INSTRUCTION stringlengths 1 8.43k | RESPONSE stringlengths 75 104k |
|---|---|
Creates connection to RabbitMQ server | def connect(self):
"""
Creates connection to RabbitMQ server
"""
if self.connecting:
log.info('PikaClient: Already connecting to RabbitMQ')
return
log.info('PikaClient: Connecting to RabbitMQ')
self.connecting = True
self.connection = Tor... |
AMQP connection callback. Creates input channel. | def on_connected(self, connection):
"""
AMQP connection callback.
Creates input channel.
Args:
connection: AMQP connection
"""
log.info('PikaClient: connected to RabbitMQ')
self.connected = True
self.in_channel = self.connection.channel(self.o... |
Input channel creation callback Queue declaration done here | def on_channel_open(self, channel):
"""
Input channel creation callback
Queue declaration done here
Args:
channel: input channel
"""
self.in_channel.exchange_declare(exchange='input_exc', type='topic', durable=True)
channel.queue_declare(callback=self... |
Input queue declaration callback. Input Queue/ Exchange binding done here | def on_input_queue_declare(self, queue):
"""
Input queue declaration callback.
Input Queue/Exchange binding done here
Args:
queue: input queue
"""
self.in_channel.queue_bind(callback=None,
exchange='input_exc',
... |
Incoming request handler. | def wsgi_app(self, request):
"""Incoming request handler.
:param request: Werkzeug request object
"""
try:
if request.method != 'POST':
abort(400)
try:
# Python 2.7 compatibility
data = request.data
... |
close opened file | def close(self, force=False):
"""
close opened file
:param force: force closing of externally opened file or buffer
"""
if self.__write:
self.write = self.__write_adhoc
self.__write = False
if not self._is_buffer or force:
self._file.... |
map unmapped atoms. | def _convert_reaction(self, reaction):
if not (reaction['reactants'] or reaction['products'] or reaction['reagents']):
raise ValueError('empty reaction')
maps = {'reactants': [], 'products': [], 'reagents': []}
for i, tmp in maps.items():
for molecule in reaction[i]:
... |
convert structure to aromatic form | def aromatize(self):
"""
convert structure to aromatic form
:return: number of processed rings
"""
rings = [x for x in self.sssr if 4 < len(x) < 7]
if not rings:
return 0
total = 0
while True:
c = self._quinonize(rings, 'order')
... |
Runs the crawl job for n rounds: param seed_list: lines of seed URLs: param n: number of rounds: return: number of successful rounds | def crawl_cmd(self, seed_list, n):
'''
Runs the crawl job for n rounds
:param seed_list: lines of seed URLs
:param n: number of rounds
:return: number of successful rounds
'''
print("Num Rounds "+str(n))
cc = self.proxy.Crawl(seed=seed_list, rounds=n)
... |
Creates a new config from xml file.: param xml_file: path to xml file. Format: nutch - site. xml or nutch - default. xml: param id:: return: config object | def load_xml_conf(self, xml_file, id):
'''
Creates a new config from xml file.
