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jrheard/madison_axi | madison_axi/axi.py | initialize | def initialize():
"""IMPORTANT: Call this function at the beginning of your program."""
try:
requests.get('http://localhost:4242/poll')
state['connected_to_bot'] = True
except requests.exceptions.ConnectionError:
state['connected_to_bot'] = False
# set up turtle
state['windo... | python | def initialize():
"""IMPORTANT: Call this function at the beginning of your program."""
try:
requests.get('http://localhost:4242/poll')
state['connected_to_bot'] = True
except requests.exceptions.ConnectionError:
state['connected_to_bot'] = False
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jrheard/madison_axi | madison_axi/axi.py | move_forward | def move_forward(num_steps):
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pjuren/pyokit | src/pyokit/statistics/online.py | RollingMean.add | def add(self, v):
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pjuren/pyokit | src/pyokit/datastruct/genomeAlignment.py | _build_trees_by_chrom | def _build_trees_by_chrom(blocks, verbose=False):
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pjuren/pyokit | src/pyokit/datastruct/genomeAlignment.py | GenomeAlignmentBlock.get_column_absolute | def get_column_absolute(self, position,
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species=None):
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pjuren/pyokit | src/pyokit/datastruct/genomeAlignment.py | GenomeAlignment.get_blocks | def get_blocks(self, chrom, start, end):
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pjuren/pyokit | src/pyokit/datastruct/genomeAlignment.py | GenomeAlignment.get_column | def get_column(self, chrom, position,
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species=None):
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pjuren/pyokit | src/pyokit/datastruct/genomeAlignment.py | JustInTimeGenomeAlignment.__get_keys | def __get_keys(self, chrom, start, end=None):
"""
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pjuren/pyokit | src/pyokit/datastruct/genomeAlignment.py | JustInTimeGenomeAlignment.get_blocks | def get_blocks(self, chrom, start, end):
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emencia/emencia_paste_djangocms_3 | emencia_paste_djangocms_3/django_buildout/project/utils/context_processors.py | get_site_metas | def get_site_metas(with_static=False, with_media=False, is_secure=False,
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Return metas from the current *Site* and settings
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cogniteev/docido-python-sdk | docido_sdk/toolbox/decorators.py | decorate_instance_methods | def decorate_instance_methods(obj, decorator, includes=None, excludes=None):
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>>> def decorate(name, f):
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edeposit/edeposit.amqp.aleph | src/edeposit/amqp/aleph/aleph.py | getListOfBases | def getListOfBases():
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edeposit/edeposit.amqp.aleph | src/edeposit/amqp/aleph/aleph.py | searchInAleph | def searchInAleph(base, phrase, considerSimilar, field):
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Request itself is pretty useless, but it can be later used as parameter
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base (str): which database you want to use
... | python | def searchInAleph(base, phrase, considerSimilar, field):
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Send request to the aleph search engine.
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edeposit/edeposit.amqp.aleph | src/edeposit/amqp/aleph/aleph.py | downloadRecords | def downloadRecords(search_result, from_doc=1):
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edeposit/edeposit.amqp.aleph | src/edeposit/amqp/aleph/aleph.py | downloadMARCXML | def downloadMARCXML(doc_id, library, base="nkc"):
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Download MARC XML document with given `doc_id` from given `library`.
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doc_id (DocumentID): You will get this from :func:`getDocumentIDs`.
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"""
Download MARC XML document with given `doc_id` from given `library`.
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doc_id (DocumentID): You will get this from :func:`getDocumentIDs`.
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edeposit/edeposit.amqp.aleph | src/edeposit/amqp/aleph/aleph.py | downloadMARCOAI | def downloadMARCOAI(doc_id, base):
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lehins/python-wepay | wepay/calls/subscription.py | Subscription.__create | def __create(self, subscription_plan_id, **kwargs):
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KnowledgeLinks/rdfframework | rdfframework/search/esloaders_temp.py | EsRdfBulkLoader._index_item | def _index_item(self, uri, num, batch_num):
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data = RdfDataset(get_all_item_data(uri, self.namespace),
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self.count += 1 | python | def _index_item(self, uri, num, batch_num):
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StanfordBioinformatics/scgpm_seqresults_dnanexus | scgpm_seqresults_dnanexus/dnanexus_utils.py | select_newest_project | def select_newest_project(dx_project_ids):
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Args:
dx_project_ids: `list` of DNAnexus project IDs.
