Search is not available for this dataset
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def pnorm(stat, stat0):
""" [P(X>pi, mu, sigma) for pi in pvalues] for normal distributed stat with
expectation value mu and std deviation sigma """
mu, sigma = mean_and_std_dev(stat0)
stat = to_one_dim_array(stat, np.float64)
args = (stat - mu) / sigma
return 1-(0.5 * (1.0 + scipy.special.erf... |
def pemp(stat, stat0):
""" Computes empirical values identically to bioconductor/qvalue empPvals """
assert len(stat0) > 0
assert len(stat) > 0
stat = np.array(stat)
stat0 = np.array(stat0)
m = len(stat)
m0 = len(stat0)
statc = np.concatenate((stat, stat0))
v = np.array([True] * ... |
def pi0est(p_values, lambda_ = np.arange(0.05,1.0,0.05), pi0_method = "smoother", smooth_df = 3, smooth_log_pi0 = False):
""" Estimate pi0 according to bioconductor/qvalue """
# Compare to bioconductor/qvalue reference implementation
# import rpy2
# import rpy2.robjects as robjects
# from rpy2.robj... |
def lfdr(p_values, pi0, trunc = True, monotone = True, transf = "probit", adj = 1.5, eps = np.power(10.0,-8)):
""" Estimate local FDR / posterior error probability from p-values according to bioconductor/qvalue """
p = np.array(p_values)
# Compare to bioconductor/qvalue reference implementation
# impor... |
def final_err_table(df, num_cut_offs=51):
""" Create artificial cutoff sample points from given range of cutoff
values in df, number of sample points is 'num_cut_offs' """
cutoffs = df.cutoff.values
min_ = min(cutoffs)
max_ = max(cutoffs)
# extend max_ and min_ by 5 % of full range
margin =... |
def summary_err_table(df, qvalues=[0, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5]):
""" Summary error table for some typical q-values """
qvalues = to_one_dim_array(qvalues)
# find best matching fows in df for given qvalues:
ix = find_nearest_matches(np.float32(df.qvalue.values), qvalues)
# extract ... |
def error_statistics(target_scores, decoy_scores, parametric, pfdr, pi0_lambda, pi0_method = "smoother", pi0_smooth_df = 3, pi0_smooth_log_pi0 = False, compute_lfdr = False, lfdr_trunc = True, lfdr_monotone = True, lfdr_transf = "probit", lfdr_adj = 1.5, lfdr_eps = np.power(10.0,-8)):
""" Takes list of decoy and ta... |
def find_cutoff(tt_scores, td_scores, cutoff_fdr, parametric, pfdr, pi0_lambda, pi0_method, pi0_smooth_df, pi0_smooth_log_pi0):
""" Finds cut off target score for specified false discovery rate fdr """
error_stat, pi0 = error_statistics(tt_scores, td_scores, parametric, pfdr, pi0_lambda, pi0_method, pi0_smooth... |
def score(infile, outfile, classifier, xgb_autotune, apply_weights, xeval_fraction, xeval_num_iter, ss_initial_fdr, ss_iteration_fdr, ss_num_iter, ss_main_score, group_id, parametric, pfdr, pi0_lambda, pi0_method, pi0_smooth_df, pi0_smooth_log_pi0, lfdr_truncate, lfdr_monotone, lfdr_transformation, lfdr_adj, lfdr_eps, ... |
def ipf(infile, outfile, ipf_ms1_scoring, ipf_ms2_scoring, ipf_h0, ipf_grouped_fdr, ipf_max_precursor_pep, ipf_max_peakgroup_pep, ipf_max_precursor_peakgroup_pep, ipf_max_transition_pep):
"""
Infer peptidoforms after scoring of MS1, MS2 and transition-level data.
"""
if outfile is None:
outfile... |
def peptide(infile, outfile, context, parametric, pfdr, pi0_lambda, pi0_method, pi0_smooth_df, pi0_smooth_log_pi0, lfdr_truncate, lfdr_monotone, lfdr_transformation, lfdr_adj, lfdr_eps):
"""
Infer peptides and conduct error-rate estimation in different contexts.