:param xml_file: path to xml file. Format : nutch-site.xml or nutch-default.xml
:param id:
:return: config object
'''
# converting nutch-site.xml to key:value pairs
import xml.... |
create sub - command: param args: cli arguments: return: | def create_cmd(self, args):
'''
'create' sub-command
:param args: cli arguments
:return:
'''
cmd = args.get('cmd_create')
if cmd == 'conf':
conf_file = args['conf_file']
conf_id = args['id']
return self.load_xml_conf(conf_file, ... |
write close tag of MRV file and close opened file | def close(self, *args, **kwargs):
"""
write close tag of MRV file and close opened file
:param force: force closing of externally opened file or buffer
"""
if not self.__finalized:
self._file.write('</cml>')
self.__finalized = True
super().close(*... |
write single molecule or reaction into file | def write(self, data):
"""
write single molecule or reaction into file
"""
self._file.write('<cml>')
self.__write(data)
self.write = self.__write |
the method is implemented for the purpose of optimization byte positions will not be re - read from a file that has already been used if the content of the file has changed and the name has been left the same the old version of byte offsets will be loaded: return: list of byte offsets from existing file | def _load_cache(self):
"""
the method is implemented for the purpose of optimization, byte positions will not be re-read from a file
that has already been used, if the content of the file has changed, and the name has been left the same,
the old version of byte offsets will be loaded
... |
_shifts dumps in/ tmp directory after reboot it will drop | def _dump_cache(self, _shifts):
"""
_shifts dumps in /tmp directory after reboot it will drop
"""
with open(self.__cache_path, 'wb') as f:
dump(_shifts, f) |
List task types for current user | def get_task_types(current):
"""
List task types for current user
.. code-block:: python
# request:
{
'view': '_zops_get_task_types',
}
# response:
{
'task_types':... |
Show task details | def get_task_detail(current):
"""
Show task details
.. code-block:: python
# request:
{
'view': '_zops_get_task_detail',
'key': key,
}
# response:
{
... |
List task types for current user | def get_task_actions(current):
"""
List task types for current user
.. code-block:: python
# request:
{
'view': '_zops_get_task_actions',
'key': key,
}
# response:
... |
List task invitations of current user | def get_tasks(current):
"""
List task invitations of current user
.. code-block:: python
# request:
{
'view': '_zops_get_tasks',
'state': string, # one of these:
# "active", "future", "finished", "expire... |
reduce memory usage of the dataframe | def reduce_memory_usage(df):
"""reduce memory usage of the dataframe
- convert runIDs to categorical
- downcast ints and floats
"""
usage_pre = df.memory_usage(deep=True).sum()
if "runIDs" in df:
df.loc[:, "runIDs"] = df.loc[:, "runIDs"].astype("category")
df_int = df.select_dtypes(... |
Check if the file supplied as input exists. | def check_existance(f):
"""Check if the file supplied as input exists."""
if not opath.isfile(f):
logging.error("Nanoget: File provided doesn't exist or the path is incorrect: {}".format(f))
sys.exit("File provided doesn't exist or the path is incorrect: {}".format(f)) |
Lists user roles as selectable except user s current role. | def list_user_roles(self):
"""
Lists user roles as selectable except user's current role.
"""
_form = JsonForm(current=self.current, title=_(u"Switch Role"))
_form.help_text = "Your current role: %s %s" % (self.current.role.unit.name,
... |
Changes user s role from current role to chosen role. | def change_user_role(self):
"""
Changes user's role from current role to chosen role.
"""
# Get chosen role_key from user form.
role_key = self.input['form']['role_options']
# Assign chosen switch role key to user's last_login_role_key field
self.current.user.las... |
Returns user s role list except current role as a tuple ( role. key role. name ) | def get_user_switchable_roles(self):
"""
Returns user's role list except current role as a tuple
(role.key, role.name)
Returns:
(list): list of tuples, user's role list except current role
"""
roles = []
for rs in self.current.user.role_set:
... |
Wrapper for es. index determines metadata needed to index from obj. If you have a raw object json string you can hard code these: index is. kibana ( as of kibana4 ) ; id can be A - Za - z0 - 9 \ - and must be unique ; doc_type is either visualization dashboard search or for settings docs: config or index - pattern. | def put_object(self, obj):
# TODO consider putting into a ES class
self.pr_dbg('put_obj: %s' % self.json_dumps(obj))
"""
Wrapper for es.index, determines metadata needed to index from obj.