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StanfordBioinformatics/scgpm_seqresults_dnanexus | scgpm_seqresults_dnanexus/dnanexus_utils.py | share_with_org | def share_with_org(project_ids, org, access_level, suppress_email_notification=False):
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StanfordBioinformatics/scgpm_seqresults_dnanexus | scgpm_seqresults_dnanexus/dnanexus_utils.py | DxSeqResults._set_dxproject_id | def _set_dxproject_id(self,latest_project=False):
"""
Searches for the project in DNAnexus based on the input arguments when instantiating the class.
If multiple projects are found based on the search criteria, an exception will be raised. A
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"""
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StanfordBioinformatics/scgpm_seqresults_dnanexus | scgpm_seqresults_dnanexus/dnanexus_utils.py | DxSeqResults.get_run_details_json | def get_run_details_json(self):
"""
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Returns:
JSON object of the run details.
"""
run_details_filename = "run_details.json"
... | python | def get_run_details_json(self):
"""
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Returns:
JSON object of the run details.
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StanfordBioinformatics/scgpm_seqresults_dnanexus | scgpm_seqresults_dnanexus/dnanexus_utils.py | DxSeqResults.get_alignment_summary_metrics | def get_alignment_summary_metrics(self, barcode):
"""
Parses the metrics in a ${barcode}alignment_summary_metrics file in the DNAnexus project
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CollectAlignmentSummaryMetrics program.
"""
filena... | python | def get_alignment_summary_metrics(self, barcode):
"""
Parses the metrics in a ${barcode}alignment_summary_metrics file in the DNAnexus project
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CollectAlignmentSummaryMetrics program.
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StanfordBioinformatics/scgpm_seqresults_dnanexus | scgpm_seqresults_dnanexus/dnanexus_utils.py | DxSeqResults.get_barcode_stats | def get_barcode_stats(self, barcode):
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"""
filename = barcode + "_stats.json"
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"""
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StanfordBioinformatics/scgpm_seqresults_dnanexus | scgpm_seqresults_dnanexus/dnanexus_utils.py | DxSeqResults.get_sample_stats_json | def get_sample_stats_json(self,barcode=None):
"""
.. deprecated:: 0.1.0
GSSC has removed the sample_stats.json file since the entire folder it was in has been
removed. Use :meth:`get_barcode_stats` instead.
Retrieves the JSON object for the stats in the file named s... | python | def get_sample_stats_json(self,barcode=None):
"""
.. deprecated:: 0.1.0
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StanfordBioinformatics/scgpm_seqresults_dnanexus | scgpm_seqresults_dnanexus/dnanexus_utils.py | DxSeqResults.download_metadata_tar | def download_metadata_tar(self,download_dir):
"""
Downloads the ${run_name}.metadata.tar file from the DNAnexus sequencing results project.
Args:
download_dir: `str` - The local directory path to download the QC report to.
Returns:
`str`: The filepath to t... | python | def download_metadata_tar(self,download_dir):
"""
Downloads the ${run_name}.metadata.tar file from the DNAnexus sequencing results project.
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StanfordBioinformatics/scgpm_seqresults_dnanexus | scgpm_seqresults_dnanexus/dnanexus_utils.py | DxSeqResults.download_fastqc_reports | def download_fastqc_reports(self,download_dir):
"""
Downloads the QC report from the DNAnexus sequencing results project.
Args:
download_dir: `str` - The local directory path to download the QC report to.
Returns:
`str`. The filepath to the downloaded ... | python | def download_fastqc_reports(self,download_dir):
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Downloads the QC report from the DNAnexus sequencing results project.
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download_dir: `str` - The local directory path to download the QC report to.