"""
if outfile is None:
outfile ... |
def protein(infile, outfile, context, parametric, pfdr, pi0_lambda, pi0_method, pi0_smooth_df, pi0_smooth_log_pi0, lfdr_truncate, lfdr_monotone, lfdr_transformation, lfdr_adj, lfdr_eps):
"""
Infer proteins and conduct error-rate estimation in different contexts.
"""
if outfile is None:
outfile ... |
def subsample(infile, outfile, subsample_ratio, test):
"""
Subsample OpenSWATH file to minimum for integrated scoring
"""
if outfile is None:
outfile = infile
else:
outfile = outfile
subsample_osw(infile, outfile, subsample_ratio, test) |
def reduce(infile, outfile):
"""
Reduce scored PyProphet file to minimum for global scoring
"""
if outfile is None:
outfile = infile
else:
outfile = outfile
reduce_osw(infile, outfile) |
def merge(infiles, outfile, same_run, templatefile):
"""
Merge multiple OSW files and (for large experiments, it is recommended to subsample first).
"""
if len(infiles) < 1:
raise click.ClickException("At least one PyProphet input file needs to be provided.")
merge_osw(infiles, outfile, te... |
def backpropagate(infile, outfile, apply_scores):
"""
Backpropagate multi-run peptide and protein scores to single files
"""
if outfile is None:
outfile = infile
else:
outfile = outfile
backpropagate_oswr(infile, outfile, apply_scores) |
def export(infile, outfile, format, outcsv, transition_quantification, max_transition_pep, ipf, ipf_max_peptidoform_pep, max_rs_peakgroup_qvalue, peptide, max_global_peptide_qvalue, protein, max_global_protein_qvalue):
"""
Export TSV/CSV tables
"""
if format == "score_plots":
export_score_plots(... |
def export_compound(infile, outfile, format, outcsv, max_rs_peakgroup_qvalue):
"""
Export Compound TSV/CSV tables
"""
if format == "score_plots":
export_score_plots(infile)
else:
if outfile is None:
if outcsv:
outfile = infile.split(".osw")[0] + ".csv"
... |
def filter(sqmassfiles, infile, max_precursor_pep, max_peakgroup_pep, max_transition_pep):
"""
Filter sqMass files
"""
filter_sqmass(sqmassfiles, infile, max_precursor_pep, max_peakgroup_pep, max_transition_pep) |
def search_groups(self, **kwargs):
"""
Returns a list of restclients.GroupReference objects matching the
passed parameters. Valid parameters are:
name: parts_of_name
name may include the wild-card (*) character.
stem: group_stem
member: member ... |
def get_group_by_id(self, group_id):
"""
Returns a restclients.Group object for the group identified by the
passed group ID.
"""
self._valid_group_id(group_id)
url = "{}/group/{}".format(self.API, group_id)
data = self._get_resource(url)
return self._gr... |
def create_group(self, group):
"""
Creates a group from the passed restclients.Group object.
"""
self._valid_group_id(group.id)
body = {"data": group.json_data()}
url = "{}/group/{}".format(self.API, group.name)
data = self._put_resource(url, headers={}, body=bo... |
def delete_group(self, group_id):
"""
Deletes the group identified by the passed group ID.
"""
self._valid_group_id(group_id)
url = "{}/group/{}".format(self.API, group_id)
self._delete_resource(url)
return True |
def get_members(self, group_id):
"""
Returns a list of restclients.GroupMember objects for the group
identified by the passed group ID.
"""
self._valid_group_id(group_id)
url = "{}/group/{}/member".format(self.API, group_id)
data = self._get_resource(url)
... |
def update_members(self, group_id, members):
"""
Updates the membership of the group represented by the passed group id.
Returns a list of members not found.