If you have a raw object json string you can hard code these:
index is .kibana (as ... |
Debug deletes obj of obj [ _type ] with id of obj [ _id ] | def del_object(self, obj):
"""Debug deletes obj of obj[_type] with id of obj['_id']"""
if obj['_index'] is None or obj['_index'] == "":
raise Exception("Invalid Object")
if obj['_id'] is None or obj['_id'] == "":
raise Exception("Invalid Object")
if obj['_type'] i... |
Serializer for consistency | def json_dumps(self, obj):
"""Serializer for consistency"""
return json.dumps(obj, sort_keys=True, indent=4, separators=(',', ': ')) |
Santize obj name into fname and verify doesn t already exist | def safe_filename(self, otype, oid):
"""Santize obj name into fname and verify doesn't already exist"""
permitted = set(['_', '-', '(', ')'])
oid = ''.join([c for c in oid if c.isalnum() or c in permitted])
while oid.find('--') != -1:
oid = oid.replace('--', '-')
ext ... |
Convert obj ( dict ) to json string and write to file | def write_object_to_file(self, obj, path='.', filename=None):
"""Convert obj (dict) to json string and write to file"""
output = self.json_dumps(obj) + '\n'
if filename is None:
filename = self.safe_filename(obj['_type'], obj['_id'])
filename = os.path.join(path, filename)
... |
Write a list of related objs to file | def write_pkg_to_file(self, name, objects, path='.', filename=None):
"""Write a list of related objs to file"""
# Kibana uses an array of docs, do the same
# as opposed to a dict of docs
pkg_objs = []
for _, obj in iteritems(objects):
pkg_objs.append(obj)
sort... |
Return all objects of type ( assumes < MAX_HITS ) | def get_objects(self, search_field, search_val):
"""Return all objects of type (assumes < MAX_HITS)"""
query = ("{ size: " + str(self.max_hits) + ", " +
"query: { filtered: { filter: { " +
search_field + ": { value: \"" + search_val + "\"" +
" } } } } }... |
Get DB and all objs needed to duplicate it | def get_dashboard_full(self, db_name):
"""Get DB and all objs needed to duplicate it"""
objects = {}
dashboards = self.get_objects("type", "dashboard")
vizs = self.get_objects("type", "visualization")
searches = self.get_objects("type", "search")
if db_name not in dashboa... |
Overrides ProcessParser. parse_node Parses and attaches the inputOutput tags that created by Camunda Modeller | def parse_node(self, node):
"""
Overrides ProcessParser.parse_node
Parses and attaches the inputOutput tags that created by Camunda Modeller
Args:
node: xml task node
Returns:
TaskSpec
"""
spec = super(CamundaProcessParser, self).parse_no... |
Tries to get WF description from collabration or process or pariticipant Returns: | def _get_description(self):
"""
Tries to get WF description from 'collabration' or 'process' or 'pariticipant'
Returns:
"""
ns = {'ns': '{%s}' % BPMN_MODEL_NS}
desc = (
self.doc_xpath('.//{ns}collaboration/{ns}documentation'.format(**ns)) or
self.... |
Tries to get WF name from process or collobration or pariticipant | def get_name(self):
"""
Tries to get WF name from 'process' or 'collobration' or 'pariticipant'
Returns:
str. WF name.
"""
ns = {'ns': '{%s}' % BPMN_MODEL_NS}
for path in ('.//{ns}process',
'.//{ns}collaboration',
'./... |
Parses inputOutput part camunda modeller extensions. Args: node: SpiffWorkflow Node object. | def _parse_input_data(self, node):
"""
Parses inputOutput part camunda modeller extensions.
Args:
node: SpiffWorkflow Node object.
Returns:
Data dict.
"""
data = DotDict()
try:
for nod in self._get_input_nodes(node):
... |
Parses the given XML node | def _get_lane_properties(self, node):
"""
Parses the given XML node
Args:
node (xml): XML node.
.. code-block:: xml
<bpmn2:lane id="Lane_8" name="Lane 8">
<bpmn2:extensionElements>
<camunda:properties>
... |
: param node: xml node: return: dict | def _parse_input_node(cls, node):
"""
:param node: xml node
:return: dict
"""
data = {}
child = node.getchildren()
if not child and node.get('name'):
val = node.text
elif child: # if tag = "{http://activiti.org/bpmn}script" then data_typ = 'sc... |
Generates wf packages from workflow diagrams. | def package_in_memory(cls, workflow_name, workflow_files):
"""
Generates wf packages from workflow diagrams.