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StanfordBioinformatics/scgpm_seqresults_dnanexus | scgpm_seqresults_dnanexus/dnanexus_utils.py | DxSeqResults.download_fastqs | def download_fastqs(self,dest_dir,barcode,overwrite=False):
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Downloads all FASTQ files in the project that match the specified barcode, or if a barcode
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StanfordBioinformatics/scgpm_seqresults_dnanexus | scgpm_seqresults_dnanexus/dnanexus_utils.py | DxSeqResults.get_fastq_dxfile_objects | def get_fastq_dxfile_objects(self,barcode=None):
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... | python | def get_fastq_dxfile_objects(self,barcode=None):
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StanfordBioinformatics/scgpm_seqresults_dnanexus | scgpm_seqresults_dnanexus/dnanexus_utils.py | DxSeqResults.get_fastq_files_props | def get_fastq_files_props(self,barcode=None):
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amcfague/webunit2 | webunit2/utils.py | parse_url | def parse_url(url):
""" Takes a URL string and returns its protocol and server """
# Verify that the protocol makes sense. We shouldn't guess!
if not RE_PROTOCOL_SERVER.match(url):
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protocol, server, path, _, _, _ = urlparse.urlparse(... | python | def parse_url(url):
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msuozzo/Aduro | aduro/store.py | EventStore.record_event | def record_event(self, event):
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file_.write(str(event) + '\n') | python | def record_event(self, event):
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b3j0f/conf | b3j0f/conf/model/param.py | Parameter.name | def name(self, value):
"""Set parameter name.
:param str value: name value.
"""
if isinstance(value, string_types):
match = Parameter._PARAM_NAME_COMPILER_MATCHER(value)
if match is None or match.group() != value:
value = re_compile(value)
... | python | def name(self, value):
"""Set parameter name.
:param str value: name value.
"""
if isinstance(value, string_types):
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if match is None or match.group() != value:
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:rtype: str
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b3j0f/conf | b3j0f/conf/model/param.py | Parameter.resolve | def resolve(
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:return: parameter value.
:raises: TypeError if serialized value is not an instance of self ptype
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scdoshi/django-bits | bits/templatetags/attribute.py | attr | def attr(object, attr):
"""
Lookup attributes in django templates dynamically
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Allows lookups such as {{ user|attr:item }} where item is a
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"""
pseudo_context = {'object': object}
try:
value = Variable('object.%s' % ... | python | def attr(object, attr):
"""
Lookup attributes in django templates dynamically
From http://stackoverflow.com/a/3466349/594269
Allows lookups such as {{ user|attr:item }} where item is a
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"""
pseudo_context = {'object': object}
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ericmjl/polcart | polcart/polcart.py | to_cartesian | def to_cartesian(r, theta, theta_units="radians"):
"""
Converts polar r, theta to cartesian x, y.
"""
assert theta_units in ['radians', 'degrees'],\
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# Convert to radians
if theta_units == "degrees":
theta = to_radians(thet... | python | def to_cartesian(r, theta, theta_units="radians"):
"""
Converts polar r, theta to cartesian x, y.
