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Semeru Lab 7

CybOXProject/mixbox

mixbox/entities.py

Entity.from_json

def from_json(cls, json_doc): """Parse a JSON string and build an entity.""" try: d = json.load(json_doc) except AttributeError: # catch the read() error d = json.loads(json_doc) return cls.from_dict(d)

python

def from_json(cls, json_doc): """Parse a JSON string and build an entity.""" try: d = json.load(json_doc) except AttributeError: # catch the read() error d = json.loads(json_doc) return cls.from_dict(d)

Parse a JSON string and build an entity.

9097dae7a433f5b98c18171c4a5598f69a7d30af

https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/entities.py#L490-L497

train

CybOXProject/mixbox

mixbox/entities.py

EntityList._multiple_field

def _multiple_field(cls): """Return the "multiple" TypedField associated with this EntityList. This also lazily sets the ``_entitylist_multiplefield`` value if it hasn't been set yet. This is set to a tuple containing one item because if we set the class attribute to the TypedField, we would effectively add a TypedField descriptor to the class, which we don't want. Raises: AssertionError: If there is more than one multiple TypedField or the the TypedField type_ is not a subclass of Entity. """ klassdict = cls.__dict__ try: # Checking for cls.entitylist_multifield would return any inherited # values, so we check the class __dict__ explicitly. return klassdict["_entitylist_multifield"][0] except (KeyError, IndexError, TypeError): from . import fields multifield_tuple = tuple(fields.find(cls, multiple=True)) assert len(multifield_tuple) == 1 # Make sure that the multiple field actually has an Entity type. multifield = multifield_tuple[0] assert issubclass(multifield.type_, Entity) # Store aside the multiple field. We wrap it in a tuple because # just doing ``cls._entitylist_multifield = multifield`` would # assign another TypedField descriptor to this class. We don't # want that. cls._entitylist_multifield = multifield_tuple # Return the multiple TypedField return multifield_tuple[0]

python

def _multiple_field(cls): """Return the "multiple" TypedField associated with this EntityList. This also lazily sets the ``_entitylist_multiplefield`` value if it hasn't been set yet. This is set to a tuple containing one item because if we set the class attribute to the TypedField, we would effectively add a TypedField descriptor to the class, which we don't want. Raises: AssertionError: If there is more than one multiple TypedField or the the TypedField type_ is not a subclass of Entity. """ klassdict = cls.__dict__ try: # Checking for cls.entitylist_multifield would return any inherited # values, so we check the class __dict__ explicitly. return klassdict["_entitylist_multifield"][0] except (KeyError, IndexError, TypeError): from . import fields multifield_tuple = tuple(fields.find(cls, multiple=True)) assert len(multifield_tuple) == 1 # Make sure that the multiple field actually has an Entity type. multifield = multifield_tuple[0] assert issubclass(multifield.type_, Entity) # Store aside the multiple field. We wrap it in a tuple because # just doing ``cls._entitylist_multifield = multifield`` would # assign another TypedField descriptor to this class. We don't # want that. cls._entitylist_multifield = multifield_tuple # Return the multiple TypedField return multifield_tuple[0]

Return the "multiple" TypedField associated with this EntityList. This also lazily sets the ``_entitylist_multiplefield`` value if it hasn't been set yet. This is set to a tuple containing one item because if we set the class attribute to the TypedField, we would effectively add a TypedField descriptor to the class, which we don't want. Raises: AssertionError: If there is more than one multiple TypedField or the the TypedField type_ is not a subclass of Entity.

9097dae7a433f5b98c18171c4a5598f69a7d30af

https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/entities.py#L594-L628

train

CybOXProject/mixbox

mixbox/entities.py

NamespaceCollector._finalize_namespaces

def _finalize_namespaces(self, ns_dict=None): """Returns a dictionary of namespaces to be exported with an XML document. This loops over all the namespaces that were discovered and built during the execution of ``collect()`` and ``_parse_collected_classes()`` and attempts to merge them all. Raises: .namespaces.DuplicatePrefixError: If namespace prefix was mapped to more than one namespace. .namespaces.NoPrefixError: If a namespace was collected that is not mapped to a prefix. """ if ns_dict: # Add the user's entries to our set for ns, alias in six.iteritems(ns_dict): self._collected_namespaces.add_namespace_uri(ns, alias) # Add the ID namespaces self._collected_namespaces.add_namespace_uri( ns_uri=idgen.get_id_namespace(), prefix=idgen.get_id_namespace_alias() ) # Remap the example namespace to the one expected by the APIs if the # sample example namespace is found. self._fix_example_namespace() # Add _input_namespaces for prefix, uri in six.iteritems(self._input_namespaces): self._collected_namespaces.add_namespace_uri(uri, prefix) # Add some default XML namespaces to make sure they're there. self._collected_namespaces.import_from(namespaces.XML_NAMESPACES) # python-stix's generateDS-generated binding classes can't handle # default namespaces. So make sure there are no preferred defaults in # the set. Get prefixes from the global namespace set if we have to. for ns_uri in self._collected_namespaces.namespace_uris: preferred_prefix = self._collected_namespaces.preferred_prefix_for_namespace(ns_uri) if preferred_prefix: continue # No preferred prefix set for namespace. Try to assign one. prefixes = self._collected_namespaces.get_prefixes(ns_uri) if prefixes: prefix = next(iter(prefixes)) else: prefix = namespaces.lookup_name(ns_uri) if prefix is None: raise namespaces.NoPrefixesError(ns_uri) self._collected_namespaces.set_preferred_prefix_for_namespace( ns_uri=ns_uri, prefix=prefix, add_if_not_exist=True )

python

def _finalize_namespaces(self, ns_dict=None): """Returns a dictionary of namespaces to be exported with an XML document. This loops over all the namespaces that were discovered and built during the execution of ``collect()`` and ``_parse_collected_classes()`` and attempts to merge them all. Raises: .namespaces.DuplicatePrefixError: If namespace prefix was mapped to more than one namespace. .namespaces.NoPrefixError: If a namespace was collected that is not mapped to a prefix. """ if ns_dict: # Add the user's entries to our set for ns, alias in six.iteritems(ns_dict): self._collected_namespaces.add_namespace_uri(ns, alias) # Add the ID namespaces self._collected_namespaces.add_namespace_uri( ns_uri=idgen.get_id_namespace(), prefix=idgen.get_id_namespace_alias() ) # Remap the example namespace to the one expected by the APIs if the # sample example namespace is found. self._fix_example_namespace() # Add _input_namespaces for prefix, uri in six.iteritems(self._input_namespaces): self._collected_namespaces.add_namespace_uri(uri, prefix) # Add some default XML namespaces to make sure they're there. self._collected_namespaces.import_from(namespaces.XML_NAMESPACES) # python-stix's generateDS-generated binding classes can't handle # default namespaces. So make sure there are no preferred defaults in # the set. Get prefixes from the global namespace set if we have to. for ns_uri in self._collected_namespaces.namespace_uris: preferred_prefix = self._collected_namespaces.preferred_prefix_for_namespace(ns_uri) if preferred_prefix: continue # No preferred prefix set for namespace. Try to assign one. prefixes = self._collected_namespaces.get_prefixes(ns_uri) if prefixes: prefix = next(iter(prefixes)) else: prefix = namespaces.lookup_name(ns_uri) if prefix is None: raise namespaces.NoPrefixesError(ns_uri) self._collected_namespaces.set_preferred_prefix_for_namespace( ns_uri=ns_uri, prefix=prefix, add_if_not_exist=True )

Returns a dictionary of namespaces to be exported with an XML document. This loops over all the namespaces that were discovered and built during the execution of ``collect()`` and ``_parse_collected_classes()`` and attempts to merge them all. Raises: .namespaces.DuplicatePrefixError: If namespace prefix was mapped to more than one namespace. .namespaces.NoPrefixError: If a namespace was collected that is not mapped to a prefix.

9097dae7a433f5b98c18171c4a5598f69a7d30af

https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/entities.py#L796-L856

train

inveniosoftware/invenio-communities

invenio_communities/views/api.py

CommunitiesResource.get

def get(self, query, sort, page, size): """Get a list of all the communities. .. http:get:: /communities/(string:id) Returns a JSON list with all the communities. **Request**: .. sourcecode:: http GET /communities HTTP/1.1 Accept: application/json Content-Type: application/json Host: localhost:5000 :reqheader Content-Type: application/json **Response**: .. sourcecode:: http HTTP/1.0 200 OK Content-Length: 334 Content-Type: application/json [ { "id": "comm1" }, { "id": "comm2" } ] :resheader Content-Type: application/json :statuscode 200: no error """ urlkwargs = { 'q': query, 'sort': sort, 'size': size, } communities = Community.filter_communities(query, sort) page = communities.paginate(page, size) links = default_links_pagination_factory(page, urlkwargs) links_headers = map(lambda key: ('link', 'ref="{0}" href="{1}"'.format( key, links[key])), links) return self.make_response( page, headers=links_headers, links_item_factory=default_links_item_factory, page=page, urlkwargs=urlkwargs, links_pagination_factory=default_links_pagination_factory, )

python

def get(self, query, sort, page, size): """Get a list of all the communities. .. http:get:: /communities/(string:id) Returns a JSON list with all the communities. **Request**: .. sourcecode:: http GET /communities HTTP/1.1 Accept: application/json Content-Type: application/json Host: localhost:5000 :reqheader Content-Type: application/json **Response**: .. sourcecode:: http HTTP/1.0 200 OK Content-Length: 334 Content-Type: application/json [ { "id": "comm1" }, { "id": "comm2" } ] :resheader Content-Type: application/json :statuscode 200: no error """ urlkwargs = { 'q': query, 'sort': sort, 'size': size, } communities = Community.filter_communities(query, sort) page = communities.paginate(page, size) links = default_links_pagination_factory(page, urlkwargs) links_headers = map(lambda key: ('link', 'ref="{0}" href="{1}"'.format( key, links[key])), links) return self.make_response( page, headers=links_headers, links_item_factory=default_links_item_factory, page=page, urlkwargs=urlkwargs, links_pagination_factory=default_links_pagination_factory, )

Get a list of all the communities. .. http:get:: /communities/(string:id) Returns a JSON list with all the communities. **Request**: .. sourcecode:: http GET /communities HTTP/1.1 Accept: application/json Content-Type: application/json Host: localhost:5000 :reqheader Content-Type: application/json **Response**: .. sourcecode:: http HTTP/1.0 200 OK Content-Length: 334 Content-Type: application/json [ { "id": "comm1" }, { "id": "comm2" } ] :resheader Content-Type: application/json :statuscode 200: no error

5c4de6783724d276ae1b6dd13a399a9e22fadc7a

https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/views/api.py#L80-L129

train

inveniosoftware/invenio-communities

invenio_communities/views/api.py

CommunityDetailsResource.get

def get(self, community_id): """Get the details of the specified community. .. http:get:: /communities/(string:id) Returns a JSON dictionary with the details of the specified community. **Request**: .. sourcecode:: http GET /communities/communities/comm1 HTTP/1.1 Accept: application/json Content-Type: application/json Host: localhost:5000 :reqheader Content-Type: application/json :query string id: ID of an specific community to get more information. **Response**: .. sourcecode:: http HTTP/1.0 200 OK Content-Length: 334 Content-Type: application/json { "id_user": 1, "description": "", "title": "", "created": "2016-04-05T14:56:37.051462", "id": "comm1", "page": "", "curation_policy": "" } :resheader Content-Type: application/json :statuscode 200: no error :statuscode 404: page not found """ community = Community.get(community_id) if not community: abort(404) etag = community.version_id self.check_etag(etag) response = self.make_response( community, links_item_factory=default_links_item_factory) response.set_etag(etag) return response

python

def get(self, community_id): """Get the details of the specified community. .. http:get:: /communities/(string:id) Returns a JSON dictionary with the details of the specified community. **Request**: .. sourcecode:: http GET /communities/communities/comm1 HTTP/1.1 Accept: application/json Content-Type: application/json Host: localhost:5000 :reqheader Content-Type: application/json :query string id: ID of an specific community to get more information. **Response**: .. sourcecode:: http HTTP/1.0 200 OK Content-Length: 334 Content-Type: application/json { "id_user": 1, "description": "", "title": "", "created": "2016-04-05T14:56:37.051462", "id": "comm1", "page": "", "curation_policy": "" } :resheader Content-Type: application/json :statuscode 200: no error :statuscode 404: page not found """ community = Community.get(community_id) if not community: abort(404) etag = community.version_id self.check_etag(etag) response = self.make_response( community, links_item_factory=default_links_item_factory) response.set_etag(etag) return response

Get the details of the specified community. .. http:get:: /communities/(string:id) Returns a JSON dictionary with the details of the specified community. **Request**: .. sourcecode:: http GET /communities/communities/comm1 HTTP/1.1 Accept: application/json Content-Type: application/json Host: localhost:5000 :reqheader Content-Type: application/json :query string id: ID of an specific community to get more information. **Response**: .. sourcecode:: http HTTP/1.0 200 OK Content-Length: 334 Content-Type: application/json { "id_user": 1, "description": "", "title": "", "created": "2016-04-05T14:56:37.051462", "id": "comm1", "page": "", "curation_policy": "" } :resheader Content-Type: application/json :statuscode 200: no error :statuscode 404: page not found

5c4de6783724d276ae1b6dd13a399a9e22fadc7a

https://github.com/inveniosoftware/invenio-communities/blob/5c4de6783724d276ae1b6dd13a399a9e22fadc7a/invenio_communities/views/api.py#L143-L185

train

OpenTreeOfLife/peyotl

peyotl/phylesystem/phylesystem_umbrella.py

Phylesystem

def Phylesystem(repos_dict=None, repos_par=None, with_caching=True, repo_nexml2json=None, git_ssh=None, pkey=None, git_action_class=PhylesystemGitAction, mirror_info=None, new_study_prefix=None, infrastructure_commit_author='OpenTree API <[email protected]>'): """Factory function for a _Phylesystem object. A wrapper around the _Phylesystem class instantiation for the most common use case: a singleton _Phylesystem. If you need distinct _Phylesystem objects, you'll need to call that class directly. """ if not repo_nexml2json: repo_nexml2json = get_config_setting('phylesystem', 'repo_nexml2json') global _THE_PHYLESYSTEM if _THE_PHYLESYSTEM is None: _THE_PHYLESYSTEM = _Phylesystem(repos_dict=repos_dict, repos_par=repos_par, with_caching=with_caching, repo_nexml2json=repo_nexml2json, git_ssh=git_ssh, pkey=pkey, git_action_class=git_action_class, mirror_info=mirror_info, new_study_prefix=new_study_prefix, infrastructure_commit_author=infrastructure_commit_author) return _THE_PHYLESYSTEM

python

def Phylesystem(repos_dict=None, repos_par=None, with_caching=True, repo_nexml2json=None, git_ssh=None, pkey=None, git_action_class=PhylesystemGitAction, mirror_info=None, new_study_prefix=None, infrastructure_commit_author='OpenTree API <[email protected]>'): """Factory function for a _Phylesystem object. A wrapper around the _Phylesystem class instantiation for the most common use case: a singleton _Phylesystem. If you need distinct _Phylesystem objects, you'll need to call that class directly. """ if not repo_nexml2json: repo_nexml2json = get_config_setting('phylesystem', 'repo_nexml2json') global _THE_PHYLESYSTEM if _THE_PHYLESYSTEM is None: _THE_PHYLESYSTEM = _Phylesystem(repos_dict=repos_dict, repos_par=repos_par, with_caching=with_caching, repo_nexml2json=repo_nexml2json, git_ssh=git_ssh, pkey=pkey, git_action_class=git_action_class, mirror_info=mirror_info, new_study_prefix=new_study_prefix, infrastructure_commit_author=infrastructure_commit_author) return _THE_PHYLESYSTEM

Factory function for a _Phylesystem object. A wrapper around the _Phylesystem class instantiation for the most common use case: a singleton _Phylesystem. If you need distinct _Phylesystem objects, you'll need to call that class directly.

5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0

https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/phylesystem/phylesystem_umbrella.py#L273-L304

train

SpotlightData/preprocessing

preprocessing/text.py

convert_html_entities

def convert_html_entities(text_string): ''' Converts HTML5 character references within text_string to their corresponding unicode characters and returns converted string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): return html.unescape(text_string).replace("&quot;", "'") else: raise InputError("string not passed as argument for text_string")

python

def convert_html_entities(text_string): ''' Converts HTML5 character references within text_string to their corresponding unicode characters and returns converted string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): return html.unescape(text_string).replace("&quot;", "'") else: raise InputError("string not passed as argument for text_string")

Converts HTML5 character references within text_string to their corresponding unicode characters and returns converted string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed

180c6472bc2642afbd7a1ece08d0b0d14968a708

https://github.com/SpotlightData/preprocessing/blob/180c6472bc2642afbd7a1ece08d0b0d14968a708/preprocessing/text.py#L33-L51

train

SpotlightData/preprocessing

preprocessing/text.py

convert_ligatures

def convert_ligatures(text_string): ''' Coverts Latin character references within text_string to their corresponding unicode characters and returns converted string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a string or NoneType not be passed as an argument ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): for i in range(0, len(LIGATURES)): text_string = text_string.replace(LIGATURES[str(i)]["ligature"], LIGATURES[str(i)]["term"]) return text_string else: raise InputError("none type or string not passed as an argument")

python

def convert_ligatures(text_string): ''' Coverts Latin character references within text_string to their corresponding unicode characters and returns converted string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a string or NoneType not be passed as an argument ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): for i in range(0, len(LIGATURES)): text_string = text_string.replace(LIGATURES[str(i)]["ligature"], LIGATURES[str(i)]["term"]) return text_string else: raise InputError("none type or string not passed as an argument")

Coverts Latin character references within text_string to their corresponding unicode characters and returns converted string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a string or NoneType not be passed as an argument

180c6472bc2642afbd7a1ece08d0b0d14968a708

https://github.com/SpotlightData/preprocessing/blob/180c6472bc2642afbd7a1ece08d0b0d14968a708/preprocessing/text.py#L53-L73

train

SpotlightData/preprocessing

preprocessing/text.py

correct_spelling

def correct_spelling(text_string): ''' Splits string and converts words not found within a pre-built dictionary to their most likely actual word based on a relative probability dictionary. Returns edited string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a string or NoneType not be passed as an argument ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): word_list = text_string.split() spellchecked_word_list = [] for word in word_list: spellchecked_word_list.append(spellcheck.correct_word(word)) return " ".join(spellchecked_word_list) else: raise InputError("none type or string not passed as an argument")

python

def correct_spelling(text_string): ''' Splits string and converts words not found within a pre-built dictionary to their most likely actual word based on a relative probability dictionary. Returns edited string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a string or NoneType not be passed as an argument ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): word_list = text_string.split() spellchecked_word_list = [] for word in word_list: spellchecked_word_list.append(spellcheck.correct_word(word)) return " ".join(spellchecked_word_list) else: raise InputError("none type or string not passed as an argument")

Splits string and converts words not found within a pre-built dictionary to their most likely actual word based on a relative probability dictionary. Returns edited string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a string or NoneType not be passed as an argument

180c6472bc2642afbd7a1ece08d0b0d14968a708

https://github.com/SpotlightData/preprocessing/blob/180c6472bc2642afbd7a1ece08d0b0d14968a708/preprocessing/text.py#L75-L98

train

SpotlightData/preprocessing

preprocessing/text.py

create_sentence_list

def create_sentence_list(text_string): ''' Splits text_string into a list of sentences based on NLTK's english.pickle tokenizer, and returns said list as type list of str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed ''' if text_string is None or text_string == "": return [] elif isinstance(text_string, str): return SENTENCE_TOKENIZER.tokenize(text_string) else: raise InputError("non-string passed as argument for create_sentence_list")

python

def create_sentence_list(text_string): ''' Splits text_string into a list of sentences based on NLTK's english.pickle tokenizer, and returns said list as type list of str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed ''' if text_string is None or text_string == "": return [] elif isinstance(text_string, str): return SENTENCE_TOKENIZER.tokenize(text_string) else: raise InputError("non-string passed as argument for create_sentence_list")

Splits text_string into a list of sentences based on NLTK's english.pickle tokenizer, and returns said list as type list of str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed

180c6472bc2642afbd7a1ece08d0b0d14968a708

https://github.com/SpotlightData/preprocessing/blob/180c6472bc2642afbd7a1ece08d0b0d14968a708/preprocessing/text.py#L100-L118

train

SpotlightData/preprocessing

preprocessing/text.py

keyword_tokenize

def keyword_tokenize(text_string): ''' Extracts keywords from text_string using NLTK's list of English stopwords, ignoring words of a length smaller than 3, and returns the new string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): return " ".join([word for word in KEYWORD_TOKENIZER.tokenize(text_string) if word not in STOPWORDS and len(word) >= 3]) else: raise InputError("string not passed as argument for text_string")

python

def keyword_tokenize(text_string): ''' Extracts keywords from text_string using NLTK's list of English stopwords, ignoring words of a length smaller than 3, and returns the new string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): return " ".join([word for word in KEYWORD_TOKENIZER.tokenize(text_string) if word not in STOPWORDS and len(word) >= 3]) else: raise InputError("string not passed as argument for text_string")

Extracts keywords from text_string using NLTK's list of English stopwords, ignoring words of a length smaller than 3, and returns the new string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed

180c6472bc2642afbd7a1ece08d0b0d14968a708

https://github.com/SpotlightData/preprocessing/blob/180c6472bc2642afbd7a1ece08d0b0d14968a708/preprocessing/text.py#L120-L138

train

SpotlightData/preprocessing

preprocessing/text.py

lemmatize

def lemmatize(text_string): ''' Returns base from of text_string using NLTK's WordNetLemmatizer as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): return LEMMATIZER.lemmatize(text_string) else: raise InputError("string not passed as primary argument")

python

def lemmatize(text_string): ''' Returns base from of text_string using NLTK's WordNetLemmatizer as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): return LEMMATIZER.lemmatize(text_string) else: raise InputError("string not passed as primary argument")

Returns base from of text_string using NLTK's WordNetLemmatizer as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed

180c6472bc2642afbd7a1ece08d0b0d14968a708

https://github.com/SpotlightData/preprocessing/blob/180c6472bc2642afbd7a1ece08d0b0d14968a708/preprocessing/text.py#L140-L157

train

SpotlightData/preprocessing

preprocessing/text.py

lowercase

def lowercase(text_string): ''' Converts text_string into lowercase and returns the converted string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): return text_string.lower() else: raise InputError("string not passed as argument for text_string")

python

def lowercase(text_string): ''' Converts text_string into lowercase and returns the converted string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): return text_string.lower() else: raise InputError("string not passed as argument for text_string")

Converts text_string into lowercase and returns the converted string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed

180c6472bc2642afbd7a1ece08d0b0d14968a708

https://github.com/SpotlightData/preprocessing/blob/180c6472bc2642afbd7a1ece08d0b0d14968a708/preprocessing/text.py#L159-L176

train

SpotlightData/preprocessing

preprocessing/text.py

preprocess_text

def preprocess_text(text_string, function_list): ''' Given each function within function_list, applies the order of functions put forward onto text_string, returning the processed string as type str. Keyword argument: - function_list: list of functions available in preprocessing.text - text_string: string instance Exceptions raised: - FunctionError: occurs should an invalid function be passed within the list of functions - InputError: occurs should text_string be non-string, or function_list be non-list ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): if isinstance(function_list, list): for func in function_list: try: text_string = func(text_string) except (NameError, TypeError): raise FunctionError("invalid function passed as element of function_list") except: raise return text_string else: raise InputError("list of functions not passed as argument for function_list") else: raise InputError("string not passed as argument for text_string")

python

def preprocess_text(text_string, function_list): ''' Given each function within function_list, applies the order of functions put forward onto text_string, returning the processed string as type str. Keyword argument: - function_list: list of functions available in preprocessing.text - text_string: string instance Exceptions raised: - FunctionError: occurs should an invalid function be passed within the list of functions - InputError: occurs should text_string be non-string, or function_list be non-list ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): if isinstance(function_list, list): for func in function_list: try: text_string = func(text_string) except (NameError, TypeError): raise FunctionError("invalid function passed as element of function_list") except: raise return text_string else: raise InputError("list of functions not passed as argument for function_list") else: raise InputError("string not passed as argument for text_string")

Given each function within function_list, applies the order of functions put forward onto text_string, returning the processed string as type str. Keyword argument: - function_list: list of functions available in preprocessing.text - text_string: string instance Exceptions raised: - FunctionError: occurs should an invalid function be passed within the list of functions - InputError: occurs should text_string be non-string, or function_list be non-list

180c6472bc2642afbd7a1ece08d0b0d14968a708

https://github.com/SpotlightData/preprocessing/blob/180c6472bc2642afbd7a1ece08d0b0d14968a708/preprocessing/text.py#L178-L208

train

SpotlightData/preprocessing

preprocessing/text.py

remove_esc_chars

def remove_esc_chars(text_string): ''' Removes any escape character within text_string and returns the new string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): return " ".join(re.sub(r'\\\w', "", text_string).split()) else: raise InputError("string not passed as argument")

python

def remove_esc_chars(text_string): ''' Removes any escape character within text_string and returns the new string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): return " ".join(re.sub(r'\\\w', "", text_string).split()) else: raise InputError("string not passed as argument")

Removes any escape character within text_string and returns the new string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed

180c6472bc2642afbd7a1ece08d0b0d14968a708

https://github.com/SpotlightData/preprocessing/blob/180c6472bc2642afbd7a1ece08d0b0d14968a708/preprocessing/text.py#L210-L227

train

SpotlightData/preprocessing

preprocessing/text.py

remove_numbers

def remove_numbers(text_string): ''' Removes any digit value discovered within text_string and returns the new string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): return " ".join(re.sub(r'\b[\d.\/,]+', "", text_string).split()) else: raise InputError("string not passed as argument")

python

def remove_numbers(text_string): ''' Removes any digit value discovered within text_string and returns the new string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): return " ".join(re.sub(r'\b[\d.\/,]+', "", text_string).split()) else: raise InputError("string not passed as argument")

Removes any digit value discovered within text_string and returns the new string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed

180c6472bc2642afbd7a1ece08d0b0d14968a708

https://github.com/SpotlightData/preprocessing/blob/180c6472bc2642afbd7a1ece08d0b0d14968a708/preprocessing/text.py#L229-L246

train

SpotlightData/preprocessing

preprocessing/text.py

remove_number_words

def remove_number_words(text_string): ''' Removes any integer represented as a word within text_string and returns the new string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): for word in NUMBER_WORDS: text_string = re.sub(r'[\S]*\b'+word+r'[\S]*', "", text_string) return " ".join(text_string.split()) else: raise InputError("string not passed as argument")

python

def remove_number_words(text_string): ''' Removes any integer represented as a word within text_string and returns the new string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): for word in NUMBER_WORDS: text_string = re.sub(r'[\S]*\b'+word+r'[\S]*', "", text_string) return " ".join(text_string.split()) else: raise InputError("string not passed as argument")

Removes any integer represented as a word within text_string and returns the new string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed

180c6472bc2642afbd7a1ece08d0b0d14968a708

https://github.com/SpotlightData/preprocessing/blob/180c6472bc2642afbd7a1ece08d0b0d14968a708/preprocessing/text.py#L248-L268

train

SpotlightData/preprocessing

preprocessing/text.py

remove_urls

def remove_urls(text_string): ''' Removes all URLs within text_string and returns the new string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): return " ".join(re.sub(r'http\S+', "", text_string).split()) else: raise InputError("string not passed as argument")

python

def remove_urls(text_string): ''' Removes all URLs within text_string and returns the new string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): return " ".join(re.sub(r'http\S+', "", text_string).split()) else: raise InputError("string not passed as argument")

Removes all URLs within text_string and returns the new string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a non-string argument be passed

180c6472bc2642afbd7a1ece08d0b0d14968a708

https://github.com/SpotlightData/preprocessing/blob/180c6472bc2642afbd7a1ece08d0b0d14968a708/preprocessing/text.py#L313-L330

train

SpotlightData/preprocessing

preprocessing/text.py

remove_whitespace

def remove_whitespace(text_string): ''' Removes all whitespace found within text_string and returns new string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a string or NoneType not be passed as an argument ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): return " ".join(text_string.split()) else: raise InputError("none type or string not passed as an argument")

python

def remove_whitespace(text_string): ''' Removes all whitespace found within text_string and returns new string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a string or NoneType not be passed as an argument ''' if text_string is None or text_string == "": return "" elif isinstance(text_string, str): return " ".join(text_string.split()) else: raise InputError("none type or string not passed as an argument")

Removes all whitespace found within text_string and returns new string as type str. Keyword argument: - text_string: string instance Exceptions raised: - InputError: occurs should a string or NoneType not be passed as an argument

180c6472bc2642afbd7a1ece08d0b0d14968a708

https://github.com/SpotlightData/preprocessing/blob/180c6472bc2642afbd7a1ece08d0b0d14968a708/preprocessing/text.py#L332-L349

train

romaryd/python-logging-mixin

loggingmixin/__init__.py

WrappedLogger.log

def log(self, level, message, *args, **kwargs): """ This is the primary method to override to ensure logging with extra options gets correctly specified. """ extra = self.extras.copy() extra.update(kwargs.pop('extra', {})) kwargs['extra'] = extra self.logger.log(level, message, *args, **kwargs)

python

def log(self, level, message, *args, **kwargs): """ This is the primary method to override to ensure logging with extra options gets correctly specified. """ extra = self.extras.copy() extra.update(kwargs.pop('extra', {})) kwargs['extra'] = extra self.logger.log(level, message, *args, **kwargs)

This is the primary method to override to ensure logging with extra options gets correctly specified.

8ac77df5731b607e6ff9ef762e71398cb5a892ea

https://github.com/romaryd/python-logging-mixin/blob/8ac77df5731b607e6ff9ef762e71398cb5a892ea/loggingmixin/__init__.py#L90-L99

train

romaryd/python-logging-mixin

loggingmixin/__init__.py

WrappedLogger.warning

def warning(self, message, *args, **kwargs): """ Specialized warnings system. If a warning subclass is passed into the keyword arguments and raise_warnings is True - the warnning will be passed to the warnings module. """ warncls = kwargs.pop('warning', None) if warncls and self.raise_warnings: warnings.warn(message, warncls) return self.log(logging.WARNING, message, *args, **kwargs)

python

def warning(self, message, *args, **kwargs): """ Specialized warnings system. If a warning subclass is passed into the keyword arguments and raise_warnings is True - the warnning will be passed to the warnings module. """ warncls = kwargs.pop('warning', None) if warncls and self.raise_warnings: warnings.warn(message, warncls) return self.log(logging.WARNING, message, *args, **kwargs)

Specialized warnings system. If a warning subclass is passed into the keyword arguments and raise_warnings is True - the warnning will be passed to the warnings module.

8ac77df5731b607e6ff9ef762e71398cb5a892ea

https://github.com/romaryd/python-logging-mixin/blob/8ac77df5731b607e6ff9ef762e71398cb5a892ea/loggingmixin/__init__.py#L107-L117

train

romaryd/python-logging-mixin

loggingmixin/__init__.py

ServiceLogger.log

def log(self, level, message, *args, **kwargs): """ Provide current user as extra context to the logger """ extra = kwargs.pop('extra', {}) extra.update({ 'user': self.user }) kwargs['extra'] = extra super(ServiceLogger, self).log(level, message, *args, **kwargs)

python

def log(self, level, message, *args, **kwargs): """ Provide current user as extra context to the logger """ extra = kwargs.pop('extra', {}) extra.update({ 'user': self.user }) kwargs['extra'] = extra super(ServiceLogger, self).log(level, message, *args, **kwargs)

Provide current user as extra context to the logger

8ac77df5731b607e6ff9ef762e71398cb5a892ea

https://github.com/romaryd/python-logging-mixin/blob/8ac77df5731b607e6ff9ef762e71398cb5a892ea/loggingmixin/__init__.py#L147-L157

train

romaryd/python-logging-mixin

loggingmixin/__init__.py

LoggingMixin.logger

def logger(self): """ Instantiates and returns a ServiceLogger instance """ if not hasattr(self, '_logger') or not self._logger: self._logger = ServiceLogger() return self._logger

python

def logger(self): """ Instantiates and returns a ServiceLogger instance """ if not hasattr(self, '_logger') or not self._logger: self._logger = ServiceLogger() return self._logger

Instantiates and returns a ServiceLogger instance

8ac77df5731b607e6ff9ef762e71398cb5a892ea

https://github.com/romaryd/python-logging-mixin/blob/8ac77df5731b607e6ff9ef762e71398cb5a892ea/loggingmixin/__init__.py#L166-L172

train

OpenTreeOfLife/peyotl

tutorials/ot-oti-find-studies.py

ot_find_studies

def ot_find_studies(arg_dict, exact=True, verbose=False, oti_wrapper=None): """Uses a peyotl wrapper around an Open Tree web service to get a list of studies including values `value` for a given property to be searched on `porperty`. The oti_wrapper can be None (in which case the default wrapper from peyotl.sugar will be used. All other arguments correspond to the arguments of the web-service call. """ if oti_wrapper is None: from peyotl.sugar import oti oti_wrapper = oti return oti_wrapper.find_studies(arg_dict, exact=exact, verbose=verbose, wrap_response=True)

python

def ot_find_studies(arg_dict, exact=True, verbose=False, oti_wrapper=None): """Uses a peyotl wrapper around an Open Tree web service to get a list of studies including values `value` for a given property to be searched on `porperty`. The oti_wrapper can be None (in which case the default wrapper from peyotl.sugar will be used. All other arguments correspond to the arguments of the web-service call. """ if oti_wrapper is None: from peyotl.sugar import oti oti_wrapper = oti return oti_wrapper.find_studies(arg_dict, exact=exact, verbose=verbose, wrap_response=True)

Uses a peyotl wrapper around an Open Tree web service to get a list of studies including values `value` for a given property to be searched on `porperty`. The oti_wrapper can be None (in which case the default wrapper from peyotl.sugar will be used. All other arguments correspond to the arguments of the web-service call.

5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0

https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/tutorials/ot-oti-find-studies.py#L12-L25

train

OpenTreeOfLife/peyotl

tutorials/ot-oti-find-studies.py

main

def main(argv): """This function sets up a command-line option parser and then calls print_matching_trees to do all of the real work. """ import argparse description = 'Uses Open Tree of Life web services to try to find a tree with the value property pair specified. ' \ 'setting --fuzzy will allow fuzzy matching' parser = argparse.ArgumentParser(prog='ot-get-tree', description=description) parser.add_argument('arg_dict', type=json.loads, help='name(s) for which we will try to find OTT IDs') parser.add_argument('--property', default=None, type=str, required=False) parser.add_argument('--fuzzy', action='store_true', default=False, required=False) # exact matching and verbose not working atm... parser.add_argument('--verbose', action='store_true', default=False, required=False) try: args = parser.parse_args(argv) arg_dict = args.arg_dict exact = not args.fuzzy verbose = args.verbose except: arg_dict = {'ot:studyId': 'ot_308'} sys.stderr.write('Running a demonstration query with {}\n'.format(arg_dict)) exact = True verbose = False print_matching_studies(arg_dict, exact=exact, verbose=verbose)

python

def main(argv): """This function sets up a command-line option parser and then calls print_matching_trees to do all of the real work. """ import argparse description = 'Uses Open Tree of Life web services to try to find a tree with the value property pair specified. ' \ 'setting --fuzzy will allow fuzzy matching' parser = argparse.ArgumentParser(prog='ot-get-tree', description=description) parser.add_argument('arg_dict', type=json.loads, help='name(s) for which we will try to find OTT IDs') parser.add_argument('--property', default=None, type=str, required=False) parser.add_argument('--fuzzy', action='store_true', default=False, required=False) # exact matching and verbose not working atm... parser.add_argument('--verbose', action='store_true', default=False, required=False) try: args = parser.parse_args(argv) arg_dict = args.arg_dict exact = not args.fuzzy verbose = args.verbose except: arg_dict = {'ot:studyId': 'ot_308'} sys.stderr.write('Running a demonstration query with {}\n'.format(arg_dict)) exact = True verbose = False print_matching_studies(arg_dict, exact=exact, verbose=verbose)

This function sets up a command-line option parser and then calls print_matching_trees to do all of the real work.

5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0

https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/tutorials/ot-oti-find-studies.py#L36-L59

train

OpenTreeOfLife/peyotl

tutorials/ot-taxo-mrca-to-root.py

main

def main(argv): """This function sets up a command-line option parser and then calls to do all of the real work. """ import argparse import codecs # have to be ready to deal with utf-8 names out = codecs.getwriter('utf-8')(sys.stdout) description = '''Takes a series of at least 2 OTT ids and reports the OTT of their least inclusive taxonomic ancestor and that taxon's ancestors.''' parser = argparse.ArgumentParser(prog='ot-taxo-mrca-to-root', description=description) parser.add_argument('ids', nargs='+', type=int, help='OTT IDs') args = parser.parse_args(argv) id_list = args.ids last_id = id_list.pop() anc_list = get_taxonomic_ancestor_ids(last_id) common_anc = set(anc_list) for curr_id in id_list: curr_anc_set = set(get_taxonomic_ancestor_ids(curr_id)) common_anc &= curr_anc_set if not common_anc: break for anc_id in anc_list: if anc_id in common_anc: out.write('{}\n'.format(anc_id))

python

def main(argv): """This function sets up a command-line option parser and then calls to do all of the real work. """ import argparse import codecs # have to be ready to deal with utf-8 names out = codecs.getwriter('utf-8')(sys.stdout) description = '''Takes a series of at least 2 OTT ids and reports the OTT of their least inclusive taxonomic ancestor and that taxon's ancestors.''' parser = argparse.ArgumentParser(prog='ot-taxo-mrca-to-root', description=description) parser.add_argument('ids', nargs='+', type=int, help='OTT IDs') args = parser.parse_args(argv) id_list = args.ids last_id = id_list.pop() anc_list = get_taxonomic_ancestor_ids(last_id) common_anc = set(anc_list) for curr_id in id_list: curr_anc_set = set(get_taxonomic_ancestor_ids(curr_id)) common_anc &= curr_anc_set if not common_anc: break for anc_id in anc_list: if anc_id in common_anc: out.write('{}\n'.format(anc_id))

This function sets up a command-line option parser and then calls to do all of the real work.

5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0

https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/tutorials/ot-taxo-mrca-to-root.py#L23-L46

train

CybOXProject/mixbox

mixbox/datautils.py

is_sequence

def is_sequence(value): """Determine if a value is a sequence type. Returns: ``True`` if `value` is a sequence type (e.g., ``list``, or ``tuple``). String types will return ``False``. NOTE: On Python 3, strings have the __iter__ defined, so a simple hasattr check is insufficient. """ return (hasattr(value, "__iter__") and not isinstance(value, (six.string_types, six.binary_type)))

python

def is_sequence(value): """Determine if a value is a sequence type. Returns: ``True`` if `value` is a sequence type (e.g., ``list``, or ``tuple``). String types will return ``False``. NOTE: On Python 3, strings have the __iter__ defined, so a simple hasattr check is insufficient. """ return (hasattr(value, "__iter__") and not isinstance(value, (six.string_types, six.binary_type)))

Determine if a value is a sequence type. Returns: ``True`` if `value` is a sequence type (e.g., ``list``, or ``tuple``). String types will return ``False``. NOTE: On Python 3, strings have the __iter__ defined, so a simple hasattr check is insufficient.

9097dae7a433f5b98c18171c4a5598f69a7d30af

https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/datautils.py#L12-L23

train

CybOXProject/mixbox

mixbox/datautils.py

import_class

def import_class(classpath): """Import the class referred to by the fully qualified class path. Args: classpath: A full "foo.bar.MyClass" path to a class definition. Returns: The class referred to by the classpath. Raises: ImportError: If an error occurs while importing the module. AttributeError: IF the class does not exist in the imported module. """ modname, classname = classpath.rsplit(".", 1) module = importlib.import_module(modname) klass = getattr(module, classname) return klass

python

def import_class(classpath): """Import the class referred to by the fully qualified class path. Args: classpath: A full "foo.bar.MyClass" path to a class definition. Returns: The class referred to by the classpath. Raises: ImportError: If an error occurs while importing the module. AttributeError: IF the class does not exist in the imported module. """ modname, classname = classpath.rsplit(".", 1) module = importlib.import_module(modname) klass = getattr(module, classname) return klass

Import the class referred to by the fully qualified class path. Args: classpath: A full "foo.bar.MyClass" path to a class definition. Returns: The class referred to by the classpath. Raises: ImportError: If an error occurs while importing the module. AttributeError: IF the class does not exist in the imported module.