Args:
workflow_name: Name of wf
workflow_files: Diagram file.
Returns:
Workflow package (file like) object
"""
s = StringIO... |
condense reaction container to CGR. see init for details about cgr_type | def compose(self, data):
"""
condense reaction container to CGR. see init for details about cgr_type
:param data: ReactionContainer
:return: CGRContainer
"""
g = self.__separate(data) if self.__cgr_type in (1, 2, 3, 4, 5, 6) else self.__condense(data)
g.meta.upda... |
new atom addition | def add_atom(self, atom, _map=None):
"""
new atom addition
"""
if _map is None:
_map = max(self, default=0) + 1
elif _map in self._node:
raise KeyError('atom with same number exists')
attr_dict = self.node_attr_dict_factory()
if isinstance... |
implementation of bond addition | def add_bond(self, atom1, atom2, bond):
"""
implementation of bond addition
"""
if atom1 == atom2:
raise KeyError('atom loops impossible')
if atom1 not in self._node or atom2 not in self._node:
raise KeyError('atoms not found')
if atom1 in self._ad... |
implementation of bond removing | def delete_bond(self, n, m):
"""
implementation of bond removing
"""
self.remove_edge(n, m)
self.flush_cache() |
pairs of ( bond atom ) connected to atom | def environment(self, atom):
"""
pairs of (bond, atom) connected to atom
:param atom: number
:return: list
"""
return tuple((bond, self._node[n]) for n, bond in self._adj[atom].items()) |
create substructure containing atoms from nbunch list | def substructure(self, atoms, meta=False, as_view=True):
"""
create substructure containing atoms from nbunch list
:param atoms: list of atoms numbers of substructure
:param meta: if True metadata will be copied to substructure
:param as_view: If True, the returned graph-view pr... |
create substructure containing atoms and their neighbors | def augmented_substructure(self, atoms, dante=False, deep=1, meta=False, as_view=True):
"""
create substructure containing atoms and their neighbors
:param atoms: list of core atoms in graph
:param dante: if True return list of graphs containing atoms, atoms + first circle, atoms + 1st ... |
split disconnected structure to connected substructures | def split(self, meta=False):
"""
split disconnected structure to connected substructures
:param meta: copy metadata to each substructure
:return: list of substructures
"""
return [self.substructure(c, meta, False) for c in connected_components(self)] |
iterate other all bonds | def bonds(self):
"""
iterate other all bonds
"""
seen = set()
for n, m_bond in self._adj.items():
seen.add(n)
for m, bond in m_bond.items():
if m not in seen:
yield n, m, bond |
need for cyclic import solving | def _get_subclass(name):
"""
need for cyclic import solving
"""
return next(x for x in BaseContainer.__subclasses__() if x.__name__ == name) |
Creates a urllib3. PoolManager object that has SSL verification enabled and uses the certifi certificates. | def _default_make_pool(http, proxy_info):
"""Creates a urllib3.PoolManager object that has SSL verification enabled
and uses the certifi certificates."""
if not http.ca_certs:
http.ca_certs = _certifi_where_for_ssl_version()
ssl_disabled = http.disable_ssl_certificate_validation
cert_reqs... |
Monkey - patches httplib2. Http to be httplib2shim. Http. | def patch(make_pool=_default_make_pool):
"""Monkey-patches httplib2.Http to be httplib2shim.Http.
This effectively makes all clients of httplib2 use urlilb3. It's preferable
to specify httplib2shim.Http explicitly where you can, but this can be
useful in situations where you do not control the construc... |
Checks if a given address is an IPv6 address. | def _is_ipv6(addr):
"""Checks if a given address is an IPv6 address."""
try:
socket.inet_pton(socket.AF_INET6, addr)
return True
except socket.error:
return False |
Gets the right location for certifi certifications for the current SSL version. | def _certifi_where_for_ssl_version():
"""Gets the right location for certifi certifications for the current SSL
version.