"""
assert theta_units in ['radians', 'degrees'],\
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rraadd88/meld | meld/dfs.py | set_index | def set_index(data,col_index):
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Sets the index if the index is not present
:param data: pandas table
:param col_index: column name which will be assigned as a index
"""
if col_index in data:
data=data.reset_index().set_index(col_index)
if 'index' in data:
del dat... | python | def set_index(data,col_index):
"""
Sets the index if the index is not present
:param data: pandas table
:param col_index: column name which will be assigned as a index
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rraadd88/meld | meld/dfs.py | del_Unnamed | def del_Unnamed(df):
"""
Deletes all the unnamed columns
:param df: pandas dataframe
"""
cols_del=[c for c in df.columns if 'Unnamed' in c]
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Deletes all the unnamed columns
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rraadd88/meld | meld/dfs.py | fhs2data_combo | def fhs2data_combo(fhs,cols,index,labels=None,col_sep=': '):
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Collates data from multiple csv files
:param fhs: list of paths to csv files
:param cols: list of column names to concatenate
:param index: name of the column name to be used as the common index of the output pandas table
"""
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DoWhileGeek/authentise-services | authentise_services/session.py | Session.__create_session | def __create_session(username=None, password=None):
"""grabs the configuration, and makes the call to Authentise to create the session"""
config = Config()
if not username or not password:
username = config.username
password = config.password
payload = {
... | python | def __create_session(username=None, password=None):
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config = Config()
if not username or not password:
username = config.username
password = config.password
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DoWhileGeek/authentise-services | authentise_services/session.py | Session.create_user | def create_user(cls, username, password, name, email):
"""utility class method to create a user"""
config = Config()
payload = {"username": username,
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"name": name,
"password": password, }
user_creation_resp = reques... | python | def create_user(cls, username, password, name, email):
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config = Config()
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mush42/mezzanine-live-tile | mezzanine_live_tile/templatetags/tile_tags.py | wrap_text | def wrap_text(paragraph, line_count, min_char_per_line=0):
"""Wraps the given text to the specified number of lines."""
one_string = strip_all_white_space(paragraph)
if min_char_per_line:
lines = wrap(one_string, width=min_char_per_line)
try:
return lines[:line_count]
except IndexError:
return lines
els... | python | def wrap_text(paragraph, line_count, min_char_per_line=0):
"""Wraps the given text to the specified number of lines."""
one_string = strip_all_white_space(paragraph)
if min_char_per_line:
lines = wrap(one_string, width=min_char_per_line)
try:
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return lines
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rsarun-uninstallio/apprequest | apprequest/AppRequest.py | AppRequest.get_request_id | def get_request_id(self, renew=False):
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"""
if not AppRequest.__request_id or renew:
self.set_request_id(uuid.uuid1())
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"""
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neuroticnerd/armory | armory/serialize.py | jsonify | def jsonify(data, pretty=False, **kwargs):
"""Serialize Python objects to JSON with optional 'pretty' formatting
Raises:
TypeError: from :mod:`json` lib
ValueError: from :mod:`json` lib
JSONDecodeError: from :mod:`json` lib
"""
isod = isinstance(data, OrderedDict)
params = {... | python | def jsonify(data, pretty=False, **kwargs):
"""Serialize Python objects to JSON with optional 'pretty' formatting
Raises:
TypeError: from :mod:`json` lib
ValueError: from :mod:`json` lib
JSONDecodeError: from :mod:`json` lib
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isod = isinstance(data, OrderedDict)
params = {... | [
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soasme/rio-client | rio_client/transports/base.py | Transport.get_emit_api | def get_emit_api(self, action):
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args = {'action': action}
args.update(self.context)
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edeposit/edeposit.amqp.aleph | src/edeposit/amqp/aleph/doc_number.py | getDocNumber | def getDocNumber(xml):
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polysquare/polysquare-generic-file-linter | polysquarelinter/cache_populate.py | main | def main(): # suppress(unused-function)
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uw-it-aca/uw-restclients-kws | uw_kws/__init__.py | KWS.get_key | def get_key(self, key_id):
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key.algorithm = data["Algorithm"]
key.cipher_mode = data["CipherMode"]
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Internal method, for creating the Key object.
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zvolsky/qrplatba-fpdf | qrplatba_fpdf.py | qrplatba | def qrplatba(pdf,
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nabeen/gswrap | gswrap/Gswrap.py | Gswrap.get_value | def get_value(self, spreadsheet_id: str, range_name: str) -> dict:
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get value by range
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ramrod-project/database-brain | schema/brain/controller/verification.py | verify_port_map | def verify_port_map(plugin):
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extra validation /
PB2 sees empty lists the same as non-existant lists
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result = True
ex_ports = plugin.get(EX_PORTS_KEY)
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"""
extra validation /
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ramrod-project/database-brain | schema/brain/controller/verification.py | verify_ports | def verify_ports(port_list):
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:param port_list: <list>
:return: <bool>
"""
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"""
ports should be of the format
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:return: <bool>
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treycucco/bidon | bidon/db/access/model_access.py | get_model_id_constraints | def get_model_id_constraints(model):
"""Returns constraints to target a specific model."""
