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def explicify_hydrogens(self):
"""
add explicit hydrogens to atoms
:return: number of added atoms
"""
tmp = []
for n, atom in self.atoms():
if atom.element != 'H':
for _ in range(atom.get_implicit_h([x.order for x in self._adj[n].values()])):
... |
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... |
def check_valence(self):
"""
check valences of all atoms
:return: list of invalid atoms
"""
return [x for x, atom in self.atoms() if not atom.check_valence(self.environment(x))] |
def _matcher(self, other):
"""
return VF2 GraphMatcher
MoleculeContainer < MoleculeContainer
MoleculeContainer < CGRContainer
"""
if isinstance(other, (self._get_subclass('CGRContainer'), MoleculeContainer)):
return GraphMatcher(other, self, lambda x, y: x ==... |
def to_datetime(date):
"""Turn a date into a datetime at midnight.
"""
return datetime.datetime.combine(date, datetime.datetime.min.time()) |
def iter_size_changes(self, issue):
"""Yield an IssueSnapshot for each time the issue size changed
"""
# Find the first size change, if any
try:
size_changes = list(filter(lambda h: h.field == 'Story Points',
itertools.chain.from_iterab... |
def iter_changes(self, issue, include_resolution_changes=True):
"""Yield an IssueSnapshot for each time the issue changed status or
resolution
"""
is_resolved = False
# Find the first status change, if any
try:
status_changes = list(filter(
l... |
def find_issues(self, criteria={}, jql=None, order='KEY ASC', verbose=False, changelog=True):
"""Return a list of issues with changelog metadata.
Searches for the `issue_types`, `project`, `valid_resolutions` and
'jql_filter' set in the passed-in `criteria` object.
Pass a JQL string to... |
def list_catalogs(self):
"""
Lists existing catalogs respect to ui view template format
"""
_form = CatalogSelectForm(current=self.current)
_form.set_choices_of('catalog', [(i, i) for i in fixture_bucket.get_keys()])
self.form_out(_form) |
def get_catalog(self):
"""
Get existing catalog and fill the form with the model data.
If given key not found as catalog, it generates an empty catalog data form.
"""
catalog_data = fixture_bucket.get(self.input['form']['catalog'])
# define add or edit based on catalog ... |
def save_catalog(self):
"""
Saves the catalog data to given key
Cancels if the cmd is cancel
Notifies user with the process.
"""
if self.input["cmd"] == 'save_catalog':
try:
edited_object = dict()
for i in self.input["form"]["Ca... |
def date_to_solr(d):
""" converts DD-MM-YYYY to YYYY-MM-DDT00:00:00Z"""
return "{y}-{m}-{day}T00:00:00Z".format(day=d[:2], m=d[3:5], y=d[6:]) if d else d |
def solr_to_date(d):
""" converts YYYY-MM-DDT00:00:00Z to DD-MM-YYYY """
return "{day}:{m}:{y}".format(y=d[:4], m=d[5:7], day=d[8:10]) if d else d |
def to_safe_str(s):
"""
converts some (tr) non-ascii chars to ascii counterparts,
then return the result as lowercase
"""
# TODO: This is insufficient as it doesn't do anything for other non-ascii chars
return re.sub(r'[^0-9a-zA-Z]+', '_', s.strip().replace(u'ğ', 'g').replace(u'ö', 'o').replace(... |
def merge_truthy(*dicts):
"""Merge multiple dictionaries, keeping the truthy values in case of key collisions.
Accepts any number of dictionaries, or any other object that returns a 2-tuple of
key and value pairs when its `.items()` method is called.
If a key exists in multiple dictionaries passed to ... |
def perform(self):
"""Perform the version upgrade on the database.
"""
db_versions = self.table.versions()
version = self.version
if (version.is_processed(db_versions) and
not self.config.force_version == self.version.number):
self.log(
... |
def _perform_version(self, version):
"""Inner method for version upgrade.
Not intended for standalone use. This method performs the actual
version upgrade with all the pre, post operations and addons upgrades.
:param version: The migration version to upgrade to
:type version: I... |
def logout(current):
"""
Log out view.
Simply deletes the session object.
