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def Client(version=__version__, resource=None, provider=None, **kwargs):
"""Initialize client object based on given version. :params version: version of CAL, def... |
versions = _CLIENTS.keys()
if version not in versions:
raise exceptions.UnsupportedVersion(
'Unknown client version or subject'
)
if provider is None:
raise exceptions.ProviderNotDefined(
'Not define Provider for Client'
)
support_types = CONF... |
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def accession(self):
""" Parse accession number from commonly supported formats. If the defline does not match one of the following formats, the entire descripti... |
accession = None
if self.defline.startswith('>gi|'):
match = re.match('>gi\|\d+\|[^\|]+\|([^\|\n ]+)', self.defline)
if match:
accession = match.group(1)
elif self.defline.startswith('>gnl|'):
match = re.match('>gnl\|[^\|]+\|([^\|\n ]+)', self... |
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def format_seq(self, outstream=None, linewidth=70):
""" Print a sequence in a readable format. :param outstream: if `None`, formatted sequence is returned as a s... |
if linewidth == 0 or len(self.seq) <= linewidth:
if outstream is None:
return self.seq
else:
print(self.seq, file=outstream)
return
i = 0
seq = ''
while i < len(self.seq):
if outstream is None:
... |
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def get_validator(filter_data):
""" ask every matcher whether it can serve such filter data :param filter_data: :return: """ |
for matcher_type, m in matchers.items():
if hasattr(m, 'can_handle') and m.can_handle(filter_data):
filter_data = m.handle(filter_data)
return filter_data |
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def run():
"""Run the examples""" |
# NOTE(kiennt): Until now, this example isn't finished yet,
# because we don't have any completed driver
# Get a network client with openstack driver.
network_client = client.Client(version=_VERSION,
resource=_RESOURCES[0], provider=_PROVIDER)
# net = networ... |
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def sort(self, attr):
"""Sort the ratings based on an attribute""" |
self.entries = Sorter(self.entries, self.category, attr).sort_entries()
return self |
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def get_title(self):
"""Title is either the chart header for a cable ratings page or above the opening description for a broadcast ratings page. """ |
if self.category == 'cable':
strings = get_strings(self.soup, 'strong')
else:
strings = get_strings(self.soup, 'b')
if len(strings) == 0:
strings = get_strings(self.soup, 'strong')
if len(strings) >= 1 and self.category == 'cable':
retur... |
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def get_json(self):
"""Serialize ratings object as JSON-formatted string""" |
ratings_dict = {
'category': self.category,
'date': self.date,
'day': self.weekday,
'next week': self.next_week,
'last week': self.last_week,
'entries': self.entries,
'url': self.url
}
return to_json(ratings_dic... |
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def _get_url_params(self, shorten=True):
"""Returns a list of each parameter to be used for the url format.""" |
cable = True if self.category == 'cable' else False
url_date = convert_month(self.date, shorten=shorten, cable=cable)
return [
BASE_URL,
self.weekday.lower(),
self.category + '-ratings',
url_date.replace(' ', '-')
] |
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def _verify_page(self):
"""Verify the ratings page matches the correct date""" |
title_date = self._get_date_in_title().lower()
split_date = self.date.lower().split()
split_date[0] = split_date[0][:3]
return all(term in title_date for term in split_date) |
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def _get_ratings_page(self):
"""Do a limited search for the correct url.""" |
# Use current posted date to build url
self._build_url()
soup = get_soup(self.url)
if soup:
return soup
# Try building url again with unshortened month
self._build_url(shorten=False)
soup = get_soup(self.url)
if soup:
return soup
... |
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def _build_url(self, shorten=True):
"""Build the url for a cable ratings page""" |
self.url = URL_FORMAT.format(*self._get_url_params(shorten=shorten)) |
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def fetch_entries(self):
"""Fetch data and parse it to build a list of cable entries.""" |
data = []
for row in self.get_rows():
# Stop fetching data if limit has been met
if exceeded_limit(self.limit, len(data)):
break
entry = row.find_all('td')
