user_model().DoesNotExist:
pass
else:
raise forms.ValidationError(
self.error_messages['duplicate_username'])
if self.cleaned_data['username'].lower() \
in defaults.ACCOUNTS_FORBIDDEN_USERNAMES:
raise forms.ValidationError(_(u'This username is not allowed.'))
return self.cleaned_data['username'] | [
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ozgurgunes/django-manifest | manifest/accounts/forms.py | RegistrationForm.clean_email | def clean_email(self):
"""
Validate that the email address is unique.
"""
if get_user_model().objects.filter(
Q(email__iexact=self.cleaned_data['email']) |
Q(email_unconfirmed__iexact=self.cleaned_data['email'])):
raise forms.ValidationError(_(u'This email address is already '
'in use. Please supply a different email.'))
return self.cleaned_data['email'] | python | def clean_email(self):
"""
Validate that the email address is unique.
"""
if get_user_model().objects.filter(
Q(email__iexact=self.cleaned_data['email']) |
Q(email_unconfirmed__iexact=self.cleaned_data['email'])):
raise forms.ValidationError(_(u'This email address is already '
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return self.cleaned_data['email'] | [
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ozgurgunes/django-manifest | manifest/accounts/forms.py | EmailForm.clean_email | def clean_email(self):
"""
Validate that the email is not already registered with another user.
"""
if self.cleaned_data['email'].lower() == self.user.email:
raise forms.ValidationError(_(u"You're already known under "
"this email address."))
if get_user_model().objects.filter(
email__iexact=self.cleaned_data['email']).exclude(
email__iexact=self.user.email):
raise forms.ValidationError(_(u'This email address is already '
'in use. Please supply a different email address.'))
return self.cleaned_data['email'] | python | def clean_email(self):
"""
Validate that the email is not already registered with another user.
"""
if self.cleaned_data['email'].lower() == self.user.email:
raise forms.ValidationError(_(u"You're already known under "
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if get_user_model().objects.filter(
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ozgurgunes/django-manifest | manifest/accounts/forms.py | ProfileForm.clean_picture | def clean_picture(self):
"""
Validates format and file size of uploaded profile picture.
"""
if self.cleaned_data.get('picture'):
picture_data = self.cleaned_data['picture']
if 'error' in picture_data:
raise forms.ValidationError(_(u'Upload a valid image. '
'The file you uploaded was either not an image '
'or a corrupted image.'))
content_type = picture_data.content_type
if content_type:
main, sub = content_type.split('/')
if not (main == 'image'
and sub in defaults.ACCOUNTS_PICTURE_FORMATS):
raise forms.ValidationError(_(u'%s only.' %
defaults.ACCOUNTS_PICTURE_FORMATS))
if picture_data.size > int(defaults.ACCOUNTS_PICTURE_MAX_FILE):
raise forms.ValidationError(_(u'Image size is too big.'))
return self.cleaned_data['picture'] | python | def clean_picture(self):
"""
Validates format and file size of uploaded profile picture.
"""
if self.cleaned_data.get('picture'):
picture_data = self.cleaned_data['picture']
if 'error' in picture_data:
raise forms.ValidationError(_(u'Upload a valid image. '
'The file you uploaded was either not an image '
'or a corrupted image.'))
content_type = picture_data.content_type
if content_type:
main, sub = content_type.split('/')
if not (main == 'image'
and sub in defaults.ACCOUNTS_PICTURE_FORMATS):
raise forms.ValidationError(_(u'%s only.' %
defaults.ACCOUNTS_PICTURE_FORMATS))
if picture_data.size > int(defaults.ACCOUNTS_PICTURE_MAX_FILE):
raise forms.ValidationError(_(u'Image size is too big.'))
return self.cleaned_data['picture'] | [
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pytroll/posttroll | posttroll/logger.py | Logger.log | def log(self):
"""Log stuff.
"""
with Subscribe(services=[""], addr_listener=True) as sub:
for msg in sub.recv(1):
if msg:
if msg.type in ["log.debug", "log.info",
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if not self.loop:
LOGGER.info("Stop logging")
break | python | def log(self):
"""Log stuff.
"""
with Subscribe(services=[""], addr_listener=True) as sub:
for msg in sub.recv(1):
if msg:
if msg.type in ["log.debug", "log.info",
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getattr(LOGGER, msg.type[4:])(msg.subject + " " +
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str(msg.time))
elif msg.binary:
LOGGER.debug("%s %s %s [binary] %s", msg.subject,
msg.sender,
msg.type,
str(msg.time))
else:
LOGGER.debug("%s %s %s %s %s", msg.subject,
msg.sender,
msg.type,
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if not self.loop:
LOGGER.info("Stop logging")
break | [
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emichael/PyREM | pyrem/task.py | cleanup | def cleanup():
"""Stop all started tasks on system exit.
Note: This only handles signals caught by the atexit module by default.
SIGKILL, for instance, will not be caught, so cleanup is not guaranteed in
all cases.
"""
to_stop = STARTED_TASKS.copy()
if to_stop:
print "Cleaning up..."
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try:
task.stop()
except: # pylint: disable=W0702
etype, value, trace = sys.exc_info()
# Disregard no such process exceptions, print out the rest
if not (isinstance(value, OSError) and value.errno == 3):
print ''.join(format_exception(etype, value, trace, None))
continue | python | def cleanup():
"""Stop all started tasks on system exit.
Note: This only handles signals caught by the atexit module by default.
SIGKILL, for instance, will not be caught, so cleanup is not guaranteed in
all cases.
"""
to_stop = STARTED_TASKS.copy()
if to_stop:
print "Cleaning up..."
for task in to_stop:
try:
task.stop()
except: # pylint: disable=W0702
etype, value, trace = sys.exc_info()
# Disregard no such process exceptions, print out the rest
if not (isinstance(value, OSError) and value.errno == 3):
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continue | [
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emichael/PyREM | pyrem/task.py | Task.wait | def wait(self):
"""Wait on a task to finish and stop it when it has finished.
Raises:
RuntimeError: If the task hasn't been started or has already been
stopped.
Returns:
The ``return_values`` of the task.
"""
if self._status is not TaskStatus.STARTED:
raise RuntimeError("Cannot wait on %s in state %s" %
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self._wait()
self.stop()
return self.return_values | python | def wait(self):
"""Wait on a task to finish and stop it when it has finished.
Raises:
RuntimeError: If the task hasn't been started or has already been
stopped.
Returns:
The ``return_values`` of the task.
"""
if self._status is not TaskStatus.STARTED:
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self._wait()
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emichael/PyREM | pyrem/task.py | Task.stop | def stop(self):
"""Stop a task immediately.
Raises:
RuntimeError: If the task hasn't been started or has already been
stopped.
"""
if self._status is TaskStatus.STOPPED:
return
if self._status is not TaskStatus.STARTED:
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self._stop()
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self._status = TaskStatus.STOPPED | python | def stop(self):
"""Stop a task immediately.
Raises:
RuntimeError: If the task hasn't been started or has already been
stopped.
"""
if self._status is TaskStatus.STOPPED:
return
if self._status is not TaskStatus.STARTED:
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emichael/PyREM | pyrem/task.py | Task.reset | def reset(self):
"""Reset a task.
Allows a task to be started again, clears the ``return_values``.
Raises:
RuntimeError: If the task has not been stopped.
"""
if self._status is not TaskStatus.STOPPED:
raise RuntimeError("Cannot reset %s in state %s" %
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self._reset()
self.return_values = {}
self._status = TaskStatus.IDLE | python | def reset(self):
"""Reset a task.
Allows a task to be started again, clears the ``return_values``.
Raises:
RuntimeError: If the task has not been stopped.
"""
if self._status is not TaskStatus.STOPPED:
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self._reset()
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emichael/PyREM | pyrem/task.py | Parallel._aggregate | def _aggregate(self):
"""Helper method to aggregate RemoteTasks into single ssh session."""
# pylint: disable=W0212
nonremote = [t for t in self._tasks if not isinstance(t, RemoteTask)]
remote = [t for t in self._tasks if isinstance(t, RemoteTask)]
host_dict = defaultdict(list)
for task in remote:
host_dict[task.host].append(task)
aggregated = []
for task_group in host_dict.values():
# Build up combined command
combined_cmd = []
for task in task_group:
if combined_cmd:
combined_cmd.append('&')
combined_cmd.append(' '.join(task._remote_command))
# Now, generated aggregate task
t0 = task_group[0] # pylint: disable=C0103
task = RemoteTask(
t0.host, combined_cmd, t0._quiet, t0._return_output,
t0._kill_remote, t0._identity_file)
aggregated.append(task)
self._tasks = nonremote + aggregated | python | def _aggregate(self):
"""Helper method to aggregate RemoteTasks into single ssh session."""
# pylint: disable=W0212
nonremote = [t for t in self._tasks if not isinstance(t, RemoteTask)]
remote = [t for t in self._tasks if isinstance(t, RemoteTask)]
host_dict = defaultdict(list)
for task in remote:
host_dict[task.host].append(task)
aggregated = []
for task_group in host_dict.values():
# Build up combined command
combined_cmd = []
for task in task_group:
if combined_cmd:
combined_cmd.append('&')
combined_cmd.append(' '.join(task._remote_command))
# Now, generated aggregate task
t0 = task_group[0] # pylint: disable=C0103
task = RemoteTask(
t0.host, combined_cmd, t0._quiet, t0._return_output,
t0._kill_remote, t0._identity_file)
aggregated.append(task)
self._tasks = nonremote + aggregated | [
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ozgurgunes/django-manifest | manifest/accounts/models.py | upload_to_picture | def upload_to_picture(instance, filename):
"""
Uploads a picture for a user to the ``ACCOUNTS_PICTURE_PATH`` and
saving it under unique hash for the image. This is for privacy
reasons so others can't just browse through the picture directory.
"""
extension = filename.split('.')[-1].lower()
salt, hash = generate_sha1(instance.id)
return '%(path)s/%(hash)s.%(extension)s' % {
'path': getattr(defaults,
'ACCOUNTS_PICTURE_PATH','%s/%s' % (
str(instance._meta.app_label),
str(instance._meta.model_name))),
'hash': hash[:10],
'extension': extension} | python | def upload_to_picture(instance, filename):
"""
Uploads a picture for a user to the ``ACCOUNTS_PICTURE_PATH`` and
saving it under unique hash for the image. This is for privacy
reasons so others can't just browse through the picture directory.