For showing logout message:
'show_logout_message' field should be True in current.task_data,
Message should be sent in current.task_data with 'logout_message' field.
Message title should be sent in current.... |
def _do_upgrade(self):
""" open websocket connection """
self.current.output['cmd'] = 'upgrade'
self.current.output['user_id'] = self.current.user_id
self.terminate_existing_login()
self.current.user.bind_private_channel(self.current.session.sess_id)
user_sess = UserSessi... |
def do_view(self):
"""
Authenticate user with given credentials.
Connects user's queue and exchange
"""
self.current.output['login_process'] = True
self.current.task_data['login_successful'] = False
if self.current.is_auth:
self._do_upgrade()
e... |
def show_view(self):
"""
Show :attr:`LoginForm` form.
"""
self.current.output['login_process'] = True
if self.current.is_auth:
self._do_upgrade()
else:
self.current.output['forms'] = LoginForm(current=self.current).serialize() |
def skip(mapping):
"""
:param mapping: generator
:return: filtered generator
"""
found = set()
for m in mapping:
matched_atoms = set(m.values())
if found.intersection(matched_atoms):
continue
found.update(matched_atoms)
yield m |
def __get_mapping(self, structures):
"""
match each pattern to each molecule.
if all patterns matches with all molecules
return generator of all possible mapping.
:param structures: disjoint molecules
:return: mapping generator
"""
for c in permutations(s... |
def get(self, default=None):
"""
return the cached value or default if it can't be found
:param default: default value
:return: cached value
"""
d = cache.get(self.key)
return ((json.loads(d.decode('utf-8')) if self.serialize else d)
if d is not N... |
def set(self, val, lifetime=None):
"""
set cache value
:param val: any picklable object
:param lifetime: exprition time in sec
:return: val
"""
cache.set(self.key,
(json.dumps(val) if self.serialize else val),
lifetime or setti... |
def add(self, val):
"""
Add given value to item (list)
Args:
val: A JSON serializable object.
Returns:
Cache backend response.
"""
return cache.lpush(self.key, json.dumps(val) if self.serialize else val) |
def get_all(self):
"""
Get all list items.
Returns:
Cache backend response.
"""
result = cache.lrange(self.key, 0, -1)
return (json.loads(item.decode('utf-8')) for item in result if
item) if self.serialize else result |
def remove_item(self, val):
"""
Removes given item from the list.
Args:
val: Item
Returns:
Cache backend response.
"""
return cache.lrem(self.key, json.dumps(val)) |
def flush(cls, *args):
"""
Removes all keys of this namespace
Without args, clears all keys starting with cls.PREFIX
if called with args, clears keys starting with given cls.PREFIX + args
Args:
*args: Arbitrary number of arguments.
Returns:
List ... |
def update_or_expire_session(self):
"""
Deletes session if keepalive request expired
otherwise updates the keepalive timestamp value
"""
if not hasattr(self, 'key'):
return
now = time.time()
timestamp = float(self.get() or 0) or now
sess_id = s... |
def send_message_for_lane_change(sender, **kwargs):
"""
Sends a message to possible owners of the current workflows
next lane.
Args:
**kwargs: ``current`` and ``possible_owners`` are required.
sender (User): User object
"""
current = kwargs['current']
owners = kwargs['possi... |
def set_password(sender, **kwargs):
"""
Encrypts password of the user.
"""
if sender.model_class.__name__ == 'User':
usr = kwargs['object']
if not usr.password.startswith('$pbkdf2'):
usr.set_password(usr.password)
usr.save() |
def channel_list(self):
"""
Main screen for channel management.
Channels listed and operations can be chosen on the screen.
If there is an error message like non-choice,
it is shown here.
"""
if self.current.task_data.get('msg', False):
if self.curre... |
def channel_choice_control(self):
"""
It controls errors. If there is an error,
returns channel list screen with error message.
"""
self.current.task_data['control'], self.current.task_data['msg'] \
= self.selection_error_control(self.input['form'])
if self.cu... |
def create_new_channel(self):
"""
Features of new channel are specified like channel's name, owner etc.
"""
self.current.task_data['new_channel'] = True
_form = NewChannelForm(Channel(), current=self.current)
_form.title = _(u"Specify Features of New Channel to Create")
... |
def save_new_channel(self):
"""
It saves new channel according to specified channel features.
