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OpenTreeOfLife/peyotl
peyotl/nexson_syntax/helper.py
_add_uniq_value_to_dict_bf
def _add_uniq_value_to_dict_bf(d, k, v): """Like _add_value_to_dict_bf but will not add v if another element in under key `k` has the same value. """ prev = d.get(k) if prev is None: d[k] = v elif isinstance(prev, list): if not isinstance(v, list): v = [v] for sel in v: found = False for el in prev: if el == sel: found = True break if not found: prev.append(sel) else: if isinstance(v, list): prev = [prev] for sel in v: found = False for el in prev: if el == sel: found = True break if not found: prev.append(sel) if len(prev) > 1: d[k] = prev elif prev != v: d[k] = [prev, v]
python
def _add_uniq_value_to_dict_bf(d, k, v): """Like _add_value_to_dict_bf but will not add v if another element in under key `k` has the same value. """ prev = d.get(k) if prev is None: d[k] = v elif isinstance(prev, list): if not isinstance(v, list): v = [v] for sel in v: found = False for el in prev: if el == sel: found = True break if not found: prev.append(sel) else: if isinstance(v, list): prev = [prev] for sel in v: found = False for el in prev: if el == sel: found = True break if not found: prev.append(sel) if len(prev) > 1: d[k] = prev elif prev != v: d[k] = [prev, v]
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Like _add_value_to_dict_bf but will not add v if another element in under key `k` has the same value.
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/nexson_syntax/helper.py#L136-L168
train
OpenTreeOfLife/peyotl
peyotl/nexson_syntax/helper.py
_debug_dump_dom
def _debug_dump_dom(el): """Debugging helper. Prints out `el` contents.""" import xml.dom.minidom s = [el.nodeName] att_container = el.attributes for i in range(att_container.length): attr = att_container.item(i) s.append(' @{a}="{v}"'.format(a=attr.name, v=attr.value)) for c in el.childNodes: if c.nodeType == xml.dom.minidom.Node.TEXT_NODE: s.append(' {a} type="TEXT" data="{d}"'.format(a=c.nodeName, d=c.data)) else: s.append(' {a} child'.format(a=c.nodeName)) return '\n'.join(s)
python
def _debug_dump_dom(el): """Debugging helper. Prints out `el` contents.""" import xml.dom.minidom s = [el.nodeName] att_container = el.attributes for i in range(att_container.length): attr = att_container.item(i) s.append(' @{a}="{v}"'.format(a=attr.name, v=attr.value)) for c in el.childNodes: if c.nodeType == xml.dom.minidom.Node.TEXT_NODE: s.append(' {a} type="TEXT" data="{d}"'.format(a=c.nodeName, d=c.data)) else: s.append(' {a} child'.format(a=c.nodeName)) return '\n'.join(s)
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Debugging helper. Prints out `el` contents.
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/nexson_syntax/helper.py#L177-L190
train
OpenTreeOfLife/peyotl
peyotl/nexson_syntax/helper.py
_convert_hbf_meta_val_for_xml
def _convert_hbf_meta_val_for_xml(key, val): """Convert to a BadgerFish-style dict for addition to a dict suitable for addition to XML tree or for v1.0 to v0.0 conversion.""" if isinstance(val, list): return [_convert_hbf_meta_val_for_xml(key, i) for i in val] is_literal = True content = None if isinstance(val, dict): ret = val if '@href' in val: is_literal = False else: content = val.get('$') if isinstance(content, dict) and _contains_hbf_meta_keys(val): is_literal = False else: ret = {} content = val if is_literal: ret.setdefault('@xsi:type', 'nex:LiteralMeta') ret.setdefault('@property', key) if content is not None: ret.setdefault('@datatype', _python_instance_to_nexml_meta_datatype(content)) if ret is not val: ret['$'] = content else: ret.setdefault('@xsi:type', 'nex:ResourceMeta') ret.setdefault('@rel', key) return ret
python
def _convert_hbf_meta_val_for_xml(key, val): """Convert to a BadgerFish-style dict for addition to a dict suitable for addition to XML tree or for v1.0 to v0.0 conversion.""" if isinstance(val, list): return [_convert_hbf_meta_val_for_xml(key, i) for i in val] is_literal = True content = None if isinstance(val, dict): ret = val if '@href' in val: is_literal = False else: content = val.get('$') if isinstance(content, dict) and _contains_hbf_meta_keys(val): is_literal = False else: ret = {} content = val if is_literal: ret.setdefault('@xsi:type', 'nex:LiteralMeta') ret.setdefault('@property', key) if content is not None: ret.setdefault('@datatype', _python_instance_to_nexml_meta_datatype(content)) if ret is not val: ret['$'] = content else: ret.setdefault('@xsi:type', 'nex:ResourceMeta') ret.setdefault('@rel', key) return ret
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Convert to a BadgerFish-style dict for addition to a dict suitable for addition to XML tree or for v1.0 to v0.0 conversion.
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/nexson_syntax/helper.py#L249-L277
train
OpenTreeOfLife/peyotl
peyotl/nexson_syntax/helper.py
find_nested_meta_first
def find_nested_meta_first(d, prop_name, version): """Returns obj. for badgerfish and val for hbf. Appropriate for nested literals""" if _is_badgerfish_version(version): return find_nested_meta_first_bf(d, prop_name) p = '^' + prop_name return d.get(p)
python
def find_nested_meta_first(d, prop_name, version): """Returns obj. for badgerfish and val for hbf. Appropriate for nested literals""" if _is_badgerfish_version(version): return find_nested_meta_first_bf(d, prop_name) p = '^' + prop_name return d.get(p)
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Returns obj. for badgerfish and val for hbf. Appropriate for nested literals
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/nexson_syntax/helper.py#L361-L366
train
PSPC-SPAC-buyandsell/von_agent
von_agent/codec.py
decode
def decode(value: str) -> Union[str, None, bool, int, float]: """ Decode encoded credential attribute value. :param value: numeric string to decode :return: decoded value, stringified if original was neither str, bool, int, nor float """ assert value.isdigit() or value[0] == '-' and value[1:].isdigit() if -I32_BOUND <= int(value) < I32_BOUND: # it's an i32: it is its own encoding return int(value) elif int(value) == I32_BOUND: return None (prefix, value) = (int(value[0]), int(value[1:])) ival = int(value) - I32_BOUND if ival == 0: return '' # special case: empty string encodes as 2**31 elif ival == 1: return False # sentinel for bool False elif ival == 2: return True # sentinel for bool True blen = ceil(log(ival, 16)/2) ibytes = unhexlify(ival.to_bytes(blen, 'big')) return DECODE_PREFIX.get(prefix, str)(ibytes.decode())
python
def decode(value: str) -> Union[str, None, bool, int, float]: """ Decode encoded credential attribute value. :param value: numeric string to decode :return: decoded value, stringified if original was neither str, bool, int, nor float """ assert value.isdigit() or value[0] == '-' and value[1:].isdigit() if -I32_BOUND <= int(value) < I32_BOUND: # it's an i32: it is its own encoding return int(value) elif int(value) == I32_BOUND: return None (prefix, value) = (int(value[0]), int(value[1:])) ival = int(value) - I32_BOUND if ival == 0: return '' # special case: empty string encodes as 2**31 elif ival == 1: return False # sentinel for bool False elif ival == 2: return True # sentinel for bool True blen = ceil(log(ival, 16)/2) ibytes = unhexlify(ival.to_bytes(blen, 'big')) return DECODE_PREFIX.get(prefix, str)(ibytes.decode())
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Decode encoded credential attribute value. :param value: numeric string to decode :return: decoded value, stringified if original was neither str, bool, int, nor float
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0b1c17cca3bd178b6e6974af84dbac1dfce5cf45
https://github.com/PSPC-SPAC-buyandsell/von_agent/blob/0b1c17cca3bd178b6e6974af84dbac1dfce5cf45/von_agent/codec.py#L70-L96
train
palantir/typedjsonrpc
typedjsonrpc/parameter_checker.py
validate_params_match
def validate_params_match(method, parameters): """Validates that the given parameters are exactly the method's declared parameters. :param method: The method to be called :type method: function :param parameters: The parameters to use in the call :type parameters: dict[str, object] | list[object] """ argspec = inspect.getargspec(method) # pylint: disable=deprecated-method default_length = len(argspec.defaults) if argspec.defaults is not None else 0 if isinstance(parameters, list): if len(parameters) > len(argspec.args) and argspec.varargs is None: raise InvalidParamsError("Too many parameters") remaining_parameters = len(argspec.args) - len(parameters) if remaining_parameters > default_length: raise InvalidParamsError("Not enough parameters") elif isinstance(parameters, dict): missing_parameters = [key for key in argspec.args if key not in parameters] default_parameters = set(argspec.args[len(argspec.args) - default_length:]) for key in missing_parameters: if key not in default_parameters: raise InvalidParamsError("Parameter {} has not been satisfied".format(key)) extra_params = [key for key in parameters if key not in argspec.args] if len(extra_params) > 0 and argspec.keywords is None: raise InvalidParamsError("Too many parameters")
python
def validate_params_match(method, parameters): """Validates that the given parameters are exactly the method's declared parameters. :param method: The method to be called :type method: function :param parameters: The parameters to use in the call :type parameters: dict[str, object] | list[object] """ argspec = inspect.getargspec(method) # pylint: disable=deprecated-method default_length = len(argspec.defaults) if argspec.defaults is not None else 0 if isinstance(parameters, list): if len(parameters) > len(argspec.args) and argspec.varargs is None: raise InvalidParamsError("Too many parameters") remaining_parameters = len(argspec.args) - len(parameters) if remaining_parameters > default_length: raise InvalidParamsError("Not enough parameters") elif isinstance(parameters, dict): missing_parameters = [key for key in argspec.args if key not in parameters] default_parameters = set(argspec.args[len(argspec.args) - default_length:]) for key in missing_parameters: if key not in default_parameters: raise InvalidParamsError("Parameter {} has not been satisfied".format(key)) extra_params = [key for key in parameters if key not in argspec.args] if len(extra_params) > 0 and argspec.keywords is None: raise InvalidParamsError("Too many parameters")
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Validates that the given parameters are exactly the method's declared parameters. :param method: The method to be called :type method: function :param parameters: The parameters to use in the call :type parameters: dict[str, object] | list[object]
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274218fcd236ff9643506caa629029c9ba25a0fb
https://github.com/palantir/typedjsonrpc/blob/274218fcd236ff9643506caa629029c9ba25a0fb/typedjsonrpc/parameter_checker.py#L27-L55
train
palantir/typedjsonrpc
typedjsonrpc/parameter_checker.py
check_types
def check_types(parameters, parameter_types, strict_floats): """Checks that the given parameters have the correct types. :param parameters: List of (name, value) pairs of the given parameters :type parameters: dict[str, object] :param parameter_types: Parameter type by name. :type parameter_types: dict[str, type] :param strict_floats: If False, treat integers as floats :type strict_floats: bool """ for name, parameter_type in parameter_types.items(): if name not in parameters: raise InvalidParamsError("Parameter '{}' is missing.".format(name)) if not _is_instance(parameters[name], parameter_type, strict_floats): raise InvalidParamsError("Value '{}' for parameter '{}' is not of expected type {}." .format(parameters[name], name, parameter_type))
python
def check_types(parameters, parameter_types, strict_floats): """Checks that the given parameters have the correct types. :param parameters: List of (name, value) pairs of the given parameters :type parameters: dict[str, object] :param parameter_types: Parameter type by name. :type parameter_types: dict[str, type] :param strict_floats: If False, treat integers as floats :type strict_floats: bool """ for name, parameter_type in parameter_types.items(): if name not in parameters: raise InvalidParamsError("Parameter '{}' is missing.".format(name)) if not _is_instance(parameters[name], parameter_type, strict_floats): raise InvalidParamsError("Value '{}' for parameter '{}' is not of expected type {}." .format(parameters[name], name, parameter_type))
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Checks that the given parameters have the correct types. :param parameters: List of (name, value) pairs of the given parameters :type parameters: dict[str, object] :param parameter_types: Parameter type by name. :type parameter_types: dict[str, type] :param strict_floats: If False, treat integers as floats :type strict_floats: bool
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274218fcd236ff9643506caa629029c9ba25a0fb
https://github.com/palantir/typedjsonrpc/blob/274218fcd236ff9643506caa629029c9ba25a0fb/typedjsonrpc/parameter_checker.py#L58-L73
train
palantir/typedjsonrpc
typedjsonrpc/parameter_checker.py
check_type_declaration
def check_type_declaration(parameter_names, parameter_types): """Checks that exactly the given parameter names have declared types. :param parameter_names: The names of the parameters in the method declaration :type parameter_names: list[str] :param parameter_types: Parameter type by name :type parameter_types: dict[str, type] """ if len(parameter_names) != len(parameter_types): raise Exception("Number of method parameters ({}) does not match number of " "declared types ({})" .format(len(parameter_names), len(parameter_types))) for parameter_name in parameter_names: if parameter_name not in parameter_types: raise Exception("Parameter '{}' does not have a declared type".format(parameter_name))
python
def check_type_declaration(parameter_names, parameter_types): """Checks that exactly the given parameter names have declared types. :param parameter_names: The names of the parameters in the method declaration :type parameter_names: list[str] :param parameter_types: Parameter type by name :type parameter_types: dict[str, type] """ if len(parameter_names) != len(parameter_types): raise Exception("Number of method parameters ({}) does not match number of " "declared types ({})" .format(len(parameter_names), len(parameter_types))) for parameter_name in parameter_names: if parameter_name not in parameter_types: raise Exception("Parameter '{}' does not have a declared type".format(parameter_name))
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Checks that exactly the given parameter names have declared types. :param parameter_names: The names of the parameters in the method declaration :type parameter_names: list[str] :param parameter_types: Parameter type by name :type parameter_types: dict[str, type]
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274218fcd236ff9643506caa629029c9ba25a0fb
https://github.com/palantir/typedjsonrpc/blob/274218fcd236ff9643506caa629029c9ba25a0fb/typedjsonrpc/parameter_checker.py#L76-L90
train
palantir/typedjsonrpc
typedjsonrpc/parameter_checker.py
check_return_type
def check_return_type(value, expected_type, strict_floats): """Checks that the given return value has the correct type. :param value: Value returned by the method :type value: object :param expected_type: Expected return type :type expected_type: type :param strict_floats: If False, treat integers as floats :type strict_floats: bool """ if expected_type is None: if value is not None: raise InvalidReturnTypeError("Returned value is '{}' but None was expected" .format(value)) elif not _is_instance(value, expected_type, strict_floats): raise InvalidReturnTypeError("Type of return value '{}' does not match expected type {}" .format(value, expected_type))
python
def check_return_type(value, expected_type, strict_floats): """Checks that the given return value has the correct type. :param value: Value returned by the method :type value: object :param expected_type: Expected return type :type expected_type: type :param strict_floats: If False, treat integers as floats :type strict_floats: bool """ if expected_type is None: if value is not None: raise InvalidReturnTypeError("Returned value is '{}' but None was expected" .format(value)) elif not _is_instance(value, expected_type, strict_floats): raise InvalidReturnTypeError("Type of return value '{}' does not match expected type {}" .format(value, expected_type))
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Checks that the given return value has the correct type. :param value: Value returned by the method :type value: object :param expected_type: Expected return type :type expected_type: type :param strict_floats: If False, treat integers as floats :type strict_floats: bool
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274218fcd236ff9643506caa629029c9ba25a0fb
https://github.com/palantir/typedjsonrpc/blob/274218fcd236ff9643506caa629029c9ba25a0fb/typedjsonrpc/parameter_checker.py#L93-L109
train
OpenTreeOfLife/peyotl
peyotl/phylesystem/helper.py
_make_phylesystem_cache_region
def _make_phylesystem_cache_region(**kwargs): """Only intended to be called by the Phylesystem singleton. """ global _CACHE_REGION_CONFIGURED, _REGION if _CACHE_REGION_CONFIGURED: return _REGION _CACHE_REGION_CONFIGURED = True try: # noinspection PyPackageRequirements from dogpile.cache import make_region except: _LOG.debug('dogpile.cache not available') return region = None trial_key = 'test_key' trial_val = {'test_val': [4, 3]} trying_redis = True if trying_redis: try: a = { 'host': 'localhost', 'port': 6379, 'db': 0, # default is 0 'redis_expiration_time': 60 * 60 * 24 * 2, # 2 days 'distributed_lock': False # True if multiple processes will use redis } region = make_region().configure('dogpile.cache.redis', arguments=a) _LOG.debug('cache region set up with cache.redis.') _LOG.debug('testing redis caching...') region.set(trial_key, trial_val) assert trial_val == region.get(trial_key) _LOG.debug('redis caching works') region.delete(trial_key) _REGION = region return region except: _LOG.debug('redis cache set up failed.') region = None trying_file_dbm = False if trying_file_dbm: _LOG.debug('Going to try dogpile.cache.dbm ...') first_par = _get_phylesystem_parent(**kwargs)[0] cache_db_dir = os.path.split(first_par)[0] cache_db = os.path.join(cache_db_dir, 'phylesystem-cachefile.dbm') _LOG.debug('dogpile.cache region using "{}"'.format(cache_db)) try: a = {'filename': cache_db} region = make_region().configure('dogpile.cache.dbm', expiration_time=36000, arguments=a) _LOG.debug('cache region set up with cache.dbm.') _LOG.debug('testing anydbm caching...') region.set(trial_key, trial_val) assert trial_val == region.get(trial_key) _LOG.debug('anydbm caching works') region.delete(trial_key) _REGION = region return region except: _LOG.debug('anydbm cache set up failed') _LOG.debug('exception in the configuration of the cache.') _LOG.debug('Phylesystem will not use caching') return None
python
def _make_phylesystem_cache_region(**kwargs): """Only intended to be called by the Phylesystem singleton. """ global _CACHE_REGION_CONFIGURED, _REGION if _CACHE_REGION_CONFIGURED: return _REGION _CACHE_REGION_CONFIGURED = True try: # noinspection PyPackageRequirements from dogpile.cache import make_region except: _LOG.debug('dogpile.cache not available') return region = None trial_key = 'test_key' trial_val = {'test_val': [4, 3]} trying_redis = True if trying_redis: try: a = { 'host': 'localhost', 'port': 6379, 'db': 0, # default is 0 'redis_expiration_time': 60 * 60 * 24 * 2, # 2 days 'distributed_lock': False # True if multiple processes will use redis } region = make_region().configure('dogpile.cache.redis', arguments=a) _LOG.debug('cache region set up with cache.redis.') _LOG.debug('testing redis caching...') region.set(trial_key, trial_val) assert trial_val == region.get(trial_key) _LOG.debug('redis caching works') region.delete(trial_key) _REGION = region return region except: _LOG.debug('redis cache set up failed.') region = None trying_file_dbm = False if trying_file_dbm: _LOG.debug('Going to try dogpile.cache.dbm ...') first_par = _get_phylesystem_parent(**kwargs)[0] cache_db_dir = os.path.split(first_par)[0] cache_db = os.path.join(cache_db_dir, 'phylesystem-cachefile.dbm') _LOG.debug('dogpile.cache region using "{}"'.format(cache_db)) try: a = {'filename': cache_db} region = make_region().configure('dogpile.cache.dbm', expiration_time=36000, arguments=a) _LOG.debug('cache region set up with cache.dbm.') _LOG.debug('testing anydbm caching...') region.set(trial_key, trial_val) assert trial_val == region.get(trial_key) _LOG.debug('anydbm caching works') region.delete(trial_key) _REGION = region return region except: _LOG.debug('anydbm cache set up failed') _LOG.debug('exception in the configuration of the cache.') _LOG.debug('Phylesystem will not use caching') return None
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Only intended to be called by the Phylesystem singleton.
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/phylesystem/helper.py#L125-L187
train
OpenTreeOfLife/peyotl
peyotl/git_storage/git_action.py
GitActionBase.path_for_doc
def path_for_doc(self, doc_id): """Returns doc_dir and doc_filepath for doc_id. """ full_path = self.path_for_doc_fn(self.repo, doc_id) # _LOG.debug('>>>>>>>>>> GitActionBase.path_for_doc_fn: {}'.format(self.path_for_doc_fn)) # _LOG.debug('>>>>>>>>>> GitActionBase.path_for_doc returning: [{}]'.format(full_path)) return full_path
python
def path_for_doc(self, doc_id): """Returns doc_dir and doc_filepath for doc_id. """ full_path = self.path_for_doc_fn(self.repo, doc_id) # _LOG.debug('>>>>>>>>>> GitActionBase.path_for_doc_fn: {}'.format(self.path_for_doc_fn)) # _LOG.debug('>>>>>>>>>> GitActionBase.path_for_doc returning: [{}]'.format(full_path)) return full_path
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Returns doc_dir and doc_filepath for doc_id.
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L143-L149
train
OpenTreeOfLife/peyotl
peyotl/git_storage/git_action.py
GitActionBase.current_branch
def current_branch(self): """Return the current branch name""" branch_name = git(self.gitdir, self.gitwd, "symbolic-ref", "HEAD") return branch_name.replace('refs/heads/', '').strip()
python
def current_branch(self): """Return the current branch name""" branch_name = git(self.gitdir, self.gitwd, "symbolic-ref", "HEAD") return branch_name.replace('refs/heads/', '').strip()
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Return the current branch name
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L169-L172
train
OpenTreeOfLife/peyotl
peyotl/git_storage/git_action.py
GitActionBase.branch_exists
def branch_exists(self, branch): """Returns true or false depending on if a branch exists""" try: git(self.gitdir, self.gitwd, "rev-parse", branch) except sh.ErrorReturnCode: return False return True
python
def branch_exists(self, branch): """Returns true or false depending on if a branch exists""" try: git(self.gitdir, self.gitwd, "rev-parse", branch) except sh.ErrorReturnCode: return False return True
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Returns true or false depending on if a branch exists
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L174-L180
train
OpenTreeOfLife/peyotl
peyotl/git_storage/git_action.py
GitActionBase.fetch
def fetch(self, remote='origin'): """fetch from a remote""" git(self.gitdir, "fetch", remote, _env=self.env())
python
def fetch(self, remote='origin'): """fetch from a remote""" git(self.gitdir, "fetch", remote, _env=self.env())
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fetch from a remote
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L204-L206
train
OpenTreeOfLife/peyotl
peyotl/git_storage/git_action.py
GitActionBase.get_version_history_for_file
def get_version_history_for_file(self, filepath): """ Return a dict representation of this file's commit history This uses specially formatted git-log output for easy parsing, as described here: http://blog.lost-theory.org/post/how-to-parse-git-log-output/ For a full list of available fields, see: http://linux.die.net/man/1/git-log """ # define the desired fields for logout output, matching the order in these lists! GIT_COMMIT_FIELDS = ['id', 'author_name', 'author_email', 'date', 'date_ISO_8601', 'relative_date', 'message_subject', 'message_body'] GIT_LOG_FORMAT = ['%H', '%an', '%ae', '%aD', '%ai', '%ar', '%s', '%b'] # make the final format string, using standard ASCII field/record delimiters GIT_LOG_FORMAT = '%x1f'.join(GIT_LOG_FORMAT) + '%x1e' try: log = git(self.gitdir, self.gitwd, '--no-pager', 'log', '--format=%s' % GIT_LOG_FORMAT, '--follow', # Track file's history when moved/renamed... '--find-renames=100%', # ... but only if the contents are identical! '--', filepath) # _LOG.debug('log said "{}"'.format(log)) log = log.strip('\n\x1e').split("\x1e") log = [row.strip().split("\x1f") for row in log] log = [dict(zip(GIT_COMMIT_FIELDS, row)) for row in log] except: _LOG.exception('git log failed') raise return log
python
def get_version_history_for_file(self, filepath): """ Return a dict representation of this file's commit history This uses specially formatted git-log output for easy parsing, as described here: http://blog.lost-theory.org/post/how-to-parse-git-log-output/ For a full list of available fields, see: http://linux.die.net/man/1/git-log """ # define the desired fields for logout output, matching the order in these lists! GIT_COMMIT_FIELDS = ['id', 'author_name', 'author_email', 'date', 'date_ISO_8601', 'relative_date', 'message_subject', 'message_body'] GIT_LOG_FORMAT = ['%H', '%an', '%ae', '%aD', '%ai', '%ar', '%s', '%b'] # make the final format string, using standard ASCII field/record delimiters GIT_LOG_FORMAT = '%x1f'.join(GIT_LOG_FORMAT) + '%x1e' try: log = git(self.gitdir, self.gitwd, '--no-pager', 'log', '--format=%s' % GIT_LOG_FORMAT, '--follow', # Track file's history when moved/renamed... '--find-renames=100%', # ... but only if the contents are identical! '--', filepath) # _LOG.debug('log said "{}"'.format(log)) log = log.strip('\n\x1e').split("\x1e") log = [row.strip().split("\x1f") for row in log] log = [dict(zip(GIT_COMMIT_FIELDS, row)) for row in log] except: _LOG.exception('git log failed') raise return log
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L235-L273
train
OpenTreeOfLife/peyotl
peyotl/git_storage/git_action.py
GitActionBase._add_and_commit
def _add_and_commit(self, doc_filepath, author, commit_msg): """Low level function used internally when you have an absolute filepath to add and commit""" try: git(self.gitdir, self.gitwd, "add", doc_filepath) git(self.gitdir, self.gitwd, "commit", author=author, message=commit_msg) except Exception as e: # We can ignore this if no changes are new, # otherwise raise a 400 if "nothing to commit" in e.message: # @EJM is this dangerous? _LOG.debug('"nothing to commit" found in error response') else: _LOG.exception('"git commit" failed') self.reset_hard() raise
python
def _add_and_commit(self, doc_filepath, author, commit_msg): """Low level function used internally when you have an absolute filepath to add and commit""" try: git(self.gitdir, self.gitwd, "add", doc_filepath) git(self.gitdir, self.gitwd, "commit", author=author, message=commit_msg) except Exception as e: # We can ignore this if no changes are new, # otherwise raise a 400 if "nothing to commit" in e.message: # @EJM is this dangerous? _LOG.debug('"nothing to commit" found in error response') else: _LOG.exception('"git commit" failed') self.reset_hard() raise
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L275-L288
train
OpenTreeOfLife/peyotl
peyotl/git_storage/git_action.py
GitActionBase._remove_document
def _remove_document(self, gh_user, doc_id, parent_sha, author, commit_msg=None): """Remove a document Remove a document on the given branch and attribute the commit to author. Returns the SHA of the commit on branch. """ # _LOG.debug("@@@@@@@@ GitActionBase._remove_document, doc_id={}".format(doc_id)) doc_filepath = self.path_for_doc(doc_id) # _LOG.debug("@@@@@@@@ GitActionBase._remove_document, doc_filepath={}".format(doc_filepath)) branch = self.create_or_checkout_branch(gh_user, doc_id, parent_sha) prev_file_sha = None if commit_msg is None: msg = "Delete document '%s' via OpenTree API" % doc_id else: msg = commit_msg if os.path.exists(doc_filepath): prev_file_sha = self.get_blob_sha_for_file(doc_filepath) if self.doc_type == 'nexson': # delete the parent directory entirely doc_dir = os.path.split(doc_filepath)[0] # _LOG.debug("@@@@@@@@ GitActionBase._remove_document, doc_dir={}".format(doc_dir)) git(self.gitdir, self.gitwd, "rm", "-rf", doc_dir) elif self.doc_type in ('collection', 'favorites', 'amendment'): # delete just the target file git(self.gitdir, self.gitwd, "rm", doc_filepath) else: raise NotImplementedError("No deletion rules for doc_type '{}'".format(self.doc_type)) git(self.gitdir, self.gitwd, "commit", author=author, message=msg) new_sha = git(self.gitdir, self.gitwd, "rev-parse", "HEAD").strip() return {'commit_sha': new_sha, 'branch': branch, 'prev_file_sha': prev_file_sha, }
python
def _remove_document(self, gh_user, doc_id, parent_sha, author, commit_msg=None): """Remove a document Remove a document on the given branch and attribute the commit to author. Returns the SHA of the commit on branch. """ # _LOG.debug("@@@@@@@@ GitActionBase._remove_document, doc_id={}".format(doc_id)) doc_filepath = self.path_for_doc(doc_id) # _LOG.debug("@@@@@@@@ GitActionBase._remove_document, doc_filepath={}".format(doc_filepath)) branch = self.create_or_checkout_branch(gh_user, doc_id, parent_sha) prev_file_sha = None if commit_msg is None: msg = "Delete document '%s' via OpenTree API" % doc_id else: msg = commit_msg if os.path.exists(doc_filepath): prev_file_sha = self.get_blob_sha_for_file(doc_filepath) if self.doc_type == 'nexson': # delete the parent directory entirely doc_dir = os.path.split(doc_filepath)[0] # _LOG.debug("@@@@@@@@ GitActionBase._remove_document, doc_dir={}".format(doc_dir)) git(self.gitdir, self.gitwd, "rm", "-rf", doc_dir) elif self.doc_type in ('collection', 'favorites', 'amendment'): # delete just the target file git(self.gitdir, self.gitwd, "rm", doc_filepath) else: raise NotImplementedError("No deletion rules for doc_type '{}'".format(self.doc_type)) git(self.gitdir, self.gitwd, "commit", author=author, message=msg) new_sha = git(self.gitdir, self.gitwd, "rev-parse", "HEAD").strip() return {'commit_sha': new_sha, 'branch': branch, 'prev_file_sha': prev_file_sha, }
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Remove a document Remove a document on the given branch and attribute the commit to author. Returns the SHA of the commit on branch.
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L429-L465
train
OpenTreeOfLife/peyotl
peyotl/git_storage/git_action.py
GitActionBase.write_document
def write_document(self, gh_user, doc_id, file_content, branch, author, commit_msg=None): """Given a document id, temporary filename of content, branch and auth_info Deprecated but needed until we merge api local-dep to master... """ parent_sha = None fc = tempfile.NamedTemporaryFile() # N.B. we currently assume file_content is text/JSON, or should be serialized from a dict if is_str_type(file_content): fc.write(file_content) else: write_as_json(file_content, fc) fc.flush() try: doc_filepath = self.path_for_doc(doc_id) doc_dir = os.path.split(doc_filepath)[0] if parent_sha is None: self.checkout_master() parent_sha = self.get_master_sha() branch = self.create_or_checkout_branch(gh_user, doc_id, parent_sha, force_branch_name=True) # create a document directory if this is a new doc EJM- what if it isn't? if not os.path.isdir(doc_dir): os.makedirs(doc_dir) shutil.copy(fc.name, doc_filepath) git(self.gitdir, self.gitwd, "add", doc_filepath) if commit_msg is None: commit_msg = "Update document '%s' via OpenTree API" % doc_id try: git(self.gitdir, self.gitwd, "commit", author=author, message=commit_msg) except Exception as e: # We can ignore this if no changes are new, # otherwise raise a 400 if "nothing to commit" in e.message: # @EJM is this dangerous? pass else: _LOG.exception('"git commit" failed') self.reset_hard() raise new_sha = git(self.gitdir, self.gitwd, "rev-parse", "HEAD") except Exception as e: _LOG.exception('write_document exception') raise GitWorkflowError("Could not write to document #%s ! Details: \n%s" % (doc_id, e.message)) finally: fc.close() return new_sha
python
def write_document(self, gh_user, doc_id, file_content, branch, author, commit_msg=None): """Given a document id, temporary filename of content, branch and auth_info Deprecated but needed until we merge api local-dep to master... """ parent_sha = None fc = tempfile.NamedTemporaryFile() # N.B. we currently assume file_content is text/JSON, or should be serialized from a dict if is_str_type(file_content): fc.write(file_content) else: write_as_json(file_content, fc) fc.flush() try: doc_filepath = self.path_for_doc(doc_id) doc_dir = os.path.split(doc_filepath)[0] if parent_sha is None: self.checkout_master() parent_sha = self.get_master_sha() branch = self.create_or_checkout_branch(gh_user, doc_id, parent_sha, force_branch_name=True) # create a document directory if this is a new doc EJM- what if it isn't? if not os.path.isdir(doc_dir): os.makedirs(doc_dir) shutil.copy(fc.name, doc_filepath) git(self.gitdir, self.gitwd, "add", doc_filepath) if commit_msg is None: commit_msg = "Update document '%s' via OpenTree API" % doc_id try: git(self.gitdir, self.gitwd, "commit", author=author, message=commit_msg) except Exception as e: # We can ignore this if no changes are new, # otherwise raise a 400 if "nothing to commit" in e.message: # @EJM is this dangerous? pass else: _LOG.exception('"git commit" failed') self.reset_hard() raise new_sha = git(self.gitdir, self.gitwd, "rev-parse", "HEAD") except Exception as e: _LOG.exception('write_document exception') raise GitWorkflowError("Could not write to document #%s ! Details: \n%s" % (doc_id, e.message)) finally: fc.close() return new_sha
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Given a document id, temporary filename of content, branch and auth_info Deprecated but needed until we merge api local-dep to master...
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L467-L516
train
OpenTreeOfLife/peyotl
peyotl/git_storage/git_action.py
GitActionBase.write_doc_from_tmpfile
def write_doc_from_tmpfile(self, doc_id, tmpfi, parent_sha, auth_info, commit_msg='', doctype_display_name="document"): """Given a doc_id, temporary filename of content, branch and auth_info """ gh_user, author = get_user_author(auth_info) doc_filepath = self.path_for_doc(doc_id) doc_dir = os.path.split(doc_filepath)[0] if parent_sha is None: self.checkout_master() parent_sha = self.get_master_sha() branch = self.create_or_checkout_branch(gh_user, doc_id, parent_sha) # build complete (probably type-specific) commit message default_commit_msg = "Update %s '%s' via OpenTree API" % (doctype_display_name, doc_id) if commit_msg: commit_msg = "%s\n\n(%s)" % (commit_msg, default_commit_msg) else: commit_msg = default_commit_msg # create a doc directory if this is a new document EJM- what if it isn't? if not os.path.isdir(doc_dir): os.makedirs(doc_dir) if os.path.exists(doc_filepath): prev_file_sha = self.get_blob_sha_for_file(doc_filepath) else: prev_file_sha = None shutil.copy(tmpfi.name, doc_filepath) self._add_and_commit(doc_filepath, author, commit_msg) new_sha = git(self.gitdir, self.gitwd, "rev-parse", "HEAD") _LOG.debug('Committed document "{i}" to branch "{b}" commit SHA: "{s}"'.format(i=doc_id, b=branch, s=new_sha.strip())) return {'commit_sha': new_sha.strip(), 'branch': branch, 'prev_file_sha': prev_file_sha, }
python
def write_doc_from_tmpfile(self, doc_id, tmpfi, parent_sha, auth_info, commit_msg='', doctype_display_name="document"): """Given a doc_id, temporary filename of content, branch and auth_info """ gh_user, author = get_user_author(auth_info) doc_filepath = self.path_for_doc(doc_id) doc_dir = os.path.split(doc_filepath)[0] if parent_sha is None: self.checkout_master() parent_sha = self.get_master_sha() branch = self.create_or_checkout_branch(gh_user, doc_id, parent_sha) # build complete (probably type-specific) commit message default_commit_msg = "Update %s '%s' via OpenTree API" % (doctype_display_name, doc_id) if commit_msg: commit_msg = "%s\n\n(%s)" % (commit_msg, default_commit_msg) else: commit_msg = default_commit_msg # create a doc directory if this is a new document EJM- what if it isn't? if not os.path.isdir(doc_dir): os.makedirs(doc_dir) if os.path.exists(doc_filepath): prev_file_sha = self.get_blob_sha_for_file(doc_filepath) else: prev_file_sha = None shutil.copy(tmpfi.name, doc_filepath) self._add_and_commit(doc_filepath, author, commit_msg) new_sha = git(self.gitdir, self.gitwd, "rev-parse", "HEAD") _LOG.debug('Committed document "{i}" to branch "{b}" commit SHA: "{s}"'.format(i=doc_id, b=branch, s=new_sha.strip())) return {'commit_sha': new_sha.strip(), 'branch': branch, 'prev_file_sha': prev_file_sha, }
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Given a doc_id, temporary filename of content, branch and auth_info
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/git_storage/git_action.py#L518-L559
train
OpenTreeOfLife/peyotl
peyotl/amendments/git_actions.py
TaxonomicAmendmentsGitAction.remove_amendment
def remove_amendment(self, first_arg, sec_arg, third_arg, fourth_arg=None, commit_msg=None): """Remove an amendment Given a amendment_id, branch and optionally an author, remove an amendment on the given branch and attribute the commit to author. Returns the SHA of the commit on branch. """ if fourth_arg is None: amendment_id, branch_name, author = first_arg, sec_arg, third_arg gh_user = branch_name.split('_amendment_')[0] parent_sha = self.get_master_sha() else: gh_user, amendment_id, parent_sha, author = first_arg, sec_arg, third_arg, fourth_arg if commit_msg is None: commit_msg = "Delete Amendment '%s' via OpenTree API" % amendment_id return self._remove_document(gh_user, amendment_id, parent_sha, author, commit_msg)
python
def remove_amendment(self, first_arg, sec_arg, third_arg, fourth_arg=None, commit_msg=None): """Remove an amendment Given a amendment_id, branch and optionally an author, remove an amendment on the given branch and attribute the commit to author. Returns the SHA of the commit on branch. """ if fourth_arg is None: amendment_id, branch_name, author = first_arg, sec_arg, third_arg gh_user = branch_name.split('_amendment_')[0] parent_sha = self.get_master_sha() else: gh_user, amendment_id, parent_sha, author = first_arg, sec_arg, third_arg, fourth_arg if commit_msg is None: commit_msg = "Delete Amendment '%s' via OpenTree API" % amendment_id return self._remove_document(gh_user, amendment_id, parent_sha, author, commit_msg)
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Remove an amendment Given a amendment_id, branch and optionally an author, remove an amendment on the given branch and attribute the commit to author. Returns the SHA of the commit on branch.
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/amendments/git_actions.py#L92-L107
train
inveniosoftware/invenio-communities
invenio_communities/models.py
InclusionRequest.create
def create(cls, community, record, user=None, expires_at=None, notify=True): """Create a record inclusion request to a community. :param community: Community object. :param record: Record API object. :param expires_at: Time after which the request expires and shouldn't be resolved anymore. """ if expires_at and expires_at < datetime.utcnow(): raise InclusionRequestExpiryTimeError( community=community, record=record) if community.has_record(record): raise InclusionRequestObsoleteError( community=community, record=record) try: # Create inclusion request with db.session.begin_nested(): obj = cls( id_community=community.id, id_record=record.id, user=user, expires_at=expires_at ) db.session.add(obj) except (IntegrityError, FlushError): raise InclusionRequestExistsError( community=community, record=record) # Send signal inclusion_request_created.send( current_app._get_current_object(), request=obj, notify=notify ) return obj
python
def create(cls, community, record, user=None, expires_at=None, notify=True): """Create a record inclusion request to a community. :param community: Community object. :param record: Record API object. :param expires_at: Time after which the request expires and shouldn't be resolved anymore. """ if expires_at and expires_at < datetime.utcnow(): raise InclusionRequestExpiryTimeError( community=community, record=record) if community.has_record(record): raise InclusionRequestObsoleteError( community=community, record=record) try: # Create inclusion request with db.session.begin_nested(): obj = cls( id_community=community.id, id_record=record.id, user=user, expires_at=expires_at ) db.session.add(obj) except (IntegrityError, FlushError): raise InclusionRequestExistsError( community=community, record=record) # Send signal inclusion_request_created.send( current_app._get_current_object(), request=obj, notify=notify ) return obj
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Create a record inclusion request to a community. :param community: Community object. :param record: Record API object. :param expires_at: Time after which the request expires and shouldn't be resolved anymore.
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L114-L152
train
inveniosoftware/invenio-communities
invenio_communities/models.py
InclusionRequest.get
def get(cls, community_id, record_uuid): """Get an inclusion request.""" return cls.query.filter_by( id_record=record_uuid, id_community=community_id ).one_or_none()
python
def get(cls, community_id, record_uuid): """Get an inclusion request.""" return cls.query.filter_by( id_record=record_uuid, id_community=community_id ).one_or_none()
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Get an inclusion request.
[ "Get", "an", "inclusion", "request", "." ]
5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L155-L159
train
inveniosoftware/invenio-communities
invenio_communities/models.py
Community.filter_communities
def filter_communities(cls, p, so, with_deleted=False): """Search for communities. Helper function which takes from database only those communities which match search criteria. Uses parameter 'so' to set communities in the correct order. Parameter 'page' is introduced to restrict results and return only slice of them for the current page. If page == 0 function will return all communities that match the pattern. """ query = cls.query if with_deleted else \ cls.query.filter(cls.deleted_at.is_(None)) if p: p = p.replace(' ', '%') query = query.filter(db.or_( cls.id.ilike('%' + p + '%'), cls.title.ilike('%' + p + '%'), cls.description.ilike('%' + p + '%'), )) if so in current_app.config['COMMUNITIES_SORTING_OPTIONS']: order = so == 'title' and db.asc or db.desc query = query.order_by(order(getattr(cls, so))) else: query = query.order_by(db.desc(cls.ranking)) return query
python
def filter_communities(cls, p, so, with_deleted=False): """Search for communities. Helper function which takes from database only those communities which match search criteria. Uses parameter 'so' to set communities in the correct order. Parameter 'page' is introduced to restrict results and return only slice of them for the current page. If page == 0 function will return all communities that match the pattern. """ query = cls.query if with_deleted else \ cls.query.filter(cls.deleted_at.is_(None)) if p: p = p.replace(' ', '%') query = query.filter(db.or_( cls.id.ilike('%' + p + '%'), cls.title.ilike('%' + p + '%'), cls.description.ilike('%' + p + '%'), )) if so in current_app.config['COMMUNITIES_SORTING_OPTIONS']: order = so == 'title' and db.asc or db.desc query = query.order_by(order(getattr(cls, so))) else: query = query.order_by(db.desc(cls.ranking)) return query
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Search for communities. Helper function which takes from database only those communities which match search criteria. Uses parameter 'so' to set communities in the correct order. Parameter 'page' is introduced to restrict results and return only slice of them for the current page. If page == 0 function will return all communities that match the pattern.
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L257-L284
train
inveniosoftware/invenio-communities
invenio_communities/models.py
Community.add_record
def add_record(self, record): """Add a record to the community. :param record: Record object. :type record: `invenio_records.api.Record` """ key = current_app.config['COMMUNITIES_RECORD_KEY'] record.setdefault(key, []) if self.has_record(record): current_app.logger.warning( 'Community addition: record {uuid} is already in community ' '"{comm}"'.format(uuid=record.id, comm=self.id)) else: record[key].append(self.id) record[key] = sorted(record[key]) if current_app.config['COMMUNITIES_OAI_ENABLED']: if not self.oaiset.has_record(record): self.oaiset.add_record(record)
python
def add_record(self, record): """Add a record to the community. :param record: Record object. :type record: `invenio_records.api.Record` """ key = current_app.config['COMMUNITIES_RECORD_KEY'] record.setdefault(key, []) if self.has_record(record): current_app.logger.warning( 'Community addition: record {uuid} is already in community ' '"{comm}"'.format(uuid=record.id, comm=self.id)) else: record[key].append(self.id) record[key] = sorted(record[key]) if current_app.config['COMMUNITIES_OAI_ENABLED']: if not self.oaiset.has_record(record): self.oaiset.add_record(record)
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Add a record to the community. :param record: Record object. :type record: `invenio_records.api.Record`
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L286-L304
train
inveniosoftware/invenio-communities
invenio_communities/models.py
Community.remove_record
def remove_record(self, record): """Remove an already accepted record from the community. :param record: Record object. :type record: `invenio_records.api.Record` """ if not self.has_record(record): current_app.logger.warning( 'Community removal: record {uuid} was not in community ' '"{comm}"'.format(uuid=record.id, comm=self.id)) else: key = current_app.config['COMMUNITIES_RECORD_KEY'] record[key] = [c for c in record[key] if c != self.id] if current_app.config['COMMUNITIES_OAI_ENABLED']: if self.oaiset.has_record(record): self.oaiset.remove_record(record)
python
def remove_record(self, record): """Remove an already accepted record from the community. :param record: Record object. :type record: `invenio_records.api.Record` """ if not self.has_record(record): current_app.logger.warning( 'Community removal: record {uuid} was not in community ' '"{comm}"'.format(uuid=record.id, comm=self.id)) else: key = current_app.config['COMMUNITIES_RECORD_KEY'] record[key] = [c for c in record[key] if c != self.id] if current_app.config['COMMUNITIES_OAI_ENABLED']: if self.oaiset.has_record(record): self.oaiset.remove_record(record)
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Remove an already accepted record from the community. :param record: Record object. :type record: `invenio_records.api.Record`
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L306-L322
train
inveniosoftware/invenio-communities
invenio_communities/models.py
Community.accept_record
def accept_record(self, record): """Accept a record for inclusion in the community. :param record: Record object. """ with db.session.begin_nested(): req = InclusionRequest.get(self.id, record.id) if req is None: raise InclusionRequestMissingError(community=self, record=record) req.delete() self.add_record(record) self.last_record_accepted = datetime.utcnow()
python
def accept_record(self, record): """Accept a record for inclusion in the community. :param record: Record object. """ with db.session.begin_nested(): req = InclusionRequest.get(self.id, record.id) if req is None: raise InclusionRequestMissingError(community=self, record=record) req.delete() self.add_record(record) self.last_record_accepted = datetime.utcnow()
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Accept a record for inclusion in the community. :param record: Record object.
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L329-L341
train
inveniosoftware/invenio-communities
invenio_communities/models.py
Community.reject_record
def reject_record(self, record): """Reject a record for inclusion in the community. :param record: Record object. """ with db.session.begin_nested(): req = InclusionRequest.get(self.id, record.id) if req is None: raise InclusionRequestMissingError(community=self, record=record) req.delete()
python
def reject_record(self, record): """Reject a record for inclusion in the community. :param record: Record object. """ with db.session.begin_nested(): req = InclusionRequest.get(self.id, record.id) if req is None: raise InclusionRequestMissingError(community=self, record=record) req.delete()
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Reject a record for inclusion in the community. :param record: Record object.
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L343-L353
train
inveniosoftware/invenio-communities
invenio_communities/models.py
Community.delete
def delete(self): """Mark the community for deletion. :param delete_time: DateTime after which to delete the community. :type delete_time: datetime.datetime :raises: CommunitiesError """ if self.deleted_at is not None: raise CommunitiesError(community=self) else: self.deleted_at = datetime.utcnow()
python
def delete(self): """Mark the community for deletion. :param delete_time: DateTime after which to delete the community. :type delete_time: datetime.datetime :raises: CommunitiesError """ if self.deleted_at is not None: raise CommunitiesError(community=self) else: self.deleted_at = datetime.utcnow()
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Mark the community for deletion. :param delete_time: DateTime after which to delete the community. :type delete_time: datetime.datetime :raises: CommunitiesError
[ "Mark", "the", "community", "for", "deletion", "." ]
5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L355-L365
train
inveniosoftware/invenio-communities
invenio_communities/models.py
Community.logo_url
def logo_url(self): """Get URL to collection logo. :returns: Path to community logo. :rtype: str """ if self.logo_ext: return '/api/files/{bucket}/{key}'.format( bucket=current_app.config['COMMUNITIES_BUCKET_UUID'], key='{0}/logo.{1}'.format(self.id, self.logo_ext), ) return None
python
def logo_url(self): """Get URL to collection logo. :returns: Path to community logo. :rtype: str """ if self.logo_ext: return '/api/files/{bucket}/{key}'.format( bucket=current_app.config['COMMUNITIES_BUCKET_UUID'], key='{0}/logo.{1}'.format(self.id, self.logo_ext), ) return None
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Get URL to collection logo. :returns: Path to community logo. :rtype: str
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L380-L391
train
inveniosoftware/invenio-communities
invenio_communities/models.py
Community.oaiset
def oaiset(self): """Return the corresponding OAISet for given community. If OAIServer is not installed this property will return None. :returns: returns OAISet object corresponding to this community. :rtype: `invenio_oaiserver.models.OAISet` or None """ if current_app.config['COMMUNITIES_OAI_ENABLED']: from invenio_oaiserver.models import OAISet return OAISet.query.filter_by(spec=self.oaiset_spec).one() else: return None
python
def oaiset(self): """Return the corresponding OAISet for given community. If OAIServer is not installed this property will return None. :returns: returns OAISet object corresponding to this community. :rtype: `invenio_oaiserver.models.OAISet` or None """ if current_app.config['COMMUNITIES_OAI_ENABLED']: from invenio_oaiserver.models import OAISet return OAISet.query.filter_by(spec=self.oaiset_spec).one() else: return None
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Return the corresponding OAISet for given community. If OAIServer is not installed this property will return None. :returns: returns OAISet object corresponding to this community. :rtype: `invenio_oaiserver.models.OAISet` or None
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L421-L433
train
inveniosoftware/invenio-communities
invenio_communities/models.py
Community.oaiset_url
def oaiset_url(self): """Return the OAISet URL for given community. :returns: URL of corresponding OAISet. :rtype: str """ return url_for( 'invenio_oaiserver.response', verb='ListRecords', metadataPrefix='oai_dc', set=self.oaiset_spec, _external=True)
python
def oaiset_url(self): """Return the OAISet URL for given community. :returns: URL of corresponding OAISet. :rtype: str """ return url_for( 'invenio_oaiserver.response', verb='ListRecords', metadataPrefix='oai_dc', set=self.oaiset_spec, _external=True)
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Return the OAISet URL for given community. :returns: URL of corresponding OAISet. :rtype: str
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L436-L445
train
inveniosoftware/invenio-communities
invenio_communities/models.py
Community.version_id
def version_id(self): """Return the version of the community. :returns: hash which encodes the community id and its las update. :rtype: str """ return hashlib.sha1('{0}__{1}'.format( self.id, self.updated).encode('utf-8')).hexdigest()
python
def version_id(self): """Return the version of the community. :returns: hash which encodes the community id and its las update. :rtype: str """ return hashlib.sha1('{0}__{1}'.format( self.id, self.updated).encode('utf-8')).hexdigest()
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Return the version of the community. :returns: hash which encodes the community id and its las update. :rtype: str
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L448-L455
train
inveniosoftware/invenio-communities
invenio_communities/models.py
FeaturedCommunity.get_featured_or_none
def get_featured_or_none(cls, start_date=None): """Get the latest featured community. :param start_date: Date after which the featuring starts :returns: Community object or None :rtype: `invenio_communities.models.Community` or None """ start_date = start_date or datetime.utcnow() comm = cls.query.filter( FeaturedCommunity.start_date <= start_date ).order_by( cls.start_date.desc() ).first() return comm if comm is None else comm.community
python
def get_featured_or_none(cls, start_date=None): """Get the latest featured community. :param start_date: Date after which the featuring starts :returns: Community object or None :rtype: `invenio_communities.models.Community` or None """ start_date = start_date or datetime.utcnow() comm = cls.query.filter( FeaturedCommunity.start_date <= start_date ).order_by( cls.start_date.desc() ).first() return comm if comm is None else comm.community
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Get the latest featured community. :param start_date: Date after which the featuring starts :returns: Community object or None :rtype: `invenio_communities.models.Community` or None
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/models.py#L486-L500
train
ARMmbed/mbed-connector-api-python
mbed_connector_api/mbed_connector_api.py
connector.getConnectorVersion
def getConnectorVersion(self): """ GET the current Connector version. :returns: asyncResult object, populates error and result fields :rtype: asyncResult """ result = asyncResult() data = self._getURL("/",versioned=False) result.fill(data) if data.status_code == 200: result.error = False else: result.error = response_codes("get_mdc_version",data.status_code) result.is_done = True return result
python
def getConnectorVersion(self): """ GET the current Connector version. :returns: asyncResult object, populates error and result fields :rtype: asyncResult """ result = asyncResult() data = self._getURL("/",versioned=False) result.fill(data) if data.status_code == 200: result.error = False else: result.error = response_codes("get_mdc_version",data.status_code) result.is_done = True return result
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GET the current Connector version. :returns: asyncResult object, populates error and result fields :rtype: asyncResult
[ "GET", "the", "current", "Connector", "version", "." ]
a5024a01dc67cc192c8bf7a70b251fcf0a3f279b
https://github.com/ARMmbed/mbed-connector-api-python/blob/a5024a01dc67cc192c8bf7a70b251fcf0a3f279b/mbed_connector_api/mbed_connector_api.py#L72-L87
train
ARMmbed/mbed-connector-api-python
mbed_connector_api/mbed_connector_api.py
connector.setHandler
def setHandler(self,handler,cbfn): ''' Register a handler for a particular notification type. These are the types of notifications that are acceptable. | 'async-responses' | 'registrations-expired' | 'de-registrations' | 'reg-updates' | 'registrations' | 'notifications' :param str handler: name of the notification type :param fnptr cbfn: function to pass the notification channel messages to. :return: Nothing. ''' if handler == "async-responses": self.async_responses_callback = cbfn elif handler == "registrations-expired": self.registrations_expired_callback = cbfn elif handler == "de-registrations": self.de_registrations_callback = cbfn elif handler == "reg-updates": self.reg_updates_callback = cbfn elif handler == "registrations": self.registrations_callback = cbfn elif handler == "notifications": self.notifications_callback = cbfn else: self.log.warn("'%s' is not a legitimate notification channel option. Please check your spelling.",handler)
python
def setHandler(self,handler,cbfn): ''' Register a handler for a particular notification type. These are the types of notifications that are acceptable. | 'async-responses' | 'registrations-expired' | 'de-registrations' | 'reg-updates' | 'registrations' | 'notifications' :param str handler: name of the notification type :param fnptr cbfn: function to pass the notification channel messages to. :return: Nothing. ''' if handler == "async-responses": self.async_responses_callback = cbfn elif handler == "registrations-expired": self.registrations_expired_callback = cbfn elif handler == "de-registrations": self.de_registrations_callback = cbfn elif handler == "reg-updates": self.reg_updates_callback = cbfn elif handler == "registrations": self.registrations_callback = cbfn elif handler == "notifications": self.notifications_callback = cbfn else: self.log.warn("'%s' is not a legitimate notification channel option. Please check your spelling.",handler)
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Register a handler for a particular notification type. These are the types of notifications that are acceptable. | 'async-responses' | 'registrations-expired' | 'de-registrations' | 'reg-updates' | 'registrations' | 'notifications' :param str handler: name of the notification type :param fnptr cbfn: function to pass the notification channel messages to. :return: Nothing.
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a5024a01dc67cc192c8bf7a70b251fcf0a3f279b
https://github.com/ARMmbed/mbed-connector-api-python/blob/a5024a01dc67cc192c8bf7a70b251fcf0a3f279b/mbed_connector_api/mbed_connector_api.py#L554-L583
train
hsolbrig/pyjsg
pyjsg/parser_impl/jsg_doc_parser.py
JSGDocParser.as_python
def as_python(self, infile, include_original_shex: bool=False): """ Return the python representation of the document """ self._context.resolve_circular_references() # add forwards for any circular entries body = '' for k in self._context.ordered_elements(): v = self._context.grammarelts[k] if isinstance(v, (JSGLexerRuleBlock, JSGObjectExpr)): body += v.as_python(k) if isinstance(v, JSGObjectExpr) and not self._context.has_typeid: self._context.directives.append(f'_CONTEXT.TYPE_EXCEPTIONS.append("{k}")') elif isinstance(v, JSGForwardRef): pass elif isinstance(v, (JSGValueType, JSGArrayExpr)): body += f"\n\n\n{k} = {v.signature_type()}" else: raise NotImplementedError("Unknown grammar elt for {}".format(k)) self._context.forward_refs.pop(k, None) body = '\n' + '\n'.join(self._context.directives) + body return _jsg_python_template.format(infile=infile, original_shex='# ' + self.text if include_original_shex else "", version=__version__, gendate=datetime.datetime.now().strftime("%Y-%m-%d %H:%M"), body=body)
python
def as_python(self, infile, include_original_shex: bool=False): """ Return the python representation of the document """ self._context.resolve_circular_references() # add forwards for any circular entries body = '' for k in self._context.ordered_elements(): v = self._context.grammarelts[k] if isinstance(v, (JSGLexerRuleBlock, JSGObjectExpr)): body += v.as_python(k) if isinstance(v, JSGObjectExpr) and not self._context.has_typeid: self._context.directives.append(f'_CONTEXT.TYPE_EXCEPTIONS.append("{k}")') elif isinstance(v, JSGForwardRef): pass elif isinstance(v, (JSGValueType, JSGArrayExpr)): body += f"\n\n\n{k} = {v.signature_type()}" else: raise NotImplementedError("Unknown grammar elt for {}".format(k)) self._context.forward_refs.pop(k, None) body = '\n' + '\n'.join(self._context.directives) + body return _jsg_python_template.format(infile=infile, original_shex='# ' + self.text if include_original_shex else "", version=__version__, gendate=datetime.datetime.now().strftime("%Y-%m-%d %H:%M"), body=body)
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Return the python representation of the document
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9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7
https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/jsg_doc_parser.py#L36-L59
train
emirozer/bowshock
bowshock/modis.py
__getDummyDateList
def __getDummyDateList(): """ Generate a dummy date list for testing without hitting the server """ D = [] for y in xrange(2001, 2010): for d in xrange(1, 365, 1): D.append('A%04d%03d' % (y, d)) return D
python
def __getDummyDateList(): """ Generate a dummy date list for testing without hitting the server """ D = [] for y in xrange(2001, 2010): for d in xrange(1, 365, 1): D.append('A%04d%03d' % (y, d)) return D
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Generate a dummy date list for testing without hitting the server
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9f5e053f1d54995b833b83616f37c67178c3e840
https://github.com/emirozer/bowshock/blob/9f5e053f1d54995b833b83616f37c67178c3e840/bowshock/modis.py#L92-L103
train
emirozer/bowshock
bowshock/modis.py
mkIntDate
def mkIntDate(s): """ Convert the webserver formatted dates to an integer format by stripping the leading char and casting """ n = s.__len__() d = int(s[-(n - 1):n]) return d
python
def mkIntDate(s): """ Convert the webserver formatted dates to an integer format by stripping the leading char and casting """ n = s.__len__() d = int(s[-(n - 1):n]) return d
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Convert the webserver formatted dates to an integer format by stripping the leading char and casting
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9f5e053f1d54995b833b83616f37c67178c3e840
https://github.com/emirozer/bowshock/blob/9f5e053f1d54995b833b83616f37c67178c3e840/bowshock/modis.py#L118-L127
train
CybOXProject/mixbox
mixbox/idgen.py
IDGenerator.create_id
def create_id(self, prefix="guid"): """Create an ID. Note that if `prefix` is not provided, it will be `guid`, even if the `method` is `METHOD_INT`. """ if self.method == IDGenerator.METHOD_UUID: id_ = str(uuid.uuid4()) elif self.method == IDGenerator.METHOD_INT: id_ = self.next_int self.next_int += 1 else: raise InvalidMethodError(self.method) return "%s:%s-%s" % (self.namespace.prefix, prefix, id_)
python
def create_id(self, prefix="guid"): """Create an ID. Note that if `prefix` is not provided, it will be `guid`, even if the `method` is `METHOD_INT`. """ if self.method == IDGenerator.METHOD_UUID: id_ = str(uuid.uuid4()) elif self.method == IDGenerator.METHOD_INT: id_ = self.next_int self.next_int += 1 else: raise InvalidMethodError(self.method) return "%s:%s-%s" % (self.namespace.prefix, prefix, id_)
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Create an ID. Note that if `prefix` is not provided, it will be `guid`, even if the `method` is `METHOD_INT`.
[ "Create", "an", "ID", "." ]
9097dae7a433f5b98c18171c4a5598f69a7d30af
https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/idgen.py#L61-L75
train
yamins81/tabular
tabular/spreadsheet.py
grayspec
def grayspec(k): """ List of gray-scale colors in HSV space as web hex triplets. For integer argument k, returns list of `k` gray-scale colors, increasingly light, linearly in the HSV color space, as web hex triplets. Technical dependency of :func:`tabular.spreadsheet.aggregate_in`. **Parameters** **k** : positive integer Number of gray-scale colors to return. **Returns** **glist** : list of strings List of `k` gray-scale colors. """ ll = .5 ul = .8 delta = (ul - ll) / k return [GrayScale(t) for t in np.arange(ll, ul, delta)]
python
def grayspec(k): """ List of gray-scale colors in HSV space as web hex triplets. For integer argument k, returns list of `k` gray-scale colors, increasingly light, linearly in the HSV color space, as web hex triplets. Technical dependency of :func:`tabular.spreadsheet.aggregate_in`. **Parameters** **k** : positive integer Number of gray-scale colors to return. **Returns** **glist** : list of strings List of `k` gray-scale colors. """ ll = .5 ul = .8 delta = (ul - ll) / k return [GrayScale(t) for t in np.arange(ll, ul, delta)]
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List of gray-scale colors in HSV space as web hex triplets. For integer argument k, returns list of `k` gray-scale colors, increasingly light, linearly in the HSV color space, as web hex triplets. Technical dependency of :func:`tabular.spreadsheet.aggregate_in`. **Parameters** **k** : positive integer Number of gray-scale colors to return. **Returns** **glist** : list of strings List of `k` gray-scale colors.
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1caf091c8c395960a9ad7078f95158b533cc52dd
https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/tabular/spreadsheet.py#L477-L502
train
yamins81/tabular
tabular/spreadsheet.py
addrecords
def addrecords(X, new): """ Append one or more records to the end of a numpy recarray or ndarray . Can take a single record, void or tuple, or a list of records, voids or tuples. Implemented by the tabarray method :func:`tabular.tab.tabarray.addrecords`. **Parameters** **X** : numpy ndarray with structured dtype or recarray The array to add records to. **new** : record, void or tuple, or list of them Record(s) to add to `X`. **Returns** **out** : numpy ndarray with structured dtype New numpy array made up of `X` plus the new records. **See also:** :func:`tabular.spreadsheet.rowstack` """ if isinstance(new, np.record) or isinstance(new, np.void) or \ isinstance(new, tuple): new = [new] return np.append(X, utils.fromrecords(new, type=np.ndarray, dtype=X.dtype), axis=0)
python
def addrecords(X, new): """ Append one or more records to the end of a numpy recarray or ndarray . Can take a single record, void or tuple, or a list of records, voids or tuples. Implemented by the tabarray method :func:`tabular.tab.tabarray.addrecords`. **Parameters** **X** : numpy ndarray with structured dtype or recarray The array to add records to. **new** : record, void or tuple, or list of them Record(s) to add to `X`. **Returns** **out** : numpy ndarray with structured dtype New numpy array made up of `X` plus the new records. **See also:** :func:`tabular.spreadsheet.rowstack` """ if isinstance(new, np.record) or isinstance(new, np.void) or \ isinstance(new, tuple): new = [new] return np.append(X, utils.fromrecords(new, type=np.ndarray, dtype=X.dtype), axis=0)
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Append one or more records to the end of a numpy recarray or ndarray . Can take a single record, void or tuple, or a list of records, voids or tuples. Implemented by the tabarray method :func:`tabular.tab.tabarray.addrecords`. **Parameters** **X** : numpy ndarray with structured dtype or recarray The array to add records to. **new** : record, void or tuple, or list of them Record(s) to add to `X`. **Returns** **out** : numpy ndarray with structured dtype New numpy array made up of `X` plus the new records. **See also:** :func:`tabular.spreadsheet.rowstack`
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1caf091c8c395960a9ad7078f95158b533cc52dd
https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/tabular/spreadsheet.py#L704-L737
train
yamins81/tabular
tabular/spreadsheet.py
addcols
def addcols(X, cols, names=None): """ Add one or more columns to a numpy ndarray. Technical dependency of :func:`tabular.spreadsheet.aggregate_in`. Implemented by the tabarray method :func:`tabular.tab.tabarray.addcols`. **Parameters** **X** : numpy ndarray with structured dtype or recarray The recarray to add columns to. **cols** : numpy ndarray, or list of arrays of columns Column(s) to add. **names**: list of strings, optional Names of the new columns. Only applicable when `cols` is a list of arrays. **Returns** **out** : numpy ndarray with structured dtype New numpy array made up of `X` plus the new columns. **See also:** :func:`tabular.spreadsheet.colstack` """ if isinstance(names,str): names = [n.strip() for n in names.split(',')] if isinstance(cols, list): if any([isinstance(x,np.ndarray) or isinstance(x,list) or \ isinstance(x,tuple) for x in cols]): assert all([len(x) == len(X) for x in cols]), \ 'Trying to add columns of wrong length.' assert names != None and len(cols) == len(names), \ 'Number of columns to add must equal number of new names.' cols = utils.fromarrays(cols,type=np.ndarray,names = names) else: assert len(cols) == len(X), 'Trying to add column of wrong length.' cols = utils.fromarrays([cols], type=np.ndarray,names=names) else: assert isinstance(cols, np.ndarray) if cols.dtype.names == None: cols = utils.fromarrays([cols],type=np.ndarray, names=names) Replacements = [a for a in cols.dtype.names if a in X.dtype.names] if len(Replacements) > 0: print('Replacing columns', [a for a in cols.dtype.names if a in X.dtype.names]) return utils.fromarrays( [X[a] if a not in cols.dtype.names else cols[a] for a in X.dtype.names] + [cols[a] for a in cols.dtype.names if a not in X.dtype.names], type=np.ndarray, names=list(X.dtype.names) + [a for a in cols.dtype.names if a not in X.dtype.names])
python
def addcols(X, cols, names=None): """ Add one or more columns to a numpy ndarray. Technical dependency of :func:`tabular.spreadsheet.aggregate_in`. Implemented by the tabarray method :func:`tabular.tab.tabarray.addcols`. **Parameters** **X** : numpy ndarray with structured dtype or recarray The recarray to add columns to. **cols** : numpy ndarray, or list of arrays of columns Column(s) to add. **names**: list of strings, optional Names of the new columns. Only applicable when `cols` is a list of arrays. **Returns** **out** : numpy ndarray with structured dtype New numpy array made up of `X` plus the new columns. **See also:** :func:`tabular.spreadsheet.colstack` """ if isinstance(names,str): names = [n.strip() for n in names.split(',')] if isinstance(cols, list): if any([isinstance(x,np.ndarray) or isinstance(x,list) or \ isinstance(x,tuple) for x in cols]): assert all([len(x) == len(X) for x in cols]), \ 'Trying to add columns of wrong length.' assert names != None and len(cols) == len(names), \ 'Number of columns to add must equal number of new names.' cols = utils.fromarrays(cols,type=np.ndarray,names = names) else: assert len(cols) == len(X), 'Trying to add column of wrong length.' cols = utils.fromarrays([cols], type=np.ndarray,names=names) else: assert isinstance(cols, np.ndarray) if cols.dtype.names == None: cols = utils.fromarrays([cols],type=np.ndarray, names=names) Replacements = [a for a in cols.dtype.names if a in X.dtype.names] if len(Replacements) > 0: print('Replacing columns', [a for a in cols.dtype.names if a in X.dtype.names]) return utils.fromarrays( [X[a] if a not in cols.dtype.names else cols[a] for a in X.dtype.names] + [cols[a] for a in cols.dtype.names if a not in X.dtype.names], type=np.ndarray, names=list(X.dtype.names) + [a for a in cols.dtype.names if a not in X.dtype.names])
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Add one or more columns to a numpy ndarray. Technical dependency of :func:`tabular.spreadsheet.aggregate_in`. Implemented by the tabarray method :func:`tabular.tab.tabarray.addcols`. **Parameters** **X** : numpy ndarray with structured dtype or recarray The recarray to add columns to. **cols** : numpy ndarray, or list of arrays of columns Column(s) to add. **names**: list of strings, optional Names of the new columns. Only applicable when `cols` is a list of arrays. **Returns** **out** : numpy ndarray with structured dtype New numpy array made up of `X` plus the new columns. **See also:** :func:`tabular.spreadsheet.colstack`
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1caf091c8c395960a9ad7078f95158b533cc52dd
https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/tabular/spreadsheet.py#L740-L803
train
yamins81/tabular
tabular/spreadsheet.py
deletecols
def deletecols(X, cols): """ Delete columns from a numpy ndarry or recarray. Can take a string giving a column name or comma-separated list of column names, or a list of string column names. Implemented by the tabarray method :func:`tabular.tab.tabarray.deletecols`. **Parameters** **X** : numpy recarray or ndarray with structured dtype The numpy array from which to delete columns. **cols** : string or list of strings Name or list of names of columns in `X`. This can be a string giving a column name or comma-separated list of column names, or a list of string column names. **Returns** **out** : numpy ndarray with structured dtype New numpy ndarray with structured dtype given by `X`, excluding the columns named in `cols`. """ if isinstance(cols, str): cols = cols.split(',') retain = [n for n in X.dtype.names if n not in cols] if len(retain) > 0: return X[retain] else: return None
python
def deletecols(X, cols): """ Delete columns from a numpy ndarry or recarray. Can take a string giving a column name or comma-separated list of column names, or a list of string column names. Implemented by the tabarray method :func:`tabular.tab.tabarray.deletecols`. **Parameters** **X** : numpy recarray or ndarray with structured dtype The numpy array from which to delete columns. **cols** : string or list of strings Name or list of names of columns in `X`. This can be a string giving a column name or comma-separated list of column names, or a list of string column names. **Returns** **out** : numpy ndarray with structured dtype New numpy ndarray with structured dtype given by `X`, excluding the columns named in `cols`. """ if isinstance(cols, str): cols = cols.split(',') retain = [n for n in X.dtype.names if n not in cols] if len(retain) > 0: return X[retain] else: return None
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Delete columns from a numpy ndarry or recarray. Can take a string giving a column name or comma-separated list of column names, or a list of string column names. Implemented by the tabarray method :func:`tabular.tab.tabarray.deletecols`. **Parameters** **X** : numpy recarray or ndarray with structured dtype The numpy array from which to delete columns. **cols** : string or list of strings Name or list of names of columns in `X`. This can be a string giving a column name or comma-separated list of column names, or a list of string column names. **Returns** **out** : numpy ndarray with structured dtype New numpy ndarray with structured dtype given by `X`, excluding the columns named in `cols`.
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1caf091c8c395960a9ad7078f95158b533cc52dd
https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/tabular/spreadsheet.py#L806-L842
train
yamins81/tabular
tabular/spreadsheet.py
renamecol
def renamecol(X, old, new): """ Rename column of a numpy ndarray with structured dtype, in-place. Implemented by the tabarray method :func:`tabular.tab.tabarray.renamecol`. **Parameters** **X** : numpy ndarray with structured dtype The numpy array for which a column is to be renamed. **old** : string Old column name, e.g. a name in `X.dtype.names`. **new** : string New column name to replace `old`. """ NewNames = tuple([n if n != old else new for n in X.dtype.names]) X.dtype.names = NewNames
python
def renamecol(X, old, new): """ Rename column of a numpy ndarray with structured dtype, in-place. Implemented by the tabarray method :func:`tabular.tab.tabarray.renamecol`. **Parameters** **X** : numpy ndarray with structured dtype The numpy array for which a column is to be renamed. **old** : string Old column name, e.g. a name in `X.dtype.names`. **new** : string New column name to replace `old`. """ NewNames = tuple([n if n != old else new for n in X.dtype.names]) X.dtype.names = NewNames
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Rename column of a numpy ndarray with structured dtype, in-place. Implemented by the tabarray method :func:`tabular.tab.tabarray.renamecol`. **Parameters** **X** : numpy ndarray with structured dtype The numpy array for which a column is to be renamed. **old** : string Old column name, e.g. a name in `X.dtype.names`. **new** : string New column name to replace `old`.
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1caf091c8c395960a9ad7078f95158b533cc52dd
https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/tabular/spreadsheet.py#L845-L868
train
yamins81/tabular
tabular/spreadsheet.py
replace
def replace(X, old, new, strict=True, cols=None, rows=None): """ Replace value `old` with `new` everywhere it appears in-place. Implemented by the tabarray method :func:`tabular.tab.tabarray.replace`. **Parameters** **X** : numpy ndarray with structured dtype Numpy array for which in-place replacement of `old` with `new` is to be done. **old** : string **new** : string **strict** : boolean, optional * If `strict` = `True`, replace only exact occurences of `old`. * If `strict` = `False`, assume `old` and `new` are strings and replace all occurences of substrings (e.g. like :func:`str.replace`) **cols** : list of strings, optional Names of columns to make replacements in; if `None`, make replacements everywhere. **rows** : list of booleans or integers, optional Rows to make replacements in; if `None`, make replacements everywhere. Note: This function does in-place replacements. Thus there are issues handling data types here when replacement dtype is larger than original dtype. This can be resolved later by making a new array when necessary ... """ if cols == None: cols = X.dtype.names elif isinstance(cols, str): cols = cols.split(',') if rows == None: rows = np.ones((len(X),), bool) if strict: new = np.array(new) for a in cols: if X.dtype[a] < new.dtype: print('WARNING: dtype of column', a, 'is inferior to dtype of ', new, 'which may cause problems.') try: X[a][(X[a] == old)[rows]] = new except: print('Replacement not made on column', a, '.') else: for a in cols: QuickRep = True try: colstr = ''.join(X[a][rows]) except TypeError: print('Not replacing in column', a, 'due to type mismatch.') else: avoid = [ord(o) for o in utils.uniqify(old + new + colstr)] ok = set(range(256)).difference(avoid) if len(ok) > 0: sep = chr(list(ok)[0]) else: ok = set(range(65536)).difference(avoid) if len(ok) > 0: sep = unichr(list(ok)[0]) else: print('All unicode characters represented in column', a, ', can\t replace quickly.') QuickRep = False if QuickRep: newrows = np.array(sep.join(X[a][rows]) .replace(old, new).split(sep)) else: newrows = np.array([aa.replace(old,new) for aa in X[a][rows]]) X[a][rows] = np.cast[X.dtype[a]](newrows) if newrows.dtype > X.dtype[a]: print('WARNING: dtype of column', a, 'is inferior to the ' 'dtype of its replacement which may cause problems ' '(ends of strings might get chopped off).')
python
def replace(X, old, new, strict=True, cols=None, rows=None): """ Replace value `old` with `new` everywhere it appears in-place. Implemented by the tabarray method :func:`tabular.tab.tabarray.replace`. **Parameters** **X** : numpy ndarray with structured dtype Numpy array for which in-place replacement of `old` with `new` is to be done. **old** : string **new** : string **strict** : boolean, optional * If `strict` = `True`, replace only exact occurences of `old`. * If `strict` = `False`, assume `old` and `new` are strings and replace all occurences of substrings (e.g. like :func:`str.replace`) **cols** : list of strings, optional Names of columns to make replacements in; if `None`, make replacements everywhere. **rows** : list of booleans or integers, optional Rows to make replacements in; if `None`, make replacements everywhere. Note: This function does in-place replacements. Thus there are issues handling data types here when replacement dtype is larger than original dtype. This can be resolved later by making a new array when necessary ... """ if cols == None: cols = X.dtype.names elif isinstance(cols, str): cols = cols.split(',') if rows == None: rows = np.ones((len(X),), bool) if strict: new = np.array(new) for a in cols: if X.dtype[a] < new.dtype: print('WARNING: dtype of column', a, 'is inferior to dtype of ', new, 'which may cause problems.') try: X[a][(X[a] == old)[rows]] = new except: print('Replacement not made on column', a, '.') else: for a in cols: QuickRep = True try: colstr = ''.join(X[a][rows]) except TypeError: print('Not replacing in column', a, 'due to type mismatch.') else: avoid = [ord(o) for o in utils.uniqify(old + new + colstr)] ok = set(range(256)).difference(avoid) if len(ok) > 0: sep = chr(list(ok)[0]) else: ok = set(range(65536)).difference(avoid) if len(ok) > 0: sep = unichr(list(ok)[0]) else: print('All unicode characters represented in column', a, ', can\t replace quickly.') QuickRep = False if QuickRep: newrows = np.array(sep.join(X[a][rows]) .replace(old, new).split(sep)) else: newrows = np.array([aa.replace(old,new) for aa in X[a][rows]]) X[a][rows] = np.cast[X.dtype[a]](newrows) if newrows.dtype > X.dtype[a]: print('WARNING: dtype of column', a, 'is inferior to the ' 'dtype of its replacement which may cause problems ' '(ends of strings might get chopped off).')
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Replace value `old` with `new` everywhere it appears in-place. Implemented by the tabarray method :func:`tabular.tab.tabarray.replace`. **Parameters** **X** : numpy ndarray with structured dtype Numpy array for which in-place replacement of `old` with `new` is to be done. **old** : string **new** : string **strict** : boolean, optional * If `strict` = `True`, replace only exact occurences of `old`. * If `strict` = `False`, assume `old` and `new` are strings and replace all occurences of substrings (e.g. like :func:`str.replace`) **cols** : list of strings, optional Names of columns to make replacements in; if `None`, make replacements everywhere. **rows** : list of booleans or integers, optional Rows to make replacements in; if `None`, make replacements everywhere. Note: This function does in-place replacements. Thus there are issues handling data types here when replacement dtype is larger than original dtype. This can be resolved later by making a new array when necessary ...
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1caf091c8c395960a9ad7078f95158b533cc52dd
https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/tabular/spreadsheet.py#L871-L964
train
yamins81/tabular
tabular/spreadsheet.py
rowstack
def rowstack(seq, mode='nulls', nullvals=None): ''' Vertically stack a sequence of numpy ndarrays with structured dtype Analog of numpy.vstack Implemented by the tabarray method :func:`tabular.tab.tabarray.rowstack` which uses :func:`tabular.tabarray.tab_rowstack`. **Parameters** **seq** : sequence of numpy recarrays List, tuple, etc. of numpy recarrays to stack vertically. **mode** : string in ['nulls', 'commons', 'abort'] Denotes how to proceed if the recarrays have different dtypes, e.g. different sets of named columns. * if `mode` == ``nulls``, the resulting set of columns is determined by the union of the dtypes of all recarrays to be stacked, and missing data is filled with null values as defined by :func:`tabular.spreadsheet.nullvalue`; this is the default mode. * elif `mode` == ``commons``, the resulting set of columns is determined by the intersection of the dtypes of all recarrays to be stacked, e.g. common columns. * elif `mode` == ``abort``, raise an error when the recarrays to stack have different dtypes. **Returns** **out** : numpy ndarray with structured dtype Result of vertically stacking the arrays in `seq`. **See also:** `numpy.vstack <http://docs.scipy.org/doc/numpy/reference/generated/numpy.vstack.html>`_. ''' if nullvals == None: nullvals = utils.DEFAULT_NULLVALUEFORMAT #newseq = [ss for ss in seq if len(ss) > 0] if len(seq) > 1: assert mode in ['commons','nulls','abort'], \ ('"mode" argument must either by "commons", "abort", or "nulls".') if mode == 'abort': if not all([set(l.dtype.names) == set(seq[0].dtype.names) for l in seq]): raise ValueError('Some column names are different.') else: mode = 'commons' if mode == 'nulls': names = utils.uniqify(utils.listunion([list(s.dtype.names) for s in seq if s.dtype.names != None])) formats = [max([s.dtype[att] for s in seq if s.dtype.names != None and att in s.dtype.names]).str for att in names] dtype = np.dtype(zip(names,formats)) return utils.fromarrays([utils.listunion([s[att].tolist() if (s.dtype.names != None and att in s.dtype.names) else [nullvals(format)] * len(s) for s in seq]) for (att, format) in zip(names, formats)], type=np.ndarray, dtype=dtype) elif mode == 'commons': names = [x for x in seq[0].dtype.names if all([x in l.dtype.names for l in seq[1:]])] formats = [max([a.dtype[att] for a in seq]).str for att in names] return utils.fromrecords(utils.listunion( [ar.tolist() for ar in seq]), type=np.ndarray, names=names, formats=formats) else: return seq[0]
python
def rowstack(seq, mode='nulls', nullvals=None): ''' Vertically stack a sequence of numpy ndarrays with structured dtype Analog of numpy.vstack Implemented by the tabarray method :func:`tabular.tab.tabarray.rowstack` which uses :func:`tabular.tabarray.tab_rowstack`. **Parameters** **seq** : sequence of numpy recarrays List, tuple, etc. of numpy recarrays to stack vertically. **mode** : string in ['nulls', 'commons', 'abort'] Denotes how to proceed if the recarrays have different dtypes, e.g. different sets of named columns. * if `mode` == ``nulls``, the resulting set of columns is determined by the union of the dtypes of all recarrays to be stacked, and missing data is filled with null values as defined by :func:`tabular.spreadsheet.nullvalue`; this is the default mode. * elif `mode` == ``commons``, the resulting set of columns is determined by the intersection of the dtypes of all recarrays to be stacked, e.g. common columns. * elif `mode` == ``abort``, raise an error when the recarrays to stack have different dtypes. **Returns** **out** : numpy ndarray with structured dtype Result of vertically stacking the arrays in `seq`. **See also:** `numpy.vstack <http://docs.scipy.org/doc/numpy/reference/generated/numpy.vstack.html>`_. ''' if nullvals == None: nullvals = utils.DEFAULT_NULLVALUEFORMAT #newseq = [ss for ss in seq if len(ss) > 0] if len(seq) > 1: assert mode in ['commons','nulls','abort'], \ ('"mode" argument must either by "commons", "abort", or "nulls".') if mode == 'abort': if not all([set(l.dtype.names) == set(seq[0].dtype.names) for l in seq]): raise ValueError('Some column names are different.') else: mode = 'commons' if mode == 'nulls': names = utils.uniqify(utils.listunion([list(s.dtype.names) for s in seq if s.dtype.names != None])) formats = [max([s.dtype[att] for s in seq if s.dtype.names != None and att in s.dtype.names]).str for att in names] dtype = np.dtype(zip(names,formats)) return utils.fromarrays([utils.listunion([s[att].tolist() if (s.dtype.names != None and att in s.dtype.names) else [nullvals(format)] * len(s) for s in seq]) for (att, format) in zip(names, formats)], type=np.ndarray, dtype=dtype) elif mode == 'commons': names = [x for x in seq[0].dtype.names if all([x in l.dtype.names for l in seq[1:]])] formats = [max([a.dtype[att] for a in seq]).str for att in names] return utils.fromrecords(utils.listunion( [ar.tolist() for ar in seq]), type=np.ndarray, names=names, formats=formats) else: return seq[0]
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Vertically stack a sequence of numpy ndarrays with structured dtype Analog of numpy.vstack Implemented by the tabarray method :func:`tabular.tab.tabarray.rowstack` which uses :func:`tabular.tabarray.tab_rowstack`. **Parameters** **seq** : sequence of numpy recarrays List, tuple, etc. of numpy recarrays to stack vertically. **mode** : string in ['nulls', 'commons', 'abort'] Denotes how to proceed if the recarrays have different dtypes, e.g. different sets of named columns. * if `mode` == ``nulls``, the resulting set of columns is determined by the union of the dtypes of all recarrays to be stacked, and missing data is filled with null values as defined by :func:`tabular.spreadsheet.nullvalue`; this is the default mode. * elif `mode` == ``commons``, the resulting set of columns is determined by the intersection of the dtypes of all recarrays to be stacked, e.g. common columns. * elif `mode` == ``abort``, raise an error when the recarrays to stack have different dtypes. **Returns** **out** : numpy ndarray with structured dtype Result of vertically stacking the arrays in `seq`. **See also:** `numpy.vstack <http://docs.scipy.org/doc/numpy/reference/generated/numpy.vstack.html>`_.
[ "Vertically", "stack", "a", "sequence", "of", "numpy", "ndarrays", "with", "structured", "dtype" ]
1caf091c8c395960a9ad7078f95158b533cc52dd
https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/tabular/spreadsheet.py#L967-L1044
train
yamins81/tabular
tabular/spreadsheet.py
colstack
def colstack(seq, mode='abort',returnnaming=False): """ Horizontally stack a sequence of numpy ndarrays with structured dtypes Analog of numpy.hstack for recarrays. Implemented by the tabarray method :func:`tabular.tab.tabarray.colstack` which uses :func:`tabular.tabarray.tab_colstack`. **Parameters** **seq** : sequence of numpy ndarray with structured dtype List, tuple, etc. of numpy recarrays to stack vertically. **mode** : string in ['first','drop','abort','rename'] Denotes how to proceed if when multiple recarrays share the same column name: * if `mode` == ``first``, take the column from the first recarray in `seq` containing the shared column name. * elif `mode` == ``abort``, raise an error when the recarrays to stack share column names; this is the default mode. * elif `mode` == ``drop``, drop any column that shares its name with any other column among the sequence of recarrays. * elif `mode` == ``rename``, for any set of all columns sharing the same name, rename all columns by appending an underscore, '_', followed by an integer, starting with '0' and incrementing by 1 for each subsequent column. **Returns** **out** : numpy ndarray with structured dtype Result of horizontally stacking the arrays in `seq`. **See also:** `numpy.hstack <http://docs.scipy.org/doc/numpy/reference/generated/numpy.hstack.html>`_. """ assert mode in ['first','drop','abort','rename'], \ 'mode argument must take on value "first","drop", "rename", or "abort".' AllNames = utils.uniqify(utils.listunion( [list(l.dtype.names) for l in seq])) NameList = [(x, [i for i in range(len(seq)) if x in seq[i].dtype.names]) for x in AllNames] Commons = [x[0] for x in NameList if len(x[1]) > 1] if len(Commons) > 0 or mode == 'first': if mode == 'abort': raise ValueError('There are common column names with differing ' + 'values in the columns') elif mode == 'drop': Names = [(L[0], x,x) for (x, L) in NameList if x not in Commons] elif mode == 'rename': NameDict = dict(NameList) Names = utils.listunion([[(i,n,n) if len(NameDict[n]) == 1 else \ (i,n,n + '_' + str(i)) for n in s.dtype.names] \ for (i,s) in enumerate(seq)]) else: Names = [(L[0], x,x) for (x, L) in NameList] if returnnaming: return utils.fromarrays([seq[i][x] for (i, x,y) in Names], type= np.ndarray,names=zip(*Names)[2]),Names else: return utils.fromarrays([seq[i][x] for (i, x,y) in Names], type= np.ndarray,names=zip(*Names)[2])
python
def colstack(seq, mode='abort',returnnaming=False): """ Horizontally stack a sequence of numpy ndarrays with structured dtypes Analog of numpy.hstack for recarrays. Implemented by the tabarray method :func:`tabular.tab.tabarray.colstack` which uses :func:`tabular.tabarray.tab_colstack`. **Parameters** **seq** : sequence of numpy ndarray with structured dtype List, tuple, etc. of numpy recarrays to stack vertically. **mode** : string in ['first','drop','abort','rename'] Denotes how to proceed if when multiple recarrays share the same column name: * if `mode` == ``first``, take the column from the first recarray in `seq` containing the shared column name. * elif `mode` == ``abort``, raise an error when the recarrays to stack share column names; this is the default mode. * elif `mode` == ``drop``, drop any column that shares its name with any other column among the sequence of recarrays. * elif `mode` == ``rename``, for any set of all columns sharing the same name, rename all columns by appending an underscore, '_', followed by an integer, starting with '0' and incrementing by 1 for each subsequent column. **Returns** **out** : numpy ndarray with structured dtype Result of horizontally stacking the arrays in `seq`. **See also:** `numpy.hstack <http://docs.scipy.org/doc/numpy/reference/generated/numpy.hstack.html>`_. """ assert mode in ['first','drop','abort','rename'], \ 'mode argument must take on value "first","drop", "rename", or "abort".' AllNames = utils.uniqify(utils.listunion( [list(l.dtype.names) for l in seq])) NameList = [(x, [i for i in range(len(seq)) if x in seq[i].dtype.names]) for x in AllNames] Commons = [x[0] for x in NameList if len(x[1]) > 1] if len(Commons) > 0 or mode == 'first': if mode == 'abort': raise ValueError('There are common column names with differing ' + 'values in the columns') elif mode == 'drop': Names = [(L[0], x,x) for (x, L) in NameList if x not in Commons] elif mode == 'rename': NameDict = dict(NameList) Names = utils.listunion([[(i,n,n) if len(NameDict[n]) == 1 else \ (i,n,n + '_' + str(i)) for n in s.dtype.names] \ for (i,s) in enumerate(seq)]) else: Names = [(L[0], x,x) for (x, L) in NameList] if returnnaming: return utils.fromarrays([seq[i][x] for (i, x,y) in Names], type= np.ndarray,names=zip(*Names)[2]),Names else: return utils.fromarrays([seq[i][x] for (i, x,y) in Names], type= np.ndarray,names=zip(*Names)[2])
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Horizontally stack a sequence of numpy ndarrays with structured dtypes Analog of numpy.hstack for recarrays. Implemented by the tabarray method :func:`tabular.tab.tabarray.colstack` which uses :func:`tabular.tabarray.tab_colstack`. **Parameters** **seq** : sequence of numpy ndarray with structured dtype List, tuple, etc. of numpy recarrays to stack vertically. **mode** : string in ['first','drop','abort','rename'] Denotes how to proceed if when multiple recarrays share the same column name: * if `mode` == ``first``, take the column from the first recarray in `seq` containing the shared column name. * elif `mode` == ``abort``, raise an error when the recarrays to stack share column names; this is the default mode. * elif `mode` == ``drop``, drop any column that shares its name with any other column among the sequence of recarrays. * elif `mode` == ``rename``, for any set of all columns sharing the same name, rename all columns by appending an underscore, '_', followed by an integer, starting with '0' and incrementing by 1 for each subsequent column. **Returns** **out** : numpy ndarray with structured dtype Result of horizontally stacking the arrays in `seq`. **See also:** `numpy.hstack <http://docs.scipy.org/doc/numpy/reference/generated/numpy.hstack.html>`_.
[ "Horizontally", "stack", "a", "sequence", "of", "numpy", "ndarrays", "with", "structured", "dtypes" ]
1caf091c8c395960a9ad7078f95158b533cc52dd
https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/tabular/spreadsheet.py#L1047-L1123
train
yamins81/tabular
tabular/spreadsheet.py
DEFAULT_RENAMER
def DEFAULT_RENAMER(L, Names=None): """ Renames overlapping column names of numpy ndarrays with structured dtypes Rename the columns by using a simple convention: * If `L` is a list, it will append the number in the list to the key associated with the array. * If `L` is a dictionary, the algorithm will append the string representation of the key associated with an array to the overlapping columns from that array. Default renamer function used by :func:`tabular.spreadsheet.join` **Parameters** **L** : list or dictionary Numpy recarrays with columns to be renamed. **Returns** **D** : dictionary of dictionaries Dictionary mapping each input numpy recarray to a dictionary mapping each original column name to its new name following the convention above. """ if isinstance(L,dict): Names = L.keys() LL = L.values() else: if Names == None: Names = range(len(L)) else: assert len(Names) == len(L) LL = L commons = Commons([l.dtype.names for l in LL]) D = {} for (i,l) in zip(Names, LL): d = {} for c in commons: if c in l.dtype.names: d[c] = c + '_' + str(i) if d: D[i] = d return D
python
def DEFAULT_RENAMER(L, Names=None): """ Renames overlapping column names of numpy ndarrays with structured dtypes Rename the columns by using a simple convention: * If `L` is a list, it will append the number in the list to the key associated with the array. * If `L` is a dictionary, the algorithm will append the string representation of the key associated with an array to the overlapping columns from that array. Default renamer function used by :func:`tabular.spreadsheet.join` **Parameters** **L** : list or dictionary Numpy recarrays with columns to be renamed. **Returns** **D** : dictionary of dictionaries Dictionary mapping each input numpy recarray to a dictionary mapping each original column name to its new name following the convention above. """ if isinstance(L,dict): Names = L.keys() LL = L.values() else: if Names == None: Names = range(len(L)) else: assert len(Names) == len(L) LL = L commons = Commons([l.dtype.names for l in LL]) D = {} for (i,l) in zip(Names, LL): d = {} for c in commons: if c in l.dtype.names: d[c] = c + '_' + str(i) if d: D[i] = d return D
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Renames overlapping column names of numpy ndarrays with structured dtypes Rename the columns by using a simple convention: * If `L` is a list, it will append the number in the list to the key associated with the array. * If `L` is a dictionary, the algorithm will append the string representation of the key associated with an array to the overlapping columns from that array. Default renamer function used by :func:`tabular.spreadsheet.join` **Parameters** **L** : list or dictionary Numpy recarrays with columns to be renamed. **Returns** **D** : dictionary of dictionaries Dictionary mapping each input numpy recarray to a dictionary mapping each original column name to its new name following the convention above.
[ "Renames", "overlapping", "column", "names", "of", "numpy", "ndarrays", "with", "structured", "dtypes" ]
1caf091c8c395960a9ad7078f95158b533cc52dd
https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/tabular/spreadsheet.py#L1520-L1571
train
emirozer/bowshock
bowshock/helioviewer.py
getjp2image
def getjp2image(date, sourceId=None, observatory=None, instrument=None, detector=None, measurement=None): ''' Helioviewer.org and JHelioviewer operate off of JPEG2000 formatted image data generated from science-quality FITS files. Use the APIs below to interact directly with these intermediary JPEG2000 files. Download a JP2 image for the specified datasource that is the closest match in time to the `date` requested. Either `sourceId` must be specified, or the combination of `observatory`, `instrument`, `detector`, and `measurement`. Request Parameters: Parameter Required Type Example Description date Required string 2014-01-01T23:59:59Z Desired date/time of the JP2 image. ISO 8601 combined UTC date and time UTC format. sourceId Optional number 14 Unique image datasource identifier. observatory Optional string SDO Observatory name. instrument Optional string AIA Instrument name. detector Optional string AIA Detector name. measurement Optional string 335 Measurement name. jpip Optional boolean false Optionally return a JPIP URI instead of the binary data of the image itself. json Optional boolean false Optionally return a JSON object. EXAMPLE: http://helioviewer.org/api/v1/getJP2Image/?date=2014-01-01T23:59:59Z&sourceId=14&jpip=true ''' base_url = 'http://helioviewer.org/api/v1/getJP2Image/?' req_url = '' try: validate_iso8601(date) if not date[-1:] == 'Z': date += 'Z' base_url += 'date=' + date except: raise ValueError( "Your date input is not in iso8601 format. ex: 2014-01-01T23:59:59") if sourceId: if not isinstance(sourceId, int): logger.error("The sourceId argument should be an int, ignoring it") else: base_url += "sourceId=" + str(sourceId) + "&" if observatory: if not isinstance(observatory, str): logger.error( "The observatory argument should be a str, ignoring it") else: base_url += "observatory=" + observatory + "&" if instrument: if not isinstance(instrument, str): logger.error( "The instrument argument should be a str, ignoring it") else: base_url += "instrument=" + instrument + "&" if detector: if not isinstance(detector, str): logger.error("The detector argument should be a str, ignoring it") else: base_url += "detector=" + detector + "&" if measurement: if not isinstance(measurement, str): logger.error( "The measurement argument should be a str, ignoring it") else: base_url += "measurement=" + detector + "&" req_url += base_url + "jpip=true" return dispatch_http_get(req_url)
python
def getjp2image(date, sourceId=None, observatory=None, instrument=None, detector=None, measurement=None): ''' Helioviewer.org and JHelioviewer operate off of JPEG2000 formatted image data generated from science-quality FITS files. Use the APIs below to interact directly with these intermediary JPEG2000 files. Download a JP2 image for the specified datasource that is the closest match in time to the `date` requested. Either `sourceId` must be specified, or the combination of `observatory`, `instrument`, `detector`, and `measurement`. Request Parameters: Parameter Required Type Example Description date Required string 2014-01-01T23:59:59Z Desired date/time of the JP2 image. ISO 8601 combined UTC date and time UTC format. sourceId Optional number 14 Unique image datasource identifier. observatory Optional string SDO Observatory name. instrument Optional string AIA Instrument name. detector Optional string AIA Detector name. measurement Optional string 335 Measurement name. jpip Optional boolean false Optionally return a JPIP URI instead of the binary data of the image itself. json Optional boolean false Optionally return a JSON object. EXAMPLE: http://helioviewer.org/api/v1/getJP2Image/?date=2014-01-01T23:59:59Z&sourceId=14&jpip=true ''' base_url = 'http://helioviewer.org/api/v1/getJP2Image/?' req_url = '' try: validate_iso8601(date) if not date[-1:] == 'Z': date += 'Z' base_url += 'date=' + date except: raise ValueError( "Your date input is not in iso8601 format. ex: 2014-01-01T23:59:59") if sourceId: if not isinstance(sourceId, int): logger.error("The sourceId argument should be an int, ignoring it") else: base_url += "sourceId=" + str(sourceId) + "&" if observatory: if not isinstance(observatory, str): logger.error( "The observatory argument should be a str, ignoring it") else: base_url += "observatory=" + observatory + "&" if instrument: if not isinstance(instrument, str): logger.error( "The instrument argument should be a str, ignoring it") else: base_url += "instrument=" + instrument + "&" if detector: if not isinstance(detector, str): logger.error("The detector argument should be a str, ignoring it") else: base_url += "detector=" + detector + "&" if measurement: if not isinstance(measurement, str): logger.error( "The measurement argument should be a str, ignoring it") else: base_url += "measurement=" + detector + "&" req_url += base_url + "jpip=true" return dispatch_http_get(req_url)
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Helioviewer.org and JHelioviewer operate off of JPEG2000 formatted image data generated from science-quality FITS files. Use the APIs below to interact directly with these intermediary JPEG2000 files. Download a JP2 image for the specified datasource that is the closest match in time to the `date` requested. Either `sourceId` must be specified, or the combination of `observatory`, `instrument`, `detector`, and `measurement`. Request Parameters: Parameter Required Type Example Description date Required string 2014-01-01T23:59:59Z Desired date/time of the JP2 image. ISO 8601 combined UTC date and time UTC format. sourceId Optional number 14 Unique image datasource identifier. observatory Optional string SDO Observatory name. instrument Optional string AIA Instrument name. detector Optional string AIA Detector name. measurement Optional string 335 Measurement name. jpip Optional boolean false Optionally return a JPIP URI instead of the binary data of the image itself. json Optional boolean false Optionally return a JSON object. EXAMPLE: http://helioviewer.org/api/v1/getJP2Image/?date=2014-01-01T23:59:59Z&sourceId=14&jpip=true
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9f5e053f1d54995b833b83616f37c67178c3e840
https://github.com/emirozer/bowshock/blob/9f5e053f1d54995b833b83616f37c67178c3e840/bowshock/helioviewer.py#L10-L85
train
hsolbrig/pyjsg
pyjsg/jsglib/loader.py
loads_loader
def loads_loader(load_module: types.ModuleType, pairs: Dict[str, str]) -> Optional[JSGValidateable]: """json loader objecthook :param load_module: Module that contains the various types :param pairs: key/value tuples (In our case, they are str/str) :return: """ cntxt = load_module._CONTEXT # If the type element is a member of the JSON, load it possible_type = pairs[cntxt.TYPE] if cntxt.TYPE in pairs else None target_class = getattr(load_module, possible_type, None) if isinstance(possible_type, str) else None if target_class: return target_class(**pairs) # See whether there are any exception types that are valid for the incoming data for type_exception in cntxt.TYPE_EXCEPTIONS: if not hasattr(load_module, type_exception): raise ValueError(UNKNOWN_TYPE_EXCEPTION.format(type_exception)) target_class = getattr(load_module, type_exception) target_strict = target_class._strict target_class._strict = False try: rval = target_class(**pairs) finally: target_class._strict = target_strict if is_valid(rval): return rval # If there is not a type variable and nothing fits, just load up the first (and perhaps only) exception # It will later fail any is_valid tests if not cntxt.TYPE and cntxt.TYPE_EXCEPTIONS: return getattr(load_module, cntxt.TYPE_EXCEPTIONS[0])(**pairs) if cntxt.TYPE in pairs: raise ValueError(f'Unknown reference type: "{cntxt.TYPE}": "{pairs[cntxt.TYPE]}"') else: raise ValueError(f'Missing "{cntxt.TYPE}" element')
python
def loads_loader(load_module: types.ModuleType, pairs: Dict[str, str]) -> Optional[JSGValidateable]: """json loader objecthook :param load_module: Module that contains the various types :param pairs: key/value tuples (In our case, they are str/str) :return: """ cntxt = load_module._CONTEXT # If the type element is a member of the JSON, load it possible_type = pairs[cntxt.TYPE] if cntxt.TYPE in pairs else None target_class = getattr(load_module, possible_type, None) if isinstance(possible_type, str) else None if target_class: return target_class(**pairs) # See whether there are any exception types that are valid for the incoming data for type_exception in cntxt.TYPE_EXCEPTIONS: if not hasattr(load_module, type_exception): raise ValueError(UNKNOWN_TYPE_EXCEPTION.format(type_exception)) target_class = getattr(load_module, type_exception) target_strict = target_class._strict target_class._strict = False try: rval = target_class(**pairs) finally: target_class._strict = target_strict if is_valid(rval): return rval # If there is not a type variable and nothing fits, just load up the first (and perhaps only) exception # It will later fail any is_valid tests if not cntxt.TYPE and cntxt.TYPE_EXCEPTIONS: return getattr(load_module, cntxt.TYPE_EXCEPTIONS[0])(**pairs) if cntxt.TYPE in pairs: raise ValueError(f'Unknown reference type: "{cntxt.TYPE}": "{pairs[cntxt.TYPE]}"') else: raise ValueError(f'Missing "{cntxt.TYPE}" element')
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9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7
https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/jsglib/loader.py#L17-L54
train
hsolbrig/pyjsg
pyjsg/jsglib/loader.py
loads
def loads(s: str, load_module: types.ModuleType, **kwargs): """ Convert a JSON string into a JSGObject :param s: string representation of JSON document :param load_module: module that contains declarations for types :param kwargs: arguments see: json.load for details :return: JSGObject representing the json string """ return json.loads(s, object_hook=lambda pairs: loads_loader(load_module, pairs), **kwargs)
python
def loads(s: str, load_module: types.ModuleType, **kwargs): """ Convert a JSON string into a JSGObject :param s: string representation of JSON document :param load_module: module that contains declarations for types :param kwargs: arguments see: json.load for details :return: JSGObject representing the json string """ return json.loads(s, object_hook=lambda pairs: loads_loader(load_module, pairs), **kwargs)
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9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7
https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/jsglib/loader.py#L57-L65
train
hsolbrig/pyjsg
pyjsg/jsglib/loader.py
load
def load(fp: Union[TextIO, str], load_module: types.ModuleType, **kwargs): """ Convert a file name or file-like object containing stringified JSON into a JSGObject :param fp: file-like object to deserialize :param load_module: module that contains declarations for types :param kwargs: arguments see: json.load for details :return: JSGObject representing the json string """ if isinstance(fp, str): with open(fp) as f: return loads(f.read(), load_module, **kwargs) else: return loads(fp.read(), load_module, **kwargs)
python
def load(fp: Union[TextIO, str], load_module: types.ModuleType, **kwargs): """ Convert a file name or file-like object containing stringified JSON into a JSGObject :param fp: file-like object to deserialize :param load_module: module that contains declarations for types :param kwargs: arguments see: json.load for details :return: JSGObject representing the json string """ if isinstance(fp, str): with open(fp) as f: return loads(f.read(), load_module, **kwargs) else: return loads(fp.read(), load_module, **kwargs)
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9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7
https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/jsglib/loader.py#L68-L80
train
hsolbrig/pyjsg
pyjsg/jsglib/loader.py
isinstance_
def isinstance_(x, A_tuple): """ native isinstance_ with the test for typing.Union overridden """ if is_union(A_tuple): return any(isinstance_(x, t) for t in A_tuple.__args__) elif getattr(A_tuple, '__origin__', None) is not None: return isinstance(x, A_tuple.__origin__) else: return isinstance(x, A_tuple)
python
def isinstance_(x, A_tuple): """ native isinstance_ with the test for typing.Union overridden """ if is_union(A_tuple): return any(isinstance_(x, t) for t in A_tuple.__args__) elif getattr(A_tuple, '__origin__', None) is not None: return isinstance(x, A_tuple.__origin__) else: return isinstance(x, A_tuple)
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9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7
https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/jsglib/loader.py#L83-L90
train
hsolbrig/pyjsg
pyjsg/jsglib/loader.py
is_valid
def is_valid(obj: JSGValidateable, log: Optional[Union[TextIO, Logger]] = None) -> bool: """ Determine whether obj is valid :param obj: Object to validate :param log: Logger to record validation failures. If absent, no information is recorded """ return obj._is_valid(log)
python
def is_valid(obj: JSGValidateable, log: Optional[Union[TextIO, Logger]] = None) -> bool: """ Determine whether obj is valid :param obj: Object to validate :param log: Logger to record validation failures. If absent, no information is recorded """ return obj._is_valid(log)
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9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7
https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/jsglib/loader.py#L93-L99
train
cydrobolt/pifx
pifx/util.py
arg_tup_to_dict
def arg_tup_to_dict(argument_tuples): """Given a set of argument tuples, set their value in a data dictionary if not blank""" data = dict() for arg_name, arg_val in argument_tuples: if arg_val is not None: if arg_val is True: arg_val = 'true' elif arg_val is False: arg_val = 'false' data[arg_name] = arg_val return data
python
def arg_tup_to_dict(argument_tuples): """Given a set of argument tuples, set their value in a data dictionary if not blank""" data = dict() for arg_name, arg_val in argument_tuples: if arg_val is not None: if arg_val is True: arg_val = 'true' elif arg_val is False: arg_val = 'false' data[arg_name] = arg_val return data
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c9de9c2695c3e6e72de4aa0de47b78fc13c457c3
https://github.com/cydrobolt/pifx/blob/c9de9c2695c3e6e72de4aa0de47b78fc13c457c3/pifx/util.py#L32-L43
train
cydrobolt/pifx
pifx/util.py
handle_error
def handle_error(response): """Raise appropriate exceptions if necessary.""" status_code = response.status_code if status_code not in A_OK_HTTP_CODES: error_explanation = A_ERROR_HTTP_CODES.get(status_code) raise_error = "{}: {}".format(status_code, error_explanation) raise Exception(raise_error) else: return True
python
def handle_error(response): """Raise appropriate exceptions if necessary.""" status_code = response.status_code if status_code not in A_OK_HTTP_CODES: error_explanation = A_ERROR_HTTP_CODES.get(status_code) raise_error = "{}: {}".format(status_code, error_explanation) raise Exception(raise_error) else: return True
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Raise appropriate exceptions if necessary.
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c9de9c2695c3e6e72de4aa0de47b78fc13c457c3
https://github.com/cydrobolt/pifx/blob/c9de9c2695c3e6e72de4aa0de47b78fc13c457c3/pifx/util.py#L54-L63
train
PSPC-SPAC-buyandsell/von_agent
von_agent/agent/base.py
_BaseAgent.open
async def open(self) -> '_BaseAgent': """ Context manager entry; open wallet. For use when keeping agent open across multiple calls. :return: current object """ LOGGER.debug('_BaseAgent.open >>>') # Do not open pool independently: let relying party decide when to go on-line and off-line await self.wallet.open() LOGGER.debug('_BaseAgent.open <<<') return self
python
async def open(self) -> '_BaseAgent': """ Context manager entry; open wallet. For use when keeping agent open across multiple calls. :return: current object """ LOGGER.debug('_BaseAgent.open >>>') # Do not open pool independently: let relying party decide when to go on-line and off-line await self.wallet.open() LOGGER.debug('_BaseAgent.open <<<') return self
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0b1c17cca3bd178b6e6974af84dbac1dfce5cf45
https://github.com/PSPC-SPAC-buyandsell/von_agent/blob/0b1c17cca3bd178b6e6974af84dbac1dfce5cf45/von_agent/agent/base.py#L129-L143
train
PSPC-SPAC-buyandsell/von_agent
von_agent/agent/base.py
_BaseAgent._get_rev_reg_def
async def _get_rev_reg_def(self, rr_id: str) -> str: """ Get revocation registry definition from ledger by its identifier. Raise AbsentRevReg for no such revocation registry, logging any error condition and raising BadLedgerTxn on bad request. Retrieve the revocation registry definition from the agent's revocation cache if it has it; cache it en passant if it does not (and such a revocation registry definition exists on the ledger). :param rr_id: (revocation registry) identifier string, of the format '<issuer-did>:4:<issuer-did>:3:CL:<schema-seq-no>:<tag>:CL_ACCUM:<tag>' :return: revocation registry definition json as retrieved from ledger """ LOGGER.debug('_BaseAgent._get_rev_reg_def >>> rr_id: %s', rr_id) rv_json = json.dumps({}) with REVO_CACHE.lock: revo_cache_entry = REVO_CACHE.get(rr_id, None) rr_def = revo_cache_entry.rev_reg_def if revo_cache_entry else None if rr_def: LOGGER.info('_BaseAgent._get_rev_reg_def: rev reg def for %s from cache', rr_id) rv_json = json.dumps(rr_def) else: get_rrd_req_json = await ledger.build_get_revoc_reg_def_request(self.did, rr_id) resp_json = await self._submit(get_rrd_req_json) try: (_, rv_json) = await ledger.parse_get_revoc_reg_def_response(resp_json) rr_def = json.loads(rv_json) except IndyError: # ledger replied, but there is no such rev reg LOGGER.debug('_BaseAgent._get_rev_reg_def: <!< no rev reg exists on %s', rr_id) raise AbsentRevReg('No rev reg exists on {}'.format(rr_id)) if revo_cache_entry is None: REVO_CACHE[rr_id] = RevoCacheEntry(rr_def, None) else: REVO_CACHE[rr_id].rev_reg_def = rr_def LOGGER.debug('_BaseAgent._get_rev_reg_def <<< %s', rv_json) return rv_json
python
async def _get_rev_reg_def(self, rr_id: str) -> str: """ Get revocation registry definition from ledger by its identifier. Raise AbsentRevReg for no such revocation registry, logging any error condition and raising BadLedgerTxn on bad request. Retrieve the revocation registry definition from the agent's revocation cache if it has it; cache it en passant if it does not (and such a revocation registry definition exists on the ledger). :param rr_id: (revocation registry) identifier string, of the format '<issuer-did>:4:<issuer-did>:3:CL:<schema-seq-no>:<tag>:CL_ACCUM:<tag>' :return: revocation registry definition json as retrieved from ledger """ LOGGER.debug('_BaseAgent._get_rev_reg_def >>> rr_id: %s', rr_id) rv_json = json.dumps({}) with REVO_CACHE.lock: revo_cache_entry = REVO_CACHE.get(rr_id, None) rr_def = revo_cache_entry.rev_reg_def if revo_cache_entry else None if rr_def: LOGGER.info('_BaseAgent._get_rev_reg_def: rev reg def for %s from cache', rr_id) rv_json = json.dumps(rr_def) else: get_rrd_req_json = await ledger.build_get_revoc_reg_def_request(self.did, rr_id) resp_json = await self._submit(get_rrd_req_json) try: (_, rv_json) = await ledger.parse_get_revoc_reg_def_response(resp_json) rr_def = json.loads(rv_json) except IndyError: # ledger replied, but there is no such rev reg LOGGER.debug('_BaseAgent._get_rev_reg_def: <!< no rev reg exists on %s', rr_id) raise AbsentRevReg('No rev reg exists on {}'.format(rr_id)) if revo_cache_entry is None: REVO_CACHE[rr_id] = RevoCacheEntry(rr_def, None) else: REVO_CACHE[rr_id].rev_reg_def = rr_def LOGGER.debug('_BaseAgent._get_rev_reg_def <<< %s', rv_json) return rv_json
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Get revocation registry definition from ledger by its identifier. Raise AbsentRevReg for no such revocation registry, logging any error condition and raising BadLedgerTxn on bad request. Retrieve the revocation registry definition from the agent's revocation cache if it has it; cache it en passant if it does not (and such a revocation registry definition exists on the ledger). :param rr_id: (revocation registry) identifier string, of the format '<issuer-did>:4:<issuer-did>:3:CL:<schema-seq-no>:<tag>:CL_ACCUM:<tag>' :return: revocation registry definition json as retrieved from ledger
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0b1c17cca3bd178b6e6974af84dbac1dfce5cf45
https://github.com/PSPC-SPAC-buyandsell/von_agent/blob/0b1c17cca3bd178b6e6974af84dbac1dfce5cf45/von_agent/agent/base.py#L289-L329
train
PSPC-SPAC-buyandsell/von_agent
von_agent/agent/base.py
_BaseAgent.get_cred_def
async def get_cred_def(self, cd_id: str) -> str: """ Get credential definition from ledger by its identifier. Raise AbsentCredDef for no such credential definition, logging any error condition and raising BadLedgerTxn on bad request. Raise ClosedPool if cred def not in cache and pool is closed. Retrieve the credential definition from the agent's credential definition cache if it has it; cache it en passant if it does not (and if there is a corresponding credential definition on the ledger). :param cd_id: (credential definition) identifier string ('<issuer-did>:3:CL:<schema-seq-no>:<tag>') :return: credential definition json as retrieved from ledger, empty production for no such cred def """ LOGGER.debug('_BaseAgent.get_cred_def >>> cd_id: %s', cd_id) rv_json = json.dumps({}) with CRED_DEF_CACHE.lock: if cd_id in CRED_DEF_CACHE: LOGGER.info('_BaseAgent.get_cred_def: got cred def for %s from cache', cd_id) rv_json = json.dumps(CRED_DEF_CACHE[cd_id]) LOGGER.debug('_BaseAgent.get_cred_def <<< %s', rv_json) return rv_json req_json = await ledger.build_get_cred_def_request(self.did, cd_id) resp_json = await self._submit(req_json) resp = json.loads(resp_json) if not ('result' in resp and resp['result'].get('data', None)): LOGGER.debug('_BaseAgent.get_cred_def: <!< no cred def exists on %s', cd_id) raise AbsentCredDef('No cred def exists on {}'.format(cd_id)) try: (_, rv_json) = await ledger.parse_get_cred_def_response(resp_json) except IndyError: # ledger replied, but there is no such cred def LOGGER.debug('_BaseAgent.get_cred_def: <!< no cred def exists on %s', cd_id) raise AbsentCredDef('No cred def exists on {}'.format(cd_id)) CRED_DEF_CACHE[cd_id] = json.loads(rv_json) LOGGER.info('_BaseAgent.get_cred_def: got cred def %s from ledger', cd_id) LOGGER.debug('_BaseAgent.get_cred_def <<< %s', rv_json) return rv_json
python
async def get_cred_def(self, cd_id: str) -> str: """ Get credential definition from ledger by its identifier. Raise AbsentCredDef for no such credential definition, logging any error condition and raising BadLedgerTxn on bad request. Raise ClosedPool if cred def not in cache and pool is closed. Retrieve the credential definition from the agent's credential definition cache if it has it; cache it en passant if it does not (and if there is a corresponding credential definition on the ledger). :param cd_id: (credential definition) identifier string ('<issuer-did>:3:CL:<schema-seq-no>:<tag>') :return: credential definition json as retrieved from ledger, empty production for no such cred def """ LOGGER.debug('_BaseAgent.get_cred_def >>> cd_id: %s', cd_id) rv_json = json.dumps({}) with CRED_DEF_CACHE.lock: if cd_id in CRED_DEF_CACHE: LOGGER.info('_BaseAgent.get_cred_def: got cred def for %s from cache', cd_id) rv_json = json.dumps(CRED_DEF_CACHE[cd_id]) LOGGER.debug('_BaseAgent.get_cred_def <<< %s', rv_json) return rv_json req_json = await ledger.build_get_cred_def_request(self.did, cd_id) resp_json = await self._submit(req_json) resp = json.loads(resp_json) if not ('result' in resp and resp['result'].get('data', None)): LOGGER.debug('_BaseAgent.get_cred_def: <!< no cred def exists on %s', cd_id) raise AbsentCredDef('No cred def exists on {}'.format(cd_id)) try: (_, rv_json) = await ledger.parse_get_cred_def_response(resp_json) except IndyError: # ledger replied, but there is no such cred def LOGGER.debug('_BaseAgent.get_cred_def: <!< no cred def exists on %s', cd_id) raise AbsentCredDef('No cred def exists on {}'.format(cd_id)) CRED_DEF_CACHE[cd_id] = json.loads(rv_json) LOGGER.info('_BaseAgent.get_cred_def: got cred def %s from ledger', cd_id) LOGGER.debug('_BaseAgent.get_cred_def <<< %s', rv_json) return rv_json
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Get credential definition from ledger by its identifier. Raise AbsentCredDef for no such credential definition, logging any error condition and raising BadLedgerTxn on bad request. Raise ClosedPool if cred def not in cache and pool is closed. Retrieve the credential definition from the agent's credential definition cache if it has it; cache it en passant if it does not (and if there is a corresponding credential definition on the ledger). :param cd_id: (credential definition) identifier string ('<issuer-did>:3:CL:<schema-seq-no>:<tag>') :return: credential definition json as retrieved from ledger, empty production for no such cred def
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0b1c17cca3bd178b6e6974af84dbac1dfce5cf45
https://github.com/PSPC-SPAC-buyandsell/von_agent/blob/0b1c17cca3bd178b6e6974af84dbac1dfce5cf45/von_agent/agent/base.py#L331-L371
train
hsolbrig/pyjsg
pyjsg/jsglib/typing_patch_37.py
is_union
def is_union(etype) -> bool: """ Determine whether etype is a Union """ return getattr(etype, '__origin__', None) is not None and \ getattr(etype.__origin__, '_name', None) and\ etype.__origin__._name == 'Union'
python
def is_union(etype) -> bool: """ Determine whether etype is a Union """ return getattr(etype, '__origin__', None) is not None and \ getattr(etype.__origin__, '_name', None) and\ etype.__origin__._name == 'Union'
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Determine whether etype is a Union
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9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7
https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/jsglib/typing_patch_37.py#L13-L17
train
CybOXProject/mixbox
mixbox/fields.py
unset
def unset(entity, *types): """Unset the TypedFields on the input `entity`. Args: entity: A mixbox.Entity object. *types: A variable-length list of TypedField subclasses. If not provided, defaults to TypedField. """ if not types: types = (TypedField,) fields = list(entity._fields.keys()) remove = (x for x in fields if isinstance(x, types)) for field in remove: del entity._fields[field]
python
def unset(entity, *types): """Unset the TypedFields on the input `entity`. Args: entity: A mixbox.Entity object. *types: A variable-length list of TypedField subclasses. If not provided, defaults to TypedField. """ if not types: types = (TypedField,) fields = list(entity._fields.keys()) remove = (x for x in fields if isinstance(x, types)) for field in remove: del entity._fields[field]
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Unset the TypedFields on the input `entity`. Args: entity: A mixbox.Entity object. *types: A variable-length list of TypedField subclasses. If not provided, defaults to TypedField.
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9097dae7a433f5b98c18171c4a5598f69a7d30af
https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/fields.py#L17-L32
train
CybOXProject/mixbox
mixbox/fields.py
_matches
def _matches(field, params): """Return True if the input TypedField `field` contains instance attributes that match the input parameters. Args: field: A TypedField instance. params: A dictionary of TypedField instance attribute-to-value mappings. Returns: True if the input TypedField matches the input parameters. """ fieldattrs = six.iteritems(params) return all(getattr(field, attr) == val for attr, val in fieldattrs)
python
def _matches(field, params): """Return True if the input TypedField `field` contains instance attributes that match the input parameters. Args: field: A TypedField instance. params: A dictionary of TypedField instance attribute-to-value mappings. Returns: True if the input TypedField matches the input parameters. """ fieldattrs = six.iteritems(params) return all(getattr(field, attr) == val for attr, val in fieldattrs)
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Return True if the input TypedField `field` contains instance attributes that match the input parameters. Args: field: A TypedField instance. params: A dictionary of TypedField instance attribute-to-value mappings. Returns: True if the input TypedField matches the input parameters.
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9097dae7a433f5b98c18171c4a5598f69a7d30af
https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/fields.py#L35-L47
train
CybOXProject/mixbox
mixbox/fields.py
iterfields
def iterfields(klass): """Iterate over the input class members and yield its TypedFields. Args: klass: A class (usually an Entity subclass). Yields: (class attribute name, TypedField instance) tuples. """ is_field = lambda x: isinstance(x, TypedField) for name, field in inspect.getmembers(klass, predicate=is_field): yield name, field
python
def iterfields(klass): """Iterate over the input class members and yield its TypedFields. Args: klass: A class (usually an Entity subclass). Yields: (class attribute name, TypedField instance) tuples. """ is_field = lambda x: isinstance(x, TypedField) for name, field in inspect.getmembers(klass, predicate=is_field): yield name, field
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Iterate over the input class members and yield its TypedFields. Args: klass: A class (usually an Entity subclass). Yields: (class attribute name, TypedField instance) tuples.
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9097dae7a433f5b98c18171c4a5598f69a7d30af
https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/fields.py#L50-L62
train
CybOXProject/mixbox
mixbox/fields.py
TypedField._clean
def _clean(self, value): """Validate and clean a candidate value for this field.""" if value is None: return None elif self.type_ is None: return value elif self.check_type(value): return value elif self.is_type_castable: # noqa return self.type_(value) error_fmt = "%s must be a %s, not a %s" error = error_fmt % (self.name, self.type_, type(value)) raise TypeError(error)
python
def _clean(self, value): """Validate and clean a candidate value for this field.""" if value is None: return None elif self.type_ is None: return value elif self.check_type(value): return value elif self.is_type_castable: # noqa return self.type_(value) error_fmt = "%s must be a %s, not a %s" error = error_fmt % (self.name, self.type_, type(value)) raise TypeError(error)
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Validate and clean a candidate value for this field.
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9097dae7a433f5b98c18171c4a5598f69a7d30af
https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/fields.py#L177-L190
train
OpenTreeOfLife/peyotl
peyotl/collections_store/git_actions.py
TreeCollectionsGitAction.remove_collection
def remove_collection(self, first_arg, sec_arg, third_arg, fourth_arg=None, commit_msg=None): """Remove a collection Given a collection_id, branch and optionally an author, remove a collection on the given branch and attribute the commit to author. Returns the SHA of the commit on branch. """ if fourth_arg is None: collection_id, branch_name, author = first_arg, sec_arg, third_arg gh_user = branch_name.split('_collection_')[0] parent_sha = self.get_master_sha() else: gh_user, collection_id, parent_sha, author = first_arg, sec_arg, third_arg, fourth_arg if commit_msg is None: commit_msg = "Delete Collection '%s' via OpenTree API" % collection_id return self._remove_document(gh_user, collection_id, parent_sha, author, commit_msg)
python
def remove_collection(self, first_arg, sec_arg, third_arg, fourth_arg=None, commit_msg=None): """Remove a collection Given a collection_id, branch and optionally an author, remove a collection on the given branch and attribute the commit to author. Returns the SHA of the commit on branch. """ if fourth_arg is None: collection_id, branch_name, author = first_arg, sec_arg, third_arg gh_user = branch_name.split('_collection_')[0] parent_sha = self.get_master_sha() else: gh_user, collection_id, parent_sha, author = first_arg, sec_arg, third_arg, fourth_arg if commit_msg is None: commit_msg = "Delete Collection '%s' via OpenTree API" % collection_id return self._remove_document(gh_user, collection_id, parent_sha, author, commit_msg)
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Remove a collection Given a collection_id, branch and optionally an author, remove a collection on the given branch and attribute the commit to author. Returns the SHA of the commit on branch.
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/collections_store/git_actions.py#L92-L107
train
PSPC-SPAC-buyandsell/von_agent
von_agent/agent/verifier.py
Verifier.load_cache
async def load_cache(self, archive: bool = False) -> int: """ Load caches and archive enough to go offline and be able to verify proof on content marked of interest in configuration. Return timestamp (epoch seconds) of cache load event, also used as subdirectory for cache archives. :param archive: whether to archive caches to disk :return: cache load event timestamp (epoch seconds) """ LOGGER.debug('Verifier.load_cache >>> archive: %s', archive) rv = int(time()) for s_id in self.cfg.get('archive-on-close', {}).get('schema_id', {}): with SCHEMA_CACHE.lock: await self.get_schema(s_id) for cd_id in self.cfg.get('archive-on-close', {}).get('cred_def_id', {}): with CRED_DEF_CACHE.lock: await self.get_cred_def(cd_id) for rr_id in self.cfg.get('archive-on-close', {}).get('rev_reg_id', {}): await self._get_rev_reg_def(rr_id) with REVO_CACHE.lock: revo_cache_entry = REVO_CACHE.get(rr_id, None) if revo_cache_entry: try: await revo_cache_entry.get_state_json(self._build_rr_state_json, rv, rv) except ClosedPool: LOGGER.warning( 'Verifier %s is offline from pool %s, cannot update revo cache reg state for %s to %s', self.wallet.name, self.pool.name, rr_id, rv) if archive: Caches.archive(self.dir_cache) LOGGER.debug('Verifier.load_cache <<< %s', rv) return rv
python
async def load_cache(self, archive: bool = False) -> int: """ Load caches and archive enough to go offline and be able to verify proof on content marked of interest in configuration. Return timestamp (epoch seconds) of cache load event, also used as subdirectory for cache archives. :param archive: whether to archive caches to disk :return: cache load event timestamp (epoch seconds) """ LOGGER.debug('Verifier.load_cache >>> archive: %s', archive) rv = int(time()) for s_id in self.cfg.get('archive-on-close', {}).get('schema_id', {}): with SCHEMA_CACHE.lock: await self.get_schema(s_id) for cd_id in self.cfg.get('archive-on-close', {}).get('cred_def_id', {}): with CRED_DEF_CACHE.lock: await self.get_cred_def(cd_id) for rr_id in self.cfg.get('archive-on-close', {}).get('rev_reg_id', {}): await self._get_rev_reg_def(rr_id) with REVO_CACHE.lock: revo_cache_entry = REVO_CACHE.get(rr_id, None) if revo_cache_entry: try: await revo_cache_entry.get_state_json(self._build_rr_state_json, rv, rv) except ClosedPool: LOGGER.warning( 'Verifier %s is offline from pool %s, cannot update revo cache reg state for %s to %s', self.wallet.name, self.pool.name, rr_id, rv) if archive: Caches.archive(self.dir_cache) LOGGER.debug('Verifier.load_cache <<< %s', rv) return rv
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0b1c17cca3bd178b6e6974af84dbac1dfce5cf45
https://github.com/PSPC-SPAC-buyandsell/von_agent/blob/0b1c17cca3bd178b6e6974af84dbac1dfce5cf45/von_agent/agent/verifier.py#L165-L204
train
inveniosoftware/invenio-communities
invenio_communities/permissions.py
_Permission.can
def can(self): """Grant permission if owner or admin.""" return str(current_user.get_id()) == str(self.community.id_user) or \ DynamicPermission(ActionNeed('admin-access')).can()
python
def can(self): """Grant permission if owner or admin.""" return str(current_user.get_id()) == str(self.community.id_user) or \ DynamicPermission(ActionNeed('admin-access')).can()
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Grant permission if owner or admin.
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/permissions.py#L46-L49
train
yamins81/tabular
tabular/utils.py
listunion
def listunion(ListOfLists): """ Take the union of a list of lists. Take a Python list of Python lists:: [[l11,l12, ...], [l21,l22, ...], ... , [ln1, ln2, ...]] and return the aggregated list:: [l11,l12, ..., l21, l22 , ...] For a list of two lists, e.g. `[a, b]`, this is like:: a.extend(b) **Parameters** **ListOfLists** : Python list Python list of Python lists. **Returns** **u** : Python list Python list created by taking the union of the lists in `ListOfLists`. """ u = [] for s in ListOfLists: if s != None: u.extend(s) return u
python
def listunion(ListOfLists): """ Take the union of a list of lists. Take a Python list of Python lists:: [[l11,l12, ...], [l21,l22, ...], ... , [ln1, ln2, ...]] and return the aggregated list:: [l11,l12, ..., l21, l22 , ...] For a list of two lists, e.g. `[a, b]`, this is like:: a.extend(b) **Parameters** **ListOfLists** : Python list Python list of Python lists. **Returns** **u** : Python list Python list created by taking the union of the lists in `ListOfLists`. """ u = [] for s in ListOfLists: if s != None: u.extend(s) return u
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Take the union of a list of lists. Take a Python list of Python lists:: [[l11,l12, ...], [l21,l22, ...], ... , [ln1, ln2, ...]] and return the aggregated list:: [l11,l12, ..., l21, l22 , ...] For a list of two lists, e.g. `[a, b]`, this is like:: a.extend(b) **Parameters** **ListOfLists** : Python list Python list of Python lists. **Returns** **u** : Python list Python list created by taking the union of the lists in `ListOfLists`.
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1caf091c8c395960a9ad7078f95158b533cc52dd
https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/tabular/utils.py#L49-L83
train
yamins81/tabular
tabular/utils.py
DEFAULT_NULLVALUE
def DEFAULT_NULLVALUE(test): """ Returns a null value for each of various kinds of test values. **Parameters** **test** : bool, int, float or string Value to test. **Returns** **null** : element in `[False, 0, 0.0, '']` Null value corresponding to the given test value: * if `test` is a `bool`, return `False` * else if `test` is an `int`, return `0` * else if `test` is a `float`, return `0.0` * else `test` is a `str`, return `''` """ return False if isinstance(test,bool) \ else 0 if isinstance(test,int) \ else 0.0 if isinstance(test,float) \ else ''
python
def DEFAULT_NULLVALUE(test): """ Returns a null value for each of various kinds of test values. **Parameters** **test** : bool, int, float or string Value to test. **Returns** **null** : element in `[False, 0, 0.0, '']` Null value corresponding to the given test value: * if `test` is a `bool`, return `False` * else if `test` is an `int`, return `0` * else if `test` is a `float`, return `0.0` * else `test` is a `str`, return `''` """ return False if isinstance(test,bool) \ else 0 if isinstance(test,int) \ else 0.0 if isinstance(test,float) \ else ''
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1caf091c8c395960a9ad7078f95158b533cc52dd
https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/tabular/utils.py#L369-L394
train
hsolbrig/pyjsg
pyjsg/parser_impl/jsg_objectexpr_parser.py
JSGObjectExpr.as_python
def as_python(self, name: str) -> str: """ Return the python representation of the class represented by this object """ if self._map_valuetype: return self.map_as_python(name) else: return self.obj_as_python(name)
python
def as_python(self, name: str) -> str: """ Return the python representation of the class represented by this object """ if self._map_valuetype: return self.map_as_python(name) else: return self.obj_as_python(name)
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Return the python representation of the class represented by this object
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9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7
https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/jsg_objectexpr_parser.py#L87-L92
train
hsolbrig/pyjsg
pyjsg/parser_impl/jsg_objectexpr_parser.py
JSGObjectExpr.members_entries
def members_entries(self, all_are_optional: bool=False) -> List[Tuple[str, str]]: """ Return an ordered list of elements for the _members section :param all_are_optional: True means we're in a choice situation so everything is optional :return: """ rval = [] if self._members: for member in self._members: rval += member.members_entries(all_are_optional) elif self._choices: for choice in self._choices: rval += self._context.reference(choice).members_entries(True) else: return [] return rval
python
def members_entries(self, all_are_optional: bool=False) -> List[Tuple[str, str]]: """ Return an ordered list of elements for the _members section :param all_are_optional: True means we're in a choice situation so everything is optional :return: """ rval = [] if self._members: for member in self._members: rval += member.members_entries(all_are_optional) elif self._choices: for choice in self._choices: rval += self._context.reference(choice).members_entries(True) else: return [] return rval
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Return an ordered list of elements for the _members section :param all_are_optional: True means we're in a choice situation so everything is optional :return:
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9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7
https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/jsg_objectexpr_parser.py#L196-L211
train
OpenTreeOfLife/peyotl
peyotl/phylesystem/phylesystem_shard.py
_get_filtered_study_ids
def _get_filtered_study_ids(shard, include_aliases=False): """Optionally filters out aliases from standard doc-id list""" from peyotl.phylesystem.helper import DIGIT_PATTERN k = shard.get_doc_ids() if shard.has_aliases and (not include_aliases): x = [] for i in k: if DIGIT_PATTERN.match(i) or ((len(i) > 1) and (i[-2] == '_')): pass else: x.append(i) return x
python
def _get_filtered_study_ids(shard, include_aliases=False): """Optionally filters out aliases from standard doc-id list""" from peyotl.phylesystem.helper import DIGIT_PATTERN k = shard.get_doc_ids() if shard.has_aliases and (not include_aliases): x = [] for i in k: if DIGIT_PATTERN.match(i) or ((len(i) > 1) and (i[-2] == '_')): pass else: x.append(i) return x
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/phylesystem/phylesystem_shard.py#L18-L29
train
OpenTreeOfLife/peyotl
peyotl/phylesystem/phylesystem_shard.py
PhylesystemShard._determine_next_study_id
def _determine_next_study_id(self): """Return the numeric part of the newest study_id Checks out master branch as a side effect! """ if self._doc_counter_lock is None: self._doc_counter_lock = Lock() prefix = self._new_study_prefix lp = len(prefix) n = 0 # this function holds the lock for quite awhile, # but it only called on the first instance of # of creating a new study with self._doc_counter_lock: with self._index_lock: for k in self.study_index.keys(): if k.startswith(prefix): try: pn = int(k[lp:]) if pn > n: n = pn except: pass nsi_contents = self._read_master_branch_resource(self._id_minting_file, is_json=True) if nsi_contents: self._next_study_id = nsi_contents['next_study_id'] if self._next_study_id <= n: m = 'next_study_id in {} is set lower than the ID of an existing study!' m = m.format(self._id_minting_file) raise RuntimeError(m) else: # legacy support for repo with no next_study_id.json file self._next_study_id = n self._advance_new_study_id()
python
def _determine_next_study_id(self): """Return the numeric part of the newest study_id Checks out master branch as a side effect! """ if self._doc_counter_lock is None: self._doc_counter_lock = Lock() prefix = self._new_study_prefix lp = len(prefix) n = 0 # this function holds the lock for quite awhile, # but it only called on the first instance of # of creating a new study with self._doc_counter_lock: with self._index_lock: for k in self.study_index.keys(): if k.startswith(prefix): try: pn = int(k[lp:]) if pn > n: n = pn except: pass nsi_contents = self._read_master_branch_resource(self._id_minting_file, is_json=True) if nsi_contents: self._next_study_id = nsi_contents['next_study_id'] if self._next_study_id <= n: m = 'next_study_id in {} is set lower than the ID of an existing study!' m = m.format(self._id_minting_file) raise RuntimeError(m) else: # legacy support for repo with no next_study_id.json file self._next_study_id = n self._advance_new_study_id()
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/phylesystem/phylesystem_shard.py#L246-L279
train
OpenTreeOfLife/peyotl
peyotl/phylesystem/phylesystem_shard.py
PhylesystemShard._advance_new_study_id
def _advance_new_study_id(self): """ ASSUMES the caller holds the _doc_counter_lock ! Returns the current numeric part of the next study ID, advances the counter to the next value, and stores that value in the file in case the server is restarted. """ c = self._next_study_id self._next_study_id = 1 + c content = u'{"next_study_id": %d}\n' % self._next_study_id # The content is JSON, but we hand-rolled the string above # so that we can use it as a commit_msg self._write_master_branch_resource(content, self._id_minting_file, commit_msg=content, is_json=False) return c
python
def _advance_new_study_id(self): """ ASSUMES the caller holds the _doc_counter_lock ! Returns the current numeric part of the next study ID, advances the counter to the next value, and stores that value in the file in case the server is restarted. """ c = self._next_study_id self._next_study_id = 1 + c content = u'{"next_study_id": %d}\n' % self._next_study_id # The content is JSON, but we hand-rolled the string above # so that we can use it as a commit_msg self._write_master_branch_resource(content, self._id_minting_file, commit_msg=content, is_json=False) return c
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ASSUMES the caller holds the _doc_counter_lock ! Returns the current numeric part of the next study ID, advances the counter to the next value, and stores that value in the file in case the server is restarted.
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/phylesystem/phylesystem_shard.py#L281-L296
train
hsolbrig/pyjsg
pyjsg/parser_impl/parser_utils.py
flatten
def flatten(l: Iterable) -> List: """Return a list of all non-list items in l :param l: list to be flattened :return: """ rval = [] for e in l: if not isinstance(e, str) and isinstance(e, Iterable): if len(list(e)): rval += flatten(e) else: rval.append(e) return rval
python
def flatten(l: Iterable) -> List: """Return a list of all non-list items in l :param l: list to be flattened :return: """ rval = [] for e in l: if not isinstance(e, str) and isinstance(e, Iterable): if len(list(e)): rval += flatten(e) else: rval.append(e) return rval
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Return a list of all non-list items in l :param l: list to be flattened :return:
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9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7
https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/parser_utils.py#L14-L27
train
hsolbrig/pyjsg
pyjsg/parser_impl/parser_utils.py
flatten_unique
def flatten_unique(l: Iterable) -> List: """ Return a list of UNIQUE non-list items in l """ rval = OrderedDict() for e in l: if not isinstance(e, str) and isinstance(e, Iterable): for ev in flatten_unique(e): rval[ev] = None else: rval[e] = None return list(rval.keys())
python
def flatten_unique(l: Iterable) -> List: """ Return a list of UNIQUE non-list items in l """ rval = OrderedDict() for e in l: if not isinstance(e, str) and isinstance(e, Iterable): for ev in flatten_unique(e): rval[ev] = None else: rval[e] = None return list(rval.keys())
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Return a list of UNIQUE non-list items in l
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9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7
https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/parser_utils.py#L30-L39
train
hsolbrig/pyjsg
pyjsg/parser_impl/parser_utils.py
as_tokens
def as_tokens(ctx: List[ParserRuleContext]) -> List[str]: """Return a stringified list of identifiers in ctx :param ctx: JSG parser item with a set of identifiers :return: """ return [as_token(e) for e in ctx]
python
def as_tokens(ctx: List[ParserRuleContext]) -> List[str]: """Return a stringified list of identifiers in ctx :param ctx: JSG parser item with a set of identifiers :return: """ return [as_token(e) for e in ctx]
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Return a stringified list of identifiers in ctx :param ctx: JSG parser item with a set of identifiers :return:
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9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7
https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/parser_utils.py#L85-L91
train
hsolbrig/pyjsg
pyjsg/parser_impl/parser_utils.py
is_valid_python
def is_valid_python(tkn: str) -> bool: """Determine whether tkn is a valid python identifier :param tkn: :return: """ try: root = ast.parse(tkn) except SyntaxError: return False return len(root.body) == 1 and isinstance(root.body[0], ast.Expr) and isinstance(root.body[0].value, ast.Name)
python
def is_valid_python(tkn: str) -> bool: """Determine whether tkn is a valid python identifier :param tkn: :return: """ try: root = ast.parse(tkn) except SyntaxError: return False return len(root.body) == 1 and isinstance(root.body[0], ast.Expr) and isinstance(root.body[0].value, ast.Name)
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Determine whether tkn is a valid python identifier :param tkn: :return:
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9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7
https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/parser_utils.py#L94-L104
train
OpenTreeOfLife/peyotl
peyotl/phylesystem/git_actions.py
PhylesystemGitAction.remove_study
def remove_study(self, first_arg, sec_arg, third_arg, fourth_arg=None, commit_msg=None): """Remove a study Given a study_id, branch and optionally an author, remove a study on the given branch and attribute the commit to author. Returns the SHA of the commit on branch. """ if fourth_arg is None: study_id, branch_name, author = first_arg, sec_arg, third_arg gh_user = branch_name.split('_study_')[0] parent_sha = self.get_master_sha() else: gh_user, study_id, parent_sha, author = first_arg, sec_arg, third_arg, fourth_arg if commit_msg is None: commit_msg = "Delete Study #%s via OpenTree API" % study_id return self._remove_document(gh_user, study_id, parent_sha, author, commit_msg)
python
def remove_study(self, first_arg, sec_arg, third_arg, fourth_arg=None, commit_msg=None): """Remove a study Given a study_id, branch and optionally an author, remove a study on the given branch and attribute the commit to author. Returns the SHA of the commit on branch. """ if fourth_arg is None: study_id, branch_name, author = first_arg, sec_arg, third_arg gh_user = branch_name.split('_study_')[0] parent_sha = self.get_master_sha() else: gh_user, study_id, parent_sha, author = first_arg, sec_arg, third_arg, fourth_arg if commit_msg is None: commit_msg = "Delete Study #%s via OpenTree API" % study_id return self._remove_document(gh_user, study_id, parent_sha, author, commit_msg)
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Remove a study Given a study_id, branch and optionally an author, remove a study on the given branch and attribute the commit to author. Returns the SHA of the commit on branch.
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/phylesystem/git_actions.py#L108-L123
train
inveniosoftware/invenio-communities
invenio_communities/cli.py
init
def init(): """Initialize the communities file storage.""" try: initialize_communities_bucket() click.secho('Community init successful.', fg='green') except FilesException as e: click.secho(e.message, fg='red')
python
def init(): """Initialize the communities file storage.""" try: initialize_communities_bucket() click.secho('Community init successful.', fg='green') except FilesException as e: click.secho(e.message, fg='red')
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Initialize the communities file storage.
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/cli.py#L50-L56
train
inveniosoftware/invenio-communities
invenio_communities/cli.py
addlogo
def addlogo(community_id, logo): """Add logo to the community.""" # Create the bucket c = Community.get(community_id) if not c: click.secho('Community {0} does not exist.'.format(community_id), fg='red') return ext = save_and_validate_logo(logo, logo.name, c.id) c.logo_ext = ext db.session.commit()
python
def addlogo(community_id, logo): """Add logo to the community.""" # Create the bucket c = Community.get(community_id) if not c: click.secho('Community {0} does not exist.'.format(community_id), fg='red') return ext = save_and_validate_logo(logo, logo.name, c.id) c.logo_ext = ext db.session.commit()
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Add logo to the community.
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/cli.py#L63-L73
train
inveniosoftware/invenio-communities
invenio_communities/cli.py
request
def request(community_id, record_id, accept): """Request a record acceptance to a community.""" c = Community.get(community_id) assert c is not None record = Record.get_record(record_id) if accept: c.add_record(record) record.commit() else: InclusionRequest.create(community=c, record=record, notify=False) db.session.commit() RecordIndexer().index_by_id(record.id)
python
def request(community_id, record_id, accept): """Request a record acceptance to a community.""" c = Community.get(community_id) assert c is not None record = Record.get_record(record_id) if accept: c.add_record(record) record.commit() else: InclusionRequest.create(community=c, record=record, notify=False) db.session.commit() RecordIndexer().index_by_id(record.id)
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Request a record acceptance to a community.
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/cli.py#L81-L93
train
inveniosoftware/invenio-communities
invenio_communities/cli.py
remove
def remove(community_id, record_id): """Remove a record from community.""" c = Community.get(community_id) assert c is not None c.remove_record(record_id) db.session.commit() RecordIndexer().index_by_id(record_id)
python
def remove(community_id, record_id): """Remove a record from community.""" c = Community.get(community_id) assert c is not None c.remove_record(record_id) db.session.commit() RecordIndexer().index_by_id(record_id)
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Remove a record from community.
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/cli.py#L100-L106
train
OpenTreeOfLife/peyotl
peyotl/__init__.py
gen_otu_dict
def gen_otu_dict(nex_obj, nexson_version=None): """Takes a NexSON object and returns a dict of otu_id -> otu_obj """ if nexson_version is None: nexson_version = detect_nexson_version(nex_obj) if _is_by_id_hbf(nexson_version): otus = nex_obj['nexml']['otusById'] if len(otus) > 1: d = {} for v in otus.values(): d.update(v['otuById']) return d else: return otus.values()[0]['otuById'] o_dict = {} for ob in nex_obj.get('otus', []): for o in ob.get('otu', []): oid = o['@id'] o_dict[oid] = o return o_dict
python
def gen_otu_dict(nex_obj, nexson_version=None): """Takes a NexSON object and returns a dict of otu_id -> otu_obj """ if nexson_version is None: nexson_version = detect_nexson_version(nex_obj) if _is_by_id_hbf(nexson_version): otus = nex_obj['nexml']['otusById'] if len(otus) > 1: d = {} for v in otus.values(): d.update(v['otuById']) return d else: return otus.values()[0]['otuById'] o_dict = {} for ob in nex_obj.get('otus', []): for o in ob.get('otu', []): oid = o['@id'] o_dict[oid] = o return o_dict
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Takes a NexSON object and returns a dict of otu_id -> otu_obj
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/__init__.py#L33-L53
train
color/django-country
django_country/views.py
set_country
def set_country(request): """ Sets the chosen country in the session or cookie. If `next' query param is present, it redirects to a given url. """ if request.method == 'POST': next = request.POST.get('next', request.GET.get('next')) if is_safe_url(url=next, host=request.get_host()): response = http.HttpResponseRedirect(next) else: response = http.HttpResponse() country_code = request.POST.get('country', '').upper() if country_code != geo.get_supported_country(country_code): return http.HttpResponseBadRequest() if hasattr(request, 'session'): request.session[geo.COUNTRY_SESSION_KEY] = country_code else: response.set_cookie(geo.COUNTRY_COOKIE_NAME, country_code, max_age=geo.COUNTRY_COOKIE_AGE, path=geo.COUNTRY_COOKIE_PATH) return response else: return http.HttpResponseNotAllowed(['POST'])
python
def set_country(request): """ Sets the chosen country in the session or cookie. If `next' query param is present, it redirects to a given url. """ if request.method == 'POST': next = request.POST.get('next', request.GET.get('next')) if is_safe_url(url=next, host=request.get_host()): response = http.HttpResponseRedirect(next) else: response = http.HttpResponse() country_code = request.POST.get('country', '').upper() if country_code != geo.get_supported_country(country_code): return http.HttpResponseBadRequest() if hasattr(request, 'session'): request.session[geo.COUNTRY_SESSION_KEY] = country_code else: response.set_cookie(geo.COUNTRY_COOKIE_NAME, country_code, max_age=geo.COUNTRY_COOKIE_AGE, path=geo.COUNTRY_COOKIE_PATH) return response else: return http.HttpResponseNotAllowed(['POST'])
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Sets the chosen country in the session or cookie. If `next' query param is present, it redirects to a given url.
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1d272a196d998e21bb8d407e2657b88211f35232
https://github.com/color/django-country/blob/1d272a196d998e21bb8d407e2657b88211f35232/django_country/views.py#L8-L34
train
hsolbrig/pyjsg
pyjsg/parser_impl/jsg_doc_context.py
JSGDocContext.reference
def reference(self, tkn: str): """ Return the element that tkn represents""" return self.grammarelts[tkn] if tkn in self.grammarelts else UndefinedElement(tkn)
python
def reference(self, tkn: str): """ Return the element that tkn represents""" return self.grammarelts[tkn] if tkn in self.grammarelts else UndefinedElement(tkn)
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Return the element that tkn represents
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9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7
https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/jsg_doc_context.py#L111-L113
train
hsolbrig/pyjsg
pyjsg/parser_impl/jsg_doc_context.py
JSGDocContext.dependency_list
def dependency_list(self, tkn: str) -> List[str]: """Return a list all of the grammarelts that depend on tkn :param tkn: :return: """ if tkn not in self.dependency_map: self.dependency_map[tkn] = [tkn] # Force a circular reference self.dependency_map[tkn] = self.reference(tkn).dependency_list() return self.dependency_map[tkn]
python
def dependency_list(self, tkn: str) -> List[str]: """Return a list all of the grammarelts that depend on tkn :param tkn: :return: """ if tkn not in self.dependency_map: self.dependency_map[tkn] = [tkn] # Force a circular reference self.dependency_map[tkn] = self.reference(tkn).dependency_list() return self.dependency_map[tkn]
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Return a list all of the grammarelts that depend on tkn :param tkn: :return:
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9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7
https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/jsg_doc_context.py#L139-L148
train
hsolbrig/pyjsg
pyjsg/parser_impl/jsg_doc_context.py
JSGDocContext.dependencies
def dependencies(self, tkn: str) -> Set[str]: """Return all the items that tkn depends on as a set :param tkn: :return: """ return set(self.dependency_list(tkn))
python
def dependencies(self, tkn: str) -> Set[str]: """Return all the items that tkn depends on as a set :param tkn: :return: """ return set(self.dependency_list(tkn))
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Return all the items that tkn depends on as a set :param tkn: :return:
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9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7
https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/jsg_doc_context.py#L150-L156
train
hsolbrig/pyjsg
pyjsg/parser_impl/jsg_doc_context.py
JSGDocContext.undefined_entries
def undefined_entries(self) -> Set[str]: """ Return the set of tokens that are referenced but not defined. """ return as_set([[d for d in self.dependencies(k) if d not in self.grammarelts] for k in self.grammarelts.keys()])
python
def undefined_entries(self) -> Set[str]: """ Return the set of tokens that are referenced but not defined. """ return as_set([[d for d in self.dependencies(k) if d not in self.grammarelts] for k in self.grammarelts.keys()])
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Return the set of tokens that are referenced but not defined.
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9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7
https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/jsg_doc_context.py#L158-L161
train
inveniosoftware/invenio-communities
invenio_communities/receivers.py
new_request
def new_request(sender, request=None, notify=True, **kwargs): """New request for inclusion.""" if current_app.config['COMMUNITIES_MAIL_ENABLED'] and notify: send_community_request_email(request)
python
def new_request(sender, request=None, notify=True, **kwargs): """New request for inclusion.""" if current_app.config['COMMUNITIES_MAIL_ENABLED'] and notify: send_community_request_email(request)
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New request for inclusion.
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/receivers.py#L36-L39
train
inveniosoftware/invenio-communities
invenio_communities/receivers.py
inject_provisional_community
def inject_provisional_community(sender, json=None, record=None, index=None, **kwargs): """Inject 'provisional_communities' key to ES index.""" if index and not index.startswith( current_app.config['COMMUNITIES_INDEX_PREFIX']): return json['provisional_communities'] = list(sorted([ r.id_community for r in InclusionRequest.get_by_record(record.id) ]))
python
def inject_provisional_community(sender, json=None, record=None, index=None, **kwargs): """Inject 'provisional_communities' key to ES index.""" if index and not index.startswith( current_app.config['COMMUNITIES_INDEX_PREFIX']): return json['provisional_communities'] = list(sorted([ r.id_community for r in InclusionRequest.get_by_record(record.id) ]))
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Inject 'provisional_communities' key to ES index.
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/receivers.py#L42-L51
train
OpenTreeOfLife/peyotl
peyotl/api/oti.py
_OTIWrapper.find_nodes
def find_nodes(self, query_dict=None, exact=False, verbose=False, **kwargs): """Query on node properties. See documentation for _OTIWrapper class.""" assert self.use_v1 return self._do_query('{p}/singlePropertySearchForTreeNodes'.format(p=self.query_prefix), query_dict=query_dict, exact=exact, verbose=verbose, valid_keys=self.node_search_term_set, kwargs=kwargs)
python
def find_nodes(self, query_dict=None, exact=False, verbose=False, **kwargs): """Query on node properties. See documentation for _OTIWrapper class.""" assert self.use_v1 return self._do_query('{p}/singlePropertySearchForTreeNodes'.format(p=self.query_prefix), query_dict=query_dict, exact=exact, verbose=verbose, valid_keys=self.node_search_term_set, kwargs=kwargs)
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Query on node properties. See documentation for _OTIWrapper class.
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/api/oti.py#L119-L127
train
OpenTreeOfLife/peyotl
peyotl/api/oti.py
_OTIWrapper.find_trees
def find_trees(self, query_dict=None, exact=False, verbose=False, wrap_response=False, **kwargs): """Query on tree properties. See documentation for _OTIWrapper class.""" if self.use_v1: uri = '{p}/singlePropertySearchForTrees'.format(p=self.query_prefix) else: uri = '{p}/find_trees'.format(p=self.query_prefix) resp = self._do_query(uri, query_dict=query_dict, exact=exact, verbose=verbose, valid_keys=self.tree_search_term_set, kwargs=kwargs) if wrap_response: return TreeRefList(resp) return resp
python
def find_trees(self, query_dict=None, exact=False, verbose=False, wrap_response=False, **kwargs): """Query on tree properties. See documentation for _OTIWrapper class.""" if self.use_v1: uri = '{p}/singlePropertySearchForTrees'.format(p=self.query_prefix) else: uri = '{p}/find_trees'.format(p=self.query_prefix) resp = self._do_query(uri, query_dict=query_dict, exact=exact, verbose=verbose, valid_keys=self.tree_search_term_set, kwargs=kwargs) if wrap_response: return TreeRefList(resp) return resp
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/api/oti.py#L129-L143
train
OpenTreeOfLife/peyotl
peyotl/api/oti.py
_OTIWrapper.find_studies
def find_studies(self, query_dict=None, exact=False, verbose=False, **kwargs): """Query on study properties. See documentation for _OTIWrapper class.""" if self.use_v1: uri = '{p}/singlePropertySearchForStudies'.format(p=self.query_prefix) else: uri = '{p}/find_studies'.format(p=self.query_prefix) return self._do_query(uri, query_dict=query_dict, exact=exact, verbose=verbose, valid_keys=self.study_search_term_set, kwargs=kwargs)
python
def find_studies(self, query_dict=None, exact=False, verbose=False, **kwargs): """Query on study properties. See documentation for _OTIWrapper class.""" if self.use_v1: uri = '{p}/singlePropertySearchForStudies'.format(p=self.query_prefix) else: uri = '{p}/find_studies'.format(p=self.query_prefix) return self._do_query(uri, query_dict=query_dict, exact=exact, verbose=verbose, valid_keys=self.study_search_term_set, kwargs=kwargs)
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Query on study properties. See documentation for _OTIWrapper class.
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/api/oti.py#L145-L156
train
SpotlightData/preprocessing
setup.py
get_requirements
def get_requirements(): '''returns requirements array for package''' packages = [] with open("requirements.txt", "r") as req_doc: for package in req_doc: packages.append(package.replace("\n", "")) return packages
python
def get_requirements(): '''returns requirements array for package''' packages = [] with open("requirements.txt", "r") as req_doc: for package in req_doc: packages.append(package.replace("\n", "")) return packages
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returns requirements array for package
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180c6472bc2642afbd7a1ece08d0b0d14968a708
https://github.com/SpotlightData/preprocessing/blob/180c6472bc2642afbd7a1ece08d0b0d14968a708/setup.py#L5-L11
train
OpenTreeOfLife/peyotl
peyotl/amendments/amendments_umbrella.py
TaxonomicAmendmentStore
def TaxonomicAmendmentStore(repos_dict=None, repos_par=None, with_caching=True, assumed_doc_version=None, git_ssh=None, pkey=None, git_action_class=TaxonomicAmendmentsGitAction, mirror_info=None, infrastructure_commit_author='OpenTree API <api@opentreeoflife.org>'): """Factory function for a _TaxonomicAmendmentStore object. A wrapper around the _TaxonomicAmendmentStore class instantiation for the most common use case: a singleton _TaxonomicAmendmentStore. If you need distinct _TaxonomicAmendmentStore objects, you'll need to call that class directly. """ global _THE_TAXONOMIC_AMENDMENT_STORE if _THE_TAXONOMIC_AMENDMENT_STORE is None: _THE_TAXONOMIC_AMENDMENT_STORE = _TaxonomicAmendmentStore(repos_dict=repos_dict, repos_par=repos_par, with_caching=with_caching, assumed_doc_version=assumed_doc_version, git_ssh=git_ssh, pkey=pkey, git_action_class=git_action_class, mirror_info=mirror_info, infrastructure_commit_author=infrastructure_commit_author) return _THE_TAXONOMIC_AMENDMENT_STORE
python
def TaxonomicAmendmentStore(repos_dict=None, repos_par=None, with_caching=True, assumed_doc_version=None, git_ssh=None, pkey=None, git_action_class=TaxonomicAmendmentsGitAction, mirror_info=None, infrastructure_commit_author='OpenTree API <api@opentreeoflife.org>'): """Factory function for a _TaxonomicAmendmentStore object. A wrapper around the _TaxonomicAmendmentStore class instantiation for the most common use case: a singleton _TaxonomicAmendmentStore. If you need distinct _TaxonomicAmendmentStore objects, you'll need to call that class directly. """ global _THE_TAXONOMIC_AMENDMENT_STORE if _THE_TAXONOMIC_AMENDMENT_STORE is None: _THE_TAXONOMIC_AMENDMENT_STORE = _TaxonomicAmendmentStore(repos_dict=repos_dict, repos_par=repos_par, with_caching=with_caching, assumed_doc_version=assumed_doc_version, git_ssh=git_ssh, pkey=pkey, git_action_class=git_action_class, mirror_info=mirror_info, infrastructure_commit_author=infrastructure_commit_author) return _THE_TAXONOMIC_AMENDMENT_STORE
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Factory function for a _TaxonomicAmendmentStore object. A wrapper around the _TaxonomicAmendmentStore class instantiation for the most common use case: a singleton _TaxonomicAmendmentStore. If you need distinct _TaxonomicAmendmentStore objects, you'll need to call that class directly.
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/amendments/amendments_umbrella.py#L352-L379
train
inveniosoftware/invenio-communities
invenio_communities/tasks.py
delete_marked_communities
def delete_marked_communities(): """Delete communities after holdout time.""" # TODO: Delete the community ID from all records metadata first raise NotImplementedError() Community.query.filter_by( Community.delete_time > datetime.utcnow()).delete() db.session.commit()
python
def delete_marked_communities(): """Delete communities after holdout time.""" # TODO: Delete the community ID from all records metadata first raise NotImplementedError() Community.query.filter_by( Community.delete_time > datetime.utcnow()).delete() db.session.commit()
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Delete communities after holdout time.
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/tasks.py#L38-L44
train
inveniosoftware/invenio-communities
invenio_communities/tasks.py
delete_expired_requests
def delete_expired_requests(): """Delete expired inclusion requests.""" InclusionRequest.query.filter_by( InclusionRequest.expiry_date > datetime.utcnow()).delete() db.session.commit()
python
def delete_expired_requests(): """Delete expired inclusion requests.""" InclusionRequest.query.filter_by( InclusionRequest.expiry_date > datetime.utcnow()).delete() db.session.commit()
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Delete expired inclusion requests.
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5c4de6783724d276ae1b6dd13a399a9e22fadc7a
https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/tasks.py#L48-L52
train
OpenTreeOfLife/peyotl
peyotl/nexson_syntax/__init__.py
create_content_spec
def create_content_spec(**kwargs): """Sugar. factory for a PhyloSchema object. Repackages the kwargs to kwargs for PhyloSchema so that our PhyloSchema.__init__ does not have to be soo rich """ format_str = kwargs.get('format', 'nexson') nexson_version = kwargs.get('nexson_version', 'native') otu_label = kwargs.get('otu_label') if otu_label is None: otu_label = kwargs.get('tip_label') content = kwargs.get('content') if content is not None: content_id = kwargs.get('content_id') if content_id is None: content_id = _get_content_id_from(**kwargs) else: content, content_id = _sniff_content_from_kwargs(**kwargs) if content is None: content = 'study' return PhyloSchema(content=content, content_id=content_id, format_str=format_str, version=nexson_version, otu_label=otu_label, repo_nexml2json=kwargs.get('repo_nexml2json'), bracket_ingroup=bool(kwargs.get('bracket_ingroup', False)), cull_nonmatching=kwargs.get('cull_nonmatching'))
python
def create_content_spec(**kwargs): """Sugar. factory for a PhyloSchema object. Repackages the kwargs to kwargs for PhyloSchema so that our PhyloSchema.__init__ does not have to be soo rich """ format_str = kwargs.get('format', 'nexson') nexson_version = kwargs.get('nexson_version', 'native') otu_label = kwargs.get('otu_label') if otu_label is None: otu_label = kwargs.get('tip_label') content = kwargs.get('content') if content is not None: content_id = kwargs.get('content_id') if content_id is None: content_id = _get_content_id_from(**kwargs) else: content, content_id = _sniff_content_from_kwargs(**kwargs) if content is None: content = 'study' return PhyloSchema(content=content, content_id=content_id, format_str=format_str, version=nexson_version, otu_label=otu_label, repo_nexml2json=kwargs.get('repo_nexml2json'), bracket_ingroup=bool(kwargs.get('bracket_ingroup', False)), cull_nonmatching=kwargs.get('cull_nonmatching'))
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Sugar. factory for a PhyloSchema object. Repackages the kwargs to kwargs for PhyloSchema so that our PhyloSchema.__init__ does not have to be soo rich
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/nexson_syntax/__init__.py#L178-L205
train
OpenTreeOfLife/peyotl
peyotl/nexson_syntax/__init__.py
convert_nexson_format
def convert_nexson_format(blob, out_nexson_format, current_format=None, remove_old_structs=True, pristine_if_invalid=False, sort_arbitrary=False): """Take a dict form of NexSON and converts its datastructures to those needed to serialize as out_nexson_format. If current_format is not specified, it will be inferred. If `remove_old_structs` is False and different honeybadgerfish varieties are selected, the `blob` will be 'fat" containing both types of lookup structures. If pristine_if_invalid is False, then the object may be corrupted if it is an invalid nexson struct. Setting this to False can result in faster translation, but if an exception is raised the object may be polluted with partially constructed fields for the out_nexson_format. """ if not current_format: current_format = detect_nexson_version(blob) out_nexson_format = resolve_nexson_format(out_nexson_format) if current_format == out_nexson_format: if sort_arbitrary: sort_arbitrarily_ordered_nexson(blob) return blob two2zero = _is_by_id_hbf(out_nexson_format) and _is_badgerfish_version(current_format) zero2two = _is_by_id_hbf(current_format) and _is_badgerfish_version(out_nexson_format) if two2zero or zero2two: # go from 0.0 -> 1.0 then the 1.0->1.2 should succeed without nexml... blob = convert_nexson_format(blob, DIRECT_HONEY_BADGERFISH, current_format=current_format, remove_old_structs=remove_old_structs, pristine_if_invalid=pristine_if_invalid) current_format = DIRECT_HONEY_BADGERFISH ccdict = {'output_format': out_nexson_format, 'input_format': current_format, 'remove_old_structs': remove_old_structs, 'pristine_if_invalid': pristine_if_invalid} ccfg = ConversionConfig(ccdict) if _is_badgerfish_version(current_format): converter = Badgerfish2DirectNexson(ccfg) elif _is_badgerfish_version(out_nexson_format): assert _is_direct_hbf(current_format) converter = Direct2BadgerfishNexson(ccfg) elif _is_direct_hbf(current_format) and (out_nexson_format == BY_ID_HONEY_BADGERFISH): converter = Direct2OptimalNexson(ccfg) elif _is_direct_hbf(out_nexson_format) and (current_format == BY_ID_HONEY_BADGERFISH): converter = Optimal2DirectNexson(ccfg) else: raise NotImplementedError('Conversion from {i} to {o}'.format(i=current_format, o=out_nexson_format)) blob = converter.convert(blob) if sort_arbitrary: sort_arbitrarily_ordered_nexson(blob) return blob
python
def convert_nexson_format(blob, out_nexson_format, current_format=None, remove_old_structs=True, pristine_if_invalid=False, sort_arbitrary=False): """Take a dict form of NexSON and converts its datastructures to those needed to serialize as out_nexson_format. If current_format is not specified, it will be inferred. If `remove_old_structs` is False and different honeybadgerfish varieties are selected, the `blob` will be 'fat" containing both types of lookup structures. If pristine_if_invalid is False, then the object may be corrupted if it is an invalid nexson struct. Setting this to False can result in faster translation, but if an exception is raised the object may be polluted with partially constructed fields for the out_nexson_format. """ if not current_format: current_format = detect_nexson_version(blob) out_nexson_format = resolve_nexson_format(out_nexson_format) if current_format == out_nexson_format: if sort_arbitrary: sort_arbitrarily_ordered_nexson(blob) return blob two2zero = _is_by_id_hbf(out_nexson_format) and _is_badgerfish_version(current_format) zero2two = _is_by_id_hbf(current_format) and _is_badgerfish_version(out_nexson_format) if two2zero or zero2two: # go from 0.0 -> 1.0 then the 1.0->1.2 should succeed without nexml... blob = convert_nexson_format(blob, DIRECT_HONEY_BADGERFISH, current_format=current_format, remove_old_structs=remove_old_structs, pristine_if_invalid=pristine_if_invalid) current_format = DIRECT_HONEY_BADGERFISH ccdict = {'output_format': out_nexson_format, 'input_format': current_format, 'remove_old_structs': remove_old_structs, 'pristine_if_invalid': pristine_if_invalid} ccfg = ConversionConfig(ccdict) if _is_badgerfish_version(current_format): converter = Badgerfish2DirectNexson(ccfg) elif _is_badgerfish_version(out_nexson_format): assert _is_direct_hbf(current_format) converter = Direct2BadgerfishNexson(ccfg) elif _is_direct_hbf(current_format) and (out_nexson_format == BY_ID_HONEY_BADGERFISH): converter = Direct2OptimalNexson(ccfg) elif _is_direct_hbf(out_nexson_format) and (current_format == BY_ID_HONEY_BADGERFISH): converter = Optimal2DirectNexson(ccfg) else: raise NotImplementedError('Conversion from {i} to {o}'.format(i=current_format, o=out_nexson_format)) blob = converter.convert(blob) if sort_arbitrary: sort_arbitrarily_ordered_nexson(blob) return blob
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Take a dict form of NexSON and converts its datastructures to those needed to serialize as out_nexson_format. If current_format is not specified, it will be inferred. If `remove_old_structs` is False and different honeybadgerfish varieties are selected, the `blob` will be 'fat" containing both types of lookup structures. If pristine_if_invalid is False, then the object may be corrupted if it is an invalid nexson struct. Setting this to False can result in faster translation, but if an exception is raised the object may be polluted with partially constructed fields for the out_nexson_format.
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5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0
https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/nexson_syntax/__init__.py#L646-L699
train