repository_name stringclasses 316
values | func_path_in_repository stringlengths 6 223 | func_name stringlengths 1 134 | language stringclasses 1
value | func_code_string stringlengths 57 65.5k | func_documentation_string stringlengths 1 46.3k | split_name stringclasses 1
value | func_code_url stringlengths 91 315 | called_functions listlengths 1 156 ⌀ | enclosing_scope stringlengths 2 1.48M |
|---|---|---|---|---|---|---|---|---|---|
solocompt/plugs-mail | plugs_mail/utils.py | to_email | python | def to_email(email_class, email, language=None, **data):
if language:
email_class().send([email], language=language, **data)
else:
email_class().send([email], translation.get_language(), **data) | Send email to specified email address | train | https://github.com/solocompt/plugs-mail/blob/6139fa79ddb437562db1769d03bd3098c25a06fa/plugs_mail/utils.py#L8-L15 | null | """
Plugs Mail Utils
"""
from django.utils import translation
from django.contrib.auth import get_user_model
def to_user(email_class, user, **data):
"""
Email user
"""
try:
email_class().send([user.email], user.language, **data)
except AttributeError:
# this is a fallback in case ... |
solocompt/plugs-mail | plugs_mail/utils.py | to_user | python | def to_user(email_class, user, **data):
try:
email_class().send([user.email], user.language, **data)
except AttributeError:
# this is a fallback in case the user model does not have the language field
email_class().send([user.email], translation.get_language(), **data) | Email user | train | https://github.com/solocompt/plugs-mail/blob/6139fa79ddb437562db1769d03bd3098c25a06fa/plugs_mail/utils.py#L17-L25 | null | """
Plugs Mail Utils
"""
from django.utils import translation
from django.contrib.auth import get_user_model
def to_email(email_class, email, language=None, **data):
"""
Send email to specified email address
"""
if language:
email_class().send([email], language=language, **data)
else:
... |
solocompt/plugs-mail | plugs_mail/utils.py | to_staff | python | def to_staff(email_class, **data):
for user in get_user_model().objects.filter(is_staff=True):
try:
email_class().send([user.email], user.language, **data)
except AttributeError:
email_class().send([user.email], translation.get_language(), **data) | Email staff users | train | https://github.com/solocompt/plugs-mail/blob/6139fa79ddb437562db1769d03bd3098c25a06fa/plugs_mail/utils.py#L27-L35 | null | """
Plugs Mail Utils
"""
from django.utils import translation
from django.contrib.auth import get_user_model
def to_email(email_class, email, language=None, **data):
"""
Send email to specified email address
"""
if language:
email_class().send([email], language=language, **data)
else:
... |
solocompt/plugs-mail | plugs_mail/utils.py | to_superuser | python | def to_superuser(email_class, **data):
for user in get_user_model().objects.filter(is_superuser=True):
try:
email_class().send([user.email], user.language, **data)
except AttributeError:
email_class().send([user.email], translation.get_language(), **data) | Email superusers | train | https://github.com/solocompt/plugs-mail/blob/6139fa79ddb437562db1769d03bd3098c25a06fa/plugs_mail/utils.py#L37-L45 | null | """
Plugs Mail Utils
"""
from django.utils import translation
from django.contrib.auth import get_user_model
def to_email(email_class, email, language=None, **data):
"""
Send email to specified email address
"""
if language:
email_class().send([email], language=language, **data)
else:
... |
solocompt/plugs-mail | plugs_mail/mail.py | PlugsMail.validate_context | python | def validate_context(self):
if self.context and len(self.context) != len(set(self.context)):
LOGGER.error('Cannot have duplicated context objects')
raise Exception('Cannot have duplicated context objects.') | Make sure there are no duplicate context objects
or we might end up with switched data
Converting the tuple to a set gets rid of the
eventual duplicate objects, comparing the length
of the original tuple and set tells us if we
have duplicates in the tuple or not | train | https://github.com/solocompt/plugs-mail/blob/6139fa79ddb437562db1769d03bd3098c25a06fa/plugs_mail/mail.py#L33-L45 | null | class PlugsMail(object):
"""
Solo mail is the class responsible for
getting and validating the context and
prepare the email for sending
"""
template = None
context = None
context_data = {}
data = None
def __init__(self):
self.validate_context()
assert self.templ... |
solocompt/plugs-mail | plugs_mail/mail.py | PlugsMail.get_instance_of | python | def get_instance_of(self, model_cls):
for obj in self.data.values():
if isinstance(obj, model_cls):
return obj
LOGGER.error('Context Not Found')
raise Exception('Context Not Found') | Search the data to find a instance
of a model specified in the template | train | https://github.com/solocompt/plugs-mail/blob/6139fa79ddb437562db1769d03bd3098c25a06fa/plugs_mail/mail.py#L47-L56 | null | class PlugsMail(object):
"""
Solo mail is the class responsible for
getting and validating the context and
prepare the email for sending
"""
template = None
context = None
context_data = {}
data = None
def __init__(self):
self.validate_context()
assert self.templ... |
solocompt/plugs-mail | plugs_mail/mail.py | PlugsMail.get_context | python | def get_context(self):
if not self.context:
return
else:
assert isinstance(self.context, tuple), 'Expected a Tuple not {0}'.format(type(self.context))
for model in self.context:
model_cls = utils.get_model_class(model)
key = utils.camel_to_snake(mo... | Create a dict with the context data
context is not required, but if it
is defined it should be a tuple | train | https://github.com/solocompt/plugs-mail/blob/6139fa79ddb437562db1769d03bd3098c25a06fa/plugs_mail/mail.py#L58-L71 | [
"def get_instance_of(self, model_cls):\n \"\"\"\n Search the data to find a instance\n of a model specified in the template\n \"\"\"\n for obj in self.data.values():\n if isinstance(obj, model_cls):\n return obj\n LOGGER.error('Context Not Found')\n raise Exception('Context No... | class PlugsMail(object):
"""
Solo mail is the class responsible for
getting and validating the context and
prepare the email for sending
"""
template = None
context = None
context_data = {}
data = None
def __init__(self):
self.validate_context()
assert self.templ... |
solocompt/plugs-mail | plugs_mail/mail.py | PlugsMail.get_context_data | python | def get_context_data(self):
self.get_context()
self.context_data.update(self.get_extra_context())
return self.context_data | Context Data is equal to context + extra_context
Merge the dicts context_data and extra_context and
update state | train | https://github.com/solocompt/plugs-mail/blob/6139fa79ddb437562db1769d03bd3098c25a06fa/plugs_mail/mail.py#L82-L90 | [
"def get_context(self):\n \"\"\"\n Create a dict with the context data\n context is not required, but if it\n is defined it should be a tuple\n \"\"\"\n if not self.context:\n return\n else:\n assert isinstance(self.context, tuple), 'Expected a Tuple not {0}'.format(type(self.cont... | class PlugsMail(object):
"""
Solo mail is the class responsible for
getting and validating the context and
prepare the email for sending
"""
template = None
context = None
context_data = {}
data = None
def __init__(self):
self.validate_context()
assert self.templ... |
solocompt/plugs-mail | plugs_mail/mail.py | PlugsMail.send | python | def send(self, to, language=None, **data):
self.data = data
self.get_context_data()
if app_settings['SEND_EMAILS']:
try:
if language:
mail.send(to, template=self.template, context=self.context_data, language=language)
else:
... | This is the method to be called | train | https://github.com/solocompt/plugs-mail/blob/6139fa79ddb437562db1769d03bd3098c25a06fa/plugs_mail/mail.py#L92-L106 | [
"def get_context_data(self):\n \"\"\"\n Context Data is equal to context + extra_context\n Merge the dicts context_data and extra_context and\n update state\n \"\"\"\n self.get_context()\n self.context_data.update(self.get_extra_context())\n return self.context_data\n"
] | class PlugsMail(object):
"""
Solo mail is the class responsible for
getting and validating the context and
prepare the email for sending
"""
template = None
context = None
context_data = {}
data = None
def __init__(self):
self.validate_context()
assert self.templ... |
solocompt/plugs-mail | plugs_mail/management/commands/load_email_templates.py | Command.override_default_templates | python | def override_default_templates(self):
if plugs_mail_settings['OVERRIDE_TEMPLATE_DIR']:
dir_ = plugs_mail_settings['OVERRIDE_TEMPLATE_DIR']
for file_ in os.listdir(dir_):
if file_.endswith(('.html', 'txt')):
self.overrides[file_] = dir_ | Override the default emails already defined by other apps | train | https://github.com/solocompt/plugs-mail/blob/6139fa79ddb437562db1769d03bd3098c25a06fa/plugs_mail/management/commands/load_email_templates.py#L29-L37 | null | class Command(BaseCommand):
overrides = {}
def handle(self, *args, **options):
self.override_default_templates()
templates = self.get_apps()
count = self.create_templates(templates)
if count:
self.stdout.write(self.style.SUCCESS('Successfully loaded %s email templat... |
solocompt/plugs-mail | plugs_mail/management/commands/load_email_templates.py | Command.get_apps | python | def get_apps(self):
templates = []
for app in settings.INSTALLED_APPS:
try:
app = import_module(app + '.emails')
templates += self.get_plugs_mail_classes(app)
except ImportError:
pass
return templates | Get the list of installed apps
and return the apps that have
an emails module | train | https://github.com/solocompt/plugs-mail/blob/6139fa79ddb437562db1769d03bd3098c25a06fa/plugs_mail/management/commands/load_email_templates.py#L39-L52 | null | class Command(BaseCommand):
overrides = {}
def handle(self, *args, **options):
self.override_default_templates()
templates = self.get_apps()
count = self.create_templates(templates)
if count:
self.stdout.write(self.style.SUCCESS('Successfully loaded %s email templat... |
solocompt/plugs-mail | plugs_mail/management/commands/load_email_templates.py | Command.get_template_files | python | def get_template_files(self, location, class_name):
template_name = utils.camel_to_snake(class_name)
dir_ = location[:-9] + 'templates/emails/'
files_ = []
for file_ in self.get_templates_files_in_dir(dir_):
if file_.startswith(template_name) and file_.endswith(('.html', '.tx... | Multilanguage support means that for each template
we can have multiple templtate files, this methods
returns all the template (html and txt) files
that match the (class) template name | train | https://github.com/solocompt/plugs-mail/blob/6139fa79ddb437562db1769d03bd3098c25a06fa/plugs_mail/management/commands/load_email_templates.py#L60-L76 | null | class Command(BaseCommand):
overrides = {}
def handle(self, *args, **options):
self.override_default_templates()
templates = self.get_apps()
count = self.create_templates(templates)
if count:
self.stdout.write(self.style.SUCCESS('Successfully loaded %s email templat... |