entry_dict = {}
show = entry[0].string
net = entry[1].str... |
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def _build_url(self, shorten=True):
"""Build the url for a broadcast ratings page""" |
url_order = self._get_url_params(shorten=shorten)
# For fast ratings, switch weekday and category in url
if self.category != 'final':
url_order[1], url_order[2] = url_order[2], url_order[1]
self.url = URL_FORMAT.format(*url_order) |
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def get_rows(self):
"""Get the rows from a broadcast ratings chart""" |
table = self.soup.find_all('tr')[1:-3]
return [row for row in table if row.contents[3].string] |
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def fetch_entries(self):
"""Fetch data and parse it to build a list of broadcast entries.""" |
current_time = ''
data = []
for row in self.get_rows():
# Stop fetching data if limit has been met
if exceeded_limit(self.limit, len(data)):
break
entry = row.find_all('td')
entry_dict = {}
show_time = entry[0].strin... |
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def get_averages(self):
"""Get the broadcast network averages for that day. Returns a dictionary: key: network name value: sub-dictionary with 'viewers', 'rating... |
networks = [unescape_html(n.string) for n in self.soup.find_all('td', width='77')]
table = self.soup.find_all('td', style=re.compile('^font'))
# Each element is a list split as [rating, share]
rateshares = [r.string.split('/') for r in table[:5] if r.string]
viewers = [v.string... |
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def _get_net(self, entry):
"""Get the network for a specific row""" |
try:
net = entry[1]
return net[net.find('(')+1:net.find(')')]
except IndexError:
return None |
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def _get_rating(self, entry):
"""Get the rating and share for a specific row""" |
r_info = ''
for string in entry[2].strings:
r_info += string
rating, share = r_info.split('/')
return (rating, share.strip('*')) |
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def _visit(self, L, marked, tempmarked):
""" Sort features topologically. This recursive function uses depth-first search to find an ordering of the features in ... |
assert not self.is_pseudo
if self in tempmarked:
raise Exception('feature graph is cyclic')
if self not in marked:
tempmarked[self] = True
features = list()
if self.siblings is not None and self.is_toplevel:
features.extend(reverse... |
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def add_child(self, child, rangecheck=False):
"""Add a child feature to this feature.""" |
assert self.seqid == child.seqid, \
(
'seqid mismatch for feature {} ({} vs {})'.format(
self.fid, self.seqid, child.seqid
)
)
if rangecheck is True:
assert self._strand == child._strand, \
('child o... |
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def pseudoify(self):
""" Derive a pseudo-feature parent from the given multi-feature. The provided multi-feature does not need to be the representative. The newl... |
assert self.is_toplevel
assert self.is_multi
assert len(self.multi_rep.siblings) > 0
rep = self.multi_rep
start = min([s.start for s in rep.siblings + [rep]])
end = max([s.end for s in rep.siblings + [rep]])
parent = Feature(None)
parent._pseudo = True
... |
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def slug(self):
""" A concise slug for this feature. Unlike the internal representation, which is 0-based half-open, the slug is a 1-based closed interval (a la ... |
return '{:s}@{:s}[{:d}, {:d}]'.format(self.type, self.seqid,
self.start + 1, self.end) |
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def add_sibling(self, sibling):
""" Designate this a multi-feature representative and add a co-feature. Some features exist discontinuously on the sequence, and ... |
assert self.is_pseudo is False
if self.siblings is None:
self.siblings = list()
self.multi_rep = self
sibling.multi_rep = self
self.siblings.append(sibling) |
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def source(self, newsource):
"""When modifying source, also update children with matching source.""" |
oldsource = self.source
for feature in self:
if feature.source == oldsource:
feature._source = newsource |
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def type(self, newtype):
"""If the feature is a multifeature, update all entries.""" |
self._type = newtype
if self.is_multi:
for sibling in self.multi_rep.siblings:
sibling._type = newtype |
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def transform(self, offset, newseqid=None):