Older versions of SSL don't support the stronger set of root certificates.
"""
if not ssl:
return
if ssl.OPENSSL_VERSION_INFO < (1, 0, 2):
warnings.warn(
... |
Maps a urllib3 response to a httplib/ httplib2 Response. | def _map_response(response, decode=False):
"""Maps a urllib3 response to a httplib/httplib2 Response."""
# This causes weird deepcopy errors, so it's commented out for now.
# item._urllib3_response = response
item = httplib2.Response(response.getheaders())
item.status = response.status
item['sta... |
Maps an exception from urlib3 to httplib2. | def _map_exception(e):
"""Maps an exception from urlib3 to httplib2."""
if isinstance(e, urllib3.exceptions.MaxRetryError):
if not e.reason:
return e
e = e.reason
message = e.args[0] if e.args else ''
if isinstance(e, urllib3.exceptions.ResponseError):
if 'too many re... |
subprocess handler | def run_workers(no_subprocess, watch_paths=None, is_background=False):
"""
subprocess handler
"""
import atexit, os, subprocess, signal
if watch_paths:
from watchdog.observers import Observer
# from watchdog.observers.fsevents import FSEventsObserver as Observer
# from watchd... |
Properly close the AMQP connections | def exit(self, signal=None, frame=None):
"""
Properly close the AMQP connections
"""
self.input_channel.close()
self.client_queue.close()
self.connection.close()
log.info("Worker exiting")
sys.exit(0) |
make amqp connection and create channels and queue binding | def connect(self):
"""
make amqp connection and create channels and queue binding
"""
self.connection = pika.BlockingConnection(BLOCKING_MQ_PARAMS)
self.client_queue = ClientQueue()
self.input_channel = self.connection.channel()
self.input_channel.exchange_declar... |
clear outs all messages from INPUT_QUEUE_NAME | def clear_queue(self):
"""
clear outs all messages from INPUT_QUEUE_NAME
"""
def remove_message(ch, method, properties, body):
print("Removed message: %s" % body)
self.input_channel.basic_consume(remove_message, queue=self.INPUT_QUEUE_NAME, no_ack=True)
try:
... |
actual consuming of incoming works starts here | def run(self):
"""
actual consuming of incoming works starts here
"""
self.input_channel.basic_consume(self.handle_message,
queue=self.INPUT_QUEUE_NAME,
no_ack=True
... |
this is a pika. basic_consumer callback handles client inputs runs appropriate workflows and views | def handle_message(self, ch, method, properties, body):
"""
this is a pika.basic_consumer callback
handles client inputs, runs appropriate workflows and views
Args:
ch: amqp channel
method: amqp method
properties:
body: message body
... |
Args: start ( DateTime ): start date finish ( DateTime ): finish date Returns: | def get_progress(start, finish):
"""
Args:
start (DateTime): start date
finish (DateTime): finish date
Returns:
"""
now = datetime.now()
dif_time_start = start - now
dif_time_finish = finish - now
if dif_time_start.days < 0 and dif_time_finish.days < 0:
return P... |
BG Job for storing wf state to DB | def sync_wf_cache(current):
"""
BG Job for storing wf state to DB
"""
wf_cache = WFCache(current)
wf_state = wf_cache.get() # unicode serialized json to dict, all values are unicode
if 'role_id' in wf_state:
# role_id inserted by engine, so it's a sign that we get it from cache not db
... |
if xml content updated create a new entry for given wf name Args: name: name of wf content: xml content | def get_or_create_by_content(cls, name, content):
"""
if xml content updated, create a new entry for given wf name
Args:
name: name of wf
content: xml content
Returns (DiagramXML(), bool): A tuple with two members.