"""
form_info = self.input['form']
channel = Channel(typ=15, name=form_info['name'],
description=form_info['description'],
owner_id=f... |
def choose_existing_channel(self):
"""
It is a channel choice list and chosen channels
at previous step shouldn't be on the screen.
"""
if self.current.task_data.get('msg', False):
self.show_warning_messages()
_form = ChannelListForm()
_form.title = ... |
def existing_choice_control(self):
"""
It controls errors. It generates an error message
if zero or more than one channels are selected.
"""
self.current.task_data['existing'] = False
self.current.task_data['msg'] = _(u"You should choose just one channel to do operation."... |
def split_channel(self):
"""
A channel can be splitted to new channel or other existing channel.
It creates subscribers list as selectable to moved.
"""
if self.current.task_data.get('msg', False):
self.show_warning_messages()
self.current.task_data['split_o... |
def subscriber_choice_control(self):
"""
It controls subscribers choice and generates
error message if there is a non-choice.
"""
self.current.task_data['option'] = None
self.current.task_data['chosen_subscribers'], names = self.return_selected_form_items(
sel... |
def move_complete_channel(self):
"""
Channels and theirs subscribers are moved
completely to new channel or existing channel.
"""
to_channel = Channel.objects.get(self.current.task_data['target_channel_key'])
chosen_channels = self.current.task_data['chosen_channels']
... |
def move_chosen_subscribers(self):
"""
After splitting operation, only chosen subscribers
are moved to new channel or existing channel.
"""
from_channel = Channel.objects.get(self.current.task_data['chosen_channels'][0])
to_channel = Channel.objects.get(self.current.task_... |
def copy_and_move_messages(from_channel, to_channel):
"""
While splitting channel and moving chosen subscribers to new channel,
old channel's messages are copied and moved to new channel.
Args:
from_channel (Channel object): move messages from channel
to_chann... |
def show_warning_messages(self, title=_(u"Incorrect Operation"), box_type='warning'):
"""
It shows incorrect operations or successful operation messages.
Args:
title (string): title of message box
box_type (string): type of message box (warning, info)
"""
... |
def return_selected_form_items(form_info):
"""
It returns chosen keys list from a given form.
Args:
form_info: serialized list of dict form data
Returns:
selected_keys(list): Chosen keys list
selected_names(list): Chosen channels' or subscribers' name... |
def selection_error_control(self, form_info):
"""
It controls the selection from the form according
to the operations, and returns an error message
if it does not comply with the rules.
Args:
form_info: Channel or subscriber form from the user
Returns: True ... |
def _eratosthenes():
"""Yields the sequence of prime numbers via the Sieve of Eratosthenes."""
d = {} # map each composite integer to its first-found prime factor
for q in count(2): # q gets 2, 3, 4, 5, ... ad infinitum
p = d.pop(q, None)
if p is None:
# q not a key in D, so q ... |
def atoms_order(self):
"""
Morgan like algorithm for graph nodes ordering
:return: dict of atom-weight pairs
"""
if not len(self): # for empty containers
return {}
elif len(self) == 1: # optimize single atom containers
return dict.fromkeys(self,... |
def init_manual(cls, pawn_value, knight_value, bishop_value, rook_value, queen_value, king_value):
"""
Manual init method for external piece values
:type: PAWN_VALUE: int
:type: KNIGHT_VALUE: int
:type: BISHOP_VALUE: int
:type: ROOK_VALUE: int
:type: QUEEN_VALUE:... |
def val(self, piece, ref_color):
"""
Finds value of ``Piece``
:type: piece: Piece
:type: ref_color: Color
:rtype: int
"""
if piece is None:
return 0
if ref_color == piece.color:
const = 1
else:
const = -1
... |
def play(self):
"""
Starts game and returns one of 3 results .
Iterates between methods ``white_move()`` and
``black_move()`` until game ends. Each
method calls the respective player's ``generate_move()``
method.
:rtype: int
"""
colors = [lambda:... |
def white_move(self):
"""
Calls the white player's ``generate_move()``
method and updates the board with the move returned.