"""
self._valid_group_id(group_id)
body = {"data": [m.json_data() for m in members]}
headers = {"If-Match... |
def get_effective_member_count(self, group_id):
"""
Returns a count of effective members for the group identified by the
passed group ID.
"""
self._valid_group_id(group_id)
url = "{}/group/{}/effective_member?view=count".format(self.API,
... |
def is_effective_member(self, group_id, netid):
"""
Returns True if the netid is in the group, False otherwise.
"""
self._valid_group_id(group_id)
# GWS doesn't accept EPPNs on effective member checks, for UW users
netid = re.sub('@washington.edu', '', netid)
ur... |
def modify_conf():
"""
pip install redbaron
"""
import redbaron
import ubelt as ub
conf_path = 'docs/conf.py'
source = ub.readfrom(conf_path)
red = redbaron.RedBaron(source)
# Insert custom extensions
extra_extensions = [
'"sphinxcontrib.napoleon"'
]
ext_node =... |
def parse_version():
""" Statically parse the version number from __init__.py """
from os.path import dirname, join
import ast
modname = setupkw['name']
init_fpath = join(dirname(__file__), modname, '__init__.py')
with open(init_fpath) as file_:
sourcecode = file_.read()
pt = ast.par... |
def create_dataset(self, name, shape=None, dtype=None, data=None,
sparse_format=None, indptr_dtype=np.int64, indices_dtype=np.int32,
**kwargs):
"""Create 3 datasets in a group to represent the sparse array.
Parameters
----------
sparse_forma... |
def cli_decrypt(context, key):
"""
Decrypts context.io_manager's stdin and sends that to
context.io_manager's stdout.
See :py:mod:`swiftly.cli.decrypt` for context usage information.
See :py:class:`CLIDecrypt` for more information.
"""
with context.io_manager.with_stdout() as stdout:
... |
def spawn(self, ident, func, *args, **kwargs):
"""
Returns immediately to the caller and begins executing the
func in the background. Use get_results and the ident given
to retrieve the results of the func. If the func causes an
exception, this exception will be caught and the
... |
def get_results(self):
"""
Returns a dict of the results currently available. The keys
are the ident values given with the calls to spawn. The
values are tuples of (exc_type, exc_value, exc_tb, result)
where:
========= ============================================
... |
def client_path_to_os_path(self, client_path):
"""
Converts a client path into the operating system's path by
replacing instances of '/' with os.path.sep.
Note: If the client path contains any instances of
os.path.sep already, they will be replaced with '-'.
"""
... |
def os_path_to_client_path(self, os_path):
"""
Converts an operating system path into a client path by
replacing instances of os.path.sep with '/'.
Note: If the client path contains any instances of '/'
already, they will be replaced with '-'.
"""
if os.path.sep ... |
def get_stdin(self, os_path=None, skip_sub_command=False):
"""
Returns a stdin-suitable file-like object based on the
optional os_path and optionally skipping any configured
sub-command.
"""
sub_command = None if skip_sub_command else self.stdin_sub_command
inn, p... |
def get_stdout(self, os_path=None, skip_sub_command=False):
"""
Returns a stdout-suitable file-like object based on the
optional os_path and optionally skipping any configured
sub-command.
"""
sub_command = None if skip_sub_command else self.stdout_sub_command
out... |
def get_stderr(self, os_path=None, skip_sub_command=False):
"""
Returns a stderr-suitable file-like object based on the
optional os_path and optionally skipping any configured
sub-command.
"""
sub_command = None if skip_sub_command else self.stderr_sub_command
out... |
def get_debug(self, os_path=None, skip_sub_command=False):
"""
Returns a debug-output-suitable file-like object based on the
optional os_path and optionally skipping any configured
sub-command.
"""
sub_command = None if skip_sub_command else self.debug_sub_command
... |
def with_stdin(self, os_path=None, skip_sub_command=False,
disk_closed_callback=None):
"""
A context manager yielding a stdin-suitable file-like object
based on the optional os_path and optionally skipping any
configured sub-command.