(DiagramXML instance and True if it's ne... |
Tries to get WF description from collabration or process or pariticipant | def get_description(self):
"""
Tries to get WF description from 'collabration' or 'process' or 'pariticipant'
Returns str: WF description
"""
paths = ['bpmn:collaboration/bpmn:participant/bpmn:documentation',
'bpmn:collaboration/bpmn:documentation',
... |
Tries to get WF name from process or collobration or pariticipant | def get_name(self):
"""
Tries to get WF name from 'process' or 'collobration' or 'pariticipant'
Returns:
str. WF name.
"""
paths = ['bpmn:process',
'bpmn:collaboration/bpmn:participant/',
'bpmn:collaboration',
]
... |
updates xml link if there aren t any running instances of this wf Args: diagram: XMLDiagram object | def set_xml(self, diagram, force=False):
"""
updates xml link if there aren't any running instances of this wf
Args:
diagram: XMLDiagram object
"""
no_of_running = WFInstance.objects.filter(wf=self, finished=False, started=True).count()
if no_of_running and no... |
Creates wf instances. Args: roles ( list ): role list | def create_wf_instances(self, roles=None):
"""
Creates wf instances.
Args:
roles (list): role list
Returns:
(list): wf instances
"""
# if roles specified then create an instance for each role
# else create only one instance
if ro... |
will create a WFInstance per object and per TaskInvitation for each role and WFInstance | def create_tasks(self):
"""
will create a WFInstance per object
and per TaskInvitation for each role and WFInstance
"""
roles = self.get_roles()
if self.task_type in ["A", "D"]:
instances = self.create_wf_instances(roles=roles)
self.create_task_in... |
returns objects keys according to self. object_query_code which can be json encoded queryset filter dict or key = value set in the following format: key = val key2 = val2 key3 = value with spaces | def get_object_query_dict(self):
"""returns objects keys according to self.object_query_code
which can be json encoded queryset filter dict or key=value set
in the following format: ```"key=val, key2 = val2 , key3= value with spaces"```
Returns:
(dict): Queryset filtering ... |
returns object keys according to task definition which can be explicitly selected one object ( self. object_key ) or result of a queryset filter. | def get_object_keys(self, wfi_role=None):
"""returns object keys according to task definition
which can be explicitly selected one object (self.object_key) or
result of a queryset filter.
Returns:
list of object keys
"""
if self.object_key:
return... |
Fetches model objects by filtering with kwargs | def get_model_objects(model, wfi_role=None, **kwargs):
"""
Fetches model objects by filtering with kwargs
If wfi_role is specified, then we expect kwargs contains a
filter value starting with role,
e.g. {'user': 'role.program.user'}
We replace this `role` key with role... |
Returns: Role instances according to task definition. | def get_roles(self):
"""
Returns:
Role instances according to task definition.
"""
if self.role.exist:
# return explicitly selected role
return [self.role]
else:
roles = []
if self.role_query_code:
# use... |
can be removed when a proper task manager admin interface implemented | def post_save(self):
"""can be removed when a proper task manager admin interface implemented"""
if self.run:
self.run = False
self.create_tasks()
self.save() |
When one person use an invitation we should delete other invitations | def delete_other_invitations(self):
"""
When one person use an invitation, we should delete other invitations
"""
# TODO: Signal logged-in users to remove the task from their task list
self.objects.filter(instance=self.instance).exclude(key=self.key).delete() |
write wf state to DB through MQ >> Worker >> _zops_sync_wf_cache | def save(self, wf_state):
"""
write wf state to DB through MQ >> Worker >> _zops_sync_wf_cache
Args:
wf_state dict: wf state
"""
self.wf_state = wf_state
self.wf_state['role_id'] = self.current.role_id
self.set(self.wf_state)
if self.wf_state[... |
Send messages through RabbitMQ s default exchange which will be delivered through routing_key ( sess_id ). | def send_to_default_exchange(self, sess_id, message=None):
"""
Send messages through RabbitMQ's default exchange,
which will be delivered through routing_key (sess_id).
This method only used for un-authenticated users, i.e. login process.
Args:
sess_id string: Sessi... |
Send messages through logged in users private exchange. | def send_to_prv_exchange(self, user_id, message=None):
"""
Send messages through logged in users private exchange.