pkname = model.primary_key_name
pkey = model.primary_key
return get_id_constraints(pkname, pkey) | python | def get_model_id_constraints(model):
"""Returns constraints to target a specific model."""
pkname = model.primary_key_name
pkey = model.primary_key
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treycucco/bidon | bidon/db/access/model_access.py | get_id_constraints | def get_id_constraints(pkname, pkey):
"""Returns primary key consraints.
:pkname: if a string, returns a dict with pkname=pkey. pkname and pkey must be enumerables of
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"""
if isinstance(pkname, str):
return {pkname: pkey}
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return dict(zip(pkname, pkey)) | python | def get_id_constraints(pkname, pkey):
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treycucco/bidon | bidon/db/access/model_access.py | ModelAccess._find_model | def _find_model(self, constructor, table_name, constraints=None, *, columns=None, order_by=None):
"""Calls DataAccess.find and passes the results to the given constructor."""
data = self.find(table_name, constraints, columns=columns, order_by=order_by)
return constructor(data) if data else None | python | def _find_model(self, constructor, table_name, constraints=None, *, columns=None, order_by=None):
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data = self.find(table_name, constraints, columns=columns, order_by=order_by)
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treycucco/bidon | bidon/db/access/model_access.py | ModelAccess._find_models | def _find_models(self, constructor, table_name, constraints=None, *, columns=None,
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"""Calls DataAccess.find_all and passes the results to the given constructor."""
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treycucco/bidon | bidon/db/access/model_access.py | ModelAccess.find_model | def find_model(self, constructor, constraints=None, *, columns=None, table_name=None,
order_by=None):
"""Specialization of DataAccess.find that returns a model instead of cursor object."""
return self._find_model(constructor, table_name or constructor.table_name, constraints,
... | python | def find_model(self, constructor, constraints=None, *, columns=None, table_name=None,
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treycucco/bidon | bidon/db/access/model_access.py | ModelAccess.find_models | def find_models(self, constructor, constraints=None, *, columns=None, order_by=None,
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"""Specialization of DataAccess.find_all that returns models instead of cursor objects."""
return self._find_models(
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treycucco/bidon | bidon/db/access/model_access.py | ModelAccess.page_models | def page_models(self, constructor, paging, constraints=None, *, columns=None, order_by=None):
"""Specialization of DataAccess.page that returns models instead of cursor objects."""
records, count = self.page(constructor.table_name, paging, constraints, columns=columns,
order_by=or... | python | def page_models(self, constructor, paging, constraints=None, *, columns=None, order_by=None):
"""Specialization of DataAccess.page that returns models instead of cursor objects."""
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treycucco/bidon | bidon/db/access/model_access.py | ModelAccess.find_model_by_id | def find_model_by_id(self, constructor, id_, *, columns=None):
"""Searches for a model by id, according to its class' primary_key_name.
If primary_key_name is a tuple, id_ must be a tuple with a matching length.
"""
return self.find_model(
constructor, get_id_constraints(constructor.primary_key_n... | python | def find_model_by_id(self, constructor, id_, *, columns=None):
"""Searches for a model by id, according to its class' primary_key_name.
If primary_key_name is a tuple, id_ must be a tuple with a matching length.
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treycucco/bidon | bidon/db/access/model_access.py | ModelAccess.refresh_model | def refresh_model(self, model, *, overwrite=False):
"""Pulls the model's record from the database. If overwrite is True, the model values are
overwritten and returns the model, otherwise a new model instance with the newer record is
returned.
"""
new_model = self.find_model_by_id(model.__class__, mo... | python | def refresh_model(self, model, *, overwrite=False):
"""Pulls the model's record from the database. If overwrite is True, the model values are
overwritten and returns the model, otherwise a new model instance with the newer record is
returned.