:param os_path: Optional p... |
def with_stdout(self, os_path=None, skip_sub_command=False,
disk_closed_callback=None):
"""
A context manager yielding a stdout-suitable file-like object
based on the optional os_path and optionally skipping any
configured sub-command.
:param os_path: Optiona... |
def with_stderr(self, os_path=None, skip_sub_command=False,
disk_closed_callback=None):
"""
A context manager yielding a stderr-suitable file-like object
based on the optional os_path and optionally skipping any
configured sub-command.
:param os_path: Optiona... |
def with_debug(self, os_path=None, skip_sub_command=False,
disk_closed_callback=None):
"""
A context manager yielding a debug-output-suitable file-like
object based on the optional os_path and optionally skipping
any configured sub-command.
:param os_path: Opt... |
def cli_empty_account(context, yes_empty_account=False, until_empty=False):
"""
Deletes all objects and containers in the account.
You must set yes_empty_account to True to verify you really want to
do this.
By default, this will perform one pass at deleting all objects and
containers; so if o... |
def cli_empty_container(context, path, until_empty=False):
"""
Deletes all objects in the container.
By default, this will perform one pass at deleting all objects in
the container; so if objects revert to previous versions or if new
objects otherwise arise during the process, the container may not... |
def cli_delete(context, path, body=None, recursive=False,
yes_empty_account=False, yes_delete_account=False,
until_empty=False):
"""
Deletes the item (account, container, or object) at the path.
See :py:mod:`swiftly.cli.delete` for context usage information.
See :py:class... |
def _stdout_filed(func):
"""
Instance method decorator to convert an optional file keyword
argument into an actual value, whether it be a passed value, a
value obtained from an io_manager, or sys.stdout.
"""
def wrapper(self, file=None):
if file:
return func(self, file=file)
... |
def _stderr_filed(func):
"""
Instance method decorator to convert an optional file keyword
argument into an actual value, whether it be a passed value, a
value obtained from an io_manager, or sys.stderr.
"""
def wrapper(self, msg, file=None):
if file:
return func(self, msg, f... |
def error(self, msg, file=None):
"""
Outputs the error msg to the file if specified, or to the
io_manager's stderr if available, or to sys.stderr.
"""
self.error_encountered = True
file.write(self.error_prefix)
file.write(msg)
file.write('\n')
file... |
def exit(self, status=0, msg=None):
"""
Immediately exits Python with the given status (or 0) as the
exit code and optionally outputs the msg using self.error.
"""
if msg:
self.error(msg)
sys.exit(status) |
def print_help(self, file=None):
"""
Outputs help information to the file if specified, or to the
io_manager's stdout if available, or to sys.stdout.
"""
optparse.OptionParser.print_help(self, file)
if self.raw_epilog:
file.write(self.raw_epilog)
file.... |
def print_usage(self, file=None):
"""
Outputs usage information to the file if specified, or to the
io_manager's stdout if available, or to sys.stdout.
"""
optparse.OptionParser.print_usage(self, file)
file.flush() |
def print_version(self, file=None):
"""
Outputs version information to the file if specified, or to
the io_manager's stdout if available, or to sys.stdout.
"""
optparse.OptionParser.print_version(self, file)
file.flush() |
def parse_args_and_create_context(self, args):
"""
Helper method that will parse the args into options and
remaining args as well as create an initial
:py:class:`swiftly.cli.context.CLIContext`.
The new context will be a copy of
:py:attr:`swiftly.cli.cli.CLI.context` wit... |
def options_list_to_lowered_dict(self, options_list):
"""
Helper function that will convert an options list into a dict
of key/values.
This is used for the quite common -hheader:value and
-qparameter=value command line options, like this::
context.headers = self.opt... |
def request(self, method, path, contents, headers, decode_json=False,
stream=False, query=None, cdn=False):
"""
Performs a direct HTTP request to the Swift service.