"""Transform the feature's coordinates by the given offset.""" |
for feature in self:
feature._range.transform(offset)
if newseqid is not None:
feature.seqid = newseqid |
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def add_attribute(self, attrkey, attrvalue, append=False, oldvalue=None):
""" Add an attribute to this feature. Feature attributes are stored as nested dictionar... |
# Handle ID/Parent relationships
if attrkey == 'ID':
if self.children is not None:
oldid = self.get_attribute('ID')
for child in self.children:
child.add_attribute('Parent', attrvalue,
oldvalue=oldid... |
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def get_attribute(self, attrkey, as_string=False, as_list=False):
""" Get the value of an attribute. By default, returns a string for ID and attributes with a si... |
assert not as_string or not as_list
if attrkey not in self._attrs:
return None
if attrkey == 'ID':
return self._attrs[attrkey]
attrvalues = list(self._attrs[attrkey])
attrvalues.sort()
if len(attrvalues) == 1 and not as_list:
return at... |
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def parse_attributes(self, attrstring):
""" Parse an attribute string. Given a string with semicolon-separated key-value pairs, populate a dictionary with the gi... |
if attrstring in [None, '', '.']:
return dict()
attributes = dict()
keyvaluepairs = attrstring.split(';')
for kvp in keyvaluepairs:
if kvp == '':
continue
key, value = kvp.split('=')
if key == 'ID':
assert ... |
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def attribute_crawl(self, key):
""" Grab all attribute values associated with the given feature. Traverse the given feature (and all of its descendants) to find ... |
union = set()
for feature in self:
values = feature.get_attribute(key, as_list=True)
if values is not None:
union.update(set(values))
return union |
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def ncbi_geneid(self):
""" Retrieve this feature's NCBI GeneID if it's present. NCBI GFF3 files contain gene IDs encoded in **Dbxref** attributes (example: `Dbxr... |
values = self.get_attribute('Dbxref', as_list=True)
if values is None:
return None
for value in values:
if value.startswith('GeneID:'):
key, geneid = value.split(':')
return geneid
return None |
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def cdslen(self):
""" Translated length of this feature. Undefined for non-mRNA features. """ |
if self.type != 'mRNA':
return None
return sum([len(c) for c in self.children if c.type == 'CDS']) |
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| def parse_querystring(msg):
'parse a querystring into keys and values'
for part in msg.querystring.strip().lstrip('?').split('&'):
key, value = part.split('=')
yield key, value |
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def AddClusterTags(r, tags, dry_run=False):
""" Adds tags to the cluster. @type tags: list of str @param tags: tags to add to the cluster @type dry_run: bool @pa... |
query = {
"dry-run": dry_run,
"tag": tags,
}
return r.request("put", "/2/tags", query=query) |
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def DeleteClusterTags(r, tags, dry_run=False):
""" Deletes tags from the cluster. @type tags: list of str @param tags: tags to delete @type dry_run: bool @param ... |
query = {
"dry-run": dry_run,
"tag": tags,
}
return r.request("delete", "/2/tags", query=query) |
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def GetInstances(r, bulk=False):
""" Gets information about instances on the cluster. @type bulk: bool @param bulk: whether to return all information about all i... |
if bulk:
return r.request("get", "/2/instances", query={"bulk": 1})
else:
instances = r.request("get", "/2/instances")
return r.applier(itemgetters("id"), instances) |
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def GetInstanceInfo(r, instance, static=None):
""" Gets information about an instance. @type instance: string @param instance: Instance name @rtype: string @retu... |
if static is None:
return r.request("get", "/2/instances/%s/info" % instance)
else:
return r.request("get", "/2/instances/%s/info" % instance,
query={"static": static}) |
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def DeleteInstance(r, instance, dry_run=False):
""" Deletes an instance. @type instance: str @param instance: the instance to delete @rtype: int @return: job id ... |
return r.request("delete", "/2/instances/%s" % instance,
query={"dry-run": dry_run}) |
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def ActivateInstanceDisks(r, instance, ignore_size=False):
""" Activates an instance's disks. @type instance: string @param instance: Instance name @type ignore_... |