"""
extension = filename.split('.')[-1].lower()
salt, hash = generate_sha1(instance.id)
return '%(path)s/%(hash)s.%(extension)s' % {
'path': getattr(defaults,
'ACCOUNTS_PICTURE_PATH','%s/%s' % (
str(instance._meta.app_label),
str(instance._meta.model_name))),
'hash': hash[:10],
'extension': extension} | [
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ozgurgunes/django-manifest | manifest/accounts/models.py | AccountActivationMixin.activation_key_expired | def activation_key_expired(self):
"""
Checks if activation key is expired.
Returns ``True`` when the ``activation_key`` of the user is expired
and ``False`` if the key is still valid.
The key is expired when it's set to the value defined in
``ACCOUNTS_ACTIVATED`` or ``activation_key_created`` is beyond the
amount of days defined in ``ACCOUNTS_ACTIVATION_DAYS``.
"""
expiration_days = datetime.timedelta(
days=defaults.ACCOUNTS_ACTIVATION_DAYS)
expiration_date = self.date_joined + expiration_days
if self.activation_key == defaults.ACCOUNTS_ACTIVATED:
return True
if get_datetime_now() >= expiration_date:
return True
return False | python | def activation_key_expired(self):
"""
Checks if activation key is expired.
Returns ``True`` when the ``activation_key`` of the user is expired
and ``False`` if the key is still valid.
The key is expired when it's set to the value defined in
``ACCOUNTS_ACTIVATED`` or ``activation_key_created`` is beyond the
amount of days defined in ``ACCOUNTS_ACTIVATION_DAYS``.
"""
expiration_days = datetime.timedelta(
days=defaults.ACCOUNTS_ACTIVATION_DAYS)
expiration_date = self.date_joined + expiration_days
if self.activation_key == defaults.ACCOUNTS_ACTIVATED:
return True
if get_datetime_now() >= expiration_date:
return True
return False | [
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ozgurgunes/django-manifest | manifest/accounts/models.py | AccountActivationMixin.send_activation_email | def send_activation_email(self):
"""
Sends a activation email to the user.
This email is send when the user wants to activate their
newly created user.
"""
context= {'user': self,
'protocol': get_protocol(),
'activation_days': defaults.ACCOUNTS_ACTIVATION_DAYS,
'activation_key': self.activation_key,
'site': Site.objects.get_current()}
subject = ''.join(render_to_string(
'accounts/emails/activation_email_subject.txt',
context).splitlines())
message = render_to_string(
'accounts/emails/activation_email_message.txt',
context)
send_mail(subject,
message,
settings.DEFAULT_FROM_EMAIL,
[self.email,]) | python | def send_activation_email(self):
"""
Sends a activation email to the user.
This email is send when the user wants to activate their
newly created user.
"""
context= {'user': self,
'protocol': get_protocol(),
'activation_days': defaults.ACCOUNTS_ACTIVATION_DAYS,
'activation_key': self.activation_key,
'site': Site.objects.get_current()}
subject = ''.join(render_to_string(
'accounts/emails/activation_email_subject.txt',
context).splitlines())
message = render_to_string(
'accounts/emails/activation_email_message.txt',
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send_mail(subject,
message,
settings.DEFAULT_FROM_EMAIL,
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ozgurgunes/django-manifest | manifest/accounts/models.py | EmailConfirmationMixin.change_email | def change_email(self, email):
"""
Changes the email address for a user.
A user needs to verify this new email address before it becomes
active. By storing the new email address in a temporary field
-- ``temporary_email`` -- we are able to set this email address
after the user has verified it by clicking on the verification URI
in the email. This email gets send out by ``send_verification_email``.
:param email:
The new email address that the user wants to use.
"""
self.email_unconfirmed = email
salt, hash = generate_sha1(self.username)
self.email_confirmation_key = hash
self.email_confirmation_key_created = get_datetime_now()
self.save()
# Send email for activation
self.send_confirmation_email()
return self | python | def change_email(self, email):
"""
Changes the email address for a user.
A user needs to verify this new email address before it becomes
active. By storing the new email address in a temporary field
-- ``temporary_email`` -- we are able to set this email address
after the user has verified it by clicking on the verification URI
in the email. This email gets send out by ``send_verification_email``.
:param email:
The new email address that the user wants to use.
"""
self.email_unconfirmed = email
salt, hash = generate_sha1(self.username)
self.email_confirmation_key = hash
self.email_confirmation_key_created = get_datetime_now()
self.save()
# Send email for activation
self.send_confirmation_email()
return self | [
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ozgurgunes/django-manifest | manifest/accounts/models.py | EmailConfirmationMixin.send_confirmation_email | def send_confirmation_email(self):
"""
Sends an email to confirm the new email address.
This method sends out two emails. One to the new email address that
contains the ``email_confirmation_key`` which is used to verify this
this email address with :func:`User.objects.confirm_email`.
The other email is to the old email address to let the user know that
a request is made to change this email address.
"""
context= {'user': self,
'new_email': self.email_unconfirmed,
'protocol': get_protocol(),
'confirmation_key': self.email_confirmation_key,
'site': Site.objects.get_current()}
# Email to the old address
subject_old = ''.join(render_to_string(
'accounts/emails/confirmation_email_subject_old.txt',
context).splitlines())
message_old = render_to_string(
'accounts/emails/confirmation_email_message_old.txt',
context)
send_mail(subject_old,
message_old,
settings.DEFAULT_FROM_EMAIL,
[self.email])
# Email to the new address
subject_new = ''.join(render_to_string(
'accounts/emails/confirmation_email_subject_new.txt',
context).splitlines())
message_new = render_to_string(
'accounts/emails/confirmation_email_message_new.txt',
context)
send_mail(subject_new,
message_new,
settings.DEFAULT_FROM_EMAIL,
[self.email_unconfirmed,]) | python | def send_confirmation_email(self):
"""
Sends an email to confirm the new email address.
This method sends out two emails. One to the new email address that
contains the ``email_confirmation_key`` which is used to verify this
this email address with :func:`User.objects.confirm_email`.
The other email is to the old email address to let the user know that
a request is made to change this email address.
"""
context= {'user': self,
'new_email': self.email_unconfirmed,
'protocol': get_protocol(),
'confirmation_key': self.email_confirmation_key,
'site': Site.objects.get_current()}
# Email to the old address
subject_old = ''.join(render_to_string(
'accounts/emails/confirmation_email_subject_old.txt',
context).splitlines())
message_old = render_to_string(
'accounts/emails/confirmation_email_message_old.txt',
context)
send_mail(subject_old,
message_old,
settings.DEFAULT_FROM_EMAIL,
[self.email])
# Email to the new address
subject_new = ''.join(render_to_string(
'accounts/emails/confirmation_email_subject_new.txt',
context).splitlines())
message_new = render_to_string(
'accounts/emails/confirmation_email_message_new.txt',
context)
send_mail(subject_new,
message_new,
settings.DEFAULT_FROM_EMAIL,
[self.email_unconfirmed,]) | [
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ozgurgunes/django-manifest | manifest/accounts/models.py | UserProfileMixin.get_picture_url | def get_picture_url(self):
"""
Returns the image containing the picture for the user.
The picture can be a uploaded image or a Gravatar.
Gravatar functionality will only be used when
``ACCOUNTS_GRAVATAR_PICTURE`` is set to ``True``.
:return:
``None`` when Gravatar is not used and no default image is
supplied by ``ACCOUNTS_GRAVATAR_DEFAULT``.
"""
# First check for a picture and if any return that.
if self.picture:
return self.picture.url
# Use Gravatar if the user wants to.
if defaults.ACCOUNTS_GRAVATAR_PICTURE:
return get_gravatar(self.email,
defaults.ACCOUNTS_GRAVATAR_SIZE,
defaults.ACCOUNTS_GRAVATAR_DEFAULT)
# Gravatar not used, check for a default image.
else:
if defaults.ACCOUNTS_GRAVATAR_DEFAULT not in ['404', 'mm',
'identicon',
'monsterid',
'wavatar']:
return defaults.ACCOUNTS_GRAVATAR_DEFAULT
else: return None | python | def get_picture_url(self):
"""
Returns the image containing the picture for the user.
The picture can be a uploaded image or a Gravatar.
Gravatar functionality will only be used when
``ACCOUNTS_GRAVATAR_PICTURE`` is set to ``True``.
:return:
``None`` when Gravatar is not used and no default image is
supplied by ``ACCOUNTS_GRAVATAR_DEFAULT``.
"""
# First check for a picture and if any return that.
if self.picture:
return self.picture.url
# Use Gravatar if the user wants to.
if defaults.ACCOUNTS_GRAVATAR_PICTURE:
return get_gravatar(self.email,
defaults.ACCOUNTS_GRAVATAR_SIZE,
defaults.ACCOUNTS_GRAVATAR_DEFAULT)
# Gravatar not used, check for a default image.
else:
if defaults.ACCOUNTS_GRAVATAR_DEFAULT not in ['404', 'mm',
'identicon',
'monsterid',
'wavatar']:
return defaults.ACCOUNTS_GRAVATAR_DEFAULT
else: return None | [
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ozgurgunes/django-manifest | manifest/accounts/models.py | UserProfileMixin.get_full_name_or_username | def get_full_name_or_username(self):
"""
Returns the full name of the user, or if none is supplied will return
the username.
Also looks at ``ACCOUNTS_WITHOUT_USERNAMES`` settings to define if it
should return the username or email address when the full name is not
supplied.
:return:
``String`` containing the full name of the user. If no name is
supplied it will return the username or email address depending on
the ``ACCOUNTS_WITHOUT_USERNAMES`` setting.