:param method: The request method ('GET', 'HEAD', etc.)
:param path: The request path.
:param cont... |
def head_account(self, headers=None, query=None, cdn=False):
"""
HEADs the account and returns the results. Useful headers
returned are:
=========================== =================================
x-account-bytes-used Object storage used for the
... |
def get_account(self, headers=None, prefix=None, delimiter=None,
marker=None, end_marker=None, limit=None, query=None,
cdn=False, decode_json=True):
"""
GETs the account and returns the results. This is done to list
the containers for the account. Some use... |
def put_account(self, headers=None, query=None, cdn=False, body=None):
"""
PUTs the account and returns the results. This is usually
done with the extract-archive bulk upload request and has no
other use I know of (but the call is left open in case there
ever is).
:param... |
def post_account(self, headers=None, query=None, cdn=False, body=None):
"""
POSTs the account and returns the results. This is usually
done to set X-Account-Meta-xxx headers. Note that any existing
X-Account-Meta-xxx headers will remain untouched. To remove an
X-Account-Meta-xxx ... |
def delete_account(self, headers=None,
yes_i_mean_delete_the_account=False, query=None,
cdn=False, body=None):
"""
Sends a DELETE request to the account and returns the results.
With ``query['bulk-delete'] = ''`` this might mean a bulk
delet... |
def head_container(self, container, headers=None, query=None, cdn=False):
"""
HEADs the container and returns the results. Useful headers
returned are:
=========================== =================================
x-container-bytes-used Object storage used for the
... |
def get_container(self, container, headers=None, prefix=None,
delimiter=None, marker=None, end_marker=None,
limit=None, query=None, cdn=False, decode_json=True):
"""
GETs the container and returns the results. This is done to
list the objects for the c... |
def put_container(self, container, headers=None, query=None, cdn=False,
body=None):
"""
PUTs the container and returns the results. This is usually
done to create new containers and can also be used to set
X-Container-Meta-xxx headers. Note that if the container
... |
def head_object(self, container, obj, headers=None, query=None, cdn=False):
"""
HEADs the object and returns the results.
:param container: The name of the container.
:param obj: The name of the object.
:param headers: Additional headers to send with the request.
:param ... |
def get_object(self, container, obj, headers=None, stream=True, query=None,
cdn=False):
"""
GETs the object and returns the results.
:param container: The name of the container.
:param obj: The name of the object.
:param headers: Additional headers to send wit... |
def put_object(self, container, obj, contents, headers=None, query=None,
cdn=False):
"""
PUTs the object and returns the results. This is used to
create or overwrite objects. X-Object-Meta-xxx can optionally
be sent to be stored with the object. Content-Type,
C... |
def post_object(self, container, obj, headers=None, query=None, cdn=False,
body=None):
"""
POSTs the object and returns the results. This is used to
update the object's header values. Note that all headers must
be sent with the POST, unlike the account and container P... |
def cli_ping(context, prefix):
"""
Performs a ping test.
See :py:mod:`swiftly.cli.ping` for context usage information.
See :py:class:`CLIPing` for more information.
:param context: The :py:class:`swiftly.cli.context.CLIContext` to
use.
:param prefix: The container name prefix to use. ... |
def cli_get_account_listing(context):
"""
Performs a GET on the account as a listing request.
See :py:mod:`swiftly.cli.get` for context usage information.
See :py:class:`CLIGet` for more information.
"""
limit = context.query.get('limit')
delimiter = context.query.get('delimiter')
pref... |
def cli_get_container_listing(context, path=None):
"""
Performs a GET on the container as a listing request.
See :py:mod:`swiftly.cli.get` for context usage information.
See :py:class:`CLIGet` for more information.
"""
path = path.strip('/') if path else None
if not path or '/' in path:
... |
def cli_get(context, path=None):
"""
Performs a GET on the item (account, container, or object).