solocompt/plugs-mail | plugs_mail/management/commands/load_email_templates.py | Command.get_plugs_mail_classes | python | def get_plugs_mail_classes(self, app):
classes = []
members = self.get_members(app)
for member in members:
name, cls = member
if inspect.isclass(cls) and issubclass(cls, PlugsMail) and name != 'PlugsMail':
files_ = self.get_template_files(app.__file__, nam... | Returns a list of tuples, but it should
return a list of dicts | train | https://github.com/solocompt/plugs-mail/blob/6139fa79ddb437562db1769d03bd3098c25a06fa/plugs_mail/management/commands/load_email_templates.py#L78-L97 | null | class Command(BaseCommand):
overrides = {}
def handle(self, *args, **options):
self.override_default_templates()
templates = self.get_apps()
count = self.create_templates(templates)
if count:
self.stdout.write(self.style.SUCCESS('Successfully loaded %s email templat... |
solocompt/plugs-mail | plugs_mail/management/commands/load_email_templates.py | Command.get_template_language | python | def get_template_language(self, file_):
stem = Path(file_).stem
language_code = stem.split('_')[-1:][0]
if len(language_code) != 2:
# TODO naive and temp implementation
# check if the two chars correspond to one of the
# available languages
raise E... | Return the template language
Every template file must end in
with the language code, and the
code must match the ISO_6301 lang code
https://en.wikipedia.org/wiki/List_of_ISO_639-1_codes
valid examples:
account_created_pt.html
payment_created_en.txt | train | https://github.com/solocompt/plugs-mail/blob/6139fa79ddb437562db1769d03bd3098c25a06fa/plugs_mail/management/commands/load_email_templates.py#L99-L118 | null | class Command(BaseCommand):
overrides = {}
def handle(self, *args, **options):
self.override_default_templates()
templates = self.get_apps()
count = self.create_templates(templates)
if count:
self.stdout.write(self.style.SUCCESS('Successfully loaded %s email templat... |
solocompt/plugs-mail | plugs_mail/management/commands/load_email_templates.py | Command.get_subject | python | def get_subject(self, text):
first_line = text.splitlines(True)[0]
# TODO second line should be empty
if first_line.startswith('SUBJECT:'):
subject = first_line[len('SUBJECT:'):]
else:
subject = first_line
return subject.strip() | Email template subject is the first
line of the email template, we can optionally
add SUBJECT: to make it clearer | train | https://github.com/solocompt/plugs-mail/blob/6139fa79ddb437562db1769d03bd3098c25a06fa/plugs_mail/management/commands/load_email_templates.py#L120-L132 | null | class Command(BaseCommand):
overrides = {}
def handle(self, *args, **options):
self.override_default_templates()
templates = self.get_apps()
count = self.create_templates(templates)
if count:
self.stdout.write(self.style.SUCCESS('Successfully loaded %s email templat... |
solocompt/plugs-mail | plugs_mail/management/commands/load_email_templates.py | Command.create_templates | python | def create_templates(self, templates):
count = 0
for template in templates:
if not self.template_exists_db(template):
name, location, description, language = template
text = self.open_file(location)
html_content = self.get_html_content(text)
... | Gets a list of templates to insert into the database | train | https://github.com/solocompt/plugs-mail/blob/6139fa79ddb437562db1769d03bd3098c25a06fa/plugs_mail/management/commands/load_email_templates.py#L141-L161 | null | class Command(BaseCommand):
overrides = {}
def handle(self, *args, **options):
self.override_default_templates()
templates = self.get_apps()
count = self.create_templates(templates)
if count:
self.stdout.write(self.style.SUCCESS('Successfully loaded %s email templat... |
solocompt/plugs-mail | plugs_mail/management/commands/load_email_templates.py | Command.open_file | python | def open_file(self, file_):
with open(file_, 'r', encoding='utf-8') as file:
text = ''
for line in file:
text += line
return text | Receives a file path has input and returns a
string with the contents of the file | train | https://github.com/solocompt/plugs-mail/blob/6139fa79ddb437562db1769d03bd3098c25a06fa/plugs_mail/management/commands/load_email_templates.py#L171-L180 | null | class Command(BaseCommand):
overrides = {}
def handle(self, *args, **options):
self.override_default_templates()
templates = self.get_apps()
count = self.create_templates(templates)
if count:
self.stdout.write(self.style.SUCCESS('Successfully loaded %s email templat... |
solocompt/plugs-mail | plugs_mail/management/commands/load_email_templates.py | Command.template_exists_db | python | def template_exists_db(self, template):
name = utils.camel_to_snake(template[0]).upper()
language = utils.camel_to_snake(template[3])
try:
models.EmailTemplate.objects.get(name=name, language=language)
except models.EmailTemplate.DoesNotExist:
return False
... | Receives a template and checks if it exists in the database
using the template name and language | train | https://github.com/solocompt/plugs-mail/blob/6139fa79ddb437562db1769d03bd3098c25a06fa/plugs_mail/management/commands/load_email_templates.py#L183-L194 | null | class Command(BaseCommand):
overrides = {}
def handle(self, *args, **options):
self.override_default_templates()
templates = self.get_apps()
count = self.create_templates(templates)
if count:
self.stdout.write(self.style.SUCCESS('Successfully loaded %s email templat... |
tetframework/Tonnikala | tonnikala/ir/generate.py | BaseIRGenerator.merge_text_nodes_on | python | def merge_text_nodes_on(self, node):
if not isinstance(node, ContainerNode) or not node.children:
return
new_children = []
text_run = []
for i in node.children:
if isinstance(i, Text) and not i.translatable:
text_run.append(i.escaped())
... | Merges all consecutive non-translatable text nodes into one | train | https://github.com/tetframework/Tonnikala/blob/99d168657da1b2372ff898254f80808ea8d1b83f/tonnikala/ir/generate.py#L57-L80 | [
"def merge_text_nodes_on(self, node):\n \"\"\"Merges all consecutive non-translatable text nodes into one\"\"\"\n\n if not isinstance(node, ContainerNode) or not node.children:\n return\n\n new_children = []\n text_run = []\n for i in node.children:\n if isinstance(i, Text) and not i.tr... | class BaseIRGenerator(object):
def __init__(self, filename=None, source=None, *a, **kw):
super(BaseIRGenerator, self).__init__(*a, **kw)
self.filename = filename
self.source = source
self.states = [{}]
self.tree = IRTree()
def syntax_error(self, message, lineno=None):
... |
tetframework/Tonnikala | tonnikala/ir/generate.py | BaseIRGenerator.push_state | python | def push_state(self):
new = dict(self.states[-1])
self.states.append(new)
return self.state | Push a copy of the topmost state on top of the state stack,
returns the new top. | train | https://github.com/tetframework/Tonnikala/blob/99d168657da1b2372ff898254f80808ea8d1b83f/tonnikala/ir/generate.py#L95-L103 | null | class BaseIRGenerator(object):
def __init__(self, filename=None, source=None, *a, **kw):
super(BaseIRGenerator, self).__init__(*a, **kw)
self.filename = filename
self.source = source
self.states = [{}]
self.tree = IRTree()
def syntax_error(self, message, lineno=None):
... |
tetframework/Tonnikala | tonnikala/ir/generate.py | BaseDOMIRGenerator.enter_node | python | def enter_node(self, ir_node):
this_is_cdata = (isinstance(ir_node, Element)
and ir_node.name in self.cdata_elements)
self.state['is_cdata'] = bool(self.state.get('is_cdata')) or this_is_cdata | Enter the given element; keeps track of `cdata`;
subclasses may extend by overriding | train | https://github.com/tetframework/Tonnikala/blob/99d168657da1b2372ff898254f80808ea8d1b83f/tonnikala/ir/generate.py#L162-L169 | null | class BaseDOMIRGenerator(BaseIRGenerator):
def __init__(self, document=None, mode='html5', *a, **kw):
super(BaseDOMIRGenerator, self).__init__(*a, **kw)
self.dom_document = document
self.mode = mode
if mode in ['html', 'html5', 'xhtml']:
self.empty_elements = html5_empty... |
tetframework/Tonnikala | tonnikala/i18n/__init__.py | extract_tonnikala | python | def extract_tonnikala(fileobj, keywords, comment_tags, options):
extractor = TonnikalaExtractor()
for msg in extractor(filename=None, fileobj=fileobj, options=Options()):
msgid = msg.msgid,
prefix = ''
if msg.msgid_plural:
msgid = (msg.msgid_plural,) + msgid
pref... | Extract messages from Tonnikala files.
:param fileobj: the file-like object the messages should be extracted
from
:param keywords: a list of keywords (i.e. function names) that should
be recognized as translation functions
:param comment_tags: a list of translator t... | train | https://github.com/tetframework/Tonnikala/blob/99d168657da1b2372ff898254f80808ea8d1b83f/tonnikala/i18n/__init__.py#L57-L84 | null | import io
from lingua.extractors import Extractor
from lingua.extractors import Message
from lingua.extractors.python import _extract_python
from tonnikala.ir.nodes import TranslatableText, Expression
from tonnikala.loader import parsers
class TonnikalaExtractor(Extractor):
"Extract strings from tonnikala templa... |
tetframework/Tonnikala | tonnikala/languages/javascript/generator.py | FreeVariableAnalyzerVisitor.visit_Identifier | python | def visit_Identifier(self, node):
if not self._is_mangle_candidate(node):
return
name = node.value
symbol = node.scope.resolve(node.value)
if symbol is None:
self.free_variables.add(name) | Mangle names. | train | https://github.com/tetframework/Tonnikala/blob/99d168657da1b2372ff898254f80808ea8d1b83f/tonnikala/languages/javascript/generator.py#L49-L58 | null | class FreeVariableAnalyzerVisitor(Visitor):
"""Mangles names.
Walks over a parsed tree and changes ID values to corresponding
mangled names.
"""
def __init__(self):
self.free_variables = set()
@staticmethod
def _is_mangle_candidate(id_node):
"""Return True if Identifier no... |
tetframework/Tonnikala | tonnikala/ir/nodes.py | Extends.add_child | python | def add_child(self, child):
if isinstance(child, Comment):
return
# ignore Text nodes with whitespace-only content
if isinstance(child, Text) and not child.text.strip():
return
super(Extends, self).add_child(child) | Add a child to the tree. Extends discards all comments
and whitespace Text. On non-whitespace Text, and any
other nodes, raise a syntax error. | train | https://github.com/tetframework/Tonnikala/blob/99d168657da1b2372ff898254f80808ea8d1b83f/tonnikala/ir/nodes.py#L334-L348 | [
"def add_child(self, child):\n \"\"\"\n Add a child to the tree. Subclasses may raise SyntaxError\n \"\"\"\n self.children.append(child)\n"
] | class Extends(ContainerNode):
def __init__(self, href):
super(Extends, self).__init__()
self.href = href
def __str__(self): # pragma: no cover
children = str(self.children)
return ', '.join([("(%s)" % self.expression), children])
def validate(self, validator):
fo... |
tetframework/Tonnikala | tonnikala/expr.py | _strip_dollars_fast | python | def _strip_dollars_fast(text):
def _sub(m):
if m.group(0) == '$$':
return '$'
raise HasExprException()
return _dollar_strip_re.sub(_sub, text) | Replace `$$` with `$`. raise immediately
if `$` starting an interpolated expression is found.