"""
move = self.player_white.generate_move(self.position)
move = make_legal(move, self.position)
self.position.update(move) |
def black_move(self):
"""
Calls the black player's ``generate_move()``
method and updates the board with the move returned.
"""
move = self.player_black.generate_move(self.position)
move = make_legal(move, self.position)
self.position.update(move) |
def get_field_cache(self, cache_type='es'):
"""Return a list of fields' mappings"""
if cache_type == 'kibana':
try:
search_results = urlopen(self.get_url).read().decode('utf-8')
except HTTPError: # as e:
# self.pr_err("get_field_cache(kibana), HTT... |
def post_field_cache(self, field_cache):
"""Where field_cache is a list of fields' mappings"""
index_pattern = self.field_cache_to_index_pattern(field_cache)
# self.pr_dbg("request/post: %s" % index_pattern)
resp = requests.post(self.post_url, data=index_pattern).text
# resp = {"... |
def field_cache_to_index_pattern(self, field_cache):
"""Return a .kibana index-pattern doc_type"""
mapping_dict = {}
mapping_dict['customFormats'] = "{}"
mapping_dict['title'] = self.index_pattern
# now post the data into .kibana
mapping_dict['fields'] = json.dumps(field_... |
def check_mapping(self, m):
"""Assert minimum set of fields in cache, does not validate contents"""
if 'name' not in m:
self.pr_dbg("Missing %s" % "name")
return False
# self.pr_dbg("Checking %s" % m['name'])
for x in ['analyzed', 'indexed', 'type', 'scripted', 'c... |
def get_index_mappings(self, index):
"""Converts all index's doc_types to .kibana"""
fields_arr = []
for (key, val) in iteritems(index):
# self.pr_dbg("\tdoc_type: %s" % key)
doc_mapping = self.get_doc_type_mappings(index[key])
# self.pr_dbg("\tdoc_mapping: %s... |
def get_doc_type_mappings(self, doc_type):
"""Converts all doc_types' fields to .kibana"""
doc_fields_arr = []
found_score = False
for (key, val) in iteritems(doc_type):
# self.pr_dbg("\t\tfield: %s" % key)
# self.pr_dbg("\tval: %s" % val)
add_it = Fal... |
def get_field_mappings(self, field):
"""Converts ES field mappings to .kibana field mappings"""
retdict = {}
retdict['indexed'] = False
retdict['analyzed'] = False
for (key, val) in iteritems(field):
if key in self.mappings:
if (key == 'type' and
... |
def is_kibana_cache_incomplete(self, es_cache, k_cache):
"""Test if k_cache is incomplete
Assume k_cache is always correct, but could be missing new
fields that es_cache has
"""
# convert list into dict, with each item's ['name'] as key
k_dict = {}
for field in k... |
def list_to_compare_dict(self, list_form):
"""Convert list into a data structure we can query easier"""
compare_dict = {}
for field in list_form:
if field['name'] in compare_dict:
self.pr_dbg("List has duplicate field %s:\n%s" %
(field['nam... |
def compare_field_caches(self, replica, original):
"""Verify original is subset of replica"""
if original is None:
original = []
if replica is None:
replica = []
self.pr_dbg("Comparing orig with %s fields to replica with %s fields" %
(len(origi... |
def start_daemon_thread(target, args=()):
"""starts a deamon thread for a given target function and arguments."""
th = Thread(target=target, args=args)
th.daemon = True
th.start()
return th |
def serialize_dict_keys(d, prefix=""):
"""returns all the keys in a dictionary.
>>> serialize_dict_keys({"a": {"b": {"c": 1, "b": 2} } })
['a', 'a.b', 'a.b.c', 'a.b.b']
"""
keys = []
for k, v in d.iteritems():
fqk = '%s%s' % (prefix, k)
keys.append(fqk)
if isinstance(v, ... |
def set_user(self, user):
"""
Writes user data to session.
Args:
user: User object
"""
self.session['user_id'] = user.key
self.session['user_data'] = user.clean_value()
role = self.get_role()
# TODO: this should be remembered from previous lo... |
def contains_opposite_color_piece(self, square, position):
"""
Finds if square on the board is occupied by a ``Piece``
belonging to the opponent.