return r.request("put", "/2/instances/%s/activate-disks" % instance,
query={"ignore_size": ignore_size}) |
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def RecreateInstanceDisks(r, instance, disks=None, nodes=None):
"""Recreate an instance's disks. @type instance: string @param instance: Instance name @type disk... |
body = {}
if disks is not None:
body["disks"] = disks
if nodes is not None:
body["nodes"] = nodes
return r.request("post", "/2/instances/%s/recreate-disks" % instance,
content=body) |
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def GrowInstanceDisk(r, instance, disk, amount, wait_for_sync=False):
""" Grows a disk of an instance. More details for parameters can be found in the RAPI docum... |
body = {
"amount": amount,
"wait_for_sync": wait_for_sync,
}
return r.request("post", "/2/instances/%s/disk/%s/grow" %
(instance, disk), content=body) |
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def AddInstanceTags(r, instance, tags, dry_run=False):
""" Adds tags to an instance. @type instance: str @param instance: instance to add tags to @type tags: lis... |
query = {
"tag": tags,
"dry-run": dry_run,
}
return r.request("put", "/2/instances/%s/tags" % instance, query=query) |
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def DeleteInstanceTags(r, instance, tags, dry_run=False):
""" Deletes tags from an instance. @type instance: str @param instance: instance to delete tags from @t... |
query = {
"tag": tags,
"dry-run": dry_run,
}
return r.request("delete", "/2/instances/%s/tags" % instance, query=query) |
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def RebootInstance(r, instance, reboot_type=None, ignore_secondaries=False, dry_run=False):
""" Reboots an instance. @type instance: str @param instance: instanc... |
query = {
"ignore_secondaries": ignore_secondaries,
"dry-run": dry_run,
}
if reboot_type:
if reboot_type not in ("hard", "soft", "full"):
raise GanetiApiError("reboot_type must be one of 'hard',"
" 'soft', or 'full'")
query["typ... |
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def ShutdownInstance(r, instance, dry_run=False, no_remember=False, timeout=120):
""" Shuts down an instance. @type instance: str @param instance: the instance t... |
query = {
"dry-run": dry_run,
"no-remember": no_remember,
}
content = {
"timeout": timeout,
}
return r.request("put", "/2/instances/%s/shutdown" % instance,
query=query, content=content) |
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def StartupInstance(r, instance, dry_run=False, no_remember=False):
""" Starts up an instance. @type instance: str @param instance: the instance to start up @typ... |
query = {
"dry-run": dry_run,
"no-remember": no_remember,
}
return r.request("put", "/2/instances/%s/startup" % instance, query=query) |
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def ReinstallInstance(r, instance, os=None, no_startup=False, osparams=None):
""" Reinstalls an instance. @type instance: str @param instance: The instance to re... |
if INST_REINSTALL_REQV1 in r.features:
body = {
"start": not no_startup,
}
if os is not None:
body["os"] = os
if osparams is not None:
body["osparams"] = osparams
return r.request("post", "/2/instances/%s/reinstall" % instance,
... |
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def ReplaceInstanceDisks(r, instance, disks=None, mode=REPLACE_DISK_AUTO, remote_node=None, iallocator=None, dry_run=False):
""" Replaces disks on an instance. @... |
if mode not in REPLACE_DISK:
raise GanetiApiError("Invalid mode %r not one of %r" % (mode,
REPLACE_DISK))
query = {
"mode": mode,
"dry-run": dry_run,
}
if disks:
query["disks"] = ",".join(str(idx) for idx... |
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def ExportInstance(r, instance, mode, destination, shutdown=None, remove_instance=None, x509_key_name=None, destination_x509_ca=None):
""" Exports an instance. @... |
body = {
"destination": destination,
"mode": mode,
}
if shutdown is not None:
body["shutdown"] = shutdown
if remove_instance is not None:
body["remove_instance"] = remove_instance
if x509_key_name is not None:
body["x509_key_name"] = x509_key_name
if... |
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def MigrateInstance(r, instance, mode=None, cleanup=None):
""" Migrates an instance. @type instance: string @param instance: Instance name @type mode: string @pa... |
body = {}
if mode is not None:
body["mode"] = mode
if cleanup is not None:
body["cleanup"] = cleanup
return r.request("put", "/2/instances/%s/migrate" % instance,
content=body) |