9097dae7a433f5b98c18171c4a5598f69a7d30af

https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/datautils.py#L26-L42

train

CybOXProject/mixbox

mixbox/datautils.py

resolve_class

def resolve_class(classref): """Attempt to return a Python class for the input class reference. If `classref` is a class or None, return it. If `classref` is a python classpath (e.g., "foo.bar.MyClass") import the class and return it. Args: classref: A fully-qualified Python path to class, or a Python class. Returns: A class. """ if classref is None: return None elif isinstance(classref, six.class_types): return classref elif isinstance(classref, six.string_types): return import_class(classref) else: raise ValueError("Unable to resolve class for '%s'" % classref)

python

def resolve_class(classref): """Attempt to return a Python class for the input class reference. If `classref` is a class or None, return it. If `classref` is a python classpath (e.g., "foo.bar.MyClass") import the class and return it. Args: classref: A fully-qualified Python path to class, or a Python class. Returns: A class. """ if classref is None: return None elif isinstance(classref, six.class_types): return classref elif isinstance(classref, six.string_types): return import_class(classref) else: raise ValueError("Unable to resolve class for '%s'" % classref)

Attempt to return a Python class for the input class reference. If `classref` is a class or None, return it. If `classref` is a python classpath (e.g., "foo.bar.MyClass") import the class and return it. Args: classref: A fully-qualified Python path to class, or a Python class. Returns: A class.

9097dae7a433f5b98c18171c4a5598f69a7d30af

https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/datautils.py#L45-L65

train

CybOXProject/mixbox

mixbox/datautils.py

needkwargs

def needkwargs(*argnames): """Function decorator which checks that the decorated function is called with a set of required kwargs. Args: *argnames: String keyword argument names. Raises: ValueError: If a required kwarg is missing in the decorated function call. """ required = set(argnames) def decorator(func): def inner(*args, **kwargs): missing = required - set(kwargs) if missing: err = "%s kwargs are missing." % list(missing) raise ValueError(err) return func(*args, **kwargs) return inner return decorator

python

def needkwargs(*argnames): """Function decorator which checks that the decorated function is called with a set of required kwargs. Args: *argnames: String keyword argument names. Raises: ValueError: If a required kwarg is missing in the decorated function call. """ required = set(argnames) def decorator(func): def inner(*args, **kwargs): missing = required - set(kwargs) if missing: err = "%s kwargs are missing." % list(missing) raise ValueError(err) return func(*args, **kwargs) return inner return decorator

Function decorator which checks that the decorated function is called with a set of required kwargs. Args: *argnames: String keyword argument names. Raises: ValueError: If a required kwarg is missing in the decorated function call.

9097dae7a433f5b98c18171c4a5598f69a7d30af

https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/datautils.py#L83-L104

train

flyte/apcaccess

apcaccess/status.py

get

def get(host="localhost", port=3551, timeout=30): """ Connect to the APCUPSd NIS and request its status. """ sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM) sock.settimeout(timeout) sock.connect((host, port)) sock.send(CMD_STATUS) buffr = "" while not buffr.endswith(EOF): buffr += sock.recv(BUFFER_SIZE).decode() sock.close() return buffr

python

def get(host="localhost", port=3551, timeout=30): """ Connect to the APCUPSd NIS and request its status. """ sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM) sock.settimeout(timeout) sock.connect((host, port)) sock.send(CMD_STATUS) buffr = "" while not buffr.endswith(EOF): buffr += sock.recv(BUFFER_SIZE).decode() sock.close() return buffr

Connect to the APCUPSd NIS and request its status.

0c8a5d5e4ba1c07110e411b4ffea4ddccef4829a

https://github.com/flyte/apcaccess/blob/0c8a5d5e4ba1c07110e411b4ffea4ddccef4829a/apcaccess/status.py#L31-L43

train

flyte/apcaccess

apcaccess/status.py

strip_units_from_lines

def strip_units_from_lines(lines): """ Removes all units from the ends of the lines. """ for line in lines: for unit in ALL_UNITS: if line.endswith(" %s" % unit): line = line[:-1-len(unit)] yield line

python

def strip_units_from_lines(lines): """ Removes all units from the ends of the lines. """ for line in lines: for unit in ALL_UNITS: if line.endswith(" %s" % unit): line = line[:-1-len(unit)] yield line

Removes all units from the ends of the lines.

0c8a5d5e4ba1c07110e411b4ffea4ddccef4829a

https://github.com/flyte/apcaccess/blob/0c8a5d5e4ba1c07110e411b4ffea4ddccef4829a/apcaccess/status.py#L69-L77

train

flyte/apcaccess

apcaccess/status.py

print_status

def print_status(raw_status, strip_units=False): """ Print the status to stdout in the same format as the original apcaccess. """ lines = split(raw_status) if strip_units: lines = strip_units_from_lines(lines) for line in lines: print(line)

python

def print_status(raw_status, strip_units=False): """ Print the status to stdout in the same format as the original apcaccess. """ lines = split(raw_status) if strip_units: lines = strip_units_from_lines(lines) for line in lines: print(line)

Print the status to stdout in the same format as the original apcaccess.

0c8a5d5e4ba1c07110e411b4ffea4ddccef4829a

https://github.com/flyte/apcaccess/blob/0c8a5d5e4ba1c07110e411b4ffea4ddccef4829a/apcaccess/status.py#L80-L88

train

OpenTreeOfLife/peyotl

peyotl/api/taxomachine.py

_TaxomachineAPIWrapper.get_cached_parent_for_taxon

def get_cached_parent_for_taxon(self, child_taxon): """If the taxa are being cached, this call will create a the lineage "spike" for taxon child_taxon Expecting child_taxon to have a non-empty _taxonomic_lineage with response dicts that can create an ancestral TaxonWrapper. """ if self._ott_id2taxon is None: resp = child_taxon._taxonomic_lineage[0] tl = child_taxon._taxonomic_lineage[1:] assert 'taxonomic_lineage' not in resp resp['taxonomic_lineage'] = tl return TaxonWrapper(taxonomy=child_taxon.taxonomy, taxomachine_wrapper=self._wr, prop_dict=resp) # TODO recursive (indirectly) else: anc = [] prev = None for resp in reversed(child_taxon._taxonomic_lineage): ott_id = resp['ot:ottId'] curr = self._ott_id2taxon.get(ott_id) if curr is None: assert 'taxonomic_lineage' not in resp assert 'parent' not in resp resp['parent'] = prev resp['taxonomic_lineage'] = anc curr = TaxonWrapper(taxonomy=child_taxon.taxonomy, taxomachine_wrapper=self._wr, prop_dict=resp) elif curr._parent is None and prev is not None: curr._parent = prev prev = curr anc.insert(0, curr) return prev

python

def get_cached_parent_for_taxon(self, child_taxon): """If the taxa are being cached, this call will create a the lineage "spike" for taxon child_taxon Expecting child_taxon to have a non-empty _taxonomic_lineage with response dicts that can create an ancestral TaxonWrapper. """ if self._ott_id2taxon is None: resp = child_taxon._taxonomic_lineage[0] tl = child_taxon._taxonomic_lineage[1:] assert 'taxonomic_lineage' not in resp resp['taxonomic_lineage'] = tl return TaxonWrapper(taxonomy=child_taxon.taxonomy, taxomachine_wrapper=self._wr, prop_dict=resp) # TODO recursive (indirectly) else: anc = [] prev = None for resp in reversed(child_taxon._taxonomic_lineage): ott_id = resp['ot:ottId'] curr = self._ott_id2taxon.get(ott_id) if curr is None: assert 'taxonomic_lineage' not in resp assert 'parent' not in resp resp['parent'] = prev resp['taxonomic_lineage'] = anc curr = TaxonWrapper(taxonomy=child_taxon.taxonomy, taxomachine_wrapper=self._wr, prop_dict=resp) elif curr._parent is None and prev is not None: curr._parent = prev prev = curr anc.insert(0, curr) return prev

If the taxa are being cached, this call will create a the lineage "spike" for taxon child_taxon Expecting child_taxon to have a non-empty _taxonomic_lineage with response dicts that can create an ancestral TaxonWrapper.

5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0

https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/api/taxomachine.py#L373-L405

train

OpenTreeOfLife/peyotl

peyotl/api/taxon.py

TaxonWrapper.update_empty_fields

def update_empty_fields(self, **kwargs): """Updates the field of info about an OTU that might not be filled in by a match_names or taxon call.""" if self._is_deprecated is None: self._is_deprecated = kwargs.get('is_deprecated') if self._is_dubious is None: self._is_dubious = kwargs.get('is_dubious') if self._is_synonym is None: self._is_synonym = kwargs.get('is_synonym') if self._synonyms is _EMPTY_TUPLE: self._synonyms = kwargs.get('synonyms') if self._synonyms is None: self._synonyms = _EMPTY_TUPLE if self.rank is None: self._rank = kwargs.get('rank') if self._nomenclature_code: self._nomenclature_code = kwargs.get('nomenclature_code') if not self._unique_name: self._unique_name = kwargs.get('unique_name') if self._taxonomic_lineage is None: self._taxonomic_lineage = kwargs.get('taxonomic_lineage') if self._parent is None: self._parent = kwargs.get('parent') if self._parent is None and self._taxomachine_wrapper is not None and self._taxonomic_lineage: self._fill_parent_attr()

python

def update_empty_fields(self, **kwargs): """Updates the field of info about an OTU that might not be filled in by a match_names or taxon call.""" if self._is_deprecated is None: self._is_deprecated = kwargs.get('is_deprecated') if self._is_dubious is None: self._is_dubious = kwargs.get('is_dubious') if self._is_synonym is None: self._is_synonym = kwargs.get('is_synonym') if self._synonyms is _EMPTY_TUPLE: self._synonyms = kwargs.get('synonyms') if self._synonyms is None: self._synonyms = _EMPTY_TUPLE if self.rank is None: self._rank = kwargs.get('rank') if self._nomenclature_code: self._nomenclature_code = kwargs.get('nomenclature_code') if not self._unique_name: self._unique_name = kwargs.get('unique_name') if self._taxonomic_lineage is None: self._taxonomic_lineage = kwargs.get('taxonomic_lineage') if self._parent is None: self._parent = kwargs.get('parent') if self._parent is None and self._taxomachine_wrapper is not None and self._taxonomic_lineage: self._fill_parent_attr()

Updates the field of info about an OTU that might not be filled in by a match_names or taxon call.

5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0

https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/api/taxon.py#L47-L70

train

OpenTreeOfLife/peyotl

scripts/nexson/prune_to_clean_mapped.py

_check_rev_dict

def _check_rev_dict(tree, ebt): """Verifyies that `ebt` is the inverse of the `edgeBySourceId` data member of `tree`""" ebs = defaultdict(dict) for edge in ebt.values(): source_id = edge['@source'] edge_id = edge['@id'] ebs[source_id][edge_id] = edge assert ebs == tree['edgeBySourceId']

python

def _check_rev_dict(tree, ebt): """Verifyies that `ebt` is the inverse of the `edgeBySourceId` data member of `tree`""" ebs = defaultdict(dict) for edge in ebt.values(): source_id = edge['@source'] edge_id = edge['@id'] ebs[source_id][edge_id] = edge assert ebs == tree['edgeBySourceId']

Verifyies that `ebt` is the inverse of the `edgeBySourceId` data member of `tree`

5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0

https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/scripts/nexson/prune_to_clean_mapped.py#L42-L49

train

OpenTreeOfLife/peyotl

scripts/nexson/prune_to_clean_mapped.py

NexsonTreeWrapper._create_edge_by_target

def _create_edge_by_target(self): """creates a edge_by_target dict with the same edge objects as the edge_by_source. Also adds an '@id' field to each edge.""" ebt = {} for edge_dict in self._edge_by_source.values(): for edge_id, edge in edge_dict.items(): target_id = edge['@target'] edge['@id'] = edge_id assert target_id not in ebt ebt[target_id] = edge # _check_rev_dict(self._tree, ebt) return ebt

python

def _create_edge_by_target(self): """creates a edge_by_target dict with the same edge objects as the edge_by_source. Also adds an '@id' field to each edge.""" ebt = {} for edge_dict in self._edge_by_source.values(): for edge_id, edge in edge_dict.items(): target_id = edge['@target'] edge['@id'] = edge_id assert target_id not in ebt ebt[target_id] = edge # _check_rev_dict(self._tree, ebt) return ebt

creates a edge_by_target dict with the same edge objects as the edge_by_source. Also adds an '@id' field to each edge.

5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0

https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/scripts/nexson/prune_to_clean_mapped.py#L86-L97

train

OpenTreeOfLife/peyotl

scripts/nexson/prune_to_clean_mapped.py

NexsonTreeWrapper.prune_to_ingroup

def prune_to_ingroup(self): """Remove nodes and edges from tree if they are not the ingroup or a descendant of it.""" # Prune to just the ingroup if not self._ingroup_node_id: _LOG.debug('No ingroup node was specified.') self._ingroup_node_id = self.root_node_id elif self._ingroup_node_id != self.root_node_id: self._do_prune_to_ingroup() self.root_node_id = self._ingroup_node_id else: _LOG.debug('Ingroup node is root.') return self.root_node_id

python

def prune_to_ingroup(self): """Remove nodes and edges from tree if they are not the ingroup or a descendant of it.""" # Prune to just the ingroup if not self._ingroup_node_id: _LOG.debug('No ingroup node was specified.') self._ingroup_node_id = self.root_node_id elif self._ingroup_node_id != self.root_node_id: self._do_prune_to_ingroup() self.root_node_id = self._ingroup_node_id else: _LOG.debug('Ingroup node is root.') return self.root_node_id

Remove nodes and edges from tree if they are not the ingroup or a descendant of it.

5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0

https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/scripts/nexson/prune_to_clean_mapped.py#L119-L130

train

OpenTreeOfLife/peyotl

scripts/nexson/prune_to_clean_mapped.py

NexsonTreeWrapper.prune_clade

def prune_clade(self, node_id): """Prune `node_id` and the edges and nodes that are tipward of it. Caller must delete the edge to node_id.""" to_del_nodes = [node_id] while bool(to_del_nodes): node_id = to_del_nodes.pop(0) self._flag_node_as_del_and_del_in_by_target(node_id) ebsd = self._edge_by_source.get(node_id) if ebsd is not None: child_edges = list(ebsd.values()) to_del_nodes.extend([i['@target'] for i in child_edges]) del self._edge_by_source[ node_id]

python

def prune_clade(self, node_id): """Prune `node_id` and the edges and nodes that are tipward of it. Caller must delete the edge to node_id.""" to_del_nodes = [node_id] while bool(to_del_nodes): node_id = to_del_nodes.pop(0) self._flag_node_as_del_and_del_in_by_target(node_id) ebsd = self._edge_by_source.get(node_id) if ebsd is not None: child_edges = list(ebsd.values()) to_del_nodes.extend([i['@target'] for i in child_edges]) del self._edge_by_source[ node_id]

Prune `node_id` and the edges and nodes that are tipward of it. Caller must delete the edge to node_id.

5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0

https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/scripts/nexson/prune_to_clean_mapped.py#L147-L159

train

OpenTreeOfLife/peyotl

scripts/nexson/prune_to_clean_mapped.py

NexsonTreeWrapper.suppress_deg_one_node

def suppress_deg_one_node(self, to_par_edge, nd_id, to_child_edge): """Deletes to_par_edge and nd_id. To be used when nd_id is an out-degree= 1 node""" # circumvent the node with nd_id to_child_edge_id = to_child_edge['@id'] par = to_par_edge['@source'] self._edge_by_source[par][to_child_edge_id] = to_child_edge to_child_edge['@source'] = par # make it a tip... del self._edge_by_source[nd_id] # delete it self._del_tip(nd_id)

python

def suppress_deg_one_node(self, to_par_edge, nd_id, to_child_edge): """Deletes to_par_edge and nd_id. To be used when nd_id is an out-degree= 1 node""" # circumvent the node with nd_id to_child_edge_id = to_child_edge['@id'] par = to_par_edge['@source'] self._edge_by_source[par][to_child_edge_id] = to_child_edge to_child_edge['@source'] = par # make it a tip... del self._edge_by_source[nd_id] # delete it self._del_tip(nd_id)

Deletes to_par_edge and nd_id. To be used when nd_id is an out-degree= 1 node

5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0

https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/scripts/nexson/prune_to_clean_mapped.py#L278-L288

train

palantir/typedjsonrpc

typedjsonrpc/method_info.py

MethodInfo.describe

def describe(self): """Describes the method. :return: Description :rtype: dict[str, object] """ return { "name": self.name, "params": self.params, "returns": self.returns, "description": self.description, }

python

def describe(self): """Describes the method. :return: Description :rtype: dict[str, object] """ return { "name": self.name, "params": self.params, "returns": self.returns, "description": self.description, }

Describes the method. :return: Description :rtype: dict[str, object]

274218fcd236ff9643506caa629029c9ba25a0fb

https://github.com/palantir/typedjsonrpc/blob/274218fcd236ff9643506caa629029c9ba25a0fb/typedjsonrpc/method_info.py#L36-L47

train

palantir/typedjsonrpc

typedjsonrpc/method_info.py

MethodInfo.params

def params(self): """The parameters for this method in a JSON-compatible format :rtype: list[dict[str, str]] """ return [{"name": p_name, "type": p_type.__name__} for (p_name, p_type) in self.signature.parameter_types]

python

def params(self): """The parameters for this method in a JSON-compatible format :rtype: list[dict[str, str]] """ return [{"name": p_name, "type": p_type.__name__} for (p_name, p_type) in self.signature.parameter_types]

The parameters for this method in a JSON-compatible format :rtype: list[dict[str, str]]

274218fcd236ff9643506caa629029c9ba25a0fb

https://github.com/palantir/typedjsonrpc/blob/274218fcd236ff9643506caa629029c9ba25a0fb/typedjsonrpc/method_info.py#L50-L56

train

palantir/typedjsonrpc

typedjsonrpc/method_info.py

MethodInfo.returns

def returns(self): """The return type for this method in a JSON-compatible format. This handles the special case of ``None`` which allows ``type(None)`` also. :rtype: str | None """ return_type = self.signature.return_type none_type = type(None) if return_type is not None and return_type is not none_type: return return_type.__name__

python

def returns(self): """The return type for this method in a JSON-compatible format. This handles the special case of ``None`` which allows ``type(None)`` also. :rtype: str | None """ return_type = self.signature.return_type none_type = type(None) if return_type is not None and return_type is not none_type: return return_type.__name__

The return type for this method in a JSON-compatible format. This handles the special case of ``None`` which allows ``type(None)`` also. :rtype: str | None

274218fcd236ff9643506caa629029c9ba25a0fb

https://github.com/palantir/typedjsonrpc/blob/274218fcd236ff9643506caa629029c9ba25a0fb/typedjsonrpc/method_info.py#L59-L69

train

palantir/typedjsonrpc

typedjsonrpc/method_info.py

MethodSignature.create

def create(parameter_names, parameter_types, return_type): """Returns a signature object ensuring order of parameter names and types. :param parameter_names: A list of ordered parameter names :type parameter_names: list[str] :param parameter_types: A dictionary of parameter names to types :type parameter_types: dict[str, type] :param return_type: The type the function returns :type return_type: type :rtype: MethodSignature """ ordered_pairs = [(name, parameter_types[name]) for name in parameter_names] return MethodSignature(ordered_pairs, return_type)

python

def create(parameter_names, parameter_types, return_type): """Returns a signature object ensuring order of parameter names and types. :param parameter_names: A list of ordered parameter names :type parameter_names: list[str] :param parameter_types: A dictionary of parameter names to types :type parameter_types: dict[str, type] :param return_type: The type the function returns :type return_type: type :rtype: MethodSignature """ ordered_pairs = [(name, parameter_types[name]) for name in parameter_names] return MethodSignature(ordered_pairs, return_type)