:type: square: Location
:type: position: Board
:rtype: bool
"""
return not position.is_square_empty(square) a... |
def gettext(message, domain=DEFAULT_DOMAIN):
"""Mark a message as translateable, and translate it.
All messages in the application that are translateable should be wrapped with this function.
When importing this function, it should be renamed to '_'. For example:
.. code-block:: python
from z... |
def gettext_lazy(message, domain=DEFAULT_DOMAIN):
"""Mark a message as translatable, but delay the translation until the message is used.
Sometimes, there are some messages that need to be translated, but the translation
can't be done at the point the message itself is written. For example, the names of
... |
def ngettext(singular, plural, n, domain=DEFAULT_DOMAIN):
"""Mark a message as translateable, and translate it considering plural forms.
Some messages may need to change based on a number. For example, consider a message
like the following:
.. code-block:: python
def alert_msg(msg_count): pri... |
def ngettext_lazy(singular, plural, n, domain=DEFAULT_DOMAIN):
"""Mark a message with plural forms translateable, and delay the translation
until the message is used.
Works the same was a `ngettext`, with a delaying functionality similiar to `gettext_lazy`.
Args:
singular (unicode): The singul... |
def _wrap_locale_formatter(fn, locale_type):
"""Wrap a Babel data formatting function to automatically format
for currently installed locale."""
def wrapped_locale_formatter(*args, **kwargs):
"""A Babel formatting function, wrapped to automatically use the
currently installed language.
... |
def install_language(cls, language_code):
"""Install the translations for language specified by `language_code`.
If we don't have translations for this language, then the default language will be used.
If the language specified is already installed, then this is a no-op.
"""
# ... |
def install_locale(cls, locale_code, locale_type):
"""Install the locale specified by `language_code`, for localizations of type `locale_type`.
If we can't perform localized formatting for the specified locale,
then the default localization format will be used.
If the locale specified ... |
def _rotate_vector(x, y, x2, y2, x1, y1):
"""
rotate x,y vector over x2-x1, y2-y1 angle
"""
angle = atan2(y2 - y1, x2 - x1)
cos_rad = cos(angle)
sin_rad = sin(angle)
return cos_rad * x + sin_rad * y, -sin_rad * x + cos_rad * y |
def _build_static_table_mapping():
"""
Build static table mapping from header name to tuple with next structure:
(<minimal index of header>, <mapping from header value to it index>).
static_table_mapping used for hash searching.
"""
static_table_mapping = {}
for index, (name, value) in enum... |
def get_by_index(self, index):
"""
Returns the entry specified by index
Note that the table is 1-based ie an index of 0 is
invalid. This is due to the fact that a zero value
index signals that a completely unindexed header
follows.
The entry will either be from... |
def add(self, name, value):
"""
Adds a new entry to the table
We reduce the table size if the entry will make the
table size greater than maxsize.
"""
# We just clear the table if the entry is too big
size = table_entry_size(name, value)
if size > self._m... |
def search(self, name, value):
"""
Searches the table for the entry specified by name
and value
Returns one of the following:
- ``None``, no match at all
- ``(index, name, None)`` for partial matches on name only.
- ``(index, name, value)`` for perfec... |
def _shrink(self):
"""
Shrinks the dynamic table to be at or below maxsize
"""
cursize = self._current_size
while cursize > self._maxsize:
name, value = self.dynamic_entries.pop()
cursize -= table_entry_size(name, value)
self._current_size = cursiz... |
def add(self, name, value):
# type: (str, str) -> None
"""Adds a new value for the given key."""
self._last_key = name
if name in self:
self._dict[name] = value
self._as_list[name].append(value)
else:
self[name] = value |
def get_all(self):
# type: () -> typing.Iterable[typing.Tuple[str, str]]
"""Returns an iterable of all (name, value) pairs.
If a header has multiple values, multiple pairs will be
returned with the same name.
"""
for name, values in six.iteritems(self._as_list):
... |
def safe_print(ustring, errors='replace', **kwargs):
""" Safely print a unicode string """
encoding = sys.stdout.encoding or 'utf-8'
if sys.version_info[0] == 3:
print(ustring, **kwargs)
else:
bytestr = ustring.encode(encoding, errors=errors)
print(bytestr, **kwargs) |
def edit_permissions(self):
"""Creates the view used to edit permissions.
To create the view, data in the following format is passed to the UI
in the objects field:
.. code-block:: python
{
"type": "tree-toggle",
"action": "set_permission",
... |
def _permission_trees(permissions):
"""Get the cached permission tree, or build a new one if necessary."""
treecache = PermissionTreeCache()
cached = treecache.get()
if not cached:
tree = PermissionTreeBuilder()
for permission in permissions:
tree.... |
def _apply_role_tree(self, perm_tree, role):
"""In permission tree, sets `'checked': True` for the permissions that the role has."""
role_permissions = role.get_permissions()
for perm in role_permissions:
self._traverse_tree(perm_tree, perm)['checked'] = True
return perm_tree |
def _traverse_tree(tree, path):
"""Traverses the permission tree, returning the permission at given permission path."""
path_steps = (step for step in path.split('.') if step != '')
# Special handling for first step, because the first step isn't under 'objects'
first_step = path_steps.ne... |
def _format_subtree(self, subtree):
"""Recursively format all subtrees."""
subtree['children'] = list(subtree['children'].values())
for child in subtree['children']:
self._format_subtree(child)
return subtree |
def apply_change(self):
"""Applies changes to the permissions of the role.
To make a change to the permission of the role, a request
in the following format should be sent:
.. code-block:: python
{
'change':
{
'id'... |
def seek(self, offset):
"""
shifts on a given number of record in the original file
:param offset: number of record
"""
if self._shifts:
if 0 <= offset < len(self._shifts):
current_pos = self._file.tell()
new_pos = self._shifts[offset]
... |
def tell(self):
"""
:return: number of records processed from the original file
"""
if self._shifts:
t = self._file.tell()
return bisect_left(self._shifts, t)
raise self._implement_error |
def write(self, data):
"""
write single molecule into file
"""
m = self._convert_structure(data)
self._file.write(self._format_mol(*m))
self._file.write('M END\n')
for k, v in data.meta.items():
self._file.write(f'> <{k}>\n{v}\n')
self._file... |
def save_workflow_to_cache(self, serialized_wf_instance):
"""
If we aren't come to the end of the wf,
saves the wf state and task_data to cache
Task_data items that starts with underscore "_" are treated as
local and does not passed to subsequent task steps.
"""
... |
def get_pool_context(self):
# TODO: Add in-process caching
"""
Builds context for the WF pool.
Returns:
Context dict.
"""
context = {self.current.lane_id: self.current.role, 'self': self.current.role}
for lane_id, role_id in self.current.pool.items():... |
def load_workflow_from_cache(self):
"""
loads the serialized wf state and data from cache
updates the self.current.task_data
"""
if not self.current.new_token:
self.wf_state = self.current.wf_cache.get(self.wf_state)
self.current.task_data = self.wf_state[... |
def serialize_workflow(self):
"""
Serializes the current WF.
Returns:
WF state data.
"""
self.workflow.refresh_waiting_tasks()
return CompactWorkflowSerializer().serialize_workflow(self.workflow,
i... |
def load_or_create_workflow(self):
"""
Tries to load the previously serialized (and saved) workflow
Creates a new one if it can't
"""
self.workflow_spec = self.get_worfklow_spec()
return self._load_workflow() or self.create_workflow() |
def find_workflow_path(self):
"""
Tries to find the path of the workflow diagram file
in `WORKFLOW_PACKAGES_PATHS`.
Returns:
Path of the workflow spec file (BPMN diagram)
"""
for pth in settings.WORKFLOW_PACKAGES_PATHS:
path = "%s/%s.bpmn" % (pth,... |
def get_worfklow_spec(self):
"""
Generates and caches the workflow spec package from
BPMN diagrams that read from disk
Returns:
SpiffWorkflow Spec object.
"""
# TODO: convert from in-process to redis based caching
if self.current.workflow_name not in ... |
def _save_or_delete_workflow(self):
"""
Calls the real save method if we pass the beggining of the wf
"""
if not self.current.task_type.startswith('Start'):
if self.current.task_name.startswith('End') and not self.are_we_in_subprocess():
self.wf_state['finishe... |
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