See :py:mod:`swiftly.cli.get` for context usage information.
See :py:class:`CLIGet` for more information.
"""
path = path.lstrip('/') if path else None
if not path:
return cli_get_accou... |
def request(self, method, path, contents, headers, decode_json=False,
stream=False, query=None, cdn=False):
"""
See :py:func:`swiftly.client.client.Client.request`
"""
if cdn:
raise Exception('CDN not yet supported with LocalClient')
if isinstance(cont... |
def _resolve_option(self, options, option_name, section_name):
"""Resolves an option value into options.
Sets options.<option_name> to a resolved value. Any value
already in options overrides a value in os.environ which
overrides self.context.conf.
:param options: The options i... |
def cli_post(context, path, body=None):
"""
Performs a POST on the item (account, container, or object).
See :py:mod:`swiftly.cli.post` for context usage information.
See :py:class:`CLIPost` for more information.
:param context: The :py:class:`swiftly.cli.context.CLIContext` to
use.
:... |
def copy(self):
"""
Returns a new CLIContext instance that is a shallow copy of
the original, much like dict's copy method.
"""
context = CLIContext()
for item in dir(self):
if item[0] != '_' and item not in ('copy', 'write_headers'):
setattr(c... |
def write_headers(self, fp, headers, mute=None):
"""
Convenience function to output headers in a formatted fashion
to a file-like fp, optionally muting any headers in the mute
list.
"""
if headers:
if not mute:
mute = []
fmt = '%%-%... |
def request(self, method, path, contents, headers, decode_json=False,
stream=False, query=None, cdn=False):
"""
See :py:func:`swiftly.client.client.Client.request`
"""
if query:
path += '?' + '&'.join(
('%s=%s' % (quote(k), quote(v)) if v else ... |
def cli_auth(context):
"""
Authenticates and then outputs the resulting information.
See :py:mod:`swiftly.cli.auth` for context usage information.
See :py:class:`CLIAuth` for more information.
"""
with context.io_manager.with_stdout() as fp:
with context.client_manager.with_client() as... |
def generate_temp_url(method, url, seconds, key):
"""
Returns a TempURL good for the given request method, url, and
number of seconds from now, signed by the given key.
"""
method = method.upper()
base_url, object_path = url.split('/v1/')
object_path = '/v1/' + object_path
expires = int(... |
def quote(value, safe='/:'):
"""
Much like parse.quote in that it returns a URL encoded string
for the given value, protecting the safe characters; but this
version also ensures the value is UTF-8 encoded.
"""
if isinstance(value, six.text_type):
value = value.encode('utf8')
elif not... |
def headers_to_dict(headers):
"""
Converts a sequence of (name, value) tuples into a dict where if
a given name occurs more than once its value in the dict will be
a list of values.
"""
hdrs = {}
for h, v in headers:
h = h.lower()
if h in hdrs:
if isinstance(hdrs[... |
def cli_fordo(context, path=None):
"""
Issues commands for each item in an account or container listing.
See :py:mod:`swiftly.cli.fordo` for context usage information.
See :py:class:`CLIForDo` for more information.
"""
path = path.lstrip('/') if path else None
if path and '/' in path:
... |
def get_client(self):
"""
Obtains a client for use, whether an existing unused client
or a brand new one if none are available.
"""
client = None
try:
client = self.clients.get(block=False)
except queue.Empty:
pass
if not client:
... |
def cli_head(context, path=None):
"""
Performs a HEAD on the item (account, container, or object).
See :py:mod:`swiftly.cli.head` for context usage information.
See :py:class:`CLIHead` for more information.
"""
path = path.lstrip('/') if path else None
with context.client_manager.with_clie... |
def aes_encrypt(key, stdin, preamble=None, chunk_size=65536,
content_length=None):
"""
Generator that encrypts a content stream using AES 256 in CBC
mode.
:param key: Any string to use as the encryption key.
:param stdin: Where to read the contents from.