@param text: the source text
@return: the text with dollars replaced, or raise
HasExprException if there are interpolated expressions | train | https://github.com/tetframework/Tonnikala/blob/99d168657da1b2372ff898254f80808ea8d1b83f/tonnikala/expr.py#L17-L32 | null | # -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function
"""Tonnikala compiler. Produces source code from XML."""
import re
from tonnikala.ir.nodes import Text, DynamicText, TranslatableText
from tonnikala.languages import python
_dollar_strip_re = re.compile(r'\$[a-zA-Z_{$]')
class... |
tetframework/Tonnikala | tonnikala/languages/python/generator.py | adjust_locations | python | def adjust_locations(ast_node, first_lineno, first_offset):
line_delta = first_lineno - 1
def _fix(node):
if 'lineno' in node._attributes:
lineno = node.lineno
col = node.col_offset
# adjust the offset on the first line
if lineno == 1:
c... | Adjust the locations of the ast nodes, offsetting them
to the new lineno and column offset | train | https://github.com/tetframework/Tonnikala/blob/99d168657da1b2372ff898254f80808ea8d1b83f/tonnikala/languages/python/generator.py#L72-L97 | [
"def _fix(node):\n if 'lineno' in node._attributes:\n lineno = node.lineno\n col = node.col_offset\n\n # adjust the offset on the first line\n if lineno == 1:\n col += first_offset\n\n lineno += line_delta\n\n node.lineno = lineno\n node.col_offset = co... | # -*- coding: utf-8 -*-
# notice: this module cannot be sanely written to take use of
# unicode_literals, bc some of the arguments need to be str on
# both python2 and 3
from __future__ import absolute_import, division, print_function
import ast
from ast import *
from collections import Iterable
from .astalyzer imp... |
tetframework/Tonnikala | tonnikala/languages/python/generator.py | coalesce_outputs | python | def coalesce_outputs(tree):
coalesce_all_outputs = True
if coalesce_all_outputs:
should_coalesce = lambda n: True
else:
should_coalesce = lambda n: n.output_args[0].__class__ is Str
class OutputCoalescer(NodeVisitor):
def visit(self, node):
# if - else expression al... | Coalesce the constant output expressions
__output__('foo')
__output__('bar')
__output__(baz)
__output__('xyzzy')
into
__output__('foobar', baz, 'xyzzy') | train | https://github.com/tetframework/Tonnikala/blob/99d168657da1b2372ff898254f80808ea8d1b83f/tonnikala/languages/python/generator.py#L560-L651 | null | # -*- coding: utf-8 -*-
# notice: this module cannot be sanely written to take use of
# unicode_literals, bc some of the arguments need to be str on
# both python2 and 3
from __future__ import absolute_import, division, print_function
import ast
from ast import *
from collections import Iterable
from .astalyzer imp... |
tetframework/Tonnikala | tonnikala/languages/python/generator.py | remove_locations | python | def remove_locations(node):
def fix(node):
if 'lineno' in node._attributes and hasattr(node, 'lineno'):
del node.lineno
if 'col_offset' in node._attributes and hasattr(node, 'col_offset'):
del node.col_offset
for child in iter_child_nodes(node):
fix(chi... | Removes locations from the given AST tree completely | train | https://github.com/tetframework/Tonnikala/blob/99d168657da1b2372ff898254f80808ea8d1b83f/tonnikala/languages/python/generator.py#L654-L669 | [
"def fix(node):\n if 'lineno' in node._attributes and hasattr(node, 'lineno'):\n del node.lineno\n\n if 'col_offset' in node._attributes and hasattr(node, 'col_offset'):\n del node.col_offset\n\n for child in iter_child_nodes(node):\n fix(child)\n"
] | # -*- coding: utf-8 -*-
# notice: this module cannot be sanely written to take use of
# unicode_literals, bc some of the arguments need to be str on
# both python2 and 3
from __future__ import absolute_import, division, print_function
import ast
from ast import *
from collections import Iterable
from .astalyzer imp... |
tetframework/Tonnikala | tonnikala/runtime/python.py | bind | python | def bind(context, block=False):
if block:
def decorate(func):
name = func.__name__.replace('__TK__block__', '')
if name not in context:
context[name] = func
return context[name]
return decorate
def decorate(func):
name = func.__name_... | Given the context, returns a decorator wrapper;
the binder replaces the wrapped func with the
value from the context OR puts this function in
the context with the name. | train | https://github.com/tetframework/Tonnikala/blob/99d168657da1b2372ff898254f80808ea8d1b83f/tonnikala/runtime/python.py#L87-L110 | null | from __future__ import absolute_import, division, print_function, \
unicode_literals
from collections import Mapping
from markupsafe import escape
from ..compat import text_type, PY3
NoneType = type(None)
class _TKPythonBufferImpl(object):
def __init__(self):
self._buffer = buffer = []
e = ... |
tetframework/Tonnikala | tonnikala/languages/javascript/jslex.py | literals | python | def literals(choices, prefix="", suffix=""):
return "|".join(prefix + re.escape(c) + suffix for c in choices.split()) | Create a regex from a space-separated list of literal `choices`.
If provided, `prefix` and `suffix` will be attached to each choice
individually. | train | https://github.com/tetframework/Tonnikala/blob/99d168657da1b2372ff898254f80808ea8d1b83f/tonnikala/languages/javascript/jslex.py#L24-L31 | null | # -*- coding: utf8 -*-
from __future__ import absolute_import, division, print_function, \
unicode_literals
"""JsLex: a lexer for Javascript"""
# From https://bitbucket.org/ned/jslex
import re
class Tok(object):
"""A specification for a token class."""
num = 0
def __init__(self, name, regex, next=... |
tetframework/Tonnikala | tonnikala/languages/javascript/jslex.py | Lexer.lex | python | def lex(self, text, start=0):
max = len(text)
eaten = start
s = self.state
r = self.regexes
toks = self.toks
while eaten < max:
for match in r[s].finditer(text, eaten):
name = match.lastgroup
tok = toks[name]
tok... | Lexically analyze `text`.
Yields pairs (`name`, `tokentext`). | train | https://github.com/tetframework/Tonnikala/blob/99d168657da1b2372ff898254f80808ea8d1b83f/tonnikala/languages/javascript/jslex.py#L52-L75 | null | class Lexer(object):
"""A generic multi-state regex-based lexer."""
def __init__(self, states, first):
self.regexes = {}
self.toks = {}
for state, rules in states.items():
parts = []
for tok in rules:
groupid = "t%d" % tok.id
self... |
tetframework/Tonnikala | tonnikala/loader.py | handle_exception | python | def handle_exception(exc_info=None, source_hint=None, tb_override=_NO):
global _make_traceback
if exc_info is None: # pragma: no cover
exc_info = sys.exc_info()
# the debugging module is imported when it's used for the first time.
# we're doing a lot of stuff there and for applications that d... | Exception handling helper. This is used internally to either raise
rewritten exceptions or return a rendered traceback for the template. | train | https://github.com/tetframework/Tonnikala/blob/99d168657da1b2372ff898254f80808ea8d1b83f/tonnikala/loader.py#L71-L93 | [
"def reraise(tp, value, tb=None): # pragma: no cover\n if value is None:\n value = tp()\n if value.__traceback__ is not tb:\n raise value.with_traceback(tb)\n raise value\n"
] | import errno
import sys
import time
import codecs
import os
from .compat import reraise
from .languages.javascript.generator import Generator as JavascriptGenerator
from .languages.python.generator import Generator as PythonGenerator
from .runtime import python, exceptions
from .syntaxes.chameleon import parse as par... |
tetframework/Tonnikala | tonnikala/loader.py | FileLoader._maybe_purge_cache | python | def _maybe_purge_cache(self):
if self._last_reload_check + MIN_CHECK_INTERVAL > time.time():
return
for name, tmpl in list(self.cache.items()):
if not os.stat(tmpl.path):
self.cache.pop(name)
continue
if os.stat(tmpl.path).st_mtime >... | If enough time since last check has elapsed, check if any
of the cached templates has changed. If any of the template
files were deleted, remove that file only. If any were
changed, then purge the entire cache. | train | https://github.com/tetframework/Tonnikala/blob/99d168657da1b2372ff898254f80808ea8d1b83f/tonnikala/loader.py#L231-L251 | null | class FileLoader(Loader):
def __init__(self, paths=[], debug=False, syntax='tonnikala', *args, **kwargs):
super(FileLoader, self).__init__(*args, debug=debug, syntax=syntax, **kwargs)
self.cache = {}
self.paths = list(paths)
self.reload = False
self._last_reload_check = time... |
tetframework/Tonnikala | tonnikala/loader.py | FileLoader.load | python | def load(self, name):
if self.reload:
self._maybe_purge_cache()
template = self.cache.get(name)
if template:
return template
path = self.resolve(name)
if not path:
raise OSError(errno.ENOENT, "File not found: %s" % name)
with codecs... | If not yet in the cache, load the named template and compiles it,
placing it into the cache.
If in cache, return the cached template. | train | https://github.com/tetframework/Tonnikala/blob/99d168657da1b2372ff898254f80808ea8d1b83f/tonnikala/loader.py#L253-L281 | [
"def load_string(self, string, filename=\"<string>\"):\n parser_func = parsers.get(self.syntax)\n if not parser_func:\n raise ValueError(\"Invalid parser syntax %s: valid syntaxes: %r\"\n % sorted(parsers.keys()))\n\n try:\n tree = parser_func(filename, string, transla... | class FileLoader(Loader):
def __init__(self, paths=[], debug=False, syntax='tonnikala', *args, **kwargs):
super(FileLoader, self).__init__(*args, debug=debug, syntax=syntax, **kwargs)
self.cache = {}
self.paths = list(paths)
self.reload = False
self._last_reload_check = time... |
tetframework/Tonnikala | tonnikala/runtime/debug.py | translate_exception | python | def translate_exception(exc_info, initial_skip=0):
tb = exc_info[2]
frames = []
# skip some internal frames if wanted
for x in range(initial_skip):
if tb is not None:
tb = tb.tb_next
initial_tb = tb
while tb is not None:
# skip frames decorated with @internalcode. ... | If passed an exc_info it will automatically rewrite the exceptions
all the way down to the correct line numbers and frames. | train | https://github.com/tetframework/Tonnikala/blob/99d168657da1b2372ff898254f80808ea8d1b83f/tonnikala/runtime/debug.py#L162-L201 | [
"def reraise(tp, value, tb=None): # pragma: no cover\n if value is None:\n value = tp()\n if value.__traceback__ is not tb:\n raise value.with_traceback(tb)\n raise value\n",
"def make_frame_proxy(frame):\n proxy = TracebackFrameProxy(frame)\n if tproxy is None:\n return proxy... | # -*- coding: utf-8 -*-
"""
tonnikala.runtime.debug
~~~~~~~~~~~~~~~~~~~~~~~
Implements the debug interface for Tonnikala. This module does some pretty
ugly stuff with the Python traceback system in order to achieve tracebacks
with correct line numbers, locals and contents.
Based on Jinja2 modu... |
tetframework/Tonnikala | tonnikala/runtime/debug.py | fake_exc_info | python | def fake_exc_info(exc_info, filename, lineno):
exc_type, exc_value, tb = exc_info
# figure the real context out
if tb is not None:
# if there is a local called __tonnikala_exception__, we get
# rid of it to not break the debug functionality.
locals = tb.tb_frame.f_locals.copy()
... | Helper for `translate_exception`. | train | https://github.com/tetframework/Tonnikala/blob/99d168657da1b2372ff898254f80808ea8d1b83f/tonnikala/runtime/debug.py#L204-L278 | null | # -*- coding: utf-8 -*-
"""
tonnikala.runtime.debug
~~~~~~~~~~~~~~~~~~~~~~~
Implements the debug interface for Tonnikala. This module does some pretty
ugly stuff with the Python traceback system in order to achieve tracebacks
with correct line numbers, locals and contents.
Based on Jinja2 modu... |
collectiveacuity/jsonModel | jsonmodel/extensions.py | tabulate | python | def tabulate(json_model):
'''
a function to add the tabulate method to a jsonModel object
:param json_model: jsonModel object
:return: jsonModel object
'''
import types
from jsonmodel._extensions import tabulate as _tabulate
try:
from tabulate import tabulate
... | a function to add the tabulate method to a jsonModel object
:param json_model: jsonModel object
:return: jsonModel object | train | https://github.com/collectiveacuity/jsonModel/blob/1ea64c36d78add3faa7b85ff82c5ec685458c940/jsonmodel/extensions.py#L6-L26 | null | ''' a package of extensions to a jsonModel class object '''
__author__ = 'rcj1492'
__created__ = '2018.03'
__license__ = 'MIT'
def tabulate(json_model):
'''
a function to add the tabulate method to a jsonModel object
:param json_model: jsonModel object
:return: jsonModel object
'''
impor... |
collectiveacuity/jsonModel | jsonmodel/validators.py | jsonModel._evaluate_field | python | def _evaluate_field(self, record_dict, field_name, field_criteria):
''' a helper method for evaluating record values based upon query criteria
:param record_dict: dictionary with model valid data to evaluate
:param field_name: string with path to root of query field
:param field_criter... | a helper method for evaluating record values based upon query criteria
:param record_dict: dictionary with model valid data to evaluate
:param field_name: string with path to root of query field
:param field_criteria: dictionary with query operators and qualifiers
:return: boolean (True... | train | https://github.com/collectiveacuity/jsonModel/blob/1ea64c36d78add3faa7b85ff82c5ec685458c940/jsonmodel/validators.py#L548-L730 | null | class jsonModel(object):
__rules__ = jsonLoader('jsonmodel', 'models/model-rules.json')
def __init__(self, data_model, query_rules=None):
'''
a method for testing data model declaration & initializing the class
:param data_model: dictionary with json model architecture
:p... |
collectiveacuity/jsonModel | jsonmodel/validators.py | jsonModel._validate_dict | python | def _validate_dict(self, input_dict, schema_dict, path_to_root, object_title=''):
''' a helper method for recursively validating keys in dictionaries
:return input_dict
'''
# reconstruct key path to current dictionary in model
rules_top_level_key = re.sub('\[\d+\]', '[0]', path_to... | a helper method for recursively validating keys in dictionaries
:return input_dict | train | https://github.com/collectiveacuity/jsonModel/blob/1ea64c36d78add3faa7b85ff82c5ec685458c940/jsonmodel/validators.py#L732-L904 | null | class jsonModel(object):
__rules__ = jsonLoader('jsonmodel', 'models/model-rules.json')
def __init__(self, data_model, query_rules=None):
'''
a method for testing data model declaration & initializing the class
:param data_model: dictionary with json model architecture
:p... |
collectiveacuity/jsonModel | jsonmodel/validators.py | jsonModel._validate_list | python | def _validate_list(self, input_list, schema_list, path_to_root, object_title=''):
'''
a helper method for recursively validating items in a list
:return: input_list
'''
# construct rules for list and items
rules_path_to_root = re.sub('\[\d+\]', '[0]', path_to_root)
... | a helper method for recursively validating items in a list
:return: input_list | train | https://github.com/collectiveacuity/jsonModel/blob/1ea64c36d78add3faa7b85ff82c5ec685458c940/jsonmodel/validators.py#L906-L998 | null | class jsonModel(object):
__rules__ = jsonLoader('jsonmodel', 'models/model-rules.json')
def __init__(self, data_model, query_rules=None):
'''
a method for testing data model declaration & initializing the class
:param data_model: dictionary with json model architecture
:p... |
collectiveacuity/jsonModel | jsonmodel/validators.py | jsonModel._validate_number | python | def _validate_number(self, input_number, path_to_root, object_title=''):
'''
a helper method for validating properties of a number
:return: input_number
'''
rules_path_to_root = re.sub('\[\d+\]', '[0]', path_to_root)
input_criteria = self.keyMap[rules_path_to_root]... | a helper method for validating properties of a number
:return: input_number | train | https://github.com/collectiveacuity/jsonModel/blob/1ea64c36d78add3faa7b85ff82c5ec685458c940/jsonmodel/validators.py#L1000-L1064 | null | class jsonModel(object):
__rules__ = jsonLoader('jsonmodel', 'models/model-rules.json')
def __init__(self, data_model, query_rules=None):
'''
a method for testing data model declaration & initializing the class
:param data_model: dictionary with json model architecture
:p... |
collectiveacuity/jsonModel | jsonmodel/validators.py | jsonModel._validate_string | python | def _validate_string(self, input_string, path_to_root, object_title=''):
'''
a helper method for validating properties of a string
:return: input_string
'''
rules_path_to_root = re.sub('\[\d+\]', '[0]', path_to_root)
input_criteria = self.keyMap[rules_path_to_root]... | a helper method for validating properties of a string
:return: input_string | train | https://github.com/collectiveacuity/jsonModel/blob/1ea64c36d78add3faa7b85ff82c5ec685458c940/jsonmodel/validators.py#L1066-L1169 | null | class jsonModel(object):
__rules__ = jsonLoader('jsonmodel', 'models/model-rules.json')
def __init__(self, data_model, query_rules=None):
'''
a method for testing data model declaration & initializing the class
:param data_model: dictionary with json model architecture
:p... |
collectiveacuity/jsonModel | jsonmodel/validators.py | jsonModel._validate_boolean | python | def _validate_boolean(self, input_boolean, path_to_root, object_title=''):
'''
a helper method for validating properties of a boolean
:return: input_boolean
'''
rules_path_to_root = re.sub('\[\d+\]', '[0]', path_to_root)
input_criteria = self.keyMap[rules_path_to_r... | a helper method for validating properties of a boolean
:return: input_boolean | train | https://github.com/collectiveacuity/jsonModel/blob/1ea64c36d78add3faa7b85ff82c5ec685458c940/jsonmodel/validators.py#L1171-L1200 | null | class jsonModel(object):
__rules__ = jsonLoader('jsonmodel', 'models/model-rules.json')
def __init__(self, data_model, query_rules=None):
'''
a method for testing data model declaration & initializing the class
:param data_model: dictionary with json model architecture
:p... |
collectiveacuity/jsonModel | jsonmodel/validators.py | jsonModel._ingest_dict | python | def _ingest_dict(self, input_dict, schema_dict, path_to_root):
'''
a helper method for ingesting keys, value pairs in a dictionary
:return: valid_dict
'''
valid_dict = {}
# construct path to root for rules
rules_path_to_root = re.sub('\[\d+\]', '[0]', path_to_... | a helper method for ingesting keys, value pairs in a dictionary
:return: valid_dict | train | https://github.com/collectiveacuity/jsonModel/blob/1ea64c36d78add3faa7b85ff82c5ec685458c940/jsonmodel/validators.py#L1202-L1272 | [
"def _ingest_dict(self, input_dict, schema_dict, path_to_root):\n\n '''\n a helper method for ingesting keys, value pairs in a dictionary\n\n :return: valid_dict\n '''\n\n valid_dict = {}\n\n# construct path to root for rules\n rules_path_to_root = re.sub('\\[\\d+\\]', '[0]', path_to_root)\n\n... | class jsonModel(object):
__rules__ = jsonLoader('jsonmodel', 'models/model-rules.json')
def __init__(self, data_model, query_rules=None):
'''
a method for testing data model declaration & initializing the class
:param data_model: dictionary with json model architecture
:p... |
collectiveacuity/jsonModel | jsonmodel/validators.py | jsonModel._ingest_list | python | def _ingest_list(self, input_list, schema_list, path_to_root):
'''
a helper method for ingesting items in a list
:return: valid_list
'''
valid_list = []
# construct max list size
max_size = None
rules_path_to_root = re.sub('\[\d+\]', '[0]', path_to_roo... | a helper method for ingesting items in a list
:return: valid_list | train | https://github.com/collectiveacuity/jsonModel/blob/1ea64c36d78add3faa7b85ff82c5ec685458c940/jsonmodel/validators.py#L1274-L1325 | null | class jsonModel(object):
__rules__ = jsonLoader('jsonmodel', 'models/model-rules.json')
def __init__(self, data_model, query_rules=None):
'''
a method for testing data model declaration & initializing the class
:param data_model: dictionary with json model architecture
:p... |
collectiveacuity/jsonModel | jsonmodel/validators.py | jsonModel._ingest_number | python | def _ingest_number(self, input_number, path_to_root):
'''
a helper method for ingesting a number
:return: valid_number
'''
valid_number = 0.0
try:
valid_number = self._validate_number(input_number, path_to_root)
except:
rules_path_t... | a helper method for ingesting a number
:return: valid_number | train | https://github.com/collectiveacuity/jsonModel/blob/1ea64c36d78add3faa7b85ff82c5ec685458c940/jsonmodel/validators.py#L1327-L1347 | null | class jsonModel(object):
__rules__ = jsonLoader('jsonmodel', 'models/model-rules.json')
def __init__(self, data_model, query_rules=None):
'''
a method for testing data model declaration & initializing the class
:param data_model: dictionary with json model architecture
:p... |
collectiveacuity/jsonModel | jsonmodel/validators.py | jsonModel._ingest_string | python | def _ingest_string(self, input_string, path_to_root):
'''
a helper method for ingesting a string
:return: valid_string
'''
valid_string = ''
try:
valid_string = self._validate_string(input_string, path_to_root)
except:
rules_path_to... | a helper method for ingesting a string
:return: valid_string | train | https://github.com/collectiveacuity/jsonModel/blob/1ea64c36d78add3faa7b85ff82c5ec685458c940/jsonmodel/validators.py#L1349-L1366 | null | class jsonModel(object):
__rules__ = jsonLoader('jsonmodel', 'models/model-rules.json')
def __init__(self, data_model, query_rules=None):
'''
a method for testing data model declaration & initializing the class
:param data_model: dictionary with json model architecture
:p... |
collectiveacuity/jsonModel | jsonmodel/validators.py | jsonModel._ingest_boolean | python | def _ingest_boolean(self, input_boolean, path_to_root):
'''
a helper method for ingesting a boolean
:return: valid_boolean
'''
valid_boolean = False
try:
valid_boolean = self._validate_boolean(input_boolean, path_to_root)
except:
ru... | a helper method for ingesting a boolean
:return: valid_boolean | train | https://github.com/collectiveacuity/jsonModel/blob/1ea64c36d78add3faa7b85ff82c5ec685458c940/jsonmodel/validators.py#L1368-L1385 | null | class jsonModel(object):
__rules__ = jsonLoader('jsonmodel', 'models/model-rules.json')
def __init__(self, data_model, query_rules=None):
'''
a method for testing data model declaration & initializing the class
:param data_model: dictionary with json model architecture
:p... |
collectiveacuity/jsonModel | jsonmodel/validators.py | jsonModel._reconstruct | python | def _reconstruct(self, path_to_root):
'''
a helper method for finding the schema endpoint from a path to root
:param path_to_root: string with dot path to root from
:return: list, dict, string, number, or boolean at path to root
'''
# split path to root into segments
... | a helper method for finding the schema endpoint from a path to root
:param path_to_root: string with dot path to root from
:return: list, dict, string, number, or boolean at path to root | train | https://github.com/collectiveacuity/jsonModel/blob/1ea64c36d78add3faa7b85ff82c5ec685458c940/jsonmodel/validators.py#L1387-L1412 | null | class jsonModel(object):
__rules__ = jsonLoader('jsonmodel', 'models/model-rules.json')
def __init__(self, data_model, query_rules=None):
'''
a method for testing data model declaration & initializing the class
:param data_model: dictionary with json model architecture
:p... |
collectiveacuity/jsonModel | jsonmodel/validators.py | jsonModel._walk | python | def _walk(self, path_to_root, record_dict):
'''
a helper method for finding the record endpoint from a path to root
:param path_to_root: string with dot path to root from
:param record_dict:
:return: list, dict, string, number, or boolean at path to root
'''
# ... | a helper method for finding the record endpoint from a path to root
:param path_to_root: string with dot path to root from
:param record_dict:
:return: list, dict, string, number, or boolean at path to root | train | https://github.com/collectiveacuity/jsonModel/blob/1ea64c36d78add3faa7b85ff82c5ec685458c940/jsonmodel/validators.py#L1414-L1468 | null | class jsonModel(object):
__rules__ = jsonLoader('jsonmodel', 'models/model-rules.json')
def __init__(self, data_model, query_rules=None):
'''
a method for testing data model declaration & initializing the class
:param data_model: dictionary with json model architecture
:p... |
collectiveacuity/jsonModel | jsonmodel/validators.py | jsonModel.validate | python | def validate(self, input_data, path_to_root='', object_title=''):
'''
a core method for validating input against the model
input_data is only returned if all data is valid
:param input_data: list, dict, string, number, or boolean to validate
:param path_to_root: [optio... | a core method for validating input against the model
input_data is only returned if all data is valid
:param input_data: list, dict, string, number, or boolean to validate
:param path_to_root: [optional] string with dot-path of model component
:param object_title: [optional] string... | train | https://github.com/collectiveacuity/jsonModel/blob/1ea64c36d78add3faa7b85ff82c5ec685458c940/jsonmodel/validators.py#L1470-L1540 | [
"def _validate_dict(self, input_dict, schema_dict, path_to_root, object_title=''):\n\n ''' a helper method for recursively validating keys in dictionaries\n\n :return input_dict\n '''\n\n# reconstruct key path to current dictionary in model\n rules_top_level_key = re.sub('\\[\\d+\\]', '[0]', path_to_roo... | class jsonModel(object):
__rules__ = jsonLoader('jsonmodel', 'models/model-rules.json')
def __init__(self, data_model, query_rules=None):
'''
a method for testing data model declaration & initializing the class
:param data_model: dictionary with json model architecture
:p... |
collectiveacuity/jsonModel | jsonmodel/validators.py | jsonModel.ingest | python | def ingest(self, **kwargs):
'''
a core method to ingest and validate arbitrary keyword data
**NOTE: data is always returned with this method**
for each key in the model, a value is returned according
to the following priority:
1. value in kwar... | a core method to ingest and validate arbitrary keyword data
**NOTE: data is always returned with this method**
for each key in the model, a value is returned according
to the following priority:
1. value in kwargs if field passes validation test
2.... | train | https://github.com/collectiveacuity/jsonModel/blob/1ea64c36d78add3faa7b85ff82c5ec685458c940/jsonmodel/validators.py#L1542-L1578 | [
"def _ingest_dict(self, input_dict, schema_dict, path_to_root):\n\n '''\n a helper method for ingesting keys, value pairs in a dictionary\n\n :return: valid_dict\n '''\n\n valid_dict = {}\n\n# construct path to root for rules\n rules_path_to_root = re.sub('\\[\\d+\\]', '[0]', path_to_root)\n\n... | class jsonModel(object):
__rules__ = jsonLoader('jsonmodel', 'models/model-rules.json')
def __init__(self, data_model, query_rules=None):
'''
a method for testing data model declaration & initializing the class
:param data_model: dictionary with json model architecture
:p... |
collectiveacuity/jsonModel | jsonmodel/validators.py | jsonModel.query | python | def query(self, query_criteria, valid_record=None):
'''
a core method for querying model valid data with criteria
**NOTE: input is only returned if all fields & qualifiers are valid for model
:param query_criteria: dictionary with model field names and query qualifiers
... | a core method for querying model valid data with criteria
**NOTE: input is only returned if all fields & qualifiers are valid for model
:param query_criteria: dictionary with model field names and query qualifiers
:param valid_record: dictionary with model valid record
... | train | https://github.com/collectiveacuity/jsonModel/blob/1ea64c36d78add3faa7b85ff82c5ec685458c940/jsonmodel/validators.py#L1580-L1666 | [
"def _validate_fields(self, fields_dict, fields_rules, declared_value=True):\n\n# validate key names in fields\n for key, value in fields_dict.items():\n\n # convert javascript dot_path to class dot_path\n if not key:\n key = '.'\n else:\n if key[0] != '.':\n ... | class jsonModel(object):
__rules__ = jsonLoader('jsonmodel', 'models/model-rules.json')
def __init__(self, data_model, query_rules=None):
'''
a method for testing data model declaration & initializing the class
:param data_model: dictionary with json model architecture
:p... |
collectiveacuity/jsonModel | jsonmodel/_extensions.py | tabulate | python | def tabulate(self, format='html', syntax=''):
'''
a function to create a table from the class model keyMap
:param format: string with format for table output
:param syntax: [optional] string with linguistic syntax
:return: string with table
'''
from tabulate import tabulate as _tabula... | a function to create a table from the class model keyMap
:param format: string with format for table output
:param syntax: [optional] string with linguistic syntax
:return: string with table | train | https://github.com/collectiveacuity/jsonModel/blob/1ea64c36d78add3faa7b85ff82c5ec685458c940/jsonmodel/_extensions.py#L34-L209 | [
"def _segment_path(dot_path):\n import re\n digit_pat = re.compile('\\[(\\d+)\\]')\n key_list = dot_path.split('.')\n segment_list = []\n for key in key_list:\n if key:\n item_list = digit_pat.split(key)\n for item in item_list:\n if item:\n ... | ''' a package of helper functions for extensions.py '''
__author__ = 'rcj1492'
__created__ = '2018.03'
__license__ = 'MIT'
def _segment_path(dot_path):
import re
digit_pat = re.compile('\[(\d+)\]')
key_list = dot_path.split('.')
segment_list = []
for key in key_list:
if key:
ite... |
fchauvel/MAD | mad/simulation/tasks.py | Task._execute | python | def _execute(self, worker):
self._assert_status_is(TaskStatus.RUNNING)
operation = worker.look_up(self.operation)
operation.invoke(self, [], worker=worker) | This method is ASSIGNED during the evaluation to control how to resume it once it has been paused | train | https://github.com/fchauvel/MAD/blob/806d5174848b1a502e5c683894995602478c448b/mad/simulation/tasks.py#L252-L258 | [
"def _assert_status_is(self, *legal_states):\n assert self.status in legal_states, \\\n \"Found status == {0.name} (expecting {1!s})\".format(self.status, [ s.name for s in legal_states ])\n"
] | class Task:
def __init__(self, service, request=None):
self.service = service
self.worker = None
self.request = request
self.status = TaskStatus.CREATED
@property
def priority(self):
return self.request.priority
@property
def identifier(self):
retur... |
fchauvel/MAD | mad/evaluation.py | Evaluation.of_think | python | def of_think(self, think):
return self._compute(
duration=think.duration,
after=self.continuation) | Simulate the worker processing the task for the specified amount of time.
The worker is not released and the task is not paused. | train | https://github.com/fchauvel/MAD/blob/806d5174848b1a502e5c683894995602478c448b/mad/evaluation.py#L209-L216 | [
"def _compute(self, duration, after):\n task = self._look_up(Symbols.TASK)\n task.compute(duration, continuation=lambda: after(Success()))\n return Busy()\n"
] | class Evaluation:
"""
Represent the future evaluation of an expression within a given environment. The expression is bound to
a continuation, that is the next evaluation to carry out.
"""
def __init__(self, environment, expression, factory, continuation=lambda x: x):
self.environment = envi... |
fchauvel/MAD | mad/parsing.py | p_definition_list | python | def p_definition_list(p):
if len(p) == 3:
p[0] = p[1] + p[2]
elif len(p) == 2:
p[0] = p[1]
else:
raise RuntimeError("Invalid production rules 'p_action_list'") | definition_list : definition definition_list
| definition | train | https://github.com/fchauvel/MAD/blob/806d5174848b1a502e5c683894995602478c448b/mad/parsing.py#L122-L132 | null | #!/usr/bin/env python
#
# This file is part of MAD.
#
# MAD is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MAD is distributed in ... |
fchauvel/MAD | mad/parsing.py | p_define_service | python | def p_define_service(p):
if len(p) == 7:
body = p[4] + p[5]
else:
body = p[4]
p[0] = DefineService(p[2], body) | define_service : SERVICE IDENTIFIER OPEN_CURLY_BRACKET settings operation_list CLOSE_CURLY_BRACKET
| SERVICE IDENTIFIER OPEN_CURLY_BRACKET operation_list CLOSE_CURLY_BRACKET | train | https://github.com/fchauvel/MAD/blob/806d5174848b1a502e5c683894995602478c448b/mad/parsing.py#L143-L152 | null | #!/usr/bin/env python
#
# This file is part of MAD.
#
# MAD is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MAD is distributed in ... |
fchauvel/MAD | mad/parsing.py | p_setting_list | python | def p_setting_list(p):
if len(p) == 3:
p[0] = merge_map(p[1], p[2])
elif len(p) == 2:
p[0] = p[1]
else:
raise RuntimeError("Invalid production rules 'p_setting_list'") | setting_list : setting setting_list
| setting | train | https://github.com/fchauvel/MAD/blob/806d5174848b1a502e5c683894995602478c448b/mad/parsing.py#L162-L172 | [
"def merge_map(map_A, map_B):\n tmp = map_A.copy()\n tmp.update(map_B)\n return tmp\n"
] | #!/usr/bin/env python
#
# This file is part of MAD.
#
# MAD is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MAD is distributed in ... |
fchauvel/MAD | mad/parsing.py | p_queue | python | def p_queue(p):
if p[3] == "LIFO":
p[0] = {"queue": LIFO()}
elif p[3] == "FIFO":
p[0] = {"queue": FIFO()}
else:
raise RuntimeError("Queue discipline '%s' is not supported!" % p[1]) | queue : QUEUE COLON LIFO
| QUEUE COLON FIFO | train | https://github.com/fchauvel/MAD/blob/806d5174848b1a502e5c683894995602478c448b/mad/parsing.py#L184-L196 | null | #!/usr/bin/env python
#
# This file is part of MAD.
#
# MAD is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MAD is distributed in ... |
fchauvel/MAD | mad/parsing.py | p_throttling | python | def p_throttling(p):
throttling = NoThrottlingSettings()
if len(p) == 7:
throttling = TailDropSettings(int(p[5]))
p[0] = {"throttling": throttling} | throttling : THROTTLING COLON NONE
| THROTTLING COLON TAIL_DROP OPEN_BRACKET NUMBER CLOSE_BRACKET | train | https://github.com/fchauvel/MAD/blob/806d5174848b1a502e5c683894995602478c448b/mad/parsing.py#L199-L207 | null | #!/usr/bin/env python
#
# This file is part of MAD.
#
# MAD is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MAD is distributed in ... |
fchauvel/MAD | mad/parsing.py | p_autoscaling_setting_list | python | def p_autoscaling_setting_list(p):
if len(p) == 3:
p[0] = merge_map(p[1], p[2])
elif len(p) == 2:
p[0] = p[1]
else:
raise RuntimeError("Invalid production in 'autoscaling_setting_list'") | autoscaling_setting_list : autoscaling_setting autoscaling_setting_list
| autoscaling_setting | train | https://github.com/fchauvel/MAD/blob/806d5174848b1a502e5c683894995602478c448b/mad/parsing.py#L217-L227 | [
"def merge_map(map_A, map_B):\n tmp = map_A.copy()\n tmp.update(map_B)\n return tmp\n"
] | #!/usr/bin/env python
#
# This file is part of MAD.
#
# MAD is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MAD is distributed in ... |
fchauvel/MAD | mad/parsing.py | p_autoscaling_setting | python | def p_autoscaling_setting(p):
if len(p) == 8:
p[0] = {"limits": (int(p[4]), int(p[6]))}
elif len(p) == 4:
p[0] = {"period": int(p[3])}
else:
raise RuntimeError("Invalid product in 'autoscaling_setting'") | autoscaling_setting : PERIOD COLON NUMBER
| LIMITS COLON OPEN_SQUARE_BRACKET NUMBER COMMA NUMBER CLOSE_SQUARE_BRACKET | train | https://github.com/fchauvel/MAD/blob/806d5174848b1a502e5c683894995602478c448b/mad/parsing.py#L230-L240 | null | #!/usr/bin/env python
#
# This file is part of MAD.
#
# MAD is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MAD is distributed in ... |
fchauvel/MAD | mad/parsing.py | p_operation_list | python | def p_operation_list(p):
if len(p) == 3:
p[0] = p[1] + p[2]
elif len(p) == 2:
p[0] = p[1]
else:
raise RuntimeError("Invalid production rules 'p_operation_list'") | operation_list : define_operation operation_list
| define_operation | train | https://github.com/fchauvel/MAD/blob/806d5174848b1a502e5c683894995602478c448b/mad/parsing.py#L243-L253 | null | #!/usr/bin/env python
#
# This file is part of MAD.
#
# MAD is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MAD is distributed in ... |
fchauvel/MAD | mad/parsing.py | p_action_list | python | def p_action_list(p):
if len(p) == 3:
p[0] = p[1] + p[2]
elif len(p) == 2:
p[0] = p[1]
else:
raise RuntimeError("Invalid production rules 'p_action_list'") | action_list : action action_list
| action | train | https://github.com/fchauvel/MAD/blob/806d5174848b1a502e5c683894995602478c448b/mad/parsing.py#L270-L280 | null | #!/usr/bin/env python
#
# This file is part of MAD.
#
# MAD is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MAD is distributed in ... |
fchauvel/MAD | mad/parsing.py | p_fail | python | def p_fail(p):
if len(p) > 2:
p[0] = Fail(float(p[2]))
else:
p[0] = Fail() | fail : FAIL NUMBER
| FAIL | train | https://github.com/fchauvel/MAD/blob/806d5174848b1a502e5c683894995602478c448b/mad/parsing.py#L302-L310 | null | #!/usr/bin/env python
#
# This file is part of MAD.
#
# MAD is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MAD is distributed in ... |
fchauvel/MAD | mad/parsing.py | p_query | python | def p_query(p):
parameters = {"service": p[2], "operation": p[4]}
if len(p) > 5:
parameters = merge_map(parameters, p[6])
p[0] = Query(**parameters) | query : QUERY IDENTIFIER SLASH IDENTIFIER
| QUERY IDENTIFIER SLASH IDENTIFIER OPEN_CURLY_BRACKET query_option_list CLOSE_CURLY_BRACKET | train | https://github.com/fchauvel/MAD/blob/806d5174848b1a502e5c683894995602478c448b/mad/parsing.py#L312-L320 | [
"def merge_map(map_A, map_B):\n tmp = map_A.copy()\n tmp.update(map_B)\n return tmp\n"
] | #!/usr/bin/env python
#
# This file is part of MAD.
#
# MAD is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MAD is distributed in ... |
fchauvel/MAD | mad/parsing.py | p_query_option_list | python | def p_query_option_list(p):
if len(p) == 2:
p[0] = p[1]
elif len(p) == 4:
p[0] = merge_map(p[1], p[3])
else:
raise RuntimeError("Invalid product rules for 'query_option_list'") | query_option_list : query_option COMMA query_option_list
| query_option | train | https://github.com/fchauvel/MAD/blob/806d5174848b1a502e5c683894995602478c448b/mad/parsing.py#L323-L333 | [
"def merge_map(map_A, map_B):\n tmp = map_A.copy()\n tmp.update(map_B)\n return tmp\n"
] | #!/usr/bin/env python
#
# This file is part of MAD.
#
# MAD is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MAD is distributed in ... |
fchauvel/MAD | mad/parsing.py | p_invoke | python | def p_invoke(p):
priority = None
if len(p) > 5:
priority = int(p[8])
p[0] = Trigger(p[2], p[4], priority) | invoke : INVOKE IDENTIFIER SLASH IDENTIFIER
| INVOKE IDENTIFIER SLASH IDENTIFIER OPEN_CURLY_BRACKET PRIORITY COLON NUMBER CLOSE_CURLY_BRACKET | train | https://github.com/fchauvel/MAD/blob/806d5174848b1a502e5c683894995602478c448b/mad/parsing.py#L358-L366 | null | #!/usr/bin/env python
#
# This file is part of MAD.
#
# MAD is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MAD is distributed in ... |
fchauvel/MAD | mad/parsing.py | p_retry | python | def p_retry(p):
if len(p) == 5:
p[0] = Retry(p[3])
elif len(p) == 8:
p[0] = Retry(p[6], **p[3])
else:
raise RuntimeError("Invalid product rules for 'retry_option_list'") | retry : RETRY OPEN_CURLY_BRACKET action_list CLOSE_CURLY_BRACKET
| RETRY OPEN_BRACKET retry_option_list CLOSE_BRACKET OPEN_CURLY_BRACKET action_list CLOSE_CURLY_BRACKET | train | https://github.com/fchauvel/MAD/blob/806d5174848b1a502e5c683894995602478c448b/mad/parsing.py#L369-L379 | null | #!/usr/bin/env python
#
# This file is part of MAD.
#
# MAD is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MAD is distributed in ... |
fchauvel/MAD | mad/parsing.py | p_retry_option_list | python | def p_retry_option_list(p):
if len(p) == 4:
p[0] = merge_map(p[1], p[3])
elif len(p) == 2:
p[0] = p[1]
else:
raise RuntimeError("Invalid production in 'retry_option_list'") | retry_option_list : retry_option COMMA retry_option_list
| retry_option | train | https://github.com/fchauvel/MAD/blob/806d5174848b1a502e5c683894995602478c448b/mad/parsing.py#L382-L392 | [
"def merge_map(map_A, map_B):\n tmp = map_A.copy()\n tmp.update(map_B)\n return tmp\n"
] | #!/usr/bin/env python
#
# This file is part of MAD.
#
# MAD is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MAD is distributed in ... |
fchauvel/MAD | mad/parsing.py | p_retry_option | python | def p_retry_option(p):
if len(p) == 4:
p[0] = {"limit": int(p[3]) }
elif len(p) == 7:
p[0] = {"delay": Delay(int(p[5]), p[3])}
else:
raise RuntimeError("Invalid production in 'retry_option'") | retry_option : LIMIT COLON NUMBER
| DELAY COLON IDENTIFIER OPEN_BRACKET NUMBER CLOSE_BRACKET | train | https://github.com/fchauvel/MAD/blob/806d5174848b1a502e5c683894995602478c448b/mad/parsing.py#L395-L405 | null | #!/usr/bin/env python
#
# This file is part of MAD.
#
# MAD is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# MAD is distributed in ... |
DomBennett/TaxonNamesResolver | taxon_names_resolver/manip_tools.py | stringClade | python | def stringClade(taxrefs, name, at):
'''Return a Newick string from a list of TaxRefs'''
string = []
for ref in taxrefs:
# distance is the difference between the taxonomic level of the ref
# and the current level of the tree growth
d = float(at-ref.level)
# ensure no spaces i... | Return a Newick string from a list of TaxRefs | train | https://github.com/DomBennett/TaxonNamesResolver/blob/a2556cc0f8b7442d83990715c92fdf6f787e1f41/taxon_names_resolver/manip_tools.py#L192-L205 | null | #! /usr/bin/env python
# D.J. Bennett
# 24/03/2014
"""
misc tools
"""
from __future__ import absolute_import
# PACKAGES
import re
from six.moves import range
# GLOBALS
# nodes on a taxonomic tree
default_taxonomy = ['subspecies', 'species', 'subgenus', 'genus', 'tribe',
'subfamily', 'family', 'sup... |
DomBennett/TaxonNamesResolver | taxon_names_resolver/manip_tools.py | taxTree | python | def taxTree(taxdict):
# the taxonomic dictionary holds the lineage of each ident in
# the same order as the taxonomy
# use hierarchy to construct a taxonomic tree
for rank in taxdict.taxonomy:
current_level = float(taxdict.taxonomy.index(rank))
# get clades at this rank in hierarchy
... | Return taxonomic Newick tree | train | https://github.com/DomBennett/TaxonNamesResolver/blob/a2556cc0f8b7442d83990715c92fdf6f787e1f41/taxon_names_resolver/manip_tools.py#L208-L241 | [
"def stringClade(taxrefs, name, at):\n '''Return a Newick string from a list of TaxRefs'''\n string = []\n for ref in taxrefs:\n # distance is the difference between the taxonomic level of the ref\n # and the current level of the tree growth\n d = float(at-ref.level)\n # ensure... | #! /usr/bin/env python
# D.J. Bennett
# 24/03/2014
"""
misc tools
"""
from __future__ import absolute_import
# PACKAGES
import re
from six.moves import range
# GLOBALS
# nodes on a taxonomic tree
default_taxonomy = ['subspecies', 'species', 'subgenus', 'genus', 'tribe',
'subfamily', 'family', 'sup... |
DomBennett/TaxonNamesResolver | taxon_names_resolver/manip_tools.py | TaxRef.change | python | def change(self, ident, rank=None):
'''Change ident'''
self.ident = ident
if rank:
self.rank = rank
self.level = self._getLevel(rank, self.taxonomy)
# count changes made to instance
self.counter += 1 | Change ident | train | https://github.com/DomBennett/TaxonNamesResolver/blob/a2556cc0f8b7442d83990715c92fdf6f787e1f41/taxon_names_resolver/manip_tools.py#L35-L42 | [
"def _getLevel(self, rank, taxonomy):\n if rank in taxonomy:\n return taxonomy.index(rank)\n # else find its closest by using the default taxonomy\n dlevel = default_taxonomy.index(rank)\n i = 1\n d = dlevel + i\n up = True\n while i <= len(default_taxonomy):\n if d > 0:\n ... | class TaxRef(object):
'''Reference for taxonimic identities'''
def __init__(self, ident, rank, taxonomy=default_taxonomy):
super(TaxRef, self).__setattr__('taxonomy', taxonomy)
super(TaxRef, self).__setattr__('ident', ident)
super(TaxRef, self).__setattr__('rank', rank)
# level i... |
DomBennett/TaxonNamesResolver | taxon_names_resolver/manip_tools.py | TaxDict._additional | python | def _additional(self, idents, kwargs):
'''Add additional data slots from **kwargs'''
if kwargs:
for name, value in list(kwargs.items()):
if not isinstance(value, list):
raise ValueError('Additional arguments must be lists of \
same length as idents')
... | Add additional data slots from **kwargs | train | https://github.com/DomBennett/TaxonNamesResolver/blob/a2556cc0f8b7442d83990715c92fdf6f787e1f41/taxon_names_resolver/manip_tools.py#L122-L130 | null | class TaxDict(dict):
'''Taxonomic Dictionary : hold and return taxonomic information'''
def __init__(self, idents, ranks, lineages, taxonomy=default_taxonomy,
**kwargs):
# add entry for each ident of lineages ordered by taxonomy
# ranks without corresponding lineage are given '... |
DomBennett/TaxonNamesResolver | taxon_names_resolver/manip_tools.py | TaxDict._slice | python | def _slice(self, level):
'''Return list of tuples of ident and lineage ident for given level
(numbered rank)'''
if level >= len(self.taxonomy):
raise IndexError('Level greater than size of taxonomy')
res = []
for ident in sorted(list(self.keys())):
res.append((sel... | Return list of tuples of ident and lineage ident for given level
(numbered rank) | train | https://github.com/DomBennett/TaxonNamesResolver/blob/a2556cc0f8b7442d83990715c92fdf6f787e1f41/taxon_names_resolver/manip_tools.py#L132-L140 | null | class TaxDict(dict):
'''Taxonomic Dictionary : hold and return taxonomic information'''
def __init__(self, idents, ranks, lineages, taxonomy=default_taxonomy,
**kwargs):
# add entry for each ident of lineages ordered by taxonomy
# ranks without corresponding lineage are given '... |
DomBennett/TaxonNamesResolver | taxon_names_resolver/manip_tools.py | TaxDict._group | python | def _group(self, taxslice):
'''Return list of lists of idents grouped by shared rank'''
res = []
while taxslice:
taxref, lident = taxslice.pop()
if lident == '':
res.append(([taxref], lident))
else:
# identify idents in the same... | Return list of lists of idents grouped by shared rank | train | https://github.com/DomBennett/TaxonNamesResolver/blob/a2556cc0f8b7442d83990715c92fdf6f787e1f41/taxon_names_resolver/manip_tools.py#L142-L160 | null | class TaxDict(dict):
'''Taxonomic Dictionary : hold and return taxonomic information'''
def __init__(self, idents, ranks, lineages, taxonomy=default_taxonomy,
**kwargs):
# add entry for each ident of lineages ordered by taxonomy
# ranks without corresponding lineage are given '... |
DomBennett/TaxonNamesResolver | taxon_names_resolver/manip_tools.py | TaxDict._hierarchy | python | def _hierarchy(self):
'''Generate dictionary of referenced idents grouped by shared rank'''
self.hierarchy = {}
for rank in self.taxonomy:
# extract lineage idents for this rank
taxslice = self._slice(level=self.taxonomy.index(rank))
# group idents by shared g... | Generate dictionary of referenced idents grouped by shared rank | train | https://github.com/DomBennett/TaxonNamesResolver/blob/a2556cc0f8b7442d83990715c92fdf6f787e1f41/taxon_names_resolver/manip_tools.py#L162-L169 | [
" def _slice(self, level):\n '''Return list of tuples of ident and lineage ident for given level\n(numbered rank)'''\n if level >= len(self.taxonomy):\n raise IndexError('Level greater than size of taxonomy')\n res = []\n for ident in sorted(list(self.keys())):\n ... | class TaxDict(dict):
'''Taxonomic Dictionary : hold and return taxonomic information'''
def __init__(self, idents, ranks, lineages, taxonomy=default_taxonomy,
**kwargs):
# add entry for each ident of lineages ordered by taxonomy
# ranks without corresponding lineage are given '... |
DomBennett/TaxonNamesResolver | taxon_names_resolver/manip_tools.py | TaxDict._contextualise | python | def _contextualise(self):
'''Determine contextual idents (cidents)'''
# loop through hierarchy identifying unique lineages
# TODO: gain other contextual information, not just ident
deja_vues = []
for rank in reversed(self.taxonomy):
# return named clades -- '' are ign... | Determine contextual idents (cidents) | train | https://github.com/DomBennett/TaxonNamesResolver/blob/a2556cc0f8b7442d83990715c92fdf6f787e1f41/taxon_names_resolver/manip_tools.py#L171-L188 | null | class TaxDict(dict):
'''Taxonomic Dictionary : hold and return taxonomic information'''
def __init__(self, idents, ranks, lineages, taxonomy=default_taxonomy,
**kwargs):
# add entry for each ident of lineages ordered by taxonomy
# ranks without corresponding lineage are given '... |
DomBennett/TaxonNamesResolver | taxon_names_resolver/gnr_tools.py | safeReadJSON | python | def safeReadJSON(url, logger, max_check=6, waittime=30):
'''Return JSON object from URL'''