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def FailoverInstance(r, instance, iallocator=None, ignore_consistency=False, target_node=None):
"""Does a failover of an instance. @type instance: string @param ... |
body = {
"ignore_consistency": ignore_consistency,
}
if iallocator is not None:
body["iallocator"] = iallocator
if target_node is not None:
body["target_node"] = target_node
return r.request("put", "/2/instances/%s/failover" % instance,
content=body) |
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def RenameInstance(r, instance, new_name, ip_check, name_check=None):
""" Changes the name of an instance. @type instance: string @param instance: Instance name ... |
body = {
"ip_check": ip_check,
"new_name": new_name,
}
if name_check is not None:
body["name_check"] = name_check
return r.request("put", "/2/instances/%s/rename" % instance, content=body) |
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def WaitForJobChange(r, job_id, fields, prev_job_info, prev_log_serial):
""" Waits for job changes. @type job_id: int @param job_id: Job ID for which to wait """ |
body = {
"fields": fields,
"previous_job_info": prev_job_info,
"previous_log_serial": prev_log_serial,
}
return r.request("get", "/2/jobs/%s/wait" % job_id, content=body) |
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def CancelJob(r, job_id, dry_run=False):
""" Cancels a job. @type job_id: int @param job_id: id of the job to delete @type dry_run: bool @param dry_run: whether ... |
return r.request("delete", "/2/jobs/%s" % job_id,
query={"dry-run": dry_run}) |
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def GetNodes(r, bulk=False):
""" Gets all nodes in the cluster. @type bulk: bool @param bulk: whether to return all information about all instances @rtype: list ... |
if bulk:
return r.request("get", "/2/nodes", query={"bulk": 1})
else:
nodes = r.request("get", "/2/nodes")
return r.applier(itemgetters("id"), nodes) |
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def EvacuateNode(r, node, iallocator=None, remote_node=None, dry_run=False, early_release=False, mode=None, accept_old=False):
""" Evacuates instances from a Gan... |
if iallocator and remote_node:
raise GanetiApiError("Only one of iallocator or remote_node can"
" be used")
query = {
"dry-run": dry_run,
}
if iallocator:
query["iallocator"] = iallocator
if remote_node:
query["remote_node"] = remote_n... |
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def MigrateNode(r, node, mode=None, dry_run=False, iallocator=None, target_node=None):
""" Migrates all primary instances from a node. @type node: str @param nod... |
query = {
"dry-run": dry_run,
}
if NODE_MIGRATE_REQV1 in r.features:
body = {}
if mode is not None:
body["mode"] = mode
if iallocator is not None:
body["iallocator"] = iallocator
if target_node is not None:
body["target_node"] =... |
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def SetNodeRole(r, node, role, force=False, auto_promote=False):
""" Sets the role for a node. @type node: str @param node: the node whose role to set @type role... |
query = {
"force": force,
"auto_promote": auto_promote,
}
return r.request("put", "/2/nodes/%s/role" % node, query=query,
content=role) |
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def PowercycleNode(r, node, force=False):
""" Powercycles a node. @type node: string @param node: Node name @type force: bool @param force: Whether to force the ... |
query = {
"force": force,
}
return r.request("post", "/2/nodes/%s/powercycle" % node, query=query) |
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def GetNodeStorageUnits(r, node, storage_type, output_fields):
""" Gets the storage units for a node. @type node: str @param node: the node whose storage units t... |
query = {
"storage_type": storage_type,
"output_fields": output_fields,
}
return r.request("get", "/2/nodes/%s/storage" % node, query=query) |
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def ModifyNodeStorageUnits(r, node, storage_type, name, allocatable=None):
""" Modifies parameters of storage units on the node. @type node: str @param node: nod... |
query = {
"storage_type": storage_type,
"name": name,
}
if allocatable is not None:
query["allocatable"] = allocatable
return r.request("put", "/2/nodes/%s/storage/modify" % node, query=query) |
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def RepairNodeStorageUnits(r, node, storage_type, name):
""" Repairs a storage unit on the node. @type node: str @param node: node whose storage units to repair ... |
query = {
"storage_type": storage_type,
"name": name,
}
return r.request("put", "/2/nodes/%s/storage/repair" % node, query=query) |
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def AddNodeTags(r, node, tags, dry_run=False):
""" Adds tags to a node. @type node: str @param node: node to add tags to @type tags: list of str @param tags: tag... |
query = {
"tag": tags,
"dry-run": dry_run,
}
return r.request("put", "/2/nodes/%s/tags" % node, query=query,
content=tags) |
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def DeleteNodeTags(r, node, tags, dry_run=False):
""" Delete tags from a node. @type node: str @param node: node to remove tags from @type tags: list of str @par... |
query = {
"tag": tags,
"dry-run": dry_run,
}
return r.request("delete", "/2/nodes/%s/tags" % node, query=query) |
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def GetGroups(r, bulk=False):
""" Gets all node groups in the cluster. @type bulk: bool @param bulk: whether to return all information about the groups @rtype: l... |
if bulk:
return r.request("get", "/2/groups", query={"bulk": 1})
else:
groups = r.request("get", "/2/groups")
return r.applier(itemgetters("name"), groups) |
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def CreateGroup(r, name, alloc_policy=None, dry_run=False):
""" Creates a new node group. @type name: str @param name: the name of node group to create @type all... |
query = {
"dry-run": dry_run,
}
body = {
"name": name,
"alloc_policy": alloc_policy
}
return r.request("post", "/2/groups", query=query, content=body) |
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def DeleteGroup(r, group, dry_run=False):
""" Deletes a node group. @type group: str @param group: the node group to delete @type dry_run: bool @param dry_run: w... |
query = {
"dry-run": dry_run,
}
return r.request("delete", "/2/groups/%s" % group, query=query) |
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def RenameGroup(r, group, new_name):
""" Changes the name of a node group. @type group: string @param group: Node group name @type new_name: string @param new_na... |
body = {
"new_name": new_name,
}
return r.request("put", "/2/groups/%s/rename" % group, content=body) |
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def AssignGroupNodes(r, group, nodes, force=False, dry_run=False):
""" Assigns nodes to a group. @type group: string @param group: Node gropu name @type nodes: l... |
query = {
"force": force,
"dry-run": dry_run,
}
body = {
"nodes": nodes,
}
return r.request("put", "/2/groups/%s/assign-nodes" % group, query=query,
content=body) |
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def AddGroupTags(r, group, tags, dry_run=False):
""" Adds tags to a node group. @type group: str @param group: group to add tags to @type tags: list of string @p... |
query = {
"dry-run": dry_run,
"tag": tags,
}
return r.request("put", "/2/groups/%s/tags" % group, query=query) |
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def DeleteGroupTags(r, group, tags, dry_run=False):
""" Deletes tags from a node group. @type group: str @param group: group to delete tags from @type tags: list... |
query = {
"dry-run": dry_run,
"tag": tags,
}
return r.request("delete", "/2/groups/%s/tags" % group, query=query) |
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def Query(r, what, fields, qfilter=None):
""" Retrieves information about resources. @type what: string @param what: Resource name, one of L{constants.QR_VIA_RAP... |
body = {
"fields": fields,
}
if qfilter is not None:
body["qfilter"] = body["filter"] = qfilter
return r.request("put", "/2/query/%s" % what, content=body) |
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def QueryFields(r, what, fields=None):
""" Retrieves available fields for a resource. @type what: string @param what: Resource name, one of L{constants.QR_VIA_RA... |
query = {}
if fields is not None:
query["fields"] = ",".join(fields)
return r.request("get", "/2/query/%s/fields" % what, query=query) |
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def createalphabet(alphabetinput=None):
""" Creates a sample alphabet containing printable ASCII characters """ |
if alphabetinput and os.path.isfile(alphabetinput):
return _load_alphabet(alphabetinput)
elif alphabetinput:
alpha = []
setlist = alphabetinput.split(',')
for alphaset in setlist:
a = int(alphaset.split('-')[0])
b = int(alphaset.split('-')[1])
... |
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def _instant_search(self):
"""Determine possible keys after a push or pop """ |
_keys = []
for k,v in self.searchables.iteritems():
if self.string in v:
_keys.append(k)
self.candidates.append(_keys) |
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def best_guess(self):