:param preamble: str to ... |
def aes_decrypt(key, stdin, chunk_size=65536):
"""
Generator that decrypts a content stream using AES 256 in CBC
mode.
:param key: Any string to use as the decryption key.
:param stdin: Where to read the encrypted data from.
:param chunk_size: Largest amount to read at once.
"""
if not ... |
def cli_put_directory_structure(context, path):
"""
Performs PUTs rooted at the path using a directory structure
pointed to by context.input\_.
See :py:mod:`swiftly.cli.put` for context usage information.
See :py:class:`CLIPut` for more information.
"""
if not context.input_:
raise... |
def cli_put_account(context):
"""
Performs a PUT on the account.
See :py:mod:`swiftly.cli.put` for context usage information.
See :py:class:`CLIPut` for more information.
"""
body = None
if context.input_:
if context.input_ == '-':
body = context.io_manager.get_stdin()
... |
def cli_put_container(context, path):
"""
Performs a PUT on the container.
See :py:mod:`swiftly.cli.put` for context usage information.
See :py:class:`CLIPut` for more information.
"""
path = path.rstrip('/')
if '/' in path:
raise ReturnCode('called cli_put_container with object %r... |
def cli_put_object(context, path):
"""
Performs a PUT on the object.
See :py:mod:`swiftly.cli.put` for context usage information.
See :py:class:`CLIPut` for more information.
"""
if context.different and context.encrypt:
raise ReturnCode(
'context.different will not work pr... |
def cli_put(context, path):
"""
Performs a PUT on the item (account, container, or object).
See :py:mod:`swiftly.cli.put` for context usage information.
See :py:class:`CLIPut` for more information.
"""
path = path.lstrip('/') if path else ''
if context.input_ and os.path.isdir(context.inpu... |
def _get_manifest_body(context, prefix, path2info, put_headers):
"""
Returns body for manifest file and modifies put_headers.
path2info is a dict like {"path": (size, etag)}
"""
if context.static_segments:
body = json.dumps([
{'path': '/' + p, 'size_bytes': s, 'etag': e}
... |
def _create_container(context, path, l_mtime, size):
"""
Creates container for segments of file with `path`
"""
new_context = context.copy()
new_context.input_ = None
new_context.headers = None
new_context.query = None
container = path.split('/', 1)[0] + '_segments'
cli_put_container... |
def cli_tempurl(context, method, path, seconds=None, use_container=False):
"""
Generates a TempURL and sends that to the context.io_manager's
stdout.
See :py:mod:`swiftly.cli.tempurl` for context usage information.
See :py:class:`CLITempURL` for more information.
:param context: The :py:class... |
def auth(self):
"""
See :py:func:`swiftly.client.client.Client.auth`
"""
self.reset()
if not self.auth_url:
raise ValueError('No Auth URL has been provided.')
funcs = []
if self.auth_methods:
for method in self.auth_methods.split(','):
... |
def request(self, method, path, contents, headers, decode_json=False,
stream=False, query=None, cdn=False):
"""
See :py:func:`swiftly.client.client.Client.request`
"""
if query:
path += '?' + '&'.join(
('%s=%s' % (quote(k), quote(v)) if v else ... |
def reset(self):
"""
See :py:func:`swiftly.client.client.Client.reset`
"""
for conn in (self.storage_conn, self.cdn_conn):
if conn:
try:
conn.close()
except Exception:
pass
self.storage_conn = Non... |
def get_account_hash(self):
"""
See :py:func:`swiftly.client.client.Client.get_account_hash`
"""
if not(self.storage_url or self.storage_path):
self.auth()
return (self.storage_url or self.storage_path).rsplit('/', 1)[1] |
def cli_trans(context, x_trans_id):
"""
Translates any information that can be determined from the
x_trans_id and sends that to the context.io_manager's stdout.
See :py:mod:`swiftly.cli.trans` for context usage information.
See :py:class:`CLITrans` for more information.
"""
with context.io... |
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