counter = 0
# try, try and try again ....
while counter < max_check:
try:
with contextlib.closing(urllib.request.urlopen(url)) as f:
res = json.loads(f.read().decode('utf8'))
... | Return JSON object from URL | train | https://github.com/DomBennett/TaxonNamesResolver/blob/a2556cc0f8b7442d83990715c92fdf6f787e1f41/taxon_names_resolver/gnr_tools.py#L18-L32 | null | #! /usr/bin/env python
# D. J. Bennett
# 16/05/2014
"""
Tools for interacting with the GNR.
"""
from __future__ import absolute_import
import time
import contextlib
import json
import os
import six
from six.moves import urllib
# FUNCTIONS
# CLASSES
class GnrDataSources(object):
"""GNR data sources class: extr... |
DomBennett/TaxonNamesResolver | taxon_names_resolver/gnr_tools.py | GnrResolver.search | python | def search(self, terms, prelim=True):
# TODO: There are now lots of additional data sources, make additional
# searching optional (11/01/2017)
if prelim: # preliminary search
res = self._resolve(terms, self.Id)
self._write(res)
return res
else: # sea... | Search terms against GNR. If prelim = False, search other datasources \
for alternative names (i.e. synonyms) with which to search main datasource.\
Return JSON object. | train | https://github.com/DomBennett/TaxonNamesResolver/blob/a2556cc0f8b7442d83990715c92fdf6f787e1f41/taxon_names_resolver/gnr_tools.py#L67-L97 | [
"def _parseNames(self, jobj):\n # return a list of tuples (term, name) from second search\n # TODO(07/06/2013): record DSs used\n alt_terms = []\n for record in jobj:\n if 'results' not in list(record.keys()):\n pass\n else:\n term = record['supplied_name_string']\n ... | class GnrResolver(object):
"""GNR resolver class: search the GNR"""
def __init__(self, logger, datasource='NCBI'):
self.logger = logger
ds = GnrDataSources(logger)
self.write_counter = 1
self.Id = ds.byName(datasource)
self.otherIds = ds.byName(datasource, invert=True)
... |
DomBennett/TaxonNamesResolver | TaxonNamesResolver.py | parseArgs | python | def parseArgs():
parser = argparse.ArgumentParser()
parser.add_argument("-names", "-n", help=".txt file of taxonomic names")
parser.add_argument("-datasource", "-d", help="taxonomic datasource by \
which names will be resolved (default NCBI)")
parser.add_argument("-taxonid", "-t", help="parent taxonomic... | Read arguments | train | https://github.com/DomBennett/TaxonNamesResolver/blob/a2556cc0f8b7442d83990715c92fdf6f787e1f41/TaxonNamesResolver.py#L30-L41 | null | #! /usr/bin/env python
# D.J. Bennett
# 16/05/2014
# Import
from __future__ import absolute_import
from __future__ import print_function
import os
import sys
import argparse
import logging
import platform
from datetime import datetime
from taxon_names_resolver import Resolver
from taxon_names_resolver import __version... |
DomBennett/TaxonNamesResolver | TaxonNamesResolver.py | logSysInfo | python | def logSysInfo():
logger.info('#' * 70)
logger.info(datetime.today().strftime("%A, %d %B %Y %I:%M%p"))
logger.info('Running on [{0}] [{1}]'.format(platform.node(),
platform.platform()))
logger.info('Python [{0}]'.format(sys.version))
logger.info('#' * ... | Write system info to log file | train | https://github.com/DomBennett/TaxonNamesResolver/blob/a2556cc0f8b7442d83990715c92fdf6f787e1f41/TaxonNamesResolver.py#L44-L51 | null | #! /usr/bin/env python
# D.J. Bennett
# 16/05/2014
# Import
from __future__ import absolute_import
from __future__ import print_function
import os
import sys
import argparse
import logging
import platform
from datetime import datetime
from taxon_names_resolver import Resolver
from taxon_names_resolver import __version... |
DomBennett/TaxonNamesResolver | TaxonNamesResolver.py | logEndTime | python | def logEndTime():
logger.info('\n' + '#' * 70)
logger.info('Complete')
logger.info(datetime.today().strftime("%A, %d %B %Y %I:%M%p"))
logger.info('#' * 70 + '\n') | Write end info to log | train | https://github.com/DomBennett/TaxonNamesResolver/blob/a2556cc0f8b7442d83990715c92fdf6f787e1f41/TaxonNamesResolver.py#L54-L59 | null | #! /usr/bin/env python
# D.J. Bennett
# 16/05/2014
# Import
from __future__ import absolute_import
from __future__ import print_function
import os
import sys
import argparse
import logging
import platform
from datetime import datetime
from taxon_names_resolver import Resolver
from taxon_names_resolver import __version... |
DomBennett/TaxonNamesResolver | taxon_names_resolver/resolver.py | Resolver._check | python | def _check(self, terms):
for t in terms:
try:
_ = urllib.parse.quote(six.text_type(t).encode('utf8'))
except:
self.logger.error('Unknown character in [{0}]!'.format(t))
self.logger.error('.... remove character and try again.')
... | Check terms do not contain unknown characters | train | https://github.com/DomBennett/TaxonNamesResolver/blob/a2556cc0f8b7442d83990715c92fdf6f787e1f41/taxon_names_resolver/resolver.py#L72-L80 | null | class Resolver(object):
"""Taxon Names Resovler class : Automatically resolves taxon names \
through GNR. All output written in 'resolved_names' folder.
See https://github.com/DomBennett/TaxonNamesResolver for details."""
def __init__(self, input_file=None, datasource='NCBI', taxon_id=None,
te... |
DomBennett/TaxonNamesResolver | taxon_names_resolver/resolver.py | Resolver.main | python | def main(self):
# TODO: Break up, too complex
primary_bool = True
no_records = True
nsearch = 1
search_terms = self.terms
original_names = []
while True:
if primary_bool:
self.logger.info('Searching [{0}] ...'.format(
... | Search and sieve query names. | train | https://github.com/DomBennett/TaxonNamesResolver/blob/a2556cc0f8b7442d83990715c92fdf6f787e1f41/taxon_names_resolver/resolver.py#L82-L127 | [
" def search(self, terms, prelim=True):\n \"\"\"Search terms against GNR. If prelim = False, search other datasources \\\nfor alternative names (i.e. synonyms) with which to search main datasource.\\\nReturn JSON object.\"\"\"\n # TODO: There are now lots of additional data sources, make additional... | class Resolver(object):
"""Taxon Names Resovler class : Automatically resolves taxon names \
through GNR. All output written in 'resolved_names' folder.
See https://github.com/DomBennett/TaxonNamesResolver for details."""
def __init__(self, input_file=None, datasource='NCBI', taxon_id=None,
te... |
DomBennett/TaxonNamesResolver | taxon_names_resolver/resolver.py | Resolver._sieve | python | def _sieve(self, multiple_records):
# TODO: Break up, too complex
GnrStore = self._store
def writeAsJson(term, results):
record = {'supplied_name_string': term}
if len(results) > 0:
record['results'] = results
return record
def boolRe... | Return json object without multiple returns per resolved name.\
Names with multiple records are reduced by finding the name in the clade of\
interest, have the highest score, have the lowest taxonomic rank (if lowrank is
true) and/or are the first item returned. | train | https://github.com/DomBennett/TaxonNamesResolver/blob/a2556cc0f8b7442d83990715c92fdf6f787e1f41/taxon_names_resolver/resolver.py#L159-L222 | null | class Resolver(object):
"""Taxon Names Resovler class : Automatically resolves taxon names \
through GNR. All output written in 'resolved_names' folder.
See https://github.com/DomBennett/TaxonNamesResolver for details."""
def __init__(self, input_file=None, datasource='NCBI', taxon_id=None,
te... |
DomBennett/TaxonNamesResolver | taxon_names_resolver/resolver.py | Resolver.write | python | def write(self):
csv_file = os.path.join(self.outdir, 'search_results.csv')
txt_file = os.path.join(self.outdir, 'unresolved.txt')
headers = self.key_terms
unresolved = []
with open(csv_file, 'w') as file:
writer = csv.writer(file)
writer.writerow(headers)... | Write csv file of resolved names and txt file of unresolved names. | train | https://github.com/DomBennett/TaxonNamesResolver/blob/a2556cc0f8b7442d83990715c92fdf6f787e1f41/taxon_names_resolver/resolver.py#L224-L258 | null | class Resolver(object):
"""Taxon Names Resovler class : Automatically resolves taxon names \
through GNR. All output written in 'resolved_names' folder.
See https://github.com/DomBennett/TaxonNamesResolver for details."""
def __init__(self, input_file=None, datasource='NCBI', taxon_id=None,
te... |
DomBennett/TaxonNamesResolver | taxon_names_resolver/resolver.py | Resolver.retrieve | python | def retrieve(self, key_term):
"""Return data for key term specified for each resolved name as a list.
Possible terms (02/12/2013): 'query_name', 'classification_path',
'data_source_title', 'match_type', 'score', 'classification_path_ranks',
'name_string', 'canonical_form',\
'classification_path_ids', 'prescore'... | Return data for key term specified for each resolved name as a list.
Possible terms (02/12/2013): 'query_name', 'classification_path',
'data_source_title', 'match_type', 'score', 'classification_path_ranks',
'name_string', 'canonical_form',\
'classification_path_ids', 'prescore', 'data_source_id', 'taxon_id',
'gni_uuid | train | https://github.com/DomBennett/TaxonNamesResolver/blob/a2556cc0f8b7442d83990715c92fdf6f787e1f41/taxon_names_resolver/resolver.py#L260-L283 | null | class Resolver(object):
"""Taxon Names Resovler class : Automatically resolves taxon names \
through GNR. All output written in 'resolved_names' folder.
See https://github.com/DomBennett/TaxonNamesResolver for details."""
def __init__(self, input_file=None, datasource='NCBI', taxon_id=None,
te... |
planetlabs/es_fluent | es_fluent/filters/core.py | Generic.add_filter | python | def add_filter(self, filter_or_string, *args, **kwargs):
self.filters.append(build_filter(filter_or_string, *args, **kwargs))
return self | Appends a filter. | train | https://github.com/planetlabs/es_fluent/blob/74f8db3a1bf9aa1d54512cf2d5e0ec58ee2f4b1c/es_fluent/filters/core.py#L27-L33 | [
"def build_filter(filter_or_string, *args, **kwargs):\n \"\"\"\n Overloaded filter construction. If ``filter_or_string`` is a string\n we look up it's corresponding class in the filter registry and return it.\n Otherwise, assume ``filter_or_string`` is an instance of a filter.\n\n :return: :class:`~e... | class Generic(Filter):
"""
Contains a generic list of filters. Serialized as a dictionary.
"""
def __init__(self):
self.filters = []
def is_empty(self):
"""
:return: ``True`` if this filter has nested clauses ``False``.
"""
return all(_filter.is_empty() for _... |
planetlabs/es_fluent | es_fluent/filters/core.py | Generic.and_filter | python | def and_filter(self, filter_or_string, *args, **kwargs):
and_filter = self.find_filter(And)
if and_filter is None:
and_filter = And()
self.filters.append(and_filter)
and_filter.add_filter(build_filter(
filter_or_string, *args, **kwargs))
return and_... | Adds a list of :class:`~es_fluent.filters.core.And` clauses, automatically
generating :class:`~es_fluent.filters.core.And` filter if it does not
exist. | train | https://github.com/planetlabs/es_fluent/blob/74f8db3a1bf9aa1d54512cf2d5e0ec58ee2f4b1c/es_fluent/filters/core.py#L35-L50 | [
"def build_filter(filter_or_string, *args, **kwargs):\n \"\"\"\n Overloaded filter construction. If ``filter_or_string`` is a string\n we look up it's corresponding class in the filter registry and return it.\n Otherwise, assume ``filter_or_string`` is an instance of a filter.\n\n :return: :class:`~e... | class Generic(Filter):
"""
Contains a generic list of filters. Serialized as a dictionary.
"""
def __init__(self):
self.filters = []
def is_empty(self):
"""
:return: ``True`` if this filter has nested clauses ``False``.
"""
return all(_filter.is_empty() for _... |
planetlabs/es_fluent | es_fluent/filters/core.py | Generic.or_filter | python | def or_filter(self, filter_or_string, *args, **kwargs):
or_filter = self.find_filter(Or)
if or_filter is None:
or_filter = Or()
self.filters.append(or_filter)
or_filter.add_filter(build_filter(
filter_or_string, *args, **kwargs
))
return or_... | Adds a list of :class:`~es_fluent.filters.core.Or` clauses, automatically
generating the an :class:`~es_fluent.filters.core.Or` filter if it does not
exist. | train | https://github.com/planetlabs/es_fluent/blob/74f8db3a1bf9aa1d54512cf2d5e0ec58ee2f4b1c/es_fluent/filters/core.py#L52-L68 | [
"def build_filter(filter_or_string, *args, **kwargs):\n \"\"\"\n Overloaded filter construction. If ``filter_or_string`` is a string\n we look up it's corresponding class in the filter registry and return it.\n Otherwise, assume ``filter_or_string`` is an instance of a filter.\n\n :return: :class:`~e... | class Generic(Filter):
"""
Contains a generic list of filters. Serialized as a dictionary.
"""
def __init__(self):
self.filters = []
def is_empty(self):
"""
:return: ``True`` if this filter has nested clauses ``False``.
"""
return all(_filter.is_empty() for _... |
planetlabs/es_fluent | es_fluent/filters/core.py | Generic.find_filter | python | def find_filter(self, filter_cls):
for filter_instance in self.filters:
if isinstance(filter_instance, filter_cls):
return filter_instance
return None | Find or create a filter instance of the provided ``filter_cls``. If it
is found, use remaining arguments to augment the filter otherwise
create a new instance of the desired type and add it to the
current :class:`~es_fluent.builder.QueryBuilder` accordingly. | train | https://github.com/planetlabs/es_fluent/blob/74f8db3a1bf9aa1d54512cf2d5e0ec58ee2f4b1c/es_fluent/filters/core.py#L70-L81 | null | class Generic(Filter):
"""
Contains a generic list of filters. Serialized as a dictionary.
"""
def __init__(self):
self.filters = []
def is_empty(self):
"""
:return: ``True`` if this filter has nested clauses ``False``.
"""
return all(_filter.is_empty() for _... |
planetlabs/es_fluent | es_fluent/filters/core.py | Dict.to_query | python | def to_query(self):
query = {}
for filter_instance in self.filters:
if filter_instance.is_empty():
continue
filter_query = filter_instance.to_query()
query.update(filter_query)
return query | Iterates over all filters and converts them to an Elastic HTTP API
suitable query.
Note: each :class:`~es_fluent.filters.Filter` is free to set it's own
filter dictionary. ESFluent does not attempt to guard against filters
that may clobber one another. If you wish to ensure that filter... | train | https://github.com/planetlabs/es_fluent/blob/74f8db3a1bf9aa1d54512cf2d5e0ec58ee2f4b1c/es_fluent/filters/core.py#L93-L112 | null | class Dict(Generic):
"""
Contains a generic dictionary of filters e.g. in a top level ES Query
we may have::
{ "filtered": {"filter": {"and": {...}, "or": {...}, "exists": {...} }
The Dict filter may represent the dictionary inside of "filtered.filter".
"""
def is_empty(self):
... |
planetlabs/es_fluent | es_fluent/filters/geometry.py | prepare_geojson | python | def prepare_geojson(geojson):
# TODO CW orientation.
geojson = deepcopy(geojson)
if geojson["type"] == "Feature":
geojson = geojson["geometry"]
if hasattr(geojson, 'properties'):
del geojson['properties']
if geojson["type"] == "FeatureCollection":
geojson["type"] = ... | Modifies incoming GeoJSON to make it Elastic friendly. This means:
1. CW orientation of polygons.
2. Re-casting of Features and FeatureCollections to Geometry and
GeometryCollections. | train | https://github.com/planetlabs/es_fluent/blob/74f8db3a1bf9aa1d54512cf2d5e0ec58ee2f4b1c/es_fluent/filters/geometry.py#L9-L32 | null | """
Geometry related filters require additional dependencies. Hence they're broken
out into their own module.
"""
from copy import deepcopy
from .core import Terminal
class GeoJSON(Terminal):
"""
Manages querying by GeoJSON. Automatically converts incoming GeoJSON
to elasticsearch friendly geometry. Thi... |
planetlabs/es_fluent | es_fluent/filters/geometry.py | IndexedShape.to_query | python | def to_query(self):
return {
"geo_shape": {
self.name: {
"indexed_shape": {
"index": self.index_name,
"type": self.doc_type,
"id": self.shape_id,
"path": self.path
... | Returns a json-serializable representation. | train | https://github.com/planetlabs/es_fluent/blob/74f8db3a1bf9aa1d54512cf2d5e0ec58ee2f4b1c/es_fluent/filters/geometry.py#L84-L99 | null | class IndexedShape(Terminal):
"""
Searches by a previously indexed Geometry.
"""
name = "indexed_geometry"
def __init__(self, name, shape_id, index_name, doc_type, path):
"""
:param string name: The field to match against the target shape.
:param string shape_id: The id of t... |
planetlabs/es_fluent | es_fluent/builder.py | QueryBuilder.and_filter | python | def and_filter(self, filter_or_string, *args, **kwargs):
self.root_filter.and_filter(filter_or_string, *args, **kwargs)
return self | Convenience method to delegate to the root_filter to generate an
:class:`~es_fluent.filters.core.And` clause.
:return: :class:`~es_fluent.builder.QueryBuilder` | train | https://github.com/planetlabs/es_fluent/blob/74f8db3a1bf9aa1d54512cf2d5e0ec58ee2f4b1c/es_fluent/builder.py#L37-L45 | [
"def and_filter(self, filter_or_string, *args, **kwargs):\n \"\"\"\n Adds a list of :class:`~es_fluent.filters.core.And` clauses, automatically\n generating :class:`~es_fluent.filters.core.And` filter if it does not\n exist.\n \"\"\"\n and_filter = self.find_filter(And)\n\n if and_filter is Non... | class QueryBuilder(object):
def __init__(self):
self.root_filter = Dict()
self.script_fields = ScriptFields()
self.fields = Fields()
self.sorts = []
self.source = True
self._size = None
@property
def size(self):
"""
Sets current size limit of... |
planetlabs/es_fluent | es_fluent/builder.py | QueryBuilder.or_filter | python | def or_filter(self, filter_or_string, *args, **kwargs):
self.root_filter.or_filter(filter_or_string, *args, **kwargs)
return self | Convenience method to delegate to the root_filter to generate an `or`
clause.
:return: :class:`~es_fluent.builder.QueryBuilder` | train | https://github.com/planetlabs/es_fluent/blob/74f8db3a1bf9aa1d54512cf2d5e0ec58ee2f4b1c/es_fluent/builder.py#L47-L55 | [
"def or_filter(self, filter_or_string, *args, **kwargs):\n \"\"\"\n Adds a list of :class:`~es_fluent.filters.core.Or` clauses, automatically\n generating the an :class:`~es_fluent.filters.core.Or` filter if it does not\n exist.\n \"\"\"\n or_filter = self.find_filter(Or)\n\n if or_filter is No... | class QueryBuilder(object):
def __init__(self):
self.root_filter = Dict()
self.script_fields = ScriptFields()
self.fields = Fields()
self.sorts = []
self.source = True
self._size = None
@property
def size(self):
"""
Sets current size limit of... |
planetlabs/es_fluent | es_fluent/builder.py | QueryBuilder.add_filter | python | def add_filter(self, filter_or_string, *args, **kwargs):
self.root_filter.add_filter(filter_or_string, *args, **kwargs)
return self | Adds a filter to the query builder's filters.
:return: :class:`~es_fluent.builder.QueryBuilder` | train | https://github.com/planetlabs/es_fluent/blob/74f8db3a1bf9aa1d54512cf2d5e0ec58ee2f4b1c/es_fluent/builder.py#L57-L64 | [
"def add_filter(self, filter_or_string, *args, **kwargs):\n \"\"\"\n Appends a filter.\n \"\"\"\n self.filters.append(build_filter(filter_or_string, *args, **kwargs))\n\n return self\n"
] | class QueryBuilder(object):
def __init__(self):
self.root_filter = Dict()
self.script_fields = ScriptFields()
self.fields = Fields()
self.sorts = []
self.source = True
self._size = None
@property
def size(self):
"""
Sets current size limit of... |
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