"""
if self.first_name or self.last_name:
# We will return this as translated string. Maybe there are some
# countries that first display the last name.
name = _(u"%(first_name)s %(last_name)s") % \
{'first_name': self.first_name,
'last_name': self.last_name}
else:
# Fallback to the username if usernames are used
if not defaults.ACCOUNTS_WITHOUT_USERNAMES:
name = "%(username)s" % {'username': self.username}
else:
name = "%(email)s" % {'email': self.email}
return name.strip() | python | def get_full_name_or_username(self):
"""
Returns the full name of the user, or if none is supplied will return
the username.
Also looks at ``ACCOUNTS_WITHOUT_USERNAMES`` settings to define if it
should return the username or email address when the full name is not
supplied.
:return:
``String`` containing the full name of the user. If no name is
supplied it will return the username or email address depending on
the ``ACCOUNTS_WITHOUT_USERNAMES`` setting.
"""
if self.first_name or self.last_name:
# We will return this as translated string. Maybe there are some
# countries that first display the last name.
name = _(u"%(first_name)s %(last_name)s") % \
{'first_name': self.first_name,
'last_name': self.last_name}
else:
# Fallback to the username if usernames are used
if not defaults.ACCOUNTS_WITHOUT_USERNAMES:
name = "%(username)s" % {'username': self.username}
else:
name = "%(email)s" % {'email': self.email}
return name.strip() | [
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contentful-labs/contentful.py | contentful/cda/client.py | Client.resolve | def resolve(self, link_resource_type, resource_id, array=None):
"""Resolve a link to a CDA resource.
Provided an `array` argument, attempt to retrieve the resource from the `mapped_items`
section of that array (containing both included and regular resources), in case the
resource cannot be found in the array (or if no `array` was provided) - attempt to fetch
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:param link_resource_type: (str) Resource type as str.
:param resource_id: (str) Remote ID of the linked resource.
:param array: (:class:`.Array`) Optional array resource.
:return: :class:`.Resource` subclass, `None` if it cannot be retrieved.
"""
result = None
if array is not None:
container = array.items_mapped.get(link_resource_type)
result = container.get(resource_id)
if result is None:
clz = utils.class_for_type(link_resource_type)
result = self.fetch(clz).where({'sys.id': resource_id}).first()
return result | python | def resolve(self, link_resource_type, resource_id, array=None):
"""Resolve a link to a CDA resource.
Provided an `array` argument, attempt to retrieve the resource from the `mapped_items`
section of that array (containing both included and regular resources), in case the
resource cannot be found in the array (or if no `array` was provided) - attempt to fetch
the resource from the API by issuing a network request.
:param link_resource_type: (str) Resource type as str.
:param resource_id: (str) Remote ID of the linked resource.
:param array: (:class:`.Array`) Optional array resource.
:return: :class:`.Resource` subclass, `None` if it cannot be retrieved.
"""
result = None
if array is not None:
container = array.items_mapped.get(link_resource_type)
result = container.get(resource_id)
if result is None:
clz = utils.class_for_type(link_resource_type)
result = self.fetch(clz).where({'sys.id': resource_id}).first()
return result | [
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:param resource_id: (str) Remote ID of the linked resource.
:param array: (:class:`.Array`) Optional array resource.
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contentful-labs/contentful.py | contentful/cda/client.py | Client.resolve_dict_link | def resolve_dict_link(self, dct, array=None):
"""Convenience method for resolving links given a dict object.
Extract link values and pass to the :func:`.resolve` method of this class.
:param dct: (dict) Dictionary with the link data.
:param array: (:class:`.Array`) Optional array resource.
:return: :class:`.Resource` subclass, `None` if it cannot be retrieved.
"""
sys = dct.get('sys')
return self.resolve(sys['linkType'], sys['id'], array) if sys is not None else None | python | def resolve_dict_link(self, dct, array=None):
"""Convenience method for resolving links given a dict object.
Extract link values and pass to the :func:`.resolve` method of this class.
:param dct: (dict) Dictionary with the link data.
:param array: (:class:`.Array`) Optional array resource.
:return: :class:`.Resource` subclass, `None` if it cannot be retrieved.
"""
sys = dct.get('sys')
return self.resolve(sys['linkType'], sys['id'], array) if sys is not None else None | [
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contentful-labs/contentful.py | contentful/cda/client.py | RequestArray.all | def all(self):
"""Attempt to retrieve all available resources matching this request.
:return: Result instance as returned by the :class:`.Dispatcher`.
"""
result = self.invoke()
if self.resolve_links:
result.resolve_links()
return result | python | def all(self):
"""Attempt to retrieve all available resources matching this request.
:return: Result instance as returned by the :class:`.Dispatcher`.
"""
result = self.invoke()
if self.resolve_links:
result.resolve_links()
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contentful-labs/contentful.py | contentful/cda/client.py | RequestArray.first | def first(self):
"""Attempt to retrieve only the first resource matching this request.
:return: Result instance, or `None` if there are no matching resources.
"""
self.params['limit'] = 1
result = self.all()
return result.items[0] if result.total > 0 else None | python | def first(self):
"""Attempt to retrieve only the first resource matching this request.
:return: Result instance, or `None` if there are no matching resources.
"""
self.params['limit'] = 1
result = self.all()
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contentful-labs/contentful.py | contentful/cda/client.py | RequestArray.where | def where(self, params):
"""Set a dict of parameters to be passed to the API when invoking this request.
:param params: (dict) query parameters.
:return: this :class:`.RequestArray` instance for convenience.
"""
self.params = dict(self.params, **params) # params overrides self.params
return self | python | def where(self, params):
"""Set a dict of parameters to be passed to the API when invoking this request.
:param params: (dict) query parameters.
:return: this :class:`.RequestArray` instance for convenience.
"""
self.params = dict(self.params, **params) # params overrides self.params
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dusktreader/py-buzz | examples/require_condition.py | complex_require_condition | def complex_require_condition():
"""
This function demonstrates a more complex usage of the require_condition
function. It shows argument interpolation and handling a more complex
boolean expression
"""
print("Demonstrating complex require_condition example")
val = 64
Buzz.require_condition(is_even(val), 'This condition should pass')
val = 81
Buzz.require_condition(is_even(val), 'Value {val} is not even', val=val) | python | def complex_require_condition():
"""
This function demonstrates a more complex usage of the require_condition
function. It shows argument interpolation and handling a more complex
boolean expression
"""
print("Demonstrating complex require_condition example")
val = 64
Buzz.require_condition(is_even(val), 'This condition should pass')
val = 81
Buzz.require_condition(is_even(val), 'Value {val} is not even', val=val) | [
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zeroSteiner/smoke-zephyr | smoke_zephyr/configuration.py | MemoryConfiguration.get | def get(self, item_name):
"""
Retrieve the value of an option.
:param str item_name: The name of the option to retrieve.
:return: The value of *item_name* in the configuration.
"""
if self.prefix:
item_name = self.prefix + self.seperator + item_name
item_names = item_name.split(self.seperator)
node = self._storage
for item_name in item_names:
node = node[item_name]
return node | python | def get(self, item_name):
"""
Retrieve the value of an option.
:param str item_name: The name of the option to retrieve.
:return: The value of *item_name* in the configuration.
"""
if self.prefix:
item_name = self.prefix + self.seperator + item_name
item_names = item_name.split(self.seperator)
node = self._storage
for item_name in item_names:
node = node[item_name]
return node | [
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zeroSteiner/smoke-zephyr | smoke_zephyr/configuration.py | MemoryConfiguration.has_option | def has_option(self, option_name):
"""
Check that an option exists.
:param str option_name: The name of the option to check.
:return: True of the option exists in the configuration.
:rtype: bool
"""
if self.prefix:
option_name = self.prefix + self.seperator + option_name
item_names = option_name.split(self.seperator)
node = self._storage
for item_name in item_names:
if node is None:
return False
if not item_name in node:
return False
node = node[item_name]
return True | python | def has_option(self, option_name):
"""
Check that an option exists.
:param str option_name: The name of the option to check.
:return: True of the option exists in the configuration.
:rtype: bool
"""
if self.prefix:
option_name = self.prefix + self.seperator + option_name
item_names = option_name.split(self.seperator)
node = self._storage
for item_name in item_names:
if node is None:
return False
if not item_name in node:
return False
node = node[item_name]
return True | [
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zeroSteiner/smoke-zephyr | smoke_zephyr/configuration.py | MemoryConfiguration.has_section | def has_section(self, section_name):
"""
Checks that an option exists and that it contains sub options.
:param str section_name: The name of the section to check.
:return: True if the section exists.
:rtype: dict
"""
if not self.has_option(section_name):
return False
return isinstance(self.get(section_name), dict) | python | def has_section(self, section_name):
"""
Checks that an option exists and that it contains sub options.
:param str section_name: The name of the section to check.
:return: True if the section exists.
:rtype: dict
"""
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return False
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zeroSteiner/smoke-zephyr | smoke_zephyr/configuration.py | MemoryConfiguration.set | def set(self, item_name, item_value):
"""
Sets the value of an option in the configuration.
:param str item_name: The name of the option to set.
:param item_value: The value of the option to set.
"""
if self.prefix:
item_name = self.prefix + self.seperator + item_name
item_names = item_name.split(self.seperator)
item_last = item_names.pop()
node = self._storage
for item_name in item_names:
if not item_name in node:
node[item_name] = {}
node = node[item_name]
node[item_last] = item_value
return | python | def set(self, item_name, item_value):
"""
Sets the value of an option in the configuration.
:param str item_name: The name of the option to set.
:param item_value: The value of the option to set.
"""
if self.prefix:
item_name = self.prefix + self.seperator + item_name
item_names = item_name.split(self.seperator)
item_last = item_names.pop()
node = self._storage
for item_name in item_names:
if not item_name in node:
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node = node[item_name]
node[item_last] = item_value
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zeroSteiner/smoke-zephyr | smoke_zephyr/configuration.py | Configuration.get_missing | def get_missing(self, verify_file):
"""
Use a verification configuration which has a list of required options
and their respective types. This information is used to identify missing
and incompatible options in the loaded configuration.
:param str verify_file: The file to load for verification data.
:return: A dictionary of missing and incompatible settings.
:rtype: dict
"""
vconf = Configuration(verify_file)
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for setting, setting_type in vconf.get('settings').items():
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missing['missing'] = missing.get('settings', [])
missing['missing'].append(setting)
elif not type(self.get(setting)).__name__ == setting_type:
missing['incompatible'] = missing.get('incompatible', [])
missing['incompatible'].append((setting, setting_type))
return missing | python | def get_missing(self, verify_file):
"""
Use a verification configuration which has a list of required options
and their respective types. This information is used to identify missing
and incompatible options in the loaded configuration.
:param str verify_file: The file to load for verification data.
:return: A dictionary of missing and incompatible settings.
:rtype: dict
"""
vconf = Configuration(verify_file)
missing = {}
for setting, setting_type in vconf.get('settings').items():
if not self.has_option(setting):
missing['missing'] = missing.get('settings', [])
missing['missing'].append(setting)
elif not type(self.get(setting)).__name__ == setting_type:
missing['incompatible'] = missing.get('incompatible', [])
missing['incompatible'].append((setting, setting_type))
return missing | [
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zeroSteiner/smoke-zephyr | smoke_zephyr/configuration.py | Configuration.save | def save(self):
"""
Save the current configuration to disk.
"""
with open(self.configuration_file, 'w') as file_h:
file_h.write(self._serializer('dumps', self._storage)) | python | def save(self):
"""
Save the current configuration to disk.
"""
with open(self.configuration_file, 'w') as file_h:
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | replace_lines | def replace_lines(regexer, handler, lines):
"""Uses replacement handler to perform replacements on lines of text
First we strip off all whitespace
We run the replacement on a clean 'content' string
Finally we replace the original content with the replaced version
This ensures that we retain the correct whitespace from the original line
"""
result = []
for line in lines:
content = line.strip()
replaced = regexer.sub(handler, content)
result.append(line.replace(content, replaced, 1))
return result | python | def replace_lines(regexer, handler, lines):
"""Uses replacement handler to perform replacements on lines of text
First we strip off all whitespace
We run the replacement on a clean 'content' string
Finally we replace the original content with the replaced version
This ensures that we retain the correct whitespace from the original line
"""
result = []
for line in lines:
content = line.strip()
replaced = regexer.sub(handler, content)
result.append(line.replace(content, replaced, 1))
return result | [
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | write_targets | def write_targets(targets, **params):
"""Writes version info into version file"""
handler = ReplacementHandler(**params)
for target, regexer in regexer_for_targets(targets):
with open(target) as fh:
lines = fh.readlines()
lines = replace_lines(regexer, handler, lines)
with open(target, "w") as fh:
fh.writelines(lines)
if handler.missing:
raise Exception(
"Failed to complete all expected replacements: %r" % handler.missing
) | python | def write_targets(targets, **params):
"""Writes version info into version file"""
handler = ReplacementHandler(**params)
for target, regexer in regexer_for_targets(targets):
with open(target) as fh:
lines = fh.readlines()
lines = replace_lines(regexer, handler, lines)
with open(target, "w") as fh:
fh.writelines(lines)
if handler.missing:
raise Exception(
"Failed to complete all expected replacements: %r" % handler.missing
) | [
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | regexer_for_targets | def regexer_for_targets(targets):
"""Pairs up target files with their correct regex"""
for target in targets:
path, file_ext = os.path.splitext(target)
regexer = config.regexers[file_ext]
yield target, regexer | python | def regexer_for_targets(targets):
"""Pairs up target files with their correct regex"""
for target in targets:
path, file_ext = os.path.splitext(target)
regexer = config.regexers[file_ext]
yield target, regexer | [
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | extract_keypairs | def extract_keypairs(lines, regexer):
"""Given some lines of text, extract key-value pairs from them"""
updates = {}
for line in lines:
# for consistency we must match the replacer and strip whitespace / newlines
match = regexer.match(line.strip())
if not match:
continue
k_v = match.groupdict()
updates[k_v[Constants.KEY_GROUP]] = k_v[Constants.VALUE_GROUP]
return updates | python | def extract_keypairs(lines, regexer):
"""Given some lines of text, extract key-value pairs from them"""
updates = {}
for line in lines:
# for consistency we must match the replacer and strip whitespace / newlines
match = regexer.match(line.strip())
if not match:
continue
k_v = match.groupdict()
updates[k_v[Constants.KEY_GROUP]] = k_v[Constants.VALUE_GROUP]
return updates | [
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | read_targets | def read_targets(targets):
"""Reads generic key-value pairs from input files"""
results = {}
for target, regexer in regexer_for_targets(targets):
with open(target) as fh:
results.update(extract_keypairs(fh.readlines(), regexer))
return results | python | def read_targets(targets):
"""Reads generic key-value pairs from input files"""
results = {}
for target, regexer in regexer_for_targets(targets):
with open(target) as fh:
results.update(extract_keypairs(fh.readlines(), regexer))
return results | [
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | detect_file_triggers | def detect_file_triggers(trigger_patterns):
"""The existence of files matching configured globs will trigger a version bump"""
triggers = set()
for trigger, pattern in trigger_patterns.items():
matches = glob.glob(pattern)
if matches:
_LOG.debug("trigger: %s bump from %r\n\t%s", trigger, pattern, matches)
triggers.add(trigger)
else:
_LOG.debug("trigger: no match on %r", pattern)
return triggers | python | def detect_file_triggers(trigger_patterns):
"""The existence of files matching configured globs will trigger a version bump"""
triggers = set()
for trigger, pattern in trigger_patterns.items():
matches = glob.glob(pattern)
if matches:
_LOG.debug("trigger: %s bump from %r\n\t%s", trigger, pattern, matches)
triggers.add(trigger)
else:
_LOG.debug("trigger: no match on %r", pattern)
return triggers | [
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | get_all_triggers | def get_all_triggers(bump, file_triggers):
"""Aggregated set of significant figures to bump"""
triggers = set()
if file_triggers:
triggers = triggers.union(detect_file_triggers(config.trigger_patterns))
if bump:
_LOG.debug("trigger: %s bump requested", bump)
triggers.add(bump)
return triggers | python | def get_all_triggers(bump, file_triggers):
"""Aggregated set of significant figures to bump"""
triggers = set()
if file_triggers:
triggers = triggers.union(detect_file_triggers(config.trigger_patterns))
if bump:
_LOG.debug("trigger: %s bump requested", bump)
triggers.add(bump)
return triggers | [
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | get_lock_behaviour | def get_lock_behaviour(triggers, all_data, lock):
"""Binary state lock protects from version increments if set"""
updates = {}
lock_key = config._forward_aliases.get(Constants.VERSION_LOCK_FIELD)
# if we are explicitly setting or locking the version, then set the lock field True anyway
if lock:
updates[Constants.VERSION_LOCK_FIELD] = config.VERSION_LOCK_VALUE
elif (
triggers
and lock_key
and str(all_data.get(lock_key)) == str(config.VERSION_LOCK_VALUE)
):
triggers.clear()
updates[Constants.VERSION_LOCK_FIELD] = config.VERSION_UNLOCK_VALUE
return updates | python | def get_lock_behaviour(triggers, all_data, lock):
"""Binary state lock protects from version increments if set"""
updates = {}
lock_key = config._forward_aliases.get(Constants.VERSION_LOCK_FIELD)
# if we are explicitly setting or locking the version, then set the lock field True anyway
if lock:
updates[Constants.VERSION_LOCK_FIELD] = config.VERSION_LOCK_VALUE
elif (
triggers
and lock_key
and str(all_data.get(lock_key)) == str(config.VERSION_LOCK_VALUE)
):
triggers.clear()
updates[Constants.VERSION_LOCK_FIELD] = config.VERSION_UNLOCK_VALUE
return updates | [
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | get_final_version_string | def get_final_version_string(release_mode, semver, commit_count=0):
"""Generates update dictionary entries for the version string"""
version_string = ".".join(semver)
maybe_dev_version_string = version_string
updates = {}
if release_mode:
# in production, we have something like `1.2.3`, as well as a flag e.g. PRODUCTION=True
updates[Constants.RELEASE_FIELD] = config.RELEASED_VALUE
else:
# in dev mode, we have a dev marker e.g. `1.2.3.dev678`
maybe_dev_version_string = config.DEVMODE_TEMPLATE.format(
version=version_string, count=commit_count
)
# make available all components of the semantic version including the full string
updates[Constants.VERSION_FIELD] = maybe_dev_version_string
updates[Constants.VERSION_STRICT_FIELD] = version_string
return updates | python | def get_final_version_string(release_mode, semver, commit_count=0):
"""Generates update dictionary entries for the version string"""
version_string = ".".join(semver)
maybe_dev_version_string = version_string
updates = {}
if release_mode:
# in production, we have something like `1.2.3`, as well as a flag e.g. PRODUCTION=True
updates[Constants.RELEASE_FIELD] = config.RELEASED_VALUE
else:
# in dev mode, we have a dev marker e.g. `1.2.3.dev678`
maybe_dev_version_string = config.DEVMODE_TEMPLATE.format(
version=version_string, count=commit_count
)
# make available all components of the semantic version including the full string
updates[Constants.VERSION_FIELD] = maybe_dev_version_string
updates[Constants.VERSION_STRICT_FIELD] = version_string
return updates | [
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | get_dvcs_info | def get_dvcs_info():
"""Gets current repository info from git"""
cmd = "git rev-list --count HEAD"
commit_count = str(
int(subprocess.check_output(shlex.split(cmd)).decode("utf8").strip())
)
cmd = "git rev-parse HEAD"
commit = str(subprocess.check_output(shlex.split(cmd)).decode("utf8").strip())
return {Constants.COMMIT_FIELD: commit, Constants.COMMIT_COUNT_FIELD: commit_count} | python | def get_dvcs_info():
"""Gets current repository info from git"""
cmd = "git rev-list --count HEAD"
commit_count = str(
int(subprocess.check_output(shlex.split(cmd)).decode("utf8").strip())
)
cmd = "git rev-parse HEAD"
commit = str(subprocess.check_output(shlex.split(cmd)).decode("utf8").strip())
return {Constants.COMMIT_FIELD: commit, Constants.COMMIT_COUNT_FIELD: commit_count} | [
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Clinical-Genomics/trailblazer | trailblazer/cli/core.py | log_cmd | def log_cmd(context, sampleinfo, sacct, quiet, config):
"""Log an analysis.