"""Return the gnomekeyring position of the closest matching """ |
best_guess_ever = (0, 0) # (key, string)
points = defaultdict(float)
points[0] = 0
if len(self.string) > 0:
for key in self.candidate_keys:
guess = self.searchables[key]
if guess == self.string:
points[key] += 100
... |
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def find_html_files(self, destination):
""" Finds all html files in the given destination. """ |
for root, dirs, files in os.walk(destination):
for f in files:
if f.endswith('.html'):
yield os.path.join(root, f) |
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def minify_file(self, target):
""" Minifies the target html file. """ |
html = open(target, 'rb').read()
enc = chardet.detect(html)['encoding']
with codecs.open(target, 'r+', enc) as f:
result = htmlmin.minify(f.read(), **self.options)
f.seek(0)
f.write(result)
f.truncate() |
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def on_after_build_all(self, builder, **extra):
""" after-build-all lektor event """ |
# NOTE(vesuvium): compatibility for lektor 2.X and 3.X
try:
is_enabled = self.is_enabled(builder.build_flags)
except AttributeError:
is_enabled = self.is_enabled(builder.extra_flags)
if not is_enabled:
return
reporter.report_generic('Startin... |
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def features(entrystream, type=None, traverse=False):
""" Pull features out of the specified entry stream. :param entrystream: a stream of entries :param type: r... |
for feature in entry_type_filter(entrystream, tag.Feature):
if traverse:
if type is None:
message = 'cannot traverse without a specific feature type'
raise ValueError(message)
if type == feature.type:
yield feature
else:
... |
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def window(featurestream, seqid, start=None, end=None, strict=True):
""" Pull features out of the designated genomic interval. This function uses 0-based half-op... |
region = None
if start and end:
region = tag.Range(start, end)
for feature in featurestream:
if feature.seqid != seqid:
continue
if region:
if strict:
if region.contains(feature._range):
yield feature
else:
... |
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def directives(entrystream, type=None):
""" Pull directives out of the specified entry stream. :param entrystream: a stream of entries :param type: retrieve only... |
for directive in entry_type_filter(entrystream, tag.Directive):
if not type or type == directive.type:
yield directive |
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def validate_driver(f):
"""Check driver on""" |
def check_driver(request):
drivers = get_all_driver()
drivers = filter(drivers, request)
if drivers:
return f(request, drivers)
else:
raise Exception('Driver is not found')
return check_driver |
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def strings_to_integers(strings: Iterable[str]) -> Iterable[int]: """ Convert a list of strings to a list of integers. :param strings: a list of string :return: a... |
return strings_to_(strings, lambda x: int(float(x))) |
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def string_to_double_precision_float(s: str) -> float: """ Double precision float in Fortran file will have form 'x.ydz' or 'x.yDz', this cannot be convert direct... |
first, second, exponential = re.match(
"(-?\d*)\.?(-?\d*)d(-?\d+)", s, re.IGNORECASE).groups()
return float(first + '.' + second + 'e' + exponential) |
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def string_to_general_float(s: str) -> float: """ Convert a string to corresponding single or double precision scientific number. :param s: a string could be '0.1... |
if 'D' in s.upper(): # Possible double precision number
try:
return string_to_double_precision_float(s)
except ValueError:
raise ValueError(
"The string '{0}' does not corresponds to a double precision number!".format(s))
else:
return float(s) |
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def match_one_string(pattern: str, s: str, *args):
""" Make sure you know only none or one string will be matched! If you are not sure, use `match_one_pattern` i... |
try:
# `match` is either an empty list or a list of string.
match, = re.findall(pattern, s)
if len(args) == 0: # If no wrapper argument is given, return directly the matched string
return match
elif len(args) == 1: # If wrapper argument is given, i.e., not empty, then ... |
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def match_one_pattern(pattern: str, s: str, *args: Optional[Callable], **flags):
""" Find a pattern in a certain string. If found and a wrapper is given, then re... |
match: Optional[List[str]] = re.findall(pattern, s,
**flags) # `match` is either an empty list or a list of strings.
if match:
if len(args) == 0: # If no wrapper argument is given, return directly the matched string
return match
elif len... |
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def all_string_like(iterable: Iterable[object]) -> bool: """ If any element of an iterable is not a string, return `True`. :param iterable: Can be a set, a tuple,... |
return all(is_string_like(_) for _ in iterable) |
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def source_filename(self, docname: str, srcdir: str):
""" Get the full filename to referenced image """ |
docpath = Path(srcdir, docname)
parent = docpath.parent
imgpath = parent.joinpath(self.filename)
# Does this exist?
if not imgpath.exists():
msg = f'Image does not exist at "{imgpath}"'
raise SphinxError(msg)
return imgpath |
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def env_updated(self, kb_app, sphinx_app: Sphinx, sphinx_env: BuildEnvironment, resource ):
""" Make images and enter them in Sphinx's output writer """ |
docname = resource.docname
srcdir = sphinx_app.env.srcdir
source_imgpath = self.source_filename(docname, srcdir)
# Copy the image to the Sphinx build directory
build_dir = sphinx_app.outdir
docpath = Path(docname)
parent = docpath.parent
target_imgpath ... |
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def catalog(self, table='', column=''):
"""Lookup the values available for querying.""" |
lookup_table = self.lookup_table
if lookup_table is not None:
if table:
if column:
column = column.upper()
return lookup_table[table][column]
return lookup_table[table]
# Show what methods are available.
... |
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def _resolve_call(self, table, column='', value='', **kwargs):
"""Internal method to resolve the API wrapper call.""" |
if not column:
return self.catalog(table)
elif not value:
return self.catalog(table, column)
# We have all the table, column, and value, and now need to
# ensure they're all strings and uppercase.
column = column.upper()
value = str(value).upper()... |
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def call_api(self, table, column, value, **kwargs):
"""Exposed method to connect and query the EPA's API.""" |
try:
output_format = kwargs.pop('output_format')
except KeyError:
output_format = self.output_format
url_list = [self.base_url, table, column,
quote(value), 'rows']
rows_count = self._number_of_rows(**kwargs)
url_list.append(rows_count... |
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def _number_of_rows(self, start=0, count=100, **kwargs):
"""Internal method to format the number of rows the EPA API returns.""" |
first = str(start)
last = str(start + count)
string_format = ':'.join([first, last])
return string_format |
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def resource_references(self, resource) -> Mapping[str, List[Any]]: """ Resolve and return reference resources pointed to by object Fields in resource.props can f... |
references = dict()
for reference_label in resource.props.references:
references[reference_label] = []
# Iterate over each value on this field, e.g.
# tags: tag1, tag2, tag3
for target_label in resource.props.references.get(reference_label):
... |
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def start(self, retry_limit=None):
""" Try to connect to Twitter's streaming API. :param retry_limit: The maximum number of retries in case of failures. Default ... |
# Run tweepy stream
wrapper_listener = TweepyWrapperListener(listener=self.listener)
stream = tweepy.Stream(auth=self.client.tweepy_api.auth, listener=wrapper_listener)
retry_counter = 0
while retry_limit is None or retry_counter <= retry_limit:
try:
... |
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def _findProteinClusters(protToPeps, pepToProts):
"""Find protein clusters in the specified protein to peptide mappings. A protein cluster is a group of proteins... |
clusters = list()
resolvingProteins = set(protToPeps)
while resolvingProteins:
protein = resolvingProteins.pop()
proteinCluster = set([protein])
peptides = set(protToPeps[protein])
parsedPeptides = set()
while len(peptides) != len(parsedPeptides):
for p... |
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def _findSamesetProteins(protToPeps, proteins=None):
"""Find proteins that are mapped to an identical set of peptides. :param protToPeps: dict, for each protein ... |
proteins = viewkeys(protToPeps) if proteins is None else proteins
equalEvidence = ddict(set)
for protein in proteins:
peptides = protToPeps[protein]
equalEvidence[tuple(sorted(peptides))].add(protein)
equalProteins = list()
for proteins in viewvalues(equalEvidence):
if len(... |
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