Args:
user_id string: User key
message dict: Message object
"""
exchange = 'prv_%s' % user_id.lower()
msg = json.dumps(message, cls... |
compose 2 graphs to CGR | def compose(self, other):
"""
compose 2 graphs to CGR
:param other: Molecule or CGR Container
:return: CGRContainer
"""
if not isinstance(other, Compose):
raise TypeError('CGRContainer or MoleculeContainer [sub]class expected')
cgr = self._get_subcla... |
decompose CGR to pair of Molecules which represents reactants and products state of reaction | def decompose(self):
"""
decompose CGR to pair of Molecules, which represents reactants and products state of reaction
:return: tuple of two molecules
"""
mc = self._get_subclass('MoleculeContainer')
reactants = mc()
products = mc()
for n, atom in self.a... |
Get data from JIRA for cycle/ flow times and story points size change. | def cycle_data(self, verbose=False, result_cycle=None, result_size=None, result_edges=None,changelog=True):
"""Get data from JIRA for cycle/flow times and story points size change.
Build a numerically indexed data frame with the following 'fixed'
columns: `key`, 'url', 'issue_type', `summary`, ... |
Return the a DataFrame indexed by day with columns containing story size for each issue. | def size_history(self,size_data):
"""Return the a DataFrame,
indexed by day, with columns containing story size for each issue.
In addition, columns are soted by Jira Issue key. First by Project and then by id number.
"""
def my_merge(df1, df2):
# http://stackoverfl... |
Return the data to build a cumulative flow diagram: a DataFrame indexed by day with columns containing cumulative counts for each of the items in the configured cycle. | def cfd(self, cycle_data,size_history= None, pointscolumn= None, stacked = True ):
"""Return the data to build a cumulative flow diagram: a DataFrame,
indexed by day, with columns containing cumulative counts for each
of the items in the configured cycle.
In addition, a column called `c... |
Return histogram data for the cycle times in cycle_data. Returns a dictionary with keys bin_values and bin_edges of numpy arrays | def histogram(self, cycle_data, bins=10):
"""Return histogram data for the cycle times in `cycle_data`. Returns
a dictionary with keys `bin_values` and `bin_edges` of numpy arrays
"""
values, edges = np.histogram(cycle_data['cycle_time'].astype('timedelta64[D]').dropna(), bins=bins)
... |
Return a data frame with columns completed_timestamp of the given frequency either count where count is the number of items sum where sum is the sum of value specified by pointscolumn. Expected to be StoryPoints completed at that timestamp ( e. g. daily ). | def throughput_data(self, cycle_data, frequency='1D',pointscolumn= None):
"""Return a data frame with columns `completed_timestamp` of the
given frequency, either
`count`, where count is the number of items
'sum', where sum is the sum of value specified by pointscolumn. Expected to be 'S... |
Return scatterplot data for the cycle times in cycle_data. Returns a data frame containing only those items in cycle_data where values are set for completed_timestamp and cycle_time and with those two columns as the first two both normalised to whole days and with completed_timestamp renamed to completed_date. | def scatterplot(self, cycle_data):
"""Return scatterplot data for the cycle times in `cycle_data`. Returns
a data frame containing only those items in `cycle_data` where values
are set for `completed_timestamp` and `cycle_time`, and with those two
columns as the first two, both normalise... |
Is NSQ running and have space to receive messages? | def _is_ready(self, topic_name):
'''
Is NSQ running and have space to receive messages?
'''
url = 'http://%s/stats?format=json&topic=%s' % (self.nsqd_http_address, topic_name)
#Cheacking for ephmeral channels
if '#' in topic_name:
topic_name, tag =topic_name.s... |
QueryContainer < MoleculeContainer QueryContainer < QueryContainer [ more general ] QueryContainer < QueryCGRContainer [ more general ] | def _matcher(self, other):
"""
QueryContainer < MoleculeContainer
QueryContainer < QueryContainer[more general]
QueryContainer < QueryCGRContainer[more general]
"""
if isinstance(other, MoleculeContainer):
return GraphMatcher(other, self, lambda x, y: y == x, ... |
QueryCGRContainer < CGRContainer QueryContainer < QueryCGRContainer [ more general ] | def _matcher(self, other):
"""
QueryCGRContainer < CGRContainer
QueryContainer < QueryCGRContainer[more general]
"""
if isinstance(other, CGRContainer):
return GraphMatcher(other, self, lambda x, y: y == x, lambda x, y: y == x)
elif isinstance(other, QueryCGRC... |
recalculate 2d coordinates. currently rings can be calculated badly. | def calculate2d(self, force=False, scale=1):
"""
recalculate 2d coordinates. currently rings can be calculated badly.
:param scale: rescale calculated positions.
:param force: ignore existing coordinates of atoms
"""
dist = {}
# length forces
for n, m_bon... |
Finds all possible knight moves: type: position Board: rtype: list | def possible_moves(self, position):
"""
Finds all possible knight moves
:type: position Board
:rtype: list
"""
for direction in [0, 1, 2, 3]:
angles = self._rotate_direction_ninety_degrees(direction)
for angle in angles:
try:
... |
get a list of lists of atoms of reaction centers | def centers_list(self):
""" get a list of lists of atoms of reaction centers
"""
center = set()
adj = defaultdict(set)
for n, atom in self.atoms():
if atom._reactant != atom._product:
center.add(n)
for n, m, bond in self.bonds():
i... |
get list of atoms of reaction center ( atoms with dynamic: bonds charges radicals ). | def center_atoms(self):
""" get list of atoms of reaction center (atoms with dynamic: bonds, charges, radicals).
"""
nodes = set()
for n, atom in self.atoms():
if atom._reactant != atom._product:
nodes.add(n)
for n, m, bond in self.bonds():
... |
get list of bonds of reaction center ( bonds with dynamic orders ). | def center_bonds(self):
""" get list of bonds of reaction center (bonds with dynamic orders).
"""
return [(n, m) for n, m, bond in self.bonds() if bond._reactant != bond._product] |
set or reset hyb and neighbors marks to atoms. | def reset_query_marks(self):
"""
set or reset hyb and neighbors marks to atoms.
"""
for i, atom in self.atoms():
neighbors = 0
hybridization = 1
p_neighbors = 0
p_hybridization = 1
# hyb 1- sp3; 2- sp2; 3- sp1; 4- aromatic
... |
create substructure containing atoms from nbunch list | def substructure(self, atoms, meta=False, as_view=True):
"""
create substructure containing atoms from nbunch list
:param atoms: list of atoms numbers of substructure
:param meta: if True metadata will be copied to substructure
:param as_view: If True, the returned graph-view pr... |
CGRContainer < CGRContainer | def _matcher(self, other):
"""
CGRContainer < CGRContainer
"""
if isinstance(other, CGRContainer):
return GraphMatcher(other, self, lambda x, y: x == y, lambda x, y: x == y)
raise TypeError('only cgr-cgr possible') |
modified NX fast BFS node generator | def __plain_bfs(adj, source):
"""modified NX fast BFS node generator"""
seen = set()
nextlevel = {source}
while nextlevel:
thislevel = nextlevel
nextlevel = set()
for v in thislevel:
if v not in seen:
yield v
... |
Returns authorization token provided by Cocaine. | def token(self):
"""
Returns authorization token provided by Cocaine.
The real meaning of the token is determined by its type. For example OAUTH2 token will
have "bearer" type.
:return: A tuple of token type and body.
"""
if self._token is None:
toke... |
Send a message lazy formatted with args. External log attributes can be passed via named attribute extra like in logging from the standart library. | def _send(self):
""" Send a message lazy formatted with args.
External log attributes can be passed via named attribute `extra`,
like in logging from the standart library.
Note:
* Attrs must be dict, otherwise the whole message would be skipped.
* The key field i... |
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