CONFIG: MIP config file for an analysis
"""
log_analysis = LogAnalysis(context.obj['store'])
try:
new_run = log_analysis(config, sampleinfo=sampleinfo, sacct=sacct)
except MissingFileError as error:
click.echo(click.style(f"Skipping, missing Sacct file: {error.message}", fg='yellow'))
return
except KeyError as error:
print(click.style(f"unexpected output, missing key: {error.args[0]}", fg='yellow'))
return
if new_run is None:
if not quiet:
click.echo(click.style('Analysis already logged', fg='yellow'))
else:
message = f"New log added: {new_run.family} ({new_run.id}) - {new_run.status}"
click.echo(click.style(message, fg='green')) | python | def log_cmd(context, sampleinfo, sacct, quiet, config):
"""Log an analysis.
CONFIG: MIP config file for an analysis
"""
log_analysis = LogAnalysis(context.obj['store'])
try:
new_run = log_analysis(config, sampleinfo=sampleinfo, sacct=sacct)
except MissingFileError as error:
click.echo(click.style(f"Skipping, missing Sacct file: {error.message}", fg='yellow'))
return
except KeyError as error:
print(click.style(f"unexpected output, missing key: {error.args[0]}", fg='yellow'))
return
if new_run is None:
if not quiet:
click.echo(click.style('Analysis already logged', fg='yellow'))
else:
message = f"New log added: {new_run.family} ({new_run.id}) - {new_run.status}"
click.echo(click.style(message, fg='green')) | [
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Clinical-Genomics/trailblazer | trailblazer/cli/core.py | start | def start(context, mip_config, email, priority, dryrun, command, start_with, family):
"""Start a new analysis."""
mip_cli = MipCli(context.obj['script'])
mip_config = mip_config or context.obj['mip_config']
email = email or environ_email()
kwargs = dict(config=mip_config, family=family, priority=priority, email=email, dryrun=dryrun, start_with=start_with)
if command:
mip_command = mip_cli.build_command(**kwargs)
click.echo(' '.join(mip_command))
else:
try:
mip_cli(**kwargs)
if not dryrun:
context.obj['store'].add_pending(family, email=email)
except MipStartError as error:
click.echo(click.style(error.message, fg='red')) | python | def start(context, mip_config, email, priority, dryrun, command, start_with, family):
"""Start a new analysis."""
mip_cli = MipCli(context.obj['script'])
mip_config = mip_config or context.obj['mip_config']
email = email or environ_email()
kwargs = dict(config=mip_config, family=family, priority=priority, email=email, dryrun=dryrun, start_with=start_with)
if command:
mip_command = mip_cli.build_command(**kwargs)
click.echo(' '.join(mip_command))
else:
try:
mip_cli(**kwargs)
if not dryrun:
context.obj['store'].add_pending(family, email=email)
except MipStartError as error:
click.echo(click.style(error.message, fg='red')) | [
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Clinical-Genomics/trailblazer | trailblazer/cli/core.py | scan | def scan(context, root_dir):
"""Scan a directory for analyses."""
root_dir = root_dir or context.obj['root']
config_files = Path(root_dir).glob('*/analysis/*_config.yaml')
for config_file in config_files:
LOG.debug("found analysis config: %s", config_file)
with config_file.open() as stream:
context.invoke(log_cmd, config=stream, quiet=True)
context.obj['store'].track_update() | python | def scan(context, root_dir):
"""Scan a directory for analyses."""
root_dir = root_dir or context.obj['root']
config_files = Path(root_dir).glob('*/analysis/*_config.yaml')
for config_file in config_files:
LOG.debug("found analysis config: %s", config_file)
with config_file.open() as stream:
context.invoke(log_cmd, config=stream, quiet=True)
context.obj['store'].track_update() | [
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Clinical-Genomics/trailblazer | trailblazer/cli/core.py | user | def user(context, name, email):
"""Add a new or display information about an existing user."""
existing_user = context.obj['store'].user(email)
if existing_user:
click.echo(existing_user.to_dict())
elif name:
new_user = context.obj['store'].add_user(name, email)
click.echo(click.style(f"New user added: {email} ({new_user.id})", fg='green'))
else:
click.echo(click.style('User not found', fg='yellow')) | python | def user(context, name, email):
"""Add a new or display information about an existing user."""
existing_user = context.obj['store'].user(email)
if existing_user:
click.echo(existing_user.to_dict())
elif name:
new_user = context.obj['store'].add_user(name, email)
click.echo(click.style(f"New user added: {email} ({new_user.id})", fg='green'))
else:
click.echo(click.style('User not found', fg='yellow')) | [
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Clinical-Genomics/trailblazer | trailblazer/cli/core.py | cancel | def cancel(context, jobs, analysis_id):
"""Cancel all jobs in a run."""
analysis_obj = context.obj['store'].analysis(analysis_id)
if analysis_obj is None:
click.echo('analysis not found')
context.abort()
elif analysis_obj.status != 'running':
click.echo(f"analysis not running: {analysis_obj.status}")
context.abort()
config_path = Path(analysis_obj.config_path)
with config_path.open() as config_stream:
config_raw = ruamel.yaml.safe_load(config_stream)
config_data = parse_config(config_raw)
log_path = Path(f"{config_data['log_path']}")
if not log_path.exists():
click.echo(f"missing MIP log file: {log_path}")
context.abort()
with log_path.open() as log_stream:
all_jobs = job_ids(log_stream)
if jobs:
for job_id in all_jobs:
click.echo(job_id)
else:
for job_id in all_jobs:
LOG.debug(f"cancelling job: {job_id}")
process = subprocess.Popen(['scancel', job_id])
process.wait()
analysis_obj.status = 'canceled'
context.obj['store'].commit()
click.echo('cancelled analysis successfully!') | python | def cancel(context, jobs, analysis_id):
"""Cancel all jobs in a run."""
analysis_obj = context.obj['store'].analysis(analysis_id)
if analysis_obj is None:
click.echo('analysis not found')
context.abort()
elif analysis_obj.status != 'running':
click.echo(f"analysis not running: {analysis_obj.status}")
context.abort()
config_path = Path(analysis_obj.config_path)
with config_path.open() as config_stream:
config_raw = ruamel.yaml.safe_load(config_stream)
config_data = parse_config(config_raw)
log_path = Path(f"{config_data['log_path']}")
if not log_path.exists():
click.echo(f"missing MIP log file: {log_path}")
context.abort()
with log_path.open() as log_stream:
all_jobs = job_ids(log_stream)
if jobs:
for job_id in all_jobs:
click.echo(job_id)
else:
for job_id in all_jobs:
LOG.debug(f"cancelling job: {job_id}")
process = subprocess.Popen(['scancel', job_id])
process.wait()
analysis_obj.status = 'canceled'
context.obj['store'].commit()
click.echo('cancelled analysis successfully!') | [
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pytroll/posttroll | posttroll/ns.py | NameServer.run | def run(self, *args):
"""Run the listener and answer to requests.
"""
del args
arec = AddressReceiver(max_age=self._max_age,
multicast_enabled=self._multicast_enabled)
arec.start()
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msg = Message.decode(msg)
self.listener.send_unicode(six.text_type(get_active_address(
msg.data["service"], arec)))
except KeyboardInterrupt:
# Needed to stop the nameserver.
pass
finally:
arec.stop()
self.stop() | python | def run(self, *args):
"""Run the listener and answer to requests.
"""
del args
arec = AddressReceiver(max_age=self._max_age,
multicast_enabled=self._multicast_enabled)
arec.start()
port = PORT
try:
with nslock:
self.listener = get_context().socket(REP)
self.listener.bind("tcp://*:" + str(port))
logger.debug('Listening on port %s', str(port))
poller = Poller()
poller.register(self.listener, POLLIN)
while self.loop:
with nslock:
socks = dict(poller.poll(1000))
if socks:
if socks.get(self.listener) == POLLIN:
msg = self.listener.recv_string()
else:
continue
logger.debug("Replying to request: " + str(msg))
msg = Message.decode(msg)
self.listener.send_unicode(six.text_type(get_active_address(
msg.data["service"], arec)))
except KeyboardInterrupt:
# Needed to stop the nameserver.
pass
finally:
arec.stop()
self.stop() | [
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pytroll/posttroll | posttroll/ns.py | NameServer.stop | def stop(self):
"""Stop the name server.
"""
self.listener.setsockopt(LINGER, 1)
self.loop = False
with nslock:
self.listener.close() | python | def stop(self):
"""Stop the name server.
"""
self.listener.setsockopt(LINGER, 1)
self.loop = False
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andrewda/frc-livescore | livescore/simpleocr_utils/segmentation.py | segments_to_numpy | def segments_to_numpy(segments):
"""given a list of 4-element tuples, transforms it into a numpy array"""
segments = numpy.array(segments, dtype=SEGMENT_DATATYPE, ndmin=2) # each segment in a row
segments = segments if SEGMENTS_DIRECTION == 0 else numpy.transpose(segments)
return segments | python | def segments_to_numpy(segments):
"""given a list of 4-element tuples, transforms it into a numpy array"""
segments = numpy.array(segments, dtype=SEGMENT_DATATYPE, ndmin=2) # each segment in a row
segments = segments if SEGMENTS_DIRECTION == 0 else numpy.transpose(segments)
return segments | [
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thespacedoctor/sherlock | sherlock/imports/marshall.py | marshall._create_dictionary_of_marshall | def _create_dictionary_of_marshall(
self,
marshallQuery,
marshallTable):
"""create a list of dictionaries containing all the rows in the marshall stream
**Key Arguments:**
- ``marshallQuery`` -- the query used to lift the required data from the marshall database.
- ``marshallTable`` -- the name of the marshall table we are lifting the data from.
**Return:**
- ``dictList`` - a list of dictionaries containing all the rows in the marshall stream
"""
self.log.debug(
'starting the ``_create_dictionary_of_marshall`` method')
dictList = []
tableName = self.dbTableName
rows = readquery(
log=self.log,
sqlQuery=marshallQuery,
dbConn=self.pmDbConn,
quiet=False
)
totalCount = len(rows)
count = 0
for row in rows:
if "dateCreated" in row:
del row["dateCreated"]
count += 1
if count > 1:
# Cursor up one line and clear line
sys.stdout.write("\x1b[1A\x1b[2K")
print "%(count)s / %(totalCount)s `%(tableName)s` data added to memory" % locals()
dictList.append(dict(row))
self.log.debug(
'completed the ``_create_dictionary_of_marshall`` method')
return dictList | python | def _create_dictionary_of_marshall(
self,
marshallQuery,
marshallTable):
"""create a list of dictionaries containing all the rows in the marshall stream
**Key Arguments:**
- ``marshallQuery`` -- the query used to lift the required data from the marshall database.
- ``marshallTable`` -- the name of the marshall table we are lifting the data from.
**Return:**
- ``dictList`` - a list of dictionaries containing all the rows in the marshall stream
"""
self.log.debug(
'starting the ``_create_dictionary_of_marshall`` method')
dictList = []
tableName = self.dbTableName
rows = readquery(
log=self.log,
sqlQuery=marshallQuery,
dbConn=self.pmDbConn,
quiet=False
)
totalCount = len(rows)
count = 0
for row in rows:
if "dateCreated" in row:
del row["dateCreated"]
count += 1
if count > 1:
# Cursor up one line and clear line
sys.stdout.write("\x1b[1A\x1b[2K")
print "%(count)s / %(totalCount)s `%(tableName)s` data added to memory" % locals()
dictList.append(dict(row))
self.log.debug(
'completed the ``_create_dictionary_of_marshall`` method')
return dictList | [
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thespacedoctor/sherlock | sherlock/imports/ned_d.py | ned_d.ingest | def ingest(self):
"""Import the ned_d catalogue into the catalogues database
The method first generates a list of python dictionaries from the ned_d datafile, imports this list of dictionaries into a database table and then generates the HTMIDs for that table.
**Usage:**
See class docstring for usage
.. todo ::
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``get`` method')
dictList = self._create_dictionary_of_ned_d()
self.primaryIdColumnName = "primaryId"
self.raColName = "raDeg"
self.declColName = "decDeg"
tableName = self.dbTableName
createStatement = u"""
CREATE TABLE `%(tableName)s` (
`primaryId` bigint(20) NOT NULL AUTO_INCREMENT COMMENT 'An internal counter',
`Method` varchar(150) DEFAULT NULL,
`dateCreated` datetime DEFAULT CURRENT_TIMESTAMP,
`dateLastModified` datetime DEFAULT CURRENT_TIMESTAMP,
`updated` varchar(45) DEFAULT '0',
`dist_derived_from_sn` varchar(150) DEFAULT NULL,
`dist_in_ned_flag` varchar(10) DEFAULT NULL,
`dist_index_id` mediumint(9) DEFAULT NULL,
`dist_mod` double DEFAULT NULL,
`dist_mod_err` double DEFAULT NULL,
`dist_mpc` double DEFAULT NULL,
`galaxy_index_id` mediumint(9) DEFAULT NULL,
`hubble_const` double DEFAULT NULL,
`lmc_mod` double DEFAULT NULL,
`notes` varchar(500) DEFAULT NULL,
`primary_ned_id` varchar(150) DEFAULT NULL,
`redshift` double DEFAULT NULL,
`ref` varchar(150) DEFAULT NULL,
`ref_date` int(11) DEFAULT NULL,
`master_row` tinyint(4) DEFAULT '0',
`major_diameter_arcmin` double DEFAULT NULL,
`ned_notes` varchar(700) DEFAULT NULL,
`object_type` varchar(100) DEFAULT NULL,
`redshift_err` double DEFAULT NULL,
`redshift_quality` varchar(100) DEFAULT NULL,
`magnitude_filter` varchar(10) DEFAULT NULL,
`minor_diameter_arcmin` double DEFAULT NULL,
`morphology` varchar(50) DEFAULT NULL,
`hierarchy` varchar(50) DEFAULT NULL,
`galaxy_morphology` varchar(50) DEFAULT NULL,
`radio_morphology` varchar(50) DEFAULT NULL,
`activity_type` varchar(50) DEFAULT NULL,
`in_ned` tinyint(4) DEFAULT NULL,
`raDeg` double DEFAULT NULL,
`decDeg` double DEFAULT NULL,
`eb_v` double DEFAULT NULL,
`sdss_coverage` TINYINT DEFAULT NULL,
PRIMARY KEY (`primaryId`),
UNIQUE KEY `galaxy_index_id_dist_index_id` (`galaxy_index_id`,`dist_index_id`)
) ENGINE=MyISAM AUTO_INCREMENT=0 DEFAULT CHARSET=latin1;
DROP VIEW IF EXISTS `view_%(tableName)s_master_recorders`;
CREATE
VIEW `view_%(tableName)s_master_recorders` AS
(SELECT
`%(tableName)s`.`primary_ned_id` AS `primary_ned_id`,
`%(tableName)s`.`object_type` AS `object_type`,
`%(tableName)s`.`raDeg` AS `raDeg`,
`%(tableName)s`.`decDeg` AS `decDeg`,
`%(tableName)s`.`dist_mpc` AS `dist_mpc`,
`%(tableName)s`.`dist_mod` AS `dist_mod`,
`%(tableName)s`.`dist_mod_err` AS `dist_mod_err`,
`%(tableName)s`.`Method` AS `dist_measurement_method`,
`%(tableName)s`.`redshift` AS `redshift`,
`%(tableName)s`.`redshift_err` AS `redshift_err`,
`%(tableName)s`.`redshift_quality` AS `redshift_quality`,
`%(tableName)s`.`major_diameter_arcmin` AS `major_diameter_arcmin`,
`%(tableName)s`.`minor_diameter_arcmin` AS `minor_diameter_arcmin`,
`%(tableName)s`.`magnitude_filter` AS `magnitude_filter`,
`%(tableName)s`.`eb_v` AS `gal_eb_v`,
`%(tableName)s`.`hierarchy` AS `hierarchy`,
`%(tableName)s`.`morphology` AS `morphology`,
`%(tableName)s`.`radio_morphology` AS `radio_morphology`,
`%(tableName)s`.`activity_type` AS `activity_type`,
`%(tableName)s`.`ned_notes` AS `ned_notes`,
`%(tableName)s`.`in_ned` AS `in_ned`,
`%(tableName)s`.`primaryId` AS `primaryId`
FROM
`%(tableName)s`
WHERE
(`%(tableName)s`.`master_row` = 1));
""" % locals()
self.add_data_to_database_table(
dictList=dictList,
createStatement=createStatement
)
self._clean_up_columns()
self._get_metadata_for_galaxies()
self._update_sdss_coverage()
self.log.debug('completed the ``get`` method')
return None | python | def ingest(self):
"""Import the ned_d catalogue into the catalogues database
The method first generates a list of python dictionaries from the ned_d datafile, imports this list of dictionaries into a database table and then generates the HTMIDs for that table.
**Usage:**
See class docstring for usage
.. todo ::
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``get`` method')
dictList = self._create_dictionary_of_ned_d()
self.primaryIdColumnName = "primaryId"
self.raColName = "raDeg"
self.declColName = "decDeg"
tableName = self.dbTableName
createStatement = u"""
CREATE TABLE `%(tableName)s` (
`primaryId` bigint(20) NOT NULL AUTO_INCREMENT COMMENT 'An internal counter',
`Method` varchar(150) DEFAULT NULL,
`dateCreated` datetime DEFAULT CURRENT_TIMESTAMP,
`dateLastModified` datetime DEFAULT CURRENT_TIMESTAMP,
`updated` varchar(45) DEFAULT '0',
`dist_derived_from_sn` varchar(150) DEFAULT NULL,
`dist_in_ned_flag` varchar(10) DEFAULT NULL,
`dist_index_id` mediumint(9) DEFAULT NULL,
`dist_mod` double DEFAULT NULL,
`dist_mod_err` double DEFAULT NULL,
`dist_mpc` double DEFAULT NULL,
`galaxy_index_id` mediumint(9) DEFAULT NULL,
`hubble_const` double DEFAULT NULL,
`lmc_mod` double DEFAULT NULL,
`notes` varchar(500) DEFAULT NULL,
`primary_ned_id` varchar(150) DEFAULT NULL,
`redshift` double DEFAULT NULL,
`ref` varchar(150) DEFAULT NULL,
`ref_date` int(11) DEFAULT NULL,
`master_row` tinyint(4) DEFAULT '0',
`major_diameter_arcmin` double DEFAULT NULL,
`ned_notes` varchar(700) DEFAULT NULL,
`object_type` varchar(100) DEFAULT NULL,
`redshift_err` double DEFAULT NULL,
`redshift_quality` varchar(100) DEFAULT NULL,
`magnitude_filter` varchar(10) DEFAULT NULL,
`minor_diameter_arcmin` double DEFAULT NULL,
`morphology` varchar(50) DEFAULT NULL,
`hierarchy` varchar(50) DEFAULT NULL,
`galaxy_morphology` varchar(50) DEFAULT NULL,
`radio_morphology` varchar(50) DEFAULT NULL,
`activity_type` varchar(50) DEFAULT NULL,
`in_ned` tinyint(4) DEFAULT NULL,
`raDeg` double DEFAULT NULL,
`decDeg` double DEFAULT NULL,
`eb_v` double DEFAULT NULL,
`sdss_coverage` TINYINT DEFAULT NULL,
PRIMARY KEY (`primaryId`),
UNIQUE KEY `galaxy_index_id_dist_index_id` (`galaxy_index_id`,`dist_index_id`)
) ENGINE=MyISAM AUTO_INCREMENT=0 DEFAULT CHARSET=latin1;
DROP VIEW IF EXISTS `view_%(tableName)s_master_recorders`;
CREATE
VIEW `view_%(tableName)s_master_recorders` AS
(SELECT
`%(tableName)s`.`primary_ned_id` AS `primary_ned_id`,
`%(tableName)s`.`object_type` AS `object_type`,
`%(tableName)s`.`raDeg` AS `raDeg`,
`%(tableName)s`.`decDeg` AS `decDeg`,
`%(tableName)s`.`dist_mpc` AS `dist_mpc`,
`%(tableName)s`.`dist_mod` AS `dist_mod`,
`%(tableName)s`.`dist_mod_err` AS `dist_mod_err`,
`%(tableName)s`.`Method` AS `dist_measurement_method`,
`%(tableName)s`.`redshift` AS `redshift`,
`%(tableName)s`.`redshift_err` AS `redshift_err`,
`%(tableName)s`.`redshift_quality` AS `redshift_quality`,
`%(tableName)s`.`major_diameter_arcmin` AS `major_diameter_arcmin`,
`%(tableName)s`.`minor_diameter_arcmin` AS `minor_diameter_arcmin`,
`%(tableName)s`.`magnitude_filter` AS `magnitude_filter`,
`%(tableName)s`.`eb_v` AS `gal_eb_v`,
`%(tableName)s`.`hierarchy` AS `hierarchy`,
`%(tableName)s`.`morphology` AS `morphology`,
`%(tableName)s`.`radio_morphology` AS `radio_morphology`,
`%(tableName)s`.`activity_type` AS `activity_type`,
`%(tableName)s`.`ned_notes` AS `ned_notes`,
`%(tableName)s`.`in_ned` AS `in_ned`,
`%(tableName)s`.`primaryId` AS `primaryId`
FROM
`%(tableName)s`
WHERE
(`%(tableName)s`.`master_row` = 1));
""" % locals()
self.add_data_to_database_table(
dictList=dictList,
createStatement=createStatement
)
self._clean_up_columns()
self._get_metadata_for_galaxies()
self._update_sdss_coverage()
self.log.debug('completed the ``get`` method')
return None | [
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**Usage:**
See class docstring for usage
.. todo ::
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring | [
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thespacedoctor/sherlock | sherlock/imports/ned_d.py | ned_d._create_dictionary_of_ned_d | def _create_dictionary_of_ned_d(
self):
"""create a list of dictionaries containing all the rows in the ned_d catalogue
**Return:**
- ``dictList`` - a list of dictionaries containing all the rows in the ned_d catalogue
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug(
'starting the ``_create_dictionary_of_ned_d`` method')
count = 0
with open(self.pathToDataFile, 'rb') as csvFile:
csvReader = csv.reader(
csvFile, dialect='excel', delimiter=',', quotechar='"')
totalRows = sum(1 for row in csvReader)
csvFile.close()
totalCount = totalRows
with open(self.pathToDataFile, 'rb') as csvFile:
csvReader = csv.reader(
csvFile, dialect='excel', delimiter=',', quotechar='"')
theseKeys = []
dictList = []
for row in csvReader:
if len(theseKeys) == 0:
totalRows -= 1
if "Exclusion Code" in row and "Hubble const." in row:
for i in row:
if i == "redshift (z)":
theseKeys.append("redshift")
elif i == "Hubble const.":
theseKeys.append("hubble_const")
elif i == "G":
theseKeys.append("galaxy_index_id")
elif i == "err":
theseKeys.append("dist_mod_err")
elif i == "D (Mpc)":
theseKeys.append("dist_mpc")
elif i == "Date (Yr. - 1980)":
theseKeys.append("ref_date")
elif i == "REFCODE":
theseKeys.append("ref")
elif i == "Exclusion Code":
theseKeys.append("dist_in_ned_flag")
elif i == "Adopted LMC modulus":
theseKeys.append("lmc_mod")
elif i == "m-M":
theseKeys.append("dist_mod")
elif i == "Notes":
theseKeys.append("notes")
elif i == "SN ID":
theseKeys.append("dist_derived_from_sn")
elif i == "method":
theseKeys.append("dist_method")
elif i == "Galaxy ID":
theseKeys.append("primary_ned_id")
elif i == "D":
theseKeys.append("dist_index_id")
else:
theseKeys.append(i)
continue
if len(theseKeys):
count += 1
if count > 1:
# Cursor up one line and clear line
sys.stdout.write("\x1b[1A\x1b[2K")
if count > totalCount:
count = totalCount
percent = (float(count) / float(totalCount)) * 100.
print "%(count)s / %(totalCount)s (%(percent)1.1f%%) rows added to memory" % locals()
rowDict = {}
for t, r in zip(theseKeys, row):
rowDict[t] = r
if t == "ref_date":
try:
rowDict[t] = int(r) + 1980
except:
rowDict[t] = None
if rowDict["dist_index_id"] != "999999":
dictList.append(rowDict)
csvFile.close()
self.log.debug(
'completed the ``_create_dictionary_of_ned_d`` method')
return dictList | python | def _create_dictionary_of_ned_d(
self):
"""create a list of dictionaries containing all the rows in the ned_d catalogue
**Return:**
- ``dictList`` - a list of dictionaries containing all the rows in the ned_d catalogue
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug(
'starting the ``_create_dictionary_of_ned_d`` method')
count = 0
with open(self.pathToDataFile, 'rb') as csvFile:
csvReader = csv.reader(
csvFile, dialect='excel', delimiter=',', quotechar='"')
totalRows = sum(1 for row in csvReader)
csvFile.close()
totalCount = totalRows
with open(self.pathToDataFile, 'rb') as csvFile:
csvReader = csv.reader(
csvFile, dialect='excel', delimiter=',', quotechar='"')
theseKeys = []
dictList = []
for row in csvReader:
if len(theseKeys) == 0:
totalRows -= 1
if "Exclusion Code" in row and "Hubble const." in row:
for i in row:
if i == "redshift (z)":
theseKeys.append("redshift")
elif i == "Hubble const.":
theseKeys.append("hubble_const")
elif i == "G":
theseKeys.append("galaxy_index_id")
elif i == "err":
theseKeys.append("dist_mod_err")
elif i == "D (Mpc)":
theseKeys.append("dist_mpc")
elif i == "Date (Yr. - 1980)":
theseKeys.append("ref_date")
elif i == "REFCODE":
theseKeys.append("ref")
elif i == "Exclusion Code":
theseKeys.append("dist_in_ned_flag")
elif i == "Adopted LMC modulus":
theseKeys.append("lmc_mod")
elif i == "m-M":
theseKeys.append("dist_mod")
elif i == "Notes":
theseKeys.append("notes")
elif i == "SN ID":
theseKeys.append("dist_derived_from_sn")
elif i == "method":
theseKeys.append("dist_method")
elif i == "Galaxy ID":
theseKeys.append("primary_ned_id")
elif i == "D":
theseKeys.append("dist_index_id")
else:
theseKeys.append(i)
continue
if len(theseKeys):
count += 1
if count > 1:
# Cursor up one line and clear line
sys.stdout.write("\x1b[1A\x1b[2K")
if count > totalCount:
count = totalCount
percent = (float(count) / float(totalCount)) * 100.
print "%(count)s / %(totalCount)s (%(percent)1.1f%%) rows added to memory" % locals()
rowDict = {}
for t, r in zip(theseKeys, row):
rowDict[t] = r
if t == "ref_date":
try:
rowDict[t] = int(r) + 1980
except:
rowDict[t] = None
if rowDict["dist_index_id"] != "999999":
dictList.append(rowDict)
csvFile.close()
self.log.debug(
'completed the ``_create_dictionary_of_ned_d`` method')
return dictList | [
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- update return values and definitions
- update usage examples and text
- update docstring text
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- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring | [
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thespacedoctor/sherlock | sherlock/imports/ned_d.py | ned_d._clean_up_columns | def _clean_up_columns(
self):
"""clean up columns of the NED table
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``_clean_up_columns`` method')
tableName = self.dbTableName
print "cleaning up %(tableName)s columns" % locals()
sqlQuery = u"""
set sql_mode="STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION";
""" % locals()
writequery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
)
sqlQuery = u"""
update %(tableName)s set dist_mod_err = null where dist_mod_err = 0;
update %(tableName)s set dist_in_ned_flag = null where dist_in_ned_flag = "";
update %(tableName)s set notes = null where notes = "";
update %(tableName)s set redshift = null where redshift = 0;
update %(tableName)s set dist_derived_from_sn = null where dist_derived_from_sn = "";
update %(tableName)s set hubble_const = null where hubble_const = 0;
update %(tableName)s set lmc_mod = null where lmc_mod = 0;
update %(tableName)s set master_row = 0;
update %(tableName)s set master_row = 1 where primaryId in (select * from (select distinct primaryId from %(tableName)s group by galaxy_index_id) as alias);
""" % locals()
writequery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
)
self.log.debug('completed the ``_clean_up_columns`` method')
return None | python | def _clean_up_columns(
self):
"""clean up columns of the NED table
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``_clean_up_columns`` method')
tableName = self.dbTableName
print "cleaning up %(tableName)s columns" % locals()
sqlQuery = u"""
set sql_mode="STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION";
""" % locals()
writequery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
)
sqlQuery = u"""
update %(tableName)s set dist_mod_err = null where dist_mod_err = 0;
update %(tableName)s set dist_in_ned_flag = null where dist_in_ned_flag = "";
update %(tableName)s set notes = null where notes = "";
update %(tableName)s set redshift = null where redshift = 0;
update %(tableName)s set dist_derived_from_sn = null where dist_derived_from_sn = "";
update %(tableName)s set hubble_const = null where hubble_const = 0;
update %(tableName)s set lmc_mod = null where lmc_mod = 0;
update %(tableName)s set master_row = 0;
update %(tableName)s set master_row = 1 where primaryId in (select * from (select distinct primaryId from %(tableName)s group by galaxy_index_id) as alias);
""" % locals()
writequery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
)
self.log.debug('completed the ``_clean_up_columns`` method')
return None | [
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- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
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thespacedoctor/sherlock | sherlock/imports/ned_d.py | ned_d._get_metadata_for_galaxies | def _get_metadata_for_galaxies(
self):
"""get metadata for galaxies
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``_get_metadata_for_galaxies`` method')
total, batches = self._count_galaxies_requiring_metadata()
print "%(total)s galaxies require metadata. Need to send %(batches)s batch requests to NED." % locals()
totalBatches = self.batches
thisCount = 0
# FOR EACH BATCH, GET THE GALAXY IDs, QUERY NED AND UPDATE THE DATABASE
while self.total:
thisCount += 1
self._get_3000_galaxies_needing_metadata()
dictList = self._query_ned_and_add_results_to_database(thisCount)
self.add_data_to_database_table(
dictList=dictList,
createStatement=False
)
self._count_galaxies_requiring_metadata()
self.log.debug('completed the ``_get_metadata_for_galaxies`` method')
return None | python | def _get_metadata_for_galaxies(
self):
"""get metadata for galaxies
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``_get_metadata_for_galaxies`` method')
total, batches = self._count_galaxies_requiring_metadata()
print "%(total)s galaxies require metadata. Need to send %(batches)s batch requests to NED." % locals()
totalBatches = self.batches
thisCount = 0
# FOR EACH BATCH, GET THE GALAXY IDs, QUERY NED AND UPDATE THE DATABASE
while self.total:
thisCount += 1
self._get_3000_galaxies_needing_metadata()
dictList = self._query_ned_and_add_results_to_database(thisCount)
self.add_data_to_database_table(
dictList=dictList,
createStatement=False
)
self._count_galaxies_requiring_metadata()
self.log.debug('completed the ``_get_metadata_for_galaxies`` method')
return None | [
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- update docstring text
- check sublime snippet exists
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- regenerate the docs and check redendering of this docstring | [
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thespacedoctor/sherlock | sherlock/imports/ned_d.py | ned_d._get_3000_galaxies_needing_metadata | def _get_3000_galaxies_needing_metadata(
self):
""" get 3000 galaxies needing metadata
**Return:**
- ``len(self.theseIds)`` -- the number of NED IDs returned
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug(
'starting the ``_get_3000_galaxies_needing_metadata`` method')
tableName = self.dbTableName
# SELECT THE DATA FROM NED TABLE
self.theseIds = {}
sqlQuery = u"""
select primaryId, primary_ned_id from %(tableName)s where master_row = 1 and in_ned is null limit 3000;
""" % locals()
rows = readquery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
quiet=False
)
for row in rows:
self.theseIds[row["primary_ned_id"]] = row["primaryId"]
self.log.debug(
'completed the ``_get_3000_galaxies_needing_metadata`` method')
return len(self.theseIds) | python | def _get_3000_galaxies_needing_metadata(
self):
""" get 3000 galaxies needing metadata
**Return:**
- ``len(self.theseIds)`` -- the number of NED IDs returned
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug(
'starting the ``_get_3000_galaxies_needing_metadata`` method')
tableName = self.dbTableName
# SELECT THE DATA FROM NED TABLE
self.theseIds = {}
sqlQuery = u"""
select primaryId, primary_ned_id from %(tableName)s where master_row = 1 and in_ned is null limit 3000;
""" % locals()
rows = readquery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
quiet=False
)
for row in rows:
self.theseIds[row["primary_ned_id"]] = row["primaryId"]
self.log.debug(
'completed the ``_get_3000_galaxies_needing_metadata`` method')
return len(self.theseIds) | [
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.. todo ::
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- update return values and definitions
- update usage examples and text
- update docstring text
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thespacedoctor/sherlock | sherlock/imports/ned_d.py | ned_d._update_sdss_coverage | def _update_sdss_coverage(
self):
""" update sdss coverage
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``_update_sdss_coverage`` method')
tableName = self.dbTableName
# SELECT THE LOCATIONS NEEDING TO BE CHECKED
sqlQuery = u"""
select primary_ned_id, primaryID, raDeg, decDeg, sdss_coverage from %(tableName)s where sdss_coverage is null and master_row = 1 and in_ned = 1 order by dist_mpc;
""" % locals()
rows = readquery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
quiet=False
)
totalCount = len(rows)
count = 0
for row in rows:
count += 1
if count > 1:
# Cursor up three lines and clear
sys.stdout.write("\x1b[1A\x1b[2K")
sys.stdout.write("\x1b[1A\x1b[2K")
sys.stdout.write("\x1b[1A\x1b[2K")
if count > totalCount:
count = totalCount
percent = (float(count) / float(totalCount)) * 100.
primaryID = row["primaryID"]
raDeg = float(row["raDeg"])
decDeg = float(row["decDeg"])
primary_ned_id = row["primary_ned_id"]
# SDSS CAN ONLY ACCEPT 60 QUERIES/MIN
time.sleep(1.1)
print "%(count)s / %(totalCount)s (%(percent)1.1f%%) NED galaxies checked for SDSS coverage" % locals()
print "NED NAME: ", primary_ned_id
# covered = True | False | 999 (i.e. not sure)
sdss_coverage = check_coverage(
log=self.log,
ra=raDeg,
dec=decDeg
).get()
if sdss_coverage == 999:
sdss_coverage_flag = "null"
elif sdss_coverage == True:
sdss_coverage_flag = 1
elif sdss_coverage == False:
sdss_coverage_flag = 0
else:
self.log.error('cound not get sdss coverage' % locals())
sys.exit(0)
# UPDATE THE DATABASE FLAG
sqlQuery = u"""
update %(tableName)s set sdss_coverage = %(sdss_coverage_flag)s where primaryID = %(primaryID)s
""" % locals()
writequery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
)
self.log.debug('completed the ``_update_sdss_coverage`` method')
return None | python | def _update_sdss_coverage(
self):
""" update sdss coverage
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``_update_sdss_coverage`` method')
tableName = self.dbTableName
# SELECT THE LOCATIONS NEEDING TO BE CHECKED
sqlQuery = u"""
select primary_ned_id, primaryID, raDeg, decDeg, sdss_coverage from %(tableName)s where sdss_coverage is null and master_row = 1 and in_ned = 1 order by dist_mpc;
""" % locals()
rows = readquery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
quiet=False
)
totalCount = len(rows)
count = 0
for row in rows:
count += 1
if count > 1:
# Cursor up three lines and clear
sys.stdout.write("\x1b[1A\x1b[2K")
sys.stdout.write("\x1b[1A\x1b[2K")
sys.stdout.write("\x1b[1A\x1b[2K")
if count > totalCount:
count = totalCount
percent = (float(count) / float(totalCount)) * 100.
primaryID = row["primaryID"]
raDeg = float(row["raDeg"])
decDeg = float(row["decDeg"])
primary_ned_id = row["primary_ned_id"]
# SDSS CAN ONLY ACCEPT 60 QUERIES/MIN
time.sleep(1.1)
print "%(count)s / %(totalCount)s (%(percent)1.1f%%) NED galaxies checked for SDSS coverage" % locals()
print "NED NAME: ", primary_ned_id
# covered = True | False | 999 (i.e. not sure)
sdss_coverage = check_coverage(
log=self.log,
ra=raDeg,
dec=decDeg
).get()
if sdss_coverage == 999:
sdss_coverage_flag = "null"
elif sdss_coverage == True:
sdss_coverage_flag = 1
elif sdss_coverage == False:
sdss_coverage_flag = 0
else:
self.log.error('cound not get sdss coverage' % locals())
sys.exit(0)
# UPDATE THE DATABASE FLAG
sqlQuery = u"""
update %(tableName)s set sdss_coverage = %(sdss_coverage_flag)s where primaryID = %(primaryID)s
""" % locals()
writequery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
)
self.log.debug('completed the ``_update_sdss_coverage`` method')
return None | [
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- regenerate the docs and check redendering of this docstring | [
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emichael/PyREM | pyrem/host.py | RemoteHost._rsync_cmd | def _rsync_cmd(self):
"""Helper method to generate base rsync command."""
cmd = ['rsync']
if self._identity_file:
cmd += ['-e', 'ssh -i ' + os.path.expanduser(self._identity_file)]
return cmd | python | def _rsync_cmd(self):
"""Helper method to generate base rsync command."""
cmd = ['rsync']
if self._identity_file:
cmd += ['-e', 'ssh -i ' + os.path.expanduser(self._identity_file)]
return cmd | [
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"."
] | 2609249ead197cd9496d164f4998ca9985503579 | https://github.com/emichael/PyREM/blob/2609249ead197cd9496d164f4998ca9985503579/pyrem/host.py#L61-L66 | train | 49,898 |
emichael/PyREM | pyrem/host.py | RemoteHost.send_file | def send_file(self, file_name, remote_destination=None, **kwargs):
"""Send a file to a remote host with rsync.
Args:
file_name (str): The relative location of the file on the local
host.
remote_destination (str): The destination for the file on the remote
host. If `None`, will be assumed to be the same as
**file_name**. Default `None`.
**kwargs: Passed to ``SubprocessTask``'s init method.
Return:
``pyrem.task.SubprocessTask``: The resulting task.
"""
if not remote_destination:
remote_destination = file_name
return SubprocessTask(
self._rsync_cmd() +
['-ut', file_name, '%s:%s' % (self.hostname, remote_destination)],
**kwargs) | python | def send_file(self, file_name, remote_destination=None, **kwargs):
"""Send a file to a remote host with rsync.
Args:
file_name (str): The relative location of the file on the local
host.
remote_destination (str): The destination for the file on the remote
host. If `None`, will be assumed to be the same as
**file_name**. Default `None`.
**kwargs: Passed to ``SubprocessTask``'s init method.
Return:
``pyrem.task.SubprocessTask``: The resulting task.
"""
if not remote_destination:
remote_destination = file_name
return SubprocessTask(
self._rsync_cmd() +
['-ut', file_name, '%s:%s' % (self.hostname, remote_destination)],
**kwargs) | [
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Args:
file_name (str): The relative location of the file on the local
host.
remote_destination (str): The destination for the file on the remote
host. If `None`, will be assumed to be the same as
**file_name**. Default `None`.
**kwargs: Passed to ``SubprocessTask``'s init method.
Return:
``pyrem.task.SubprocessTask``: The resulting task. | [
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] | 2609249ead197cd9496d164f4998ca9985503579 | https://github.com/emichael/PyREM/blob/2609249ead197cd9496d164f4998ca9985503579/pyrem/host.py#L68-L90 | train | 49,899 |
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