"""
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treycucco/bidon | bidon/db/access/model_access.py | ModelAccess.update_model | def update_model(self, model, *, include_keys=None):
"""Updates a model.
:include_keys: if given, only updates the given attributes. Otherwise, updates all non-id
attributes.
"""
id_constraints = get_model_id_constraints(model)
if include_keys is None:
include_keys = set(
model.a... | python | def update_model(self, model, *, include_keys=None):
"""Updates a model.
:include_keys: if given, only updates the given attributes. Otherwise, updates all non-id
attributes.
"""
id_constraints = get_model_id_constraints(model)
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treycucco/bidon | bidon/db/access/model_access.py | ModelAccess.insert_model | def insert_model(self, model, *, upsert=None):
"""Inserts a record for the given model.
If model's primary key is auto, the primary key will be set appropriately.
"""
pkname = model.primary_key_name
include_keys = set(model.attrs.keys()).difference(model.exclude_keys_sql)
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"""
pkname = model.primary_key_name
include_keys = set(model.attrs.keys()).difference(model.exclude_keys_sql)
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treycucco/bidon | bidon/db/access/model_access.py | ModelAccess.delete_model | def delete_model(self, model_or_type, id_=None):
"""Deletes a model.
:model_or_type: if a model, delete that model. If it is a ModelBase subclass, id_ must be
specified, and the associated record is deleted.
"""
if not id_:
constraints = get_model_id_constraints(model_or_type)
else:
... | python | def delete_model(self, model_or_type, id_=None):
"""Deletes a model.
:model_or_type: if a model, delete that model. If it is a ModelBase subclass, id_ must be
specified, and the associated record is deleted.
"""
if not id_:
constraints = get_model_id_constraints(model_or_type)
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treycucco/bidon | bidon/db/access/model_access.py | ModelAccess.find_or_build | def find_or_build(self, constructor, props):
"""Looks for a model that matches the given dictionary constraints. If it is not found, a new
model of the given type is constructed and returned.
"""
model = self.find_model(constructor, props)
return model or constructor(**props) | python | def find_or_build(self, constructor, props):
"""Looks for a model that matches the given dictionary constraints. If it is not found, a new
model of the given type is constructed and returned.
"""
model = self.find_model(constructor, props)
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treycucco/bidon | bidon/db/access/model_access.py | ModelAccess.find_or_create | def find_or_create(self, constructor, props, *, comp=None):
"""Looks for a model taht matches the given dictionary constraints. If it is not found, a new
model of the given type is created and saved to the database, then returned.
"""
model = self.find_model(constructor, comp or props)
if model is N... | python | def find_or_create(self, constructor, props, *, comp=None):
"""Looks for a model taht matches the given dictionary constraints. If it is not found, a new
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chrisdrackett/django-support | support/forms/processing.py | process_form | def process_form(request, form_class, form_dict=None, save_kwargs=None, *a, **kw):
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success, form = process_form(request, DiscussionForm, in... | python | def process_form(request, form_class, form_dict=None, save_kwargs=None, *a, **kw):
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etcher-be/elib_config | elib_config/_value/_config_value_path.py | ConfigValuePath.friendly_type_name | def friendly_type_name(self) -> str:
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limiear/soyprice | soyprice/bots/presenter_bot.py | Presenter.tweet | def tweet(self, status, images):
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minhhoit/yacms | yacms/pages/managers.py | PageManager.published | def published(self, for_user=None, include_login_required=False):
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stevemarple/python-atomiccreate | atomiccreate/__init__.py | atomic_symlink | def atomic_symlink(src, dst):
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dst_dir = os.path.dirname(dst)
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msuozzo/Aduro | main.py | run | def run(): #pylint: disable=too-many-locals
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contains-io/containment | containment/builder.py | CommandLineInterface._os_install | def _os_install(self, package_file):
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"containment",
"pave_project"
] | train | https://github.com/contains-io/containment/blob/4f7e2c2338e0ca7c107a7b3a9913bb5e6e07245f/containment/builder.py#L110-L124 |
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