Returns a signature object ensuring order of parameter names and types. :param parameter_names: A list of ordered parameter names :type parameter_names: list[str] :param parameter_types: A dictionary of parameter names to types :type parameter_types: dict[str, type] :param return_type: The type the function returns :type return_type: type :rtype: MethodSignature

274218fcd236ff9643506caa629029c9ba25a0fb

https://github.com/palantir/typedjsonrpc/blob/274218fcd236ff9643506caa629029c9ba25a0fb/typedjsonrpc/method_info.py#L90-L102

train

OpenTreeOfLife/peyotl

peyotl/nexson_syntax/nexml2nexson.py

Nexml2Nexson._hbf_handle_child_elements

def _hbf_handle_child_elements(self, obj, ntl): """ Indirect recursion through _gen_hbf_el """ # accumulate a list of the children names in ko, and # the a dictionary of tag to xml elements. # repetition of a tag means that it will map to a list of # xml elements cd = {} ko = [] ks = set() for child in ntl: k = child.nodeName if k == 'meta' and (not self._badgerfish_style_conversion): matk, matv = self._transform_meta_key_value(child) if matk is not None: _add_value_to_dict_bf(obj, matk, matv) else: if k not in ks: ko.append(k) ks.add(k) _add_value_to_dict_bf(cd, k, child) # Converts the child XML elements to dicts by recursion and # adds these to the dict. for k in ko: v = _index_list_of_values(cd, k) dcl = [] ct = None for xc in v: ct, dc = self._gen_hbf_el(xc) dcl.append(dc) # this assertion will trip is the hacky stripping of namespaces # results in a name clash among the tags of the children assert ct not in obj obj[ct] = dcl # delete redundant about attributes that are used in XML, but not JSON (last rule of HoneyBadgerFish) _cull_redundant_about(obj) return obj

python

def _hbf_handle_child_elements(self, obj, ntl): """ Indirect recursion through _gen_hbf_el """ # accumulate a list of the children names in ko, and # the a dictionary of tag to xml elements. # repetition of a tag means that it will map to a list of # xml elements cd = {} ko = [] ks = set() for child in ntl: k = child.nodeName if k == 'meta' and (not self._badgerfish_style_conversion): matk, matv = self._transform_meta_key_value(child) if matk is not None: _add_value_to_dict_bf(obj, matk, matv) else: if k not in ks: ko.append(k) ks.add(k) _add_value_to_dict_bf(cd, k, child) # Converts the child XML elements to dicts by recursion and # adds these to the dict. for k in ko: v = _index_list_of_values(cd, k) dcl = [] ct = None for xc in v: ct, dc = self._gen_hbf_el(xc) dcl.append(dc) # this assertion will trip is the hacky stripping of namespaces # results in a name clash among the tags of the children assert ct not in obj obj[ct] = dcl # delete redundant about attributes that are used in XML, but not JSON (last rule of HoneyBadgerFish) _cull_redundant_about(obj) return obj

Indirect recursion through _gen_hbf_el

5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0

https://github.com/OpenTreeOfLife/peyotl/blob/5e4e52a0fdbd17f490aa644ad79fda6ea2eda7c0/peyotl/nexson_syntax/nexml2nexson.py#L169-L208

train

CybOXProject/mixbox

mixbox/xml.py

get_xml_parser

def get_xml_parser(encoding=None): """Returns an ``etree.ETCompatXMLParser`` instance.""" parser = etree.ETCompatXMLParser( huge_tree=True, remove_comments=True, strip_cdata=False, remove_blank_text=True, resolve_entities=False, encoding=encoding ) return parser

python

def get_xml_parser(encoding=None): """Returns an ``etree.ETCompatXMLParser`` instance.""" parser = etree.ETCompatXMLParser( huge_tree=True, remove_comments=True, strip_cdata=False, remove_blank_text=True, resolve_entities=False, encoding=encoding ) return parser

Returns an ``etree.ETCompatXMLParser`` instance.

9097dae7a433f5b98c18171c4a5598f69a7d30af

https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/xml.py#L34-L45

train

CybOXProject/mixbox

mixbox/xml.py

get_etree_root

def get_etree_root(doc, encoding=None): """Returns an instance of lxml.etree._Element for the given `doc` input. Args: doc: The input XML document. Can be an instance of ``lxml.etree._Element``, ``lxml.etree._ElementTree``, a file-like object, or a string filename. encoding: The character encoding of `doc`. If ``None``, an attempt will be made to determine the character encoding by the XML parser. Returns: An ``lxml.etree._Element`` instance for `doc`. Raises: IOError: If `doc` cannot be found. lxml.ParseError: If `doc` is a malformed XML document. """ tree = get_etree(doc, encoding) root = tree.getroot() return root

python

def get_etree_root(doc, encoding=None): """Returns an instance of lxml.etree._Element for the given `doc` input. Args: doc: The input XML document. Can be an instance of ``lxml.etree._Element``, ``lxml.etree._ElementTree``, a file-like object, or a string filename. encoding: The character encoding of `doc`. If ``None``, an attempt will be made to determine the character encoding by the XML parser. Returns: An ``lxml.etree._Element`` instance for `doc`. Raises: IOError: If `doc` cannot be found. lxml.ParseError: If `doc` is a malformed XML document. """ tree = get_etree(doc, encoding) root = tree.getroot() return root

Returns an instance of lxml.etree._Element for the given `doc` input. Args: doc: The input XML document. Can be an instance of ``lxml.etree._Element``, ``lxml.etree._ElementTree``, a file-like object, or a string filename. encoding: The character encoding of `doc`. If ``None``, an attempt will be made to determine the character encoding by the XML parser. Returns: An ``lxml.etree._Element`` instance for `doc`. Raises: IOError: If `doc` cannot be found. lxml.ParseError: If `doc` is a malformed XML document.

9097dae7a433f5b98c18171c4a5598f69a7d30af

https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/xml.py#L58-L80

train

CybOXProject/mixbox

mixbox/xml.py

strip_cdata

def strip_cdata(text): """Removes all CDATA blocks from `text` if it contains them. Note: If the function contains escaped XML characters outside of a CDATA block, they will be unescaped. Args: A string containing one or more CDATA blocks. Returns: An XML unescaped string with CDATA block qualifiers removed. """ if not is_cdata(text): return text xml = "<e>{0}</e>".format(text) node = etree.fromstring(xml) return node.text

python

def strip_cdata(text): """Removes all CDATA blocks from `text` if it contains them. Note: If the function contains escaped XML characters outside of a CDATA block, they will be unescaped. Args: A string containing one or more CDATA blocks. Returns: An XML unescaped string with CDATA block qualifiers removed. """ if not is_cdata(text): return text xml = "<e>{0}</e>".format(text) node = etree.fromstring(xml) return node.text

Removes all CDATA blocks from `text` if it contains them. Note: If the function contains escaped XML characters outside of a CDATA block, they will be unescaped. Args: A string containing one or more CDATA blocks. Returns: An XML unescaped string with CDATA block qualifiers removed.

9097dae7a433f5b98c18171c4a5598f69a7d30af

https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/xml.py#L114-L133

train

CybOXProject/mixbox

mixbox/typedlist.py

TypedList._is_valid

def _is_valid(self, value): """Return True if the input value is valid for insertion into the inner list. Args: value: An object about to be inserted. """ # Entities have an istypeof method that can perform more sophisticated # type checking. if hasattr(self._type, "istypeof"): return self._type.istypeof(value) else: return isinstance(value, self._type)

python

def _is_valid(self, value): """Return True if the input value is valid for insertion into the inner list. Args: value: An object about to be inserted. """ # Entities have an istypeof method that can perform more sophisticated # type checking. if hasattr(self._type, "istypeof"): return self._type.istypeof(value) else: return isinstance(value, self._type)

Return True if the input value is valid for insertion into the inner list. Args: value: An object about to be inserted.

9097dae7a433f5b98c18171c4a5598f69a7d30af

https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/typedlist.py#L40-L53

train

CybOXProject/mixbox

mixbox/typedlist.py

TypedList._fix_value

def _fix_value(self, value): """Attempt to coerce value into the correct type. Subclasses can override this function. """ try: return self._castfunc(value) except: error = "Can't put '{0}' ({1}) into a {2}. Expected a {3} object." error = error.format( value, # Input value type(value), # Type of input value type(self), # Type of collection self._type # Expected type of input value ) six.reraise(TypeError, TypeError(error), sys.exc_info()[-1])

python

def _fix_value(self, value): """Attempt to coerce value into the correct type. Subclasses can override this function. """ try: return self._castfunc(value) except: error = "Can't put '{0}' ({1}) into a {2}. Expected a {3} object." error = error.format( value, # Input value type(value), # Type of input value type(self), # Type of collection self._type # Expected type of input value ) six.reraise(TypeError, TypeError(error), sys.exc_info()[-1])

Attempt to coerce value into the correct type. Subclasses can override this function.

9097dae7a433f5b98c18171c4a5598f69a7d30af

https://github.com/CybOXProject/mixbox/blob/9097dae7a433f5b98c18171c4a5598f69a7d30af/mixbox/typedlist.py#L55-L70

train

hsolbrig/pyjsg

pyjsg/parser_impl/jsg_pairdef_parser.py

JSGPairDef.members_entries

def members_entries(self, all_are_optional: Optional[bool] = False) -> List[Tuple[str, str]]: """ Generate a list quoted raw name, signature type entries for this pairdef, recursively traversing reference types :param all_are_optional: If true, all types are forced optional :return: raw name/ signature type for all elements in this pair """ if self._type_reference: rval: List[Tuple[str, str]] = [] for n, t in self._context.reference(self._type_reference).members_entries(all_are_optional): rval.append((n, self._ebnf.signature_cardinality(t, all_are_optional).format(name=n))) return rval else: sig = self._ebnf.signature_cardinality(self._typ.reference_type(), all_are_optional) return [(name, sig.format(name=name)) for name in self._names]

python

def members_entries(self, all_are_optional: Optional[bool] = False) -> List[Tuple[str, str]]: """ Generate a list quoted raw name, signature type entries for this pairdef, recursively traversing reference types :param all_are_optional: If true, all types are forced optional :return: raw name/ signature type for all elements in this pair """ if self._type_reference: rval: List[Tuple[str, str]] = [] for n, t in self._context.reference(self._type_reference).members_entries(all_are_optional): rval.append((n, self._ebnf.signature_cardinality(t, all_are_optional).format(name=n))) return rval else: sig = self._ebnf.signature_cardinality(self._typ.reference_type(), all_are_optional) return [(name, sig.format(name=name)) for name in self._names]

Generate a list quoted raw name, signature type entries for this pairdef, recursively traversing reference types :param all_are_optional: If true, all types are forced optional :return: raw name/ signature type for all elements in this pair

9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7

https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/jsg_pairdef_parser.py#L43-L57

train

hsolbrig/pyjsg

pyjsg/parser_impl/jsg_pairdef_parser.py

JSGPairDef._initializer_for

def _initializer_for(self, raw_name: str, cooked_name: str, prefix: Optional[str]) -> List[str]: """Create an initializer entry for the entry :param raw_name: name unadjusted for python compatibility. :param cooked_name: name that may or may not be python compatible :param prefix: owner of the element - used when objects passed as arguments :return: Initialization statements """ mt_val = self._ebnf.mt_value(self._typ) rval = [] if is_valid_python(raw_name): if prefix: # If a prefix exists, the input has already been processed - no if clause is necessary rval.append(f"self.{raw_name} = {prefix}.{raw_name}") else: cons = raw_name rval.append(f"self.{raw_name} = {cons}") elif is_valid_python(cooked_name): if prefix: rval.append(f"setattr(self, '{raw_name}', getattr({prefix}, '{raw_name}')") else: cons = f"{cooked_name} if {cooked_name} is not {mt_val} else _kwargs.get('{raw_name}', {mt_val})" rval.append(f"setattr(self, '{raw_name}', {cons})") else: getter = f"_kwargs.get('{raw_name}', {mt_val})" if prefix: rval.append(f"setattr(self, '{raw_name}', getattr({prefix}, '{getter}')") else: rval.append(f"setattr(self, '{raw_name}', {getter})") return rval

python

def _initializer_for(self, raw_name: str, cooked_name: str, prefix: Optional[str]) -> List[str]: """Create an initializer entry for the entry :param raw_name: name unadjusted for python compatibility. :param cooked_name: name that may or may not be python compatible :param prefix: owner of the element - used when objects passed as arguments :return: Initialization statements """ mt_val = self._ebnf.mt_value(self._typ) rval = [] if is_valid_python(raw_name): if prefix: # If a prefix exists, the input has already been processed - no if clause is necessary rval.append(f"self.{raw_name} = {prefix}.{raw_name}") else: cons = raw_name rval.append(f"self.{raw_name} = {cons}") elif is_valid_python(cooked_name): if prefix: rval.append(f"setattr(self, '{raw_name}', getattr({prefix}, '{raw_name}')") else: cons = f"{cooked_name} if {cooked_name} is not {mt_val} else _kwargs.get('{raw_name}', {mt_val})" rval.append(f"setattr(self, '{raw_name}', {cons})") else: getter = f"_kwargs.get('{raw_name}', {mt_val})" if prefix: rval.append(f"setattr(self, '{raw_name}', getattr({prefix}, '{getter}')") else: rval.append(f"setattr(self, '{raw_name}', {getter})") return rval

Create an initializer entry for the entry :param raw_name: name unadjusted for python compatibility. :param cooked_name: name that may or may not be python compatible :param prefix: owner of the element - used when objects passed as arguments :return: Initialization statements

9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7

https://github.com/hsolbrig/pyjsg/blob/9b2b8fa8e3b8448abe70b09f804a79f0f31b32b7/pyjsg/parser_impl/jsg_pairdef_parser.py#L96-L129

train

PSPC-SPAC-buyandsell/von_agent

von_agent/agent/holder_prover.py

HolderProver._assert_link_secret

def _assert_link_secret(self, action: str): """ Raise AbsentLinkSecret if link secret is not set. :param action: action requiring link secret """ if self._link_secret is None: LOGGER.debug('HolderProver._assert_link_secret: action %s requires link secret but it is not set', action) raise AbsentLinkSecret('Action {} requires link secret but it is not set'.format(action))

python

def _assert_link_secret(self, action: str): """ Raise AbsentLinkSecret if link secret is not set. :param action: action requiring link secret """ if self._link_secret is None: LOGGER.debug('HolderProver._assert_link_secret: action %s requires link secret but it is not set', action) raise AbsentLinkSecret('Action {} requires link secret but it is not set'.format(action))

Raise AbsentLinkSecret if link secret is not set. :param action: action requiring link secret

0b1c17cca3bd178b6e6974af84dbac1dfce5cf45

https://github.com/PSPC-SPAC-buyandsell/von_agent/blob/0b1c17cca3bd178b6e6974af84dbac1dfce5cf45/von_agent/agent/holder_prover.py#L90-L99

train

PSPC-SPAC-buyandsell/von_agent

von_agent/agent/holder_prover.py

HolderProver.rev_regs

def rev_regs(self) -> list: """ Return list of revocation registry identifiers for which HolderProver has tails files. :return: list of revocation registry identifiers for which HolderProver has tails files """ LOGGER.debug('HolderProver.rev_regs >>>') rv = [basename(f) for f in Tails.links(self._dir_tails)] LOGGER.debug('HolderProver.rev_regs <<< %s', rv) return rv

python

def rev_regs(self) -> list: """ Return list of revocation registry identifiers for which HolderProver has tails files. :return: list of revocation registry identifiers for which HolderProver has tails files """ LOGGER.debug('HolderProver.rev_regs >>>') rv = [basename(f) for f in Tails.links(self._dir_tails)] LOGGER.debug('HolderProver.rev_regs <<< %s', rv) return rv

Return list of revocation registry identifiers for which HolderProver has tails files. :return: list of revocation registry identifiers for which HolderProver has tails files

0b1c17cca3bd178b6e6974af84dbac1dfce5cf45

https://github.com/PSPC-SPAC-buyandsell/von_agent/blob/0b1c17cca3bd178b6e6974af84dbac1dfce5cf45/von_agent/agent/holder_prover.py#L539-L550

train

PSPC-SPAC-buyandsell/von_agent

von_agent/agent/holder_prover.py

HolderProver.create_cred_req

async def create_cred_req(self, cred_offer_json: str, cd_id: str) -> (str, str): """ Create credential request as HolderProver and store in wallet; return credential json and metadata json. Raise AbsentLinkSecret if link secret not set. :param cred_offer_json: credential offer json :param cd_id: credential definition identifier :return: cred request json and corresponding metadata json as created and stored in wallet """ LOGGER.debug('HolderProver.create_cred_req >>> cred_offer_json: %s, cd_id: %s', cred_offer_json, cd_id) self._assert_link_secret('create_cred_req') # Check that ledger has schema on ledger where cred def expects - in case of pool reset with extant wallet cred_def_json = await self.get_cred_def(cd_id) schema_seq_no = int(json.loads(cred_def_json)['schemaId']) schema_json = await self.get_schema(schema_seq_no) schema = json.loads(schema_json) if not schema: LOGGER.debug( 'HolderProver.create_cred_req: <!< absent schema@#%s, cred req may be for another ledger', schema_seq_no) raise AbsentSchema('Absent schema@#{}, cred req may be for another ledger'.format(schema_seq_no)) (cred_req_json, cred_req_metadata_json) = await anoncreds.prover_create_credential_req( self.wallet.handle, self.did, cred_offer_json, cred_def_json, self._link_secret) rv = (cred_req_json, cred_req_metadata_json) LOGGER.debug('HolderProver.create_cred_req <<< %s', rv) return rv

python

async def create_cred_req(self, cred_offer_json: str, cd_id: str) -> (str, str): """ Create credential request as HolderProver and store in wallet; return credential json and metadata json. Raise AbsentLinkSecret if link secret not set. :param cred_offer_json: credential offer json :param cd_id: credential definition identifier :return: cred request json and corresponding metadata json as created and stored in wallet """ LOGGER.debug('HolderProver.create_cred_req >>> cred_offer_json: %s, cd_id: %s', cred_offer_json, cd_id) self._assert_link_secret('create_cred_req') # Check that ledger has schema on ledger where cred def expects - in case of pool reset with extant wallet cred_def_json = await self.get_cred_def(cd_id) schema_seq_no = int(json.loads(cred_def_json)['schemaId']) schema_json = await self.get_schema(schema_seq_no) schema = json.loads(schema_json) if not schema: LOGGER.debug( 'HolderProver.create_cred_req: <!< absent schema@#%s, cred req may be for another ledger', schema_seq_no) raise AbsentSchema('Absent schema@#{}, cred req may be for another ledger'.format(schema_seq_no)) (cred_req_json, cred_req_metadata_json) = await anoncreds.prover_create_credential_req( self.wallet.handle, self.did, cred_offer_json, cred_def_json, self._link_secret) rv = (cred_req_json, cred_req_metadata_json) LOGGER.debug('HolderProver.create_cred_req <<< %s', rv) return rv

Create credential request as HolderProver and store in wallet; return credential json and metadata json. Raise AbsentLinkSecret if link secret not set. :param cred_offer_json: credential offer json :param cd_id: credential definition identifier :return: cred request json and corresponding metadata json as created and stored in wallet

0b1c17cca3bd178b6e6974af84dbac1dfce5cf45

https://github.com/PSPC-SPAC-buyandsell/von_agent/blob/0b1c17cca3bd178b6e6974af84dbac1dfce5cf45/von_agent/agent/holder_prover.py#L578-L612

train

PSPC-SPAC-buyandsell/von_agent

von_agent/agent/holder_prover.py

HolderProver.load_cache

async def load_cache(self, archive: bool = False) -> int: """ Load caches and archive enough to go offline and be able to generate proof on all credentials in wallet. Return timestamp (epoch seconds) of cache load event, also used as subdirectory for cache archives. :return: cache load event timestamp (epoch seconds) """ LOGGER.debug('HolderProver.load_cache >>> archive: %s', archive) rv = int(time()) box_ids = json.loads(await self.get_box_ids_json()) for s_id in box_ids['schema_id']: with SCHEMA_CACHE.lock: await self.get_schema(s_id) for cd_id in box_ids['cred_def_id']: with CRED_DEF_CACHE.lock: await self.get_cred_def(cd_id) for rr_id in box_ids['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_delta_json(self._build_rr_delta_json, rv, rv) except ClosedPool: LOGGER.warning( 'Holder-Prover %s is offline from pool %s, cannot update revo cache reg delta for %s to %s', self.wallet.name, self.pool.name, rr_id, rv) if archive: Caches.archive(self.dir_cache) LOGGER.debug('HolderProver.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 generate proof on all credentials in wallet. Return timestamp (epoch seconds) of cache load event, also used as subdirectory for cache archives. :return: cache load event timestamp (epoch seconds) """ LOGGER.debug('HolderProver.load_cache >>> archive: %s', archive) rv = int(time()) box_ids = json.loads(await self.get_box_ids_json()) for s_id in box_ids['schema_id']: with SCHEMA_CACHE.lock: await self.get_schema(s_id) for cd_id in box_ids['cred_def_id']: with CRED_DEF_CACHE.lock: await self.get_cred_def(cd_id) for rr_id in box_ids['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_delta_json(self._build_rr_delta_json, rv, rv) except ClosedPool: LOGGER.warning( 'Holder-Prover %s is offline from pool %s, cannot update revo cache reg delta for %s to %s', self.wallet.name, self.pool.name, rr_id, rv) if archive: Caches.archive(self.dir_cache) LOGGER.debug('HolderProver.load_cache <<< %s', rv) return rv

Load caches and archive enough to go offline and be able to generate proof on all credentials in wallet. Return timestamp (epoch seconds) of cache load event, also used as subdirectory for cache archives. :return: cache load event timestamp (epoch seconds)

0b1c17cca3bd178b6e6974af84dbac1dfce5cf45

https://github.com/PSPC-SPAC-buyandsell/von_agent/blob/0b1c17cca3bd178b6e6974af84dbac1dfce5cf45/von_agent/agent/holder_prover.py#L649-L688

train

PSPC-SPAC-buyandsell/von_agent

von_agent/agent/holder_prover.py

HolderProver.get_creds

async def get_creds(self, proof_req_json: str, filt: dict = None, filt_dflt_incl: bool = False) -> (Set[str], str): """ Get credentials from HolderProver wallet corresponding to proof request and filter criteria; return credential identifiers from wallet and credentials json. Return empty set and empty production for no such credentials. :param proof_req_json: proof request json as Verifier creates; has entries for proof request's nonce, name, and version; plus credential's requested attributes, requested predicates. I.e., :: { 'nonce': string, # indy-sdk makes no semantic specification on this value 'name': string, # indy-sdk makes no semantic specification on this value 'version': numeric-string, # indy-sdk makes no semantic specification on this value 'requested_attributes': { '<attr_uuid>': { # aka attr_referent, a proof-request local identifier 'name': string, # attribute name (matches case- and space-insensitively) 'restrictions' [ # optional { "schema_id": string, # optional "schema_issuer_did": string, # optional "schema_name": string, # optional "schema_version": string, # optional "issuer_did": string, # optional "cred_def_id": string # optional }, { ... # if more than one restriction given, combined disjunctively (i.e., via OR) } ], 'non_revoked': { # optional - indy-sdk ignores when getting creds from wallet 'from': int, # optional, epoch seconds 'to': int # optional, epoch seconds } }, ... }, 'requested_predicates': { '<pred_uuid>': { # aka predicate_referent, a proof-request local predicate identifier 'name': string, # attribute name (matches case- and space-insensitively) 'p_type': '>=', 'p_value': int, # predicate value 'restrictions': [ # optional { "schema_id": string, # optional "schema_issuer_did": string, # optional "schema_name": string, # optional "schema_version": string, # optional "issuer_did": string, # optional "cred_def_id": string # optional }, { ... # if more than one restriction given, combined disjunctively (i.e., via OR) } ], 'non_revoked': { # optional - indy-sdk ignores when getting creds from wallet 'from': int, # optional, epoch seconds 'to': int # optional, epoch seconds } }, ... }, 'non_revoked': { # optional - indy-sdk ignores when getting creds from wallet 'from': Optional<int>, 'to': Optional<int> } } :param filt: filter for matching attribute-value pairs and predicates; dict mapping each cred def id to dict (specify empty dict or none for no filter, matching all) mapping attributes to values to match or compare. E.g., :: { 'Vx4E82R17q...:3:CL:16:0': { 'attr-match': { 'name': 'Alex', 'sex': 'M', 'favouriteDrink': None }, 'minima': { # if both attr-match and minima present, combined conjunctively (i.e., via AND) 'favouriteNumber' : 10, 'score': '100' # nicety: implementation converts to int for caller }, }, 'R17v42T4pk...:3:CL:19:0': { 'attr-match': { 'height': 175, 'birthdate': '1975-11-15' # combined conjunctively (i.e., via AND) } }, 'Z9ccax812j...:3:CL:27:0': { 'attr-match': {} # match all attributes on this cred def } ... } :param filt_dflt_incl: whether to include (True) all credentials from wallet that filter does not identify by cred def, or to exclude (False) all such credentials :return: tuple with (set of referents, creds json for input proof request); empty set and empty production for no such credential """ LOGGER.debug('HolderProver.get_creds >>> proof_req_json: %s, filt: %s', proof_req_json, filt) if filt is None: filt = {} rv = None creds_json = await anoncreds.prover_get_credentials_for_proof_req(self.wallet.handle, proof_req_json) creds = json.loads(creds_json) cred_ids = set() if filt: for cd_id in filt: try: json.loads(await self.get_cred_def(cd_id)) except AbsentCredDef: LOGGER.warning('HolderProver.get_creds: ignoring filter criterion, no cred def on %s', cd_id) filt.pop(cd_id) for inner_creds in {**creds['attrs'], **creds['predicates']}.values(): for cred in inner_creds: # cred is a dict in a list of dicts cred_info = cred['cred_info'] if filt: cred_cd_id = cred_info['cred_def_id'] if cred_cd_id not in filt: if filt_dflt_incl: cred_ids.add(cred_info['referent']) continue if 'attr-match' in (filt[cred_cd_id] or {}): # maybe filt[cred_cd_id]: None if not {k: str(filt[cred_cd_id].get('attr-match', {})[k]) for k in filt[cred_cd_id].get('attr-match', {})}.items() <= cred_info['attrs'].items(): continue if 'minima' in (filt[cred_cd_id] or {}): # maybe filt[cred_cd_id]: None minima = filt[cred_cd_id].get('minima', {}) try: if any((attr not in cred_info['attrs']) or (int(cred_info['attrs'][attr]) < int(minima[attr])) for attr in minima): continue except ValueError: continue # int conversion failed - reject candidate cred_ids.add(cred_info['referent']) else: cred_ids.add(cred_info['referent']) if filt: creds = json.loads(prune_creds_json(creds, cred_ids)) rv = (cred_ids, json.dumps(creds)) LOGGER.debug('HolderProver.get_creds <<< %s', rv) return rv

python

async def get_creds(self, proof_req_json: str, filt: dict = None, filt_dflt_incl: bool = False) -> (Set[str], str): """ Get credentials from HolderProver wallet corresponding to proof request and filter criteria; return credential identifiers from wallet and credentials json. Return empty set and empty production for no such credentials. :param proof_req_json: proof request json as Verifier creates; has entries for proof request's nonce, name, and version; plus credential's requested attributes, requested predicates. I.e., :: { 'nonce': string, # indy-sdk makes no semantic specification on this value 'name': string, # indy-sdk makes no semantic specification on this value 'version': numeric-string, # indy-sdk makes no semantic specification on this value 'requested_attributes': { '<attr_uuid>': { # aka attr_referent, a proof-request local identifier 'name': string, # attribute name (matches case- and space-insensitively) 'restrictions' [ # optional { "schema_id": string, # optional "schema_issuer_did": string, # optional "schema_name": string, # optional "schema_version": string, # optional "issuer_did": string, # optional "cred_def_id": string # optional }, { ... # if more than one restriction given, combined disjunctively (i.e., via OR) } ], 'non_revoked': { # optional - indy-sdk ignores when getting creds from wallet 'from': int, # optional, epoch seconds 'to': int # optional, epoch seconds } }, ... }, 'requested_predicates': { '<pred_uuid>': { # aka predicate_referent, a proof-request local predicate identifier 'name': string, # attribute name (matches case- and space-insensitively) 'p_type': '>=', 'p_value': int, # predicate value 'restrictions': [ # optional { "schema_id": string, # optional "schema_issuer_did": string, # optional "schema_name": string, # optional "schema_version": string, # optional "issuer_did": string, # optional "cred_def_id": string # optional }, { ... # if more than one restriction given, combined disjunctively (i.e., via OR) } ], 'non_revoked': { # optional - indy-sdk ignores when getting creds from wallet 'from': int, # optional, epoch seconds 'to': int # optional, epoch seconds } }, ... }, 'non_revoked': { # optional - indy-sdk ignores when getting creds from wallet 'from': Optional<int>, 'to': Optional<int> } } :param filt: filter for matching attribute-value pairs and predicates; dict mapping each cred def id to dict (specify empty dict or none for no filter, matching all) mapping attributes to values to match or compare. E.g., :: { 'Vx4E82R17q...:3:CL:16:0': { 'attr-match': { 'name': 'Alex', 'sex': 'M', 'favouriteDrink': None }, 'minima': { # if both attr-match and minima present, combined conjunctively (i.e., via AND) 'favouriteNumber' : 10, 'score': '100' # nicety: implementation converts to int for caller }, }, 'R17v42T4pk...:3:CL:19:0': { 'attr-match': { 'height': 175, 'birthdate': '1975-11-15' # combined conjunctively (i.e., via AND) } }, 'Z9ccax812j...:3:CL:27:0': { 'attr-match': {} # match all attributes on this cred def } ... } :param filt_dflt_incl: whether to include (True) all credentials from wallet that filter does not identify by cred def, or to exclude (False) all such credentials :return: tuple with (set of referents, creds json for input proof request); empty set and empty production for no such credential """ LOGGER.debug('HolderProver.get_creds >>> proof_req_json: %s, filt: %s', proof_req_json, filt) if filt is None: filt = {} rv = None creds_json = await anoncreds.prover_get_credentials_for_proof_req(self.wallet.handle, proof_req_json) creds = json.loads(creds_json) cred_ids = set() if filt: for cd_id in filt: try: json.loads(await self.get_cred_def(cd_id)) except AbsentCredDef: LOGGER.warning('HolderProver.get_creds: ignoring filter criterion, no cred def on %s', cd_id) filt.pop(cd_id) for inner_creds in {**creds['attrs'], **creds['predicates']}.values(): for cred in inner_creds: # cred is a dict in a list of dicts cred_info = cred['cred_info'] if filt: cred_cd_id = cred_info['cred_def_id'] if cred_cd_id not in filt: if filt_dflt_incl: cred_ids.add(cred_info['referent']) continue if 'attr-match' in (filt[cred_cd_id] or {}): # maybe filt[cred_cd_id]: None if not {k: str(filt[cred_cd_id].get('attr-match', {})[k]) for k in filt[cred_cd_id].get('attr-match', {})}.items() <= cred_info['attrs'].items(): continue if 'minima' in (filt[cred_cd_id] or {}): # maybe filt[cred_cd_id]: None minima = filt[cred_cd_id].get('minima', {}) try: if any((attr not in cred_info['attrs']) or (int(cred_info['attrs'][attr]) < int(minima[attr])) for attr in minima): continue except ValueError: continue # int conversion failed - reject candidate cred_ids.add(cred_info['referent']) else: cred_ids.add(cred_info['referent']) if filt: creds = json.loads(prune_creds_json(creds, cred_ids)) rv = (cred_ids, json.dumps(creds)) LOGGER.debug('HolderProver.get_creds <<< %s', rv) return rv

Get credentials from HolderProver wallet corresponding to proof request and filter criteria; return credential identifiers from wallet and credentials json. Return empty set and empty production for no such credentials. :param proof_req_json: proof request json as Verifier creates; has entries for proof request's nonce, name, and version; plus credential's requested attributes, requested predicates. I.e., :: { 'nonce': string, # indy-sdk makes no semantic specification on this value 'name': string, # indy-sdk makes no semantic specification on this value 'version': numeric-string, # indy-sdk makes no semantic specification on this value 'requested_attributes': { '<attr_uuid>': { # aka attr_referent, a proof-request local identifier 'name': string, # attribute name (matches case- and space-insensitively) 'restrictions' [ # optional { "schema_id": string, # optional "schema_issuer_did": string, # optional "schema_name": string, # optional "schema_version": string, # optional "issuer_did": string, # optional "cred_def_id": string # optional }, { ... # if more than one restriction given, combined disjunctively (i.e., via OR) } ], 'non_revoked': { # optional - indy-sdk ignores when getting creds from wallet 'from': int, # optional, epoch seconds 'to': int # optional, epoch seconds } }, ... }, 'requested_predicates': { '<pred_uuid>': { # aka predicate_referent, a proof-request local predicate identifier 'name': string, # attribute name (matches case- and space-insensitively) 'p_type': '>=', 'p_value': int, # predicate value 'restrictions': [ # optional { "schema_id": string, # optional "schema_issuer_did": string, # optional "schema_name": string, # optional "schema_version": string, # optional "issuer_did": string, # optional "cred_def_id": string # optional }, { ... # if more than one restriction given, combined disjunctively (i.e., via OR) } ], 'non_revoked': { # optional - indy-sdk ignores when getting creds from wallet 'from': int, # optional, epoch seconds 'to': int # optional, epoch seconds } }, ... }, 'non_revoked': { # optional - indy-sdk ignores when getting creds from wallet 'from': Optional<int>, 'to': Optional<int> } } :param filt: filter for matching attribute-value pairs and predicates; dict mapping each cred def id to dict (specify empty dict or none for no filter, matching all) mapping attributes to values to match or compare. E.g., :: { 'Vx4E82R17q...:3:CL:16:0': { 'attr-match': { 'name': 'Alex', 'sex': 'M', 'favouriteDrink': None }, 'minima': { # if both attr-match and minima present, combined conjunctively (i.e., via AND) 'favouriteNumber' : 10, 'score': '100' # nicety: implementation converts to int for caller }, }, 'R17v42T4pk...:3:CL:19:0': { 'attr-match': { 'height': 175, 'birthdate': '1975-11-15' # combined conjunctively (i.e., via AND) } }, 'Z9ccax812j...:3:CL:27:0': { 'attr-match': {} # match all attributes on this cred def } ... } :param filt_dflt_incl: whether to include (True) all credentials from wallet that filter does not identify by cred def, or to exclude (False) all such credentials :return: tuple with (set of referents, creds json for input proof request); empty set and empty production for no such credential

0b1c17cca3bd178b6e6974af84dbac1dfce5cf45

https://github.com/PSPC-SPAC-buyandsell/von_agent/blob/0b1c17cca3bd178b6e6974af84dbac1dfce5cf45/von_agent/agent/holder_prover.py#L784-L937

train

PSPC-SPAC-buyandsell/von_agent

von_agent/agent/holder_prover.py

HolderProver.get_creds_by_id

async def get_creds_by_id(self, proof_req_json: str, cred_ids: set) -> str: """ Get creds structure from HolderProver wallet by credential identifiers. :param proof_req_json: proof request as per get_creds() above :param cred_ids: set of credential identifiers of interest :return: json with cred(s) for input credential identifier(s) """ LOGGER.debug('HolderProver.get_creds_by_id >>> proof_req_json: %s, cred_ids: %s', proof_req_json, cred_ids) creds_json = await anoncreds.prover_get_credentials_for_proof_req(self.wallet.handle, proof_req_json) # retain only creds of interest: find corresponding referents rv_json = prune_creds_json(json.loads(creds_json), cred_ids) LOGGER.debug('HolderProver.get_cred_by_referent <<< %s', rv_json) return rv_json

python

async def get_creds_by_id(self, proof_req_json: str, cred_ids: set) -> str: """ Get creds structure from HolderProver wallet by credential identifiers. :param proof_req_json: proof request as per get_creds() above :param cred_ids: set of credential identifiers of interest :return: json with cred(s) for input credential identifier(s) """ LOGGER.debug('HolderProver.get_creds_by_id >>> proof_req_json: %s, cred_ids: %s', proof_req_json, cred_ids) creds_json = await anoncreds.prover_get_credentials_for_proof_req(self.wallet.handle, proof_req_json) # retain only creds of interest: find corresponding referents rv_json = prune_creds_json(json.loads(creds_json), cred_ids) LOGGER.debug('HolderProver.get_cred_by_referent <<< %s', rv_json) return rv_json

Get creds structure from HolderProver wallet by credential identifiers. :param proof_req_json: proof request as per get_creds() above :param cred_ids: set of credential identifiers of interest :return: json with cred(s) for input credential identifier(s)

0b1c17cca3bd178b6e6974af84dbac1dfce5cf45

https://github.com/PSPC-SPAC-buyandsell/von_agent/blob/0b1c17cca3bd178b6e6974af84dbac1dfce5cf45/von_agent/agent/holder_prover.py#L939-L955

train

palantir/typedjsonrpc

contrib/multi-module-example/typedjsonrpc_example/valid.py

histogram

def histogram(data): """Returns a histogram of your data. :param data: The data to histogram :type data: list[object] :return: The histogram :rtype: dict[object, int] """ ret = {} for datum in data: if datum in ret: ret[datum] += 1 else: ret[datum] = 1 return ret

python

def histogram(data): """Returns a histogram of your data. :param data: The data to histogram :type data: list[object] :return: The histogram :rtype: dict[object, int] """ ret = {} for datum in data: if datum in ret: ret[datum] += 1 else: ret[datum] = 1 return ret

Returns a histogram of your data. :param data: The data to histogram :type data: list[object] :return: The histogram :rtype: dict[object, int]

274218fcd236ff9643506caa629029c9ba25a0fb

https://github.com/palantir/typedjsonrpc/blob/274218fcd236ff9643506caa629029c9ba25a0fb/contrib/multi-module-example/typedjsonrpc_example/valid.py#L22-L36

train

palantir/typedjsonrpc

contrib/multi-module-example/typedjsonrpc_example/valid.py

print_data

def print_data(data): """Prints object key-value pairs in a custom format :param data: The dict to print :type data: dict :rtype: None """ print(", ".join(["{}=>{}".format(key, value) for key, value in data]))

python

def print_data(data): """Prints object key-value pairs in a custom format :param data: The dict to print :type data: dict :rtype: None """ print(", ".join(["{}=>{}".format(key, value) for key, value in data]))

Prints object key-value pairs in a custom format :param data: The dict to print :type data: dict :rtype: None

274218fcd236ff9643506caa629029c9ba25a0fb

https://github.com/palantir/typedjsonrpc/blob/274218fcd236ff9643506caa629029c9ba25a0fb/contrib/multi-module-example/typedjsonrpc_example/valid.py#L65-L72

train

yamins81/tabular

setup.py

subdir_findall

def subdir_findall(dir, subdir): """ Find all files in a subdirectory and return paths relative to dir This is similar to (and uses) setuptools.findall However, the paths returned are in the form needed for package_data """ strip_n = len(dir.split('/')) path = '/'.join((dir, subdir)) return ['/'.join(s.split('/')[strip_n:]) for s in setuptools.findall(path)]

python

def subdir_findall(dir, subdir): """ Find all files in a subdirectory and return paths relative to dir This is similar to (and uses) setuptools.findall However, the paths returned are in the form needed for package_data """ strip_n = len(dir.split('/')) path = '/'.join((dir, subdir)) return ['/'.join(s.split('/')[strip_n:]) for s in setuptools.findall(path)]

Find all files in a subdirectory and return paths relative to dir This is similar to (and uses) setuptools.findall However, the paths returned are in the form needed for package_data

1caf091c8c395960a9ad7078f95158b533cc52dd

https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/setup.py#L82-L91

train

yamins81/tabular

setup.py

find_package_data

def find_package_data(packages): """ For a list of packages, find the package_data This function scans the subdirectories of a package and considers all non-submodule subdirectories as resources, including them in the package_data Returns a dictionary suitable for setup(package_data=<result>) """ package_data = {} for package in packages: package_data[package] = [] for subdir in find_subdirectories(package): if '.'.join((package, subdir)) in packages: # skip submodules logging.debug("skipping submodule %s/%s" % (package, subdir)) continue if skip_tests and (subdir == 'tests'): # skip tests logging.debug("skipping tests %s/%s" % (package, subdir)) continue package_data[package] += subdir_findall(package_to_path(package), subdir) return package_data

python

def find_package_data(packages): """ For a list of packages, find the package_data This function scans the subdirectories of a package and considers all non-submodule subdirectories as resources, including them in the package_data Returns a dictionary suitable for setup(package_data=<result>) """ package_data = {} for package in packages: package_data[package] = [] for subdir in find_subdirectories(package): if '.'.join((package, subdir)) in packages: # skip submodules logging.debug("skipping submodule %s/%s" % (package, subdir)) continue if skip_tests and (subdir == 'tests'): # skip tests logging.debug("skipping tests %s/%s" % (package, subdir)) continue package_data[package] += subdir_findall(package_to_path(package), subdir) return package_data

For a list of packages, find the package_data This function scans the subdirectories of a package and considers all non-submodule subdirectories as resources, including them in the package_data Returns a dictionary suitable for setup(package_data=<result>)

1caf091c8c395960a9ad7078f95158b533cc52dd

https://github.com/yamins81/tabular/blob/1caf091c8c395960a9ad7078f95158b533cc52dd/setup.py#L93-L114

train

finklabs/metrics

metrics/metrics_utils.py

process_file_metrics

def process_file_metrics(context, file_processors): """Main routine for metrics.""" file_metrics = OrderedDict() # TODO make available the includes and excludes feature gitignore = [] if os.path.isfile('.gitignore'): with open('.gitignore', 'r') as ifile: gitignore = ifile.read().splitlines() in_files = glob_files(context['root_dir'], context['in_file_names'], gitignore=gitignore) # main loop for in_file, key in in_files: # print 'file %i: %s' % (i, in_file) try: with open(in_file, 'rb') as ifile: code = ifile.read() # lookup lexicographical scanner to use for this run try: lex = guess_lexer_for_filename(in_file, code, encoding='guess') # encoding is 'guess', chardet', 'utf-8' except: pass else: token_list = lex.get_tokens(code) # parse code file_metrics[key] = OrderedDict() file_metrics[key].update(compute_file_metrics(file_processors, lex.name, key, token_list)) file_metrics[key]['language'] = lex.name except IOError as e: sys.stderr.writelines(str(e) + " -- Skipping input file.\n\n") return file_metrics

python

def process_file_metrics(context, file_processors): """Main routine for metrics.""" file_metrics = OrderedDict() # TODO make available the includes and excludes feature gitignore = [] if os.path.isfile('.gitignore'): with open('.gitignore', 'r') as ifile: gitignore = ifile.read().splitlines() in_files = glob_files(context['root_dir'], context['in_file_names'], gitignore=gitignore) # main loop for in_file, key in in_files: # print 'file %i: %s' % (i, in_file) try: with open(in_file, 'rb') as ifile: code = ifile.read() # lookup lexicographical scanner to use for this run try: lex = guess_lexer_for_filename(in_file, code, encoding='guess') # encoding is 'guess', chardet', 'utf-8' except: pass else: token_list = lex.get_tokens(code) # parse code file_metrics[key] = OrderedDict() file_metrics[key].update(compute_file_metrics(file_processors, lex.name, key, token_list)) file_metrics[key]['language'] = lex.name except IOError as e: sys.stderr.writelines(str(e) + " -- Skipping input file.\n\n") return file_metrics

Main routine for metrics.

fd9974af498831664b9ae8e8f3834e1ec2e8a699

https://github.com/finklabs/metrics/blob/fd9974af498831664b9ae8e8f3834e1ec2e8a699/metrics/metrics_utils.py#L117-L150

train

finklabs/metrics

metrics/metrics_utils.py

process_build_metrics

def process_build_metrics(context, build_processors): """use processors to collect build metrics.""" build_metrics = OrderedDict() # reset all processors for p in build_processors: p.reset() # collect metrics from all processors for p in build_processors: build_metrics.update(p.build_metrics) return build_metrics

python

def process_build_metrics(context, build_processors): """use processors to collect build metrics.""" build_metrics = OrderedDict() # reset all processors for p in build_processors: p.reset() # collect metrics from all processors for p in build_processors: build_metrics.update(p.build_metrics) return build_metrics

use processors to collect build metrics.

fd9974af498831664b9ae8e8f3834e1ec2e8a699

https://github.com/finklabs/metrics/blob/fd9974af498831664b9ae8e8f3834e1ec2e8a699/metrics/metrics_utils.py#L153-L165

train

finklabs/metrics

metrics/metrics_utils.py

summary

def summary(processors, metrics, context): """Print the summary""" # display aggregated metric values on language level def display_header(processors, before='', after=''): """Display the header for the summary results.""" print(before, end=' ') for processor in processors: processor.display_header() print(after) def display_separator(processors, before='', after=''): """Display the header for the summary results.""" print(before, end=' ') for processor in processors: processor.display_separator() print(after) def display_metrics(processors, before='', after='', metrics=[]): """Display the header for the summary results.""" print(before, end=' ') for processor in processors: processor.display_metrics(metrics) print(after) summary = {} for m in metrics: lang = metrics[m]['language'] has_key = lang in summary if not has_key: summary[lang] = {'file_count': 0, 'language': lang} summary[lang]['file_count'] += 1 for i in metrics[m]: if i not in ['sloc', 'comments', 'mccabe']: # include metrics to be used continue if not has_key: summary[lang][i] = 0 summary[lang][i] += metrics[m][i] total = {'language': 'Total'} for m in summary: for i in summary[m]: if i == 'language': continue if i not in total: total[i] = 0 total[i] += summary[m][i] print('Metrics Summary:') display_header(processors, 'Files', '') display_separator(processors, '-'*5, '') for k in sorted(summary.keys(), key=str.lower): display_metrics(processors, '%5d' % summary[k]['file_count'], '', summary[k]) display_separator(processors, '-'*5, '') display_metrics(processors, '%5d' % total['file_count'], '', total)

python

def summary(processors, metrics, context): """Print the summary""" # display aggregated metric values on language level def display_header(processors, before='', after=''): """Display the header for the summary results.""" print(before, end=' ') for processor in processors: processor.display_header() print(after) def display_separator(processors, before='', after=''): """Display the header for the summary results.""" print(before, end=' ') for processor in processors: processor.display_separator() print(after) def display_metrics(processors, before='', after='', metrics=[]): """Display the header for the summary results.""" print(before, end=' ') for processor in processors: processor.display_metrics(metrics) print(after) summary = {} for m in metrics: lang = metrics[m]['language'] has_key = lang in summary if not has_key: summary[lang] = {'file_count': 0, 'language': lang} summary[lang]['file_count'] += 1 for i in metrics[m]: if i not in ['sloc', 'comments', 'mccabe']: # include metrics to be used continue if not has_key: summary[lang][i] = 0 summary[lang][i] += metrics[m][i] total = {'language': 'Total'} for m in summary: for i in summary[m]: if i == 'language': continue if i not in total: total[i] = 0 total[i] += summary[m][i] print('Metrics Summary:') display_header(processors, 'Files', '') display_separator(processors, '-'*5, '') for k in sorted(summary.keys(), key=str.lower): display_metrics(processors, '%5d' % summary[k]['file_count'], '', summary[k]) display_separator(processors, '-'*5, '') display_metrics(processors, '%5d' % total['file_count'], '', total)

Print the summary

fd9974af498831664b9ae8e8f3834e1ec2e8a699

https://github.com/finklabs/metrics/blob/fd9974af498831664b9ae8e8f3834e1ec2e8a699/metrics/metrics_utils.py#L168-L224

train

rwl/pylon

examples/pyreto/thesis/ex6_1.py

get_portfolios3

def get_portfolios3(): """ Returns portfolios with U12 and U20 generators removed and generators of the same type at the same bus aggregated. """ g1 = [0] g2 = [1] g7 = [2] g13 = [3] g14 = [4] # sync cond g15 = [5] g16 = [6] g18 = [7] g21 = [8] g22 = [9] g23 = [10, 11] portfolios = [g1 + g15 + g18, g2 + g16 + g21, g13 + g22, g7 + g23] passive = g14 # sync_cond return portfolios, passive

python

def get_portfolios3(): """ Returns portfolios with U12 and U20 generators removed and generators of the same type at the same bus aggregated. """ g1 = [0] g2 = [1] g7 = [2] g13 = [3] g14 = [4] # sync cond g15 = [5] g16 = [6] g18 = [7] g21 = [8] g22 = [9] g23 = [10, 11] portfolios = [g1 + g15 + g18, g2 + g16 + g21, g13 + g22, g7 + g23] passive = g14 # sync_cond return portfolios, passive

Returns portfolios with U12 and U20 generators removed and generators of the same type at the same bus aggregated.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/examples/pyreto/thesis/ex6_1.py#L95-L118

train

pymoca/pymoca

src/pymoca/backends/xml/parser.py

ModelListener.call

def call(self, tag_name: str, *args, **kwargs): """Convenience method for calling methods with walker.""" if hasattr(self, tag_name): getattr(self, tag_name)(*args, **kwargs)

python

def call(self, tag_name: str, *args, **kwargs): """Convenience method for calling methods with walker.""" if hasattr(self, tag_name): getattr(self, tag_name)(*args, **kwargs)

Convenience method for calling methods with walker.

14b5eb7425e96689de6cc5c10f400895d586a978

https://github.com/pymoca/pymoca/blob/14b5eb7425e96689de6cc5c10f400895d586a978/src/pymoca/backends/xml/parser.py#L85-L88

train

pymoca/pymoca

src/pymoca/backends/xml/parser.py

ModelListener.der

def der(self, x: Sym): """Get the derivative of the variable, create it if it doesn't exist.""" name = 'der({:s})'.format(x.name()) if name not in self.scope['dvar'].keys(): self.scope['dvar'][name] = self.sym.sym(name, *x.shape) self.scope['states'].append(x.name()) return self.scope['dvar'][name]

python

def der(self, x: Sym): """Get the derivative of the variable, create it if it doesn't exist.""" name = 'der({:s})'.format(x.name()) if name not in self.scope['dvar'].keys(): self.scope['dvar'][name] = self.sym.sym(name, *x.shape) self.scope['states'].append(x.name()) return self.scope['dvar'][name]

Get the derivative of the variable, create it if it doesn't exist.

14b5eb7425e96689de6cc5c10f400895d586a978

https://github.com/pymoca/pymoca/blob/14b5eb7425e96689de6cc5c10f400895d586a978/src/pymoca/backends/xml/parser.py#L94-L100

train

pymoca/pymoca

src/pymoca/backends/xml/parser.py

ModelListener.noise_gaussian

def noise_gaussian(self, mean, std): """Create a gaussian noise variable""" assert std > 0 ng = self.sym.sym('ng_{:d}'.format(len(self.scope['ng']))) self.scope['ng'].append(ng) return mean + std*ng

python

def noise_gaussian(self, mean, std): """Create a gaussian noise variable""" assert std > 0 ng = self.sym.sym('ng_{:d}'.format(len(self.scope['ng']))) self.scope['ng'].append(ng) return mean + std*ng

Create a gaussian noise variable

14b5eb7425e96689de6cc5c10f400895d586a978

https://github.com/pymoca/pymoca/blob/14b5eb7425e96689de6cc5c10f400895d586a978/src/pymoca/backends/xml/parser.py#L126-L131

train

pymoca/pymoca

src/pymoca/backends/xml/parser.py

ModelListener.noise_uniform

def noise_uniform(self, lower_bound, upper_bound): """Create a uniform noise variable""" assert upper_bound > lower_bound nu = self.sym.sym('nu_{:d}'.format(len(self.scope['nu']))) self.scope['nu'].append(nu) return lower_bound + nu*(upper_bound - lower_bound)

python

def noise_uniform(self, lower_bound, upper_bound): """Create a uniform noise variable""" assert upper_bound > lower_bound nu = self.sym.sym('nu_{:d}'.format(len(self.scope['nu']))) self.scope['nu'].append(nu) return lower_bound + nu*(upper_bound - lower_bound)

Create a uniform noise variable

14b5eb7425e96689de6cc5c10f400895d586a978

https://github.com/pymoca/pymoca/blob/14b5eb7425e96689de6cc5c10f400895d586a978/src/pymoca/backends/xml/parser.py#L133-L138

train

pymoca/pymoca

src/pymoca/backends/xml/parser.py

ModelListener.log

def log(self, *args, **kwargs): """Convenience function for printing indenting debug output.""" if self.verbose: print(' ' * self.depth, *args, **kwargs)

python

def log(self, *args, **kwargs): """Convenience function for printing indenting debug output.""" if self.verbose: print(' ' * self.depth, *args, **kwargs)

Convenience function for printing indenting debug output.

14b5eb7425e96689de6cc5c10f400895d586a978

https://github.com/pymoca/pymoca/blob/14b5eb7425e96689de6cc5c10f400895d586a978/src/pymoca/backends/xml/parser.py#L158-L161

train

rwl/pylon

examples/pyreto/thesis/common.py

get_case6ww

def get_case6ww(): """ Returns the 6 bus case from Wood & Wollenberg PG&C. """ path = os.path.dirname(pylon.__file__) path = os.path.join(path, "test", "data") path = os.path.join(path, "case6ww", "case6ww.pkl") case = pylon.Case.load(path) case.generators[0].p_cost = (0.0, 4.0, 200.0) case.generators[1].p_cost = (0.0, 3.0, 200.0) # case.generators[0].p_cost = (0.0, 5.1, 200.0) # 10% # case.generators[1].p_cost = (0.0, 4.5, 200.0) # 30% case.generators[2].p_cost = (0.0, 6.0, 200.0) # passive # case.generators[0].c_shutdown = 100.0 # case.generators[1].c_shutdown = 100.0 # case.generators[2].c_shutdown = 100.0 case.generators[0].p_min = 0.0 # TODO: Unit-decommitment. case.generators[1].p_min = 0.0 case.generators[2].p_min = 0.0 case.generators[0].p_max = 110.0 case.generators[1].p_max = 110.0 case.generators[2].p_max = 220.0 # passive # FIXME: Correct generator naming order. for g in case.generators: g.name #pyreto.util.plotGenCost(case.generators) return case

python

def get_case6ww(): """ Returns the 6 bus case from Wood & Wollenberg PG&C. """ path = os.path.dirname(pylon.__file__) path = os.path.join(path, "test", "data") path = os.path.join(path, "case6ww", "case6ww.pkl") case = pylon.Case.load(path) case.generators[0].p_cost = (0.0, 4.0, 200.0) case.generators[1].p_cost = (0.0, 3.0, 200.0) # case.generators[0].p_cost = (0.0, 5.1, 200.0) # 10% # case.generators[1].p_cost = (0.0, 4.5, 200.0) # 30% case.generators[2].p_cost = (0.0, 6.0, 200.0) # passive # case.generators[0].c_shutdown = 100.0 # case.generators[1].c_shutdown = 100.0 # case.generators[2].c_shutdown = 100.0 case.generators[0].p_min = 0.0 # TODO: Unit-decommitment. case.generators[1].p_min = 0.0 case.generators[2].p_min = 0.0 case.generators[0].p_max = 110.0 case.generators[1].p_max = 110.0 case.generators[2].p_max = 220.0 # passive # FIXME: Correct generator naming order. for g in case.generators: g.name #pyreto.util.plotGenCost(case.generators) return case

Returns the 6 bus case from Wood & Wollenberg PG&C.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/examples/pyreto/thesis/common.py#L36-L70

train

rwl/pylon

examples/pyreto/thesis/common.py

get_case24_ieee_rts

def get_case24_ieee_rts(): """ Returns the 24 bus IEEE Reliability Test System. """ path = os.path.dirname(pylon.__file__) path = os.path.join(path, "test", "data") path = os.path.join(path, "case24_ieee_rts", "case24_ieee_rts.pkl") case = pylon.Case.load(path) # FIXME: Correct generator naming order. for g in case.generators: g.name return case

python

def get_case24_ieee_rts(): """ Returns the 24 bus IEEE Reliability Test System. """ path = os.path.dirname(pylon.__file__) path = os.path.join(path, "test", "data") path = os.path.join(path, "case24_ieee_rts", "case24_ieee_rts.pkl") case = pylon.Case.load(path) # FIXME: Correct generator naming order. for g in case.generators: g.name return case

Returns the 24 bus IEEE Reliability Test System.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/examples/pyreto/thesis/common.py#L107-L120

train

rwl/pylon

examples/pyreto/thesis/common.py

get_discrete_task_agent

def get_discrete_task_agent(generators, market, nStates, nOffer, markups, withholds, maxSteps, learner, Pd0=None, Pd_min=0.0): """ Returns a tuple of task and agent for the given learner. """ env = pyreto.discrete.MarketEnvironment(generators, market, numStates=nStates, numOffbids=nOffer, markups=markups, withholds=withholds, Pd0=Pd0, Pd_min=Pd_min) task = pyreto.discrete.ProfitTask(env, maxSteps=maxSteps) nActions = len(env._allActions) module = ActionValueTable(numStates=nStates, numActions=nActions) agent = LearningAgent(module, learner) return task, agent

python

def get_discrete_task_agent(generators, market, nStates, nOffer, markups, withholds, maxSteps, learner, Pd0=None, Pd_min=0.0): """ Returns a tuple of task and agent for the given learner. """ env = pyreto.discrete.MarketEnvironment(generators, market, numStates=nStates, numOffbids=nOffer, markups=markups, withholds=withholds, Pd0=Pd0, Pd_min=Pd_min) task = pyreto.discrete.ProfitTask(env, maxSteps=maxSteps) nActions = len(env._allActions) module = ActionValueTable(numStates=nStates, numActions=nActions) agent = LearningAgent(module, learner) return task, agent

Returns a tuple of task and agent for the given learner.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/examples/pyreto/thesis/common.py#L166-L184

train

rwl/pylon

examples/pyreto/thesis/common.py

get_zero_task_agent

def get_zero_task_agent(generators, market, nOffer, maxSteps): """ Returns a task-agent tuple whose action is always zero. """ env = pyreto.discrete.MarketEnvironment(generators, market, nOffer) task = pyreto.discrete.ProfitTask(env, maxSteps=maxSteps) agent = pyreto.util.ZeroAgent(env.outdim, env.indim) return task, agent

python

def get_zero_task_agent(generators, market, nOffer, maxSteps): """ Returns a task-agent tuple whose action is always zero. """ env = pyreto.discrete.MarketEnvironment(generators, market, nOffer) task = pyreto.discrete.ProfitTask(env, maxSteps=maxSteps) agent = pyreto.util.ZeroAgent(env.outdim, env.indim) return task, agent

Returns a task-agent tuple whose action is always zero.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/examples/pyreto/thesis/common.py#L211-L217

train

rwl/pylon

examples/pyreto/thesis/common.py

get_neg_one_task_agent

def get_neg_one_task_agent(generators, market, nOffer, maxSteps): """ Returns a task-agent tuple whose action is always minus one. """ env = pyreto.discrete.MarketEnvironment(generators, market, nOffer) task = pyreto.discrete.ProfitTask(env, maxSteps=maxSteps) agent = pyreto.util.NegOneAgent(env.outdim, env.indim) return task, agent

python

def get_neg_one_task_agent(generators, market, nOffer, maxSteps): """ Returns a task-agent tuple whose action is always minus one. """ env = pyreto.discrete.MarketEnvironment(generators, market, nOffer) task = pyreto.discrete.ProfitTask(env, maxSteps=maxSteps) agent = pyreto.util.NegOneAgent(env.outdim, env.indim) return task, agent

Returns a task-agent tuple whose action is always minus one.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/examples/pyreto/thesis/common.py#L220-L226

train

rwl/pylon

examples/pyreto/thesis/common.py

run_experiment

def run_experiment(experiment, roleouts, episodes, in_cloud=False, dynProfile=None): """ Runs the given experiment and returns the results. """ def run(): if dynProfile is None: maxsteps = len(experiment.profile) # episode length else: maxsteps = dynProfile.shape[1] na = len(experiment.agents) ni = roleouts * episodes * maxsteps all_action = zeros((na, 0)) all_reward = zeros((na, 0)) epsilon = zeros((na, ni)) # exploration rate # Converts to action vector in percentage markup values. vmarkup = vectorize(get_markup) for roleout in range(roleouts): if dynProfile is not None: # Apply new load profile before each roleout (week). i = roleout * episodes # index of first profile value experiment.profile = dynProfile[i:i + episodes, :] # print "PROFILE:", experiment.profile, episodes experiment.doEpisodes(episodes) # number of samples per learning step nei = episodes * maxsteps # num interactions per role epi_action = zeros((0, nei)) epi_reward = zeros((0, nei)) for i, (task, agent) in \ enumerate(zip(experiment.tasks, experiment.agents)): action = copy(agent.history["action"]) reward = copy(agent.history["reward"]) for j in range(nei): if isinstance(agent.learner, DirectSearchLearner): action[j, :] = task.denormalize(action[j, :]) k = nei * roleout epsilon[i, k:k + nei] = agent.learner.explorer.sigma[0] elif isinstance(agent.learner, ValueBasedLearner): action[j, :] = vmarkup(action[j, :], task) k = nei * roleout epsilon[i, k:k + nei] = agent.learner.explorer.epsilon else: action = vmarkup(action, task) # FIXME: Only stores action[0] for all interactions. epi_action = c_[epi_action.T, action[:, 0].flatten()].T epi_reward = c_[epi_reward.T, reward.flatten()].T if hasattr(agent, "module"): print "PARAMS:", agent.module.params agent.learn() agent.reset() all_action = c_[all_action, epi_action] all_reward = c_[all_reward, epi_reward] return all_action, all_reward, epsilon if in_cloud: import cloud job_id = cloud.call(run, _high_cpu=False) result = cloud.result(job_id) all_action, all_reward, epsilon = result else: all_action, all_reward, epsilon = run() return all_action, all_reward, epsilon

python

def run_experiment(experiment, roleouts, episodes, in_cloud=False, dynProfile=None): """ Runs the given experiment and returns the results. """ def run(): if dynProfile is None: maxsteps = len(experiment.profile) # episode length else: maxsteps = dynProfile.shape[1] na = len(experiment.agents) ni = roleouts * episodes * maxsteps all_action = zeros((na, 0)) all_reward = zeros((na, 0)) epsilon = zeros((na, ni)) # exploration rate # Converts to action vector in percentage markup values. vmarkup = vectorize(get_markup) for roleout in range(roleouts): if dynProfile is not None: # Apply new load profile before each roleout (week). i = roleout * episodes # index of first profile value experiment.profile = dynProfile[i:i + episodes, :] # print "PROFILE:", experiment.profile, episodes experiment.doEpisodes(episodes) # number of samples per learning step nei = episodes * maxsteps # num interactions per role epi_action = zeros((0, nei)) epi_reward = zeros((0, nei)) for i, (task, agent) in \ enumerate(zip(experiment.tasks, experiment.agents)): action = copy(agent.history["action"]) reward = copy(agent.history["reward"]) for j in range(nei): if isinstance(agent.learner, DirectSearchLearner): action[j, :] = task.denormalize(action[j, :]) k = nei * roleout epsilon[i, k:k + nei] = agent.learner.explorer.sigma[0] elif isinstance(agent.learner, ValueBasedLearner): action[j, :] = vmarkup(action[j, :], task) k = nei * roleout epsilon[i, k:k + nei] = agent.learner.explorer.epsilon else: action = vmarkup(action, task) # FIXME: Only stores action[0] for all interactions. epi_action = c_[epi_action.T, action[:, 0].flatten()].T epi_reward = c_[epi_reward.T, reward.flatten()].T if hasattr(agent, "module"): print "PARAMS:", agent.module.params agent.learn() agent.reset() all_action = c_[all_action, epi_action] all_reward = c_[all_reward, epi_reward] return all_action, all_reward, epsilon if in_cloud: import cloud job_id = cloud.call(run, _high_cpu=False) result = cloud.result(job_id) all_action, all_reward, epsilon = result else: all_action, all_reward, epsilon = run() return all_action, all_reward, epsilon

Runs the given experiment and returns the results.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/examples/pyreto/thesis/common.py#L241-L314

train

rwl/pylon

examples/pyreto/thesis/common.py

get_full_year

def get_full_year(): """ Returns percentages of peak load for all hours of the year. @return: Numpy array of doubles with length 8736. """ weekly = get_weekly() daily = get_daily() hourly_winter_wkdy, hourly_winter_wknd = get_winter_hourly() hourly_summer_wkdy, hourly_summer_wknd = get_summer_hourly() hourly_spring_autumn_wkdy, hourly_spring_autumn_wknd = \ get_spring_autumn_hourly() fullyear = zeros(364 * 24) c = 0 l = [(0, 7, hourly_winter_wkdy, hourly_winter_wknd), (8, 16, hourly_spring_autumn_wkdy, hourly_spring_autumn_wknd), (17, 29, hourly_summer_wkdy, hourly_summer_wknd), (30, 42, hourly_spring_autumn_wkdy, hourly_spring_autumn_wknd), (43, 51, hourly_winter_wkdy, hourly_winter_wknd)] for start, end, wkdy, wknd in l: for w in weekly[start:end + 1]: for d in daily[:5]: for h in wkdy: fullyear[c] = w * (d / 100.0) * (h / 100.0) c += 1 for d in daily[5:]: for h in wknd: fullyear[c] = w * (d / 100.0) * (h / 100.0) c += 1 return fullyear

python

def get_full_year(): """ Returns percentages of peak load for all hours of the year. @return: Numpy array of doubles with length 8736. """ weekly = get_weekly() daily = get_daily() hourly_winter_wkdy, hourly_winter_wknd = get_winter_hourly() hourly_summer_wkdy, hourly_summer_wknd = get_summer_hourly() hourly_spring_autumn_wkdy, hourly_spring_autumn_wknd = \ get_spring_autumn_hourly() fullyear = zeros(364 * 24) c = 0 l = [(0, 7, hourly_winter_wkdy, hourly_winter_wknd), (8, 16, hourly_spring_autumn_wkdy, hourly_spring_autumn_wknd), (17, 29, hourly_summer_wkdy, hourly_summer_wknd), (30, 42, hourly_spring_autumn_wkdy, hourly_spring_autumn_wknd), (43, 51, hourly_winter_wkdy, hourly_winter_wknd)] for start, end, wkdy, wknd in l: for w in weekly[start:end + 1]: for d in daily[:5]: for h in wkdy: fullyear[c] = w * (d / 100.0) * (h / 100.0) c += 1 for d in daily[5:]: for h in wknd: fullyear[c] = w * (d / 100.0) * (h / 100.0) c += 1 return fullyear

Returns percentages of peak load for all hours of the year. @return: Numpy array of doubles with length 8736.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/examples/pyreto/thesis/common.py#L426-L457

train

rwl/pylon

examples/pyreto/thesis/common.py

get_all_days

def get_all_days(): """ Returns percentages of peak load for all days of the year. Data from the IEEE RTS. """ weekly = get_weekly() daily = get_daily() return [w * (d / 100.0) for w in weekly for d in daily]

python

def get_all_days(): """ Returns percentages of peak load for all days of the year. Data from the IEEE RTS. """ weekly = get_weekly() daily = get_daily() return [w * (d / 100.0) for w in weekly for d in daily]

Returns percentages of peak load for all days of the year. Data from the IEEE RTS.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/examples/pyreto/thesis/common.py#L460-L467

train

rwl/pylon

examples/pyreto/thesis/ex5_1.py

get_q_experiment

def get_q_experiment(case, minor=1): """ Returns an experiment that uses Q-learning. """ gen = case.generators profile = array([1.0]) maxSteps = len(profile) if minor == 1: alpha = 0.3 # Learning rate. gamma = 0.99 # Discount factor # The closer epsilon gets to 0, the more greedy and less explorative. epsilon = 0.9 decay = 0.97 tau = 150.0 # Boltzmann temperature. qlambda = 0.9 elif minor == 2: alpha = 0.1 # Learning rate. gamma = 0.99 # Discount factor # The closer epsilon gets to 0, the more greedy and less explorative. epsilon = 0.9 decay = 0.99 tau = 150.0 # Boltzmann temperature. qlambda = 0.9 else: raise ValueError market = pyreto.SmartMarket(case, priceCap=cap, decommit=decommit, auctionType=auctionType) experiment = pyreto.continuous.MarketExperiment([], [], market, profile) for g in gen[0:2]: learner = Q(alpha, gamma) # learner = QLambda(alpha, gamma, qlambda) # learner = SARSA(alpha, gamma) learner.explorer.epsilon = epsilon learner.explorer.decay = decay # learner.explorer = BoltzmannExplorer(tau, decay) task, agent = get_discrete_task_agent([g], market, nStates, nOffer, markups, withholds, maxSteps, learner) experiment.tasks.append(task) experiment.agents.append(agent) # Passive agent. task, agent = get_zero_task_agent(gen[2:3], market, nOffer, maxSteps) experiment.tasks.append(task) experiment.agents.append(agent) return experiment

python

def get_q_experiment(case, minor=1): """ Returns an experiment that uses Q-learning. """ gen = case.generators profile = array([1.0]) maxSteps = len(profile) if minor == 1: alpha = 0.3 # Learning rate. gamma = 0.99 # Discount factor # The closer epsilon gets to 0, the more greedy and less explorative. epsilon = 0.9 decay = 0.97 tau = 150.0 # Boltzmann temperature. qlambda = 0.9 elif minor == 2: alpha = 0.1 # Learning rate. gamma = 0.99 # Discount factor # The closer epsilon gets to 0, the more greedy and less explorative. epsilon = 0.9 decay = 0.99 tau = 150.0 # Boltzmann temperature. qlambda = 0.9 else: raise ValueError market = pyreto.SmartMarket(case, priceCap=cap, decommit=decommit, auctionType=auctionType) experiment = pyreto.continuous.MarketExperiment([], [], market, profile) for g in gen[0:2]: learner = Q(alpha, gamma) # learner = QLambda(alpha, gamma, qlambda) # learner = SARSA(alpha, gamma) learner.explorer.epsilon = epsilon learner.explorer.decay = decay # learner.explorer = BoltzmannExplorer(tau, decay) task, agent = get_discrete_task_agent([g], market, nStates, nOffer, markups, withholds, maxSteps, learner) experiment.tasks.append(task) experiment.agents.append(agent) # Passive agent. task, agent = get_zero_task_agent(gen[2:3], market, nOffer, maxSteps) experiment.tasks.append(task) experiment.agents.append(agent) return experiment

Returns an experiment that uses Q-learning.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/examples/pyreto/thesis/ex5_1.py#L79-L133

train

rwl/pylon

pylon/generator.py

Generator.q_limited

def q_limited(self): """ Is the machine at it's limit of reactive power? """ if (self.q >= self.q_max) or (self.q <= self.q_min): return True else: return False

python

def q_limited(self): """ Is the machine at it's limit of reactive power? """ if (self.q >= self.q_max) or (self.q <= self.q_min): return True else: return False

Is the machine at it's limit of reactive power?

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/pylon/generator.py#L156-L162

train

rwl/pylon

pylon/generator.py

Generator.total_cost

def total_cost(self, p=None, p_cost=None, pcost_model=None): """ Computes total cost for the generator at the given output level. """ p = self.p if p is None else p p_cost = self.p_cost if p_cost is None else p_cost pcost_model = self.pcost_model if pcost_model is None else pcost_model p = 0.0 if not self.online else p if pcost_model == PW_LINEAR: n_segments = len(p_cost) - 1 # Iterate over the piece-wise linear segments. for i in range(n_segments): x1, y1 = p_cost[i] x2, y2 = p_cost[i + 1] m = (y2 - y1) / (x2 - x1) c = y1 - m * x1 if x1 <= p <= x2: result = m*p + c break else: # print "TOTC:", self.name, p, self.p_max, p_cost # raise ValueError, "Value [%f] outwith pwl cost curve." % p # Use the last segment for values outwith the cost curve. logger.error("Value [%f] outside pwl cost curve [%s]." % (p, p_cost[-1][0])) result = m*p + c elif pcost_model == POLYNOMIAL: # result = p_cost[-1] # for i in range(1, len(p_cost)): # result += p_cost[-(i + 1)] * p**i result = polyval(p_cost, p) else: raise ValueError if self.is_load: return -result else: return result

python

def total_cost(self, p=None, p_cost=None, pcost_model=None): """ Computes total cost for the generator at the given output level. """ p = self.p if p is None else p p_cost = self.p_cost if p_cost is None else p_cost pcost_model = self.pcost_model if pcost_model is None else pcost_model p = 0.0 if not self.online else p if pcost_model == PW_LINEAR: n_segments = len(p_cost) - 1 # Iterate over the piece-wise linear segments. for i in range(n_segments): x1, y1 = p_cost[i] x2, y2 = p_cost[i + 1] m = (y2 - y1) / (x2 - x1) c = y1 - m * x1 if x1 <= p <= x2: result = m*p + c break else: # print "TOTC:", self.name, p, self.p_max, p_cost # raise ValueError, "Value [%f] outwith pwl cost curve." % p # Use the last segment for values outwith the cost curve. logger.error("Value [%f] outside pwl cost curve [%s]." % (p, p_cost[-1][0])) result = m*p + c elif pcost_model == POLYNOMIAL: # result = p_cost[-1] # for i in range(1, len(p_cost)): # result += p_cost[-(i + 1)] * p**i result = polyval(p_cost, p) else: raise ValueError if self.is_load: return -result else: return result

Computes total cost for the generator at the given output level.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/pylon/generator.py#L180-L220

train

rwl/pylon

pylon/generator.py

Generator.poly_to_pwl

def poly_to_pwl(self, n_points=4): """ Sets the piece-wise linear cost attribute, converting the polynomial cost variable by evaluating at zero and then at n_points evenly spaced points between p_min and p_max. """ assert self.pcost_model == POLYNOMIAL p_min = self.p_min p_max = self.p_max p_cost = [] if p_min > 0.0: # Make the first segment go from the origin to p_min. step = (p_max - p_min) / (n_points - 2) y0 = self.total_cost(0.0) p_cost.append((0.0, y0)) x = p_min n_points -= 1 else: step = (p_max - p_min) / (n_points - 1) x = 0.0 for _ in range(n_points): y = self.total_cost(x) p_cost.append((x, y)) x += step # Change the cost model and set the new cost. self.pcost_model = PW_LINEAR self.p_cost = p_cost

python

def poly_to_pwl(self, n_points=4): """ Sets the piece-wise linear cost attribute, converting the polynomial cost variable by evaluating at zero and then at n_points evenly spaced points between p_min and p_max. """ assert self.pcost_model == POLYNOMIAL p_min = self.p_min p_max = self.p_max p_cost = [] if p_min > 0.0: # Make the first segment go from the origin to p_min. step = (p_max - p_min) / (n_points - 2) y0 = self.total_cost(0.0) p_cost.append((0.0, y0)) x = p_min n_points -= 1 else: step = (p_max - p_min) / (n_points - 1) x = 0.0 for _ in range(n_points): y = self.total_cost(x) p_cost.append((x, y)) x += step # Change the cost model and set the new cost. self.pcost_model = PW_LINEAR self.p_cost = p_cost

Sets the piece-wise linear cost attribute, converting the polynomial cost variable by evaluating at zero and then at n_points evenly spaced points between p_min and p_max.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/pylon/generator.py#L278-L308

train

rwl/pylon

pylon/generator.py

Generator.get_offers

def get_offers(self, n_points=6): """ Returns quantity and price offers created from the cost function. """ from pyreto.smart_market import Offer qtyprc = self._get_qtyprc(n_points) return [Offer(self, qty, prc) for qty, prc in qtyprc]

python

def get_offers(self, n_points=6): """ Returns quantity and price offers created from the cost function. """ from pyreto.smart_market import Offer qtyprc = self._get_qtyprc(n_points) return [Offer(self, qty, prc) for qty, prc in qtyprc]

Returns quantity and price offers created from the cost function.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/pylon/generator.py#L311-L317

train

rwl/pylon

pylon/generator.py

Generator.get_bids

def get_bids(self, n_points=6): """ Returns quantity and price bids created from the cost function. """ from pyreto.smart_market import Bid qtyprc = self._get_qtyprc(n_points) return [Bid(self, qty, prc) for qty, prc in qtyprc]

python

def get_bids(self, n_points=6): """ Returns quantity and price bids created from the cost function. """ from pyreto.smart_market import Bid qtyprc = self._get_qtyprc(n_points) return [Bid(self, qty, prc) for qty, prc in qtyprc]

Returns quantity and price bids created from the cost function.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/pylon/generator.py#L320-L326

train

rwl/pylon

pylon/generator.py

Generator.offers_to_pwl

def offers_to_pwl(self, offers): """ Updates the piece-wise linear total cost function using the given offer blocks. Based on off2case.m from MATPOWER by Ray Zimmerman, developed at PSERC Cornell. See U{http://www.pserc.cornell.edu/matpower/} for more info. """ assert not self.is_load # Only apply offers associated with this generator. g_offers = [offer for offer in offers if offer.generator == self] # Fliter out zero quantity offers. gt_zero = [offr for offr in g_offers if round(offr.quantity, 4) > 0.0] # Ignore withheld offers. valid = [offer for offer in gt_zero if not offer.withheld] p_offers = [v for v in valid if not v.reactive] q_offers = [v for v in valid if v.reactive] if p_offers: self.p_cost = self._offbids_to_points(p_offers) self.pcost_model = PW_LINEAR self.online = True else: self.p_cost = [(0.0, 0.0), (self.p_max, 0.0)] self.pcost_model = PW_LINEAR if q_offers: # Dispatch at zero real power without shutting down # if capacity offered for reactive power. self.p_min = 0.0 self.p_max = 0.0 self.online = True else: self.online = False if q_offers: self.q_cost = self._offbids_to_points(q_offers) self.qcost_model = PW_LINEAR else: self.q_cost = None#[(0.0, 0.0), (self.q_max, 0.0)] self.qcost_model = PW_LINEAR if not len(p_offers) and not len(q_offers): logger.info("No valid offers for generator [%s], shutting down." % self.name) self.online = False self._adjust_limits()

python

def offers_to_pwl(self, offers): """ Updates the piece-wise linear total cost function using the given offer blocks. Based on off2case.m from MATPOWER by Ray Zimmerman, developed at PSERC Cornell. See U{http://www.pserc.cornell.edu/matpower/} for more info. """ assert not self.is_load # Only apply offers associated with this generator. g_offers = [offer for offer in offers if offer.generator == self] # Fliter out zero quantity offers. gt_zero = [offr for offr in g_offers if round(offr.quantity, 4) > 0.0] # Ignore withheld offers. valid = [offer for offer in gt_zero if not offer.withheld] p_offers = [v for v in valid if not v.reactive] q_offers = [v for v in valid if v.reactive] if p_offers: self.p_cost = self._offbids_to_points(p_offers) self.pcost_model = PW_LINEAR self.online = True else: self.p_cost = [(0.0, 0.0), (self.p_max, 0.0)] self.pcost_model = PW_LINEAR if q_offers: # Dispatch at zero real power without shutting down # if capacity offered for reactive power. self.p_min = 0.0 self.p_max = 0.0 self.online = True else: self.online = False if q_offers: self.q_cost = self._offbids_to_points(q_offers) self.qcost_model = PW_LINEAR else: self.q_cost = None#[(0.0, 0.0), (self.q_max, 0.0)] self.qcost_model = PW_LINEAR if not len(p_offers) and not len(q_offers): logger.info("No valid offers for generator [%s], shutting down." % self.name) self.online = False self._adjust_limits()

Updates the piece-wise linear total cost function using the given offer blocks. Based on off2case.m from MATPOWER by Ray Zimmerman, developed at PSERC Cornell. See U{http://www.pserc.cornell.edu/matpower/} for more info.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/pylon/generator.py#L420-L466

train

rwl/pylon

pylon/generator.py

Generator.bids_to_pwl

def bids_to_pwl(self, bids): """ Updates the piece-wise linear total cost function using the given bid blocks. Based on off2case.m from MATPOWER by Ray Zimmerman, developed at PSERC Cornell. See U{http://www.pserc.cornell.edu/matpower/} for more info. """ assert self.is_load # Apply only those bids associated with this dispatchable load. vl_bids = [bid for bid in bids if bid.vLoad == self] # Filter out zero quantity bids. gt_zero = [bid for bid in vl_bids if round(bid.quantity, 4) > 0.0] # Ignore withheld offers. valid_bids = [bid for bid in gt_zero if not bid.withheld] p_bids = [v for v in valid_bids if not v.reactive] q_bids = [v for v in valid_bids if v.reactive] if p_bids: self.p_cost = self._offbids_to_points(p_bids, True) self.pcost_model = PW_LINEAR self.online = True else: self.p_cost = [(0.0, 0.0), (self.p_max, 0.0)] self.pcost_model = PW_LINEAR logger.info("No valid active power bids for dispatchable load " "[%s], shutting down." % self.name) self.online = False if q_bids: self.q_cost = self._offbids_to_points(q_bids, True) self.qcost_model = PW_LINEAR self.online = True else: self.q_cost = [(self.q_min, 0.0), (0.0, 0.0), (self.q_max, 0.0)] self.qcost_model = PW_LINEAR # logger.info("No valid bids for dispatchable load, shutting down.") # self.online = False self._adjust_limits()

python

def bids_to_pwl(self, bids): """ Updates the piece-wise linear total cost function using the given bid blocks. Based on off2case.m from MATPOWER by Ray Zimmerman, developed at PSERC Cornell. See U{http://www.pserc.cornell.edu/matpower/} for more info. """ assert self.is_load # Apply only those bids associated with this dispatchable load. vl_bids = [bid for bid in bids if bid.vLoad == self] # Filter out zero quantity bids. gt_zero = [bid for bid in vl_bids if round(bid.quantity, 4) > 0.0] # Ignore withheld offers. valid_bids = [bid for bid in gt_zero if not bid.withheld] p_bids = [v for v in valid_bids if not v.reactive] q_bids = [v for v in valid_bids if v.reactive] if p_bids: self.p_cost = self._offbids_to_points(p_bids, True) self.pcost_model = PW_LINEAR self.online = True else: self.p_cost = [(0.0, 0.0), (self.p_max, 0.0)] self.pcost_model = PW_LINEAR logger.info("No valid active power bids for dispatchable load " "[%s], shutting down." % self.name) self.online = False if q_bids: self.q_cost = self._offbids_to_points(q_bids, True) self.qcost_model = PW_LINEAR self.online = True else: self.q_cost = [(self.q_min, 0.0), (0.0, 0.0), (self.q_max, 0.0)] self.qcost_model = PW_LINEAR # logger.info("No valid bids for dispatchable load, shutting down.") # self.online = False self._adjust_limits()

Updates the piece-wise linear total cost function using the given bid blocks. Based on off2case.m from MATPOWER by Ray Zimmerman, developed at PSERC Cornell. See U{http://www.pserc.cornell.edu/matpower/} for more info.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/pylon/generator.py#L469-L508

train

rwl/pylon

pylon/generator.py

Generator._adjust_limits

def _adjust_limits(self): """ Sets the active power limits, 'p_max' and 'p_min', according to the pwl cost function points. """ if not self.is_load: # self.p_min = min([point[0] for point in self.p_cost]) self.p_max = max([point[0] for point in self.p_cost]) else: p_min = min([point[0] for point in self.p_cost]) self.p_max = 0.0 self.q_min = self.q_min * p_min / self.p_min self.q_max = self.q_max * p_min / self.p_min self.p_min = p_min

python

def _adjust_limits(self): """ Sets the active power limits, 'p_max' and 'p_min', according to the pwl cost function points. """ if not self.is_load: # self.p_min = min([point[0] for point in self.p_cost]) self.p_max = max([point[0] for point in self.p_cost]) else: p_min = min([point[0] for point in self.p_cost]) self.p_max = 0.0 self.q_min = self.q_min * p_min / self.p_min self.q_max = self.q_max * p_min / self.p_min self.p_min = p_min

Sets the active power limits, 'p_max' and 'p_min', according to the pwl cost function points.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/pylon/generator.py#L537-L549

train

rwl/pylon

pyreto/continuous/environment.py

MarketEnvironment.indim

def indim(self): """ The number of action values that the environment accepts. """ indim = self.numOffbids * len(self.generators) if self.maxWithhold is not None: return indim * 2 else: return indim

python

def indim(self): """ The number of action values that the environment accepts. """ indim = self.numOffbids * len(self.generators) if self.maxWithhold is not None: return indim * 2 else: return indim

The number of action values that the environment accepts.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/pyreto/continuous/environment.py#L103-L111

train

rwl/pylon

pyreto/continuous/environment.py

MarketEnvironment._getBusVoltageLambdaSensor

def _getBusVoltageLambdaSensor(self): """ Returns an array of length nb where each value is the sum of the Lagrangian multipliers on the upper and the negative of the Lagrangian multipliers on the lower voltage limits. """ muVmin = array([b.mu_vmin for b in self.market.case.connected_buses]) muVmax = array([b.mu_vmax for b in self.market.case.connected_buses]) muVmin = -1.0 * muVmin diff = muVmin + muVmax return diff

python

def _getBusVoltageLambdaSensor(self): """ Returns an array of length nb where each value is the sum of the Lagrangian multipliers on the upper and the negative of the Lagrangian multipliers on the lower voltage limits. """ muVmin = array([b.mu_vmin for b in self.market.case.connected_buses]) muVmax = array([b.mu_vmax for b in self.market.case.connected_buses]) muVmin = -1.0 * muVmin diff = muVmin + muVmax return diff

Returns an array of length nb where each value is the sum of the Lagrangian multipliers on the upper and the negative of the Lagrangian multipliers on the lower voltage limits.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/pyreto/continuous/environment.py#L177-L185

train

melizalab/libtfr

site_scons/site_tools/doxygen.py

DoxyfileParse

def DoxyfileParse(file_contents): """ Parse a Doxygen source file and return a dictionary of all the values. Values will be strings and lists of strings. """ data = {} import shlex lex = shlex.shlex(instream = file_contents, posix = True) lex.wordchars += "*+./-:" lex.whitespace = lex.whitespace.replace("\n", "") lex.escape = "" lineno = lex.lineno token = lex.get_token() key = token # the first token should be a key last_token = "" key_token = False next_key = False new_data = True def append_data(data, key, new_data, token): if new_data or len(data[key]) == 0: data[key].append(token) else: data[key][-1] += token while token: if token in ['\n']: if last_token not in ['\\']: key_token = True elif token in ['\\']: pass elif key_token: key = token key_token = False else: if token == "+=": if not data.has_key(key): data[key] = list() elif token == "=": if key == "TAGFILES" and data.has_key(key): append_data( data, key, False, "=" ) new_data=False else: data[key] = list() else: append_data( data, key, new_data, token ) new_data = True last_token = token token = lex.get_token() if last_token == '\\' and token != '\n': new_data = False append_data( data, key, new_data, '\\' ) # compress lists of len 1 into single strings for (k, v) in data.items(): if len(v) == 0: data.pop(k) # items in the following list will be kept as lists and not converted to strings if k in ["INPUT", "FILE_PATTERNS", "EXCLUDE_PATTERNS", "TAGFILES"]: continue if len(v) == 1: data[k] = v[0] return data

python

def DoxyfileParse(file_contents): """ Parse a Doxygen source file and return a dictionary of all the values. Values will be strings and lists of strings. """ data = {} import shlex lex = shlex.shlex(instream = file_contents, posix = True) lex.wordchars += "*+./-:" lex.whitespace = lex.whitespace.replace("\n", "") lex.escape = "" lineno = lex.lineno token = lex.get_token() key = token # the first token should be a key last_token = "" key_token = False next_key = False new_data = True def append_data(data, key, new_data, token): if new_data or len(data[key]) == 0: data[key].append(token) else: data[key][-1] += token while token: if token in ['\n']: if last_token not in ['\\']: key_token = True elif token in ['\\']: pass elif key_token: key = token key_token = False else: if token == "+=": if not data.has_key(key): data[key] = list() elif token == "=": if key == "TAGFILES" and data.has_key(key): append_data( data, key, False, "=" ) new_data=False else: data[key] = list() else: append_data( data, key, new_data, token ) new_data = True last_token = token token = lex.get_token() if last_token == '\\' and token != '\n': new_data = False append_data( data, key, new_data, '\\' ) # compress lists of len 1 into single strings for (k, v) in data.items(): if len(v) == 0: data.pop(k) # items in the following list will be kept as lists and not converted to strings if k in ["INPUT", "FILE_PATTERNS", "EXCLUDE_PATTERNS", "TAGFILES"]: continue if len(v) == 1: data[k] = v[0] return data

Parse a Doxygen source file and return a dictionary of all the values. Values will be strings and lists of strings.

9f7e7705793d258a0b205f185b20e3bbcda473da

https://github.com/melizalab/libtfr/blob/9f7e7705793d258a0b205f185b20e3bbcda473da/site_scons/site_tools/doxygen.py#L28-L97

train

melizalab/libtfr

site_scons/site_tools/doxygen.py

DoxySourceScan

def DoxySourceScan(node, env, path): """ Doxygen Doxyfile source scanner. This should scan the Doxygen file and add any files used to generate docs to the list of source files. """ default_file_patterns = [ '*.c', '*.cc', '*.cxx', '*.cpp', '*.c++', '*.java', '*.ii', '*.ixx', '*.ipp', '*.i++', '*.inl', '*.h', '*.hh ', '*.hxx', '*.hpp', '*.h++', '*.idl', '*.odl', '*.cs', '*.php', '*.php3', '*.inc', '*.m', '*.mm', '*.py', ] default_exclude_patterns = [ '*~', ] sources = [] data = DoxyfileParse(node.get_contents()) if data.get("RECURSIVE", "NO") == "YES": recursive = True else: recursive = False file_patterns = data.get("FILE_PATTERNS", default_file_patterns) exclude_patterns = data.get("EXCLUDE_PATTERNS", default_exclude_patterns) # We're running in the top-level directory, but the doxygen # configuration file is in the same directory as node; this means # that relative pathnames in node must be adjusted before they can # go onto the sources list conf_dir = os.path.dirname(str(node)) for node in data.get("INPUT", []): if not os.path.isabs(node): node = os.path.join(conf_dir, node) if os.path.isfile(node): sources.append(node) elif os.path.isdir(node): if recursive: for root, dirs, files in os.walk(node): for f in files: filename = os.path.join(root, f) pattern_check = reduce(lambda x, y: x or bool(fnmatch(filename, y)), file_patterns, False) exclude_check = reduce(lambda x, y: x and fnmatch(filename, y), exclude_patterns, True) if pattern_check and not exclude_check: sources.append(filename) else: for pattern in file_patterns: sources.extend(glob.glob("/".join([node, pattern]))) # Add tagfiles to the list of source files: for node in data.get("TAGFILES", []): file = node.split("=")[0] if not os.path.isabs(file): file = os.path.join(conf_dir, file) sources.append(file) # Add additional files to the list of source files: def append_additional_source(option): file = data.get(option, "") if file != "": if not os.path.isabs(file): file = os.path.join(conf_dir, file) if os.path.isfile(file): sources.append(file) append_additional_source("HTML_STYLESHEET") append_additional_source("HTML_HEADER") append_additional_source("HTML_FOOTER") sources = map( lambda path: env.File(path), sources ) return sources

python

def DoxySourceScan(node, env, path): """ Doxygen Doxyfile source scanner. This should scan the Doxygen file and add any files used to generate docs to the list of source files. """ default_file_patterns = [ '*.c', '*.cc', '*.cxx', '*.cpp', '*.c++', '*.java', '*.ii', '*.ixx', '*.ipp', '*.i++', '*.inl', '*.h', '*.hh ', '*.hxx', '*.hpp', '*.h++', '*.idl', '*.odl', '*.cs', '*.php', '*.php3', '*.inc', '*.m', '*.mm', '*.py', ] default_exclude_patterns = [ '*~', ] sources = [] data = DoxyfileParse(node.get_contents()) if data.get("RECURSIVE", "NO") == "YES": recursive = True else: recursive = False file_patterns = data.get("FILE_PATTERNS", default_file_patterns) exclude_patterns = data.get("EXCLUDE_PATTERNS", default_exclude_patterns) # We're running in the top-level directory, but the doxygen # configuration file is in the same directory as node; this means # that relative pathnames in node must be adjusted before they can # go onto the sources list conf_dir = os.path.dirname(str(node)) for node in data.get("INPUT", []): if not os.path.isabs(node): node = os.path.join(conf_dir, node) if os.path.isfile(node): sources.append(node) elif os.path.isdir(node): if recursive: for root, dirs, files in os.walk(node): for f in files: filename = os.path.join(root, f) pattern_check = reduce(lambda x, y: x or bool(fnmatch(filename, y)), file_patterns, False) exclude_check = reduce(lambda x, y: x and fnmatch(filename, y), exclude_patterns, True) if pattern_check and not exclude_check: sources.append(filename) else: for pattern in file_patterns: sources.extend(glob.glob("/".join([node, pattern]))) # Add tagfiles to the list of source files: for node in data.get("TAGFILES", []): file = node.split("=")[0] if not os.path.isabs(file): file = os.path.join(conf_dir, file) sources.append(file) # Add additional files to the list of source files: def append_additional_source(option): file = data.get(option, "") if file != "": if not os.path.isabs(file): file = os.path.join(conf_dir, file) if os.path.isfile(file): sources.append(file) append_additional_source("HTML_STYLESHEET") append_additional_source("HTML_HEADER") append_additional_source("HTML_FOOTER") sources = map( lambda path: env.File(path), sources ) return sources

Doxygen Doxyfile source scanner. This should scan the Doxygen file and add any files used to generate docs to the list of source files.

9f7e7705793d258a0b205f185b20e3bbcda473da

https://github.com/melizalab/libtfr/blob/9f7e7705793d258a0b205f185b20e3bbcda473da/site_scons/site_tools/doxygen.py#L99-L174

train

melizalab/libtfr

site_scons/site_tools/doxygen.py

DoxyEmitter

def DoxyEmitter(source, target, env): """Doxygen Doxyfile emitter""" # possible output formats and their default values and output locations output_formats = { "HTML": ("YES", "html"), "LATEX": ("YES", "latex"), "RTF": ("NO", "rtf"), "MAN": ("YES", "man"), "XML": ("NO", "xml"), } data = DoxyfileParse(source[0].get_contents()) targets = [] out_dir = data.get("OUTPUT_DIRECTORY", ".") if not os.path.isabs(out_dir): conf_dir = os.path.dirname(str(source[0])) out_dir = os.path.join(conf_dir, out_dir) # add our output locations for (k, v) in output_formats.items(): if data.get("GENERATE_" + k, v[0]) == "YES": targets.append(env.Dir( os.path.join(out_dir, data.get(k + "_OUTPUT", v[1]))) ) # add the tag file if neccessary: tagfile = data.get("GENERATE_TAGFILE", "") if tagfile != "": if not os.path.isabs(tagfile): conf_dir = os.path.dirname(str(source[0])) tagfile = os.path.join(conf_dir, tagfile) targets.append(env.File(tagfile)) # don't clobber targets for node in targets: env.Precious(node) # set up cleaning stuff for node in targets: env.Clean(node, node) return (targets, source)

python

def DoxyEmitter(source, target, env): """Doxygen Doxyfile emitter""" # possible output formats and their default values and output locations output_formats = { "HTML": ("YES", "html"), "LATEX": ("YES", "latex"), "RTF": ("NO", "rtf"), "MAN": ("YES", "man"), "XML": ("NO", "xml"), } data = DoxyfileParse(source[0].get_contents()) targets = [] out_dir = data.get("OUTPUT_DIRECTORY", ".") if not os.path.isabs(out_dir): conf_dir = os.path.dirname(str(source[0])) out_dir = os.path.join(conf_dir, out_dir) # add our output locations for (k, v) in output_formats.items(): if data.get("GENERATE_" + k, v[0]) == "YES": targets.append(env.Dir( os.path.join(out_dir, data.get(k + "_OUTPUT", v[1]))) ) # add the tag file if neccessary: tagfile = data.get("GENERATE_TAGFILE", "") if tagfile != "": if not os.path.isabs(tagfile): conf_dir = os.path.dirname(str(source[0])) tagfile = os.path.join(conf_dir, tagfile) targets.append(env.File(tagfile)) # don't clobber targets for node in targets: env.Precious(node) # set up cleaning stuff for node in targets: env.Clean(node, node) return (targets, source)

Doxygen Doxyfile emitter

9f7e7705793d258a0b205f185b20e3bbcda473da

https://github.com/melizalab/libtfr/blob/9f7e7705793d258a0b205f185b20e3bbcda473da/site_scons/site_tools/doxygen.py#L181-L221

train

melizalab/libtfr

site_scons/site_tools/doxygen.py

generate

def generate(env): """ Add builders and construction variables for the Doxygen tool. This is currently for Doxygen 1.4.6. """ doxyfile_scanner = env.Scanner( DoxySourceScan, "DoxySourceScan", scan_check = DoxySourceScanCheck, ) import SCons.Builder doxyfile_builder = SCons.Builder.Builder( action = "cd ${SOURCE.dir} && ${DOXYGEN} ${SOURCE.file}", emitter = DoxyEmitter, target_factory = env.fs.Entry, single_source = True, source_scanner = doxyfile_scanner, ) env.Append(BUILDERS = { 'Doxygen': doxyfile_builder, }) env.AppendUnique( DOXYGEN = 'doxygen', )

python

def generate(env): """ Add builders and construction variables for the Doxygen tool. This is currently for Doxygen 1.4.6. """ doxyfile_scanner = env.Scanner( DoxySourceScan, "DoxySourceScan", scan_check = DoxySourceScanCheck, ) import SCons.Builder doxyfile_builder = SCons.Builder.Builder( action = "cd ${SOURCE.dir} && ${DOXYGEN} ${SOURCE.file}", emitter = DoxyEmitter, target_factory = env.fs.Entry, single_source = True, source_scanner = doxyfile_scanner, ) env.Append(BUILDERS = { 'Doxygen': doxyfile_builder, }) env.AppendUnique( DOXYGEN = 'doxygen', )

Add builders and construction variables for the Doxygen tool. This is currently for Doxygen 1.4.6.

9f7e7705793d258a0b205f185b20e3bbcda473da

https://github.com/melizalab/libtfr/blob/9f7e7705793d258a0b205f185b20e3bbcda473da/site_scons/site_tools/doxygen.py#L223-L249

train

finklabs/metrics

metrics/position.py

PosMetric.reset

def reset(self): """Reset metric counter.""" self._positions = [] self._line = 1 self._curr = None # current scope we are analyzing self._scope = 0 self.language = None

python

def reset(self): """Reset metric counter.""" self._positions = [] self._line = 1 self._curr = None # current scope we are analyzing self._scope = 0 self.language = None

Reset metric counter.

fd9974af498831664b9ae8e8f3834e1ec2e8a699

https://github.com/finklabs/metrics/blob/fd9974af498831664b9ae8e8f3834e1ec2e8a699/metrics/position.py#L87-L93

train

finklabs/metrics

metrics/position.py

PosMetric.add_scope

def add_scope(self, scope_type, scope_name, scope_start, is_method=False): """we identified a scope and add it to positions.""" if self._curr is not None: self._curr['end'] = scope_start - 1 # close last scope self._curr = { 'type': scope_type, 'name': scope_name, 'start': scope_start, 'end': scope_start } if is_method and self._positions: last = self._positions[-1] if not 'methods' in last: last['methods'] = [] last['methods'].append(self._curr) else: self._positions.append(self._curr)

python

def add_scope(self, scope_type, scope_name, scope_start, is_method=False): """we identified a scope and add it to positions.""" if self._curr is not None: self._curr['end'] = scope_start - 1 # close last scope self._curr = { 'type': scope_type, 'name': scope_name, 'start': scope_start, 'end': scope_start } if is_method and self._positions: last = self._positions[-1] if not 'methods' in last: last['methods'] = [] last['methods'].append(self._curr) else: self._positions.append(self._curr)

we identified a scope and add it to positions.

fd9974af498831664b9ae8e8f3834e1ec2e8a699

https://github.com/finklabs/metrics/blob/fd9974af498831664b9ae8e8f3834e1ec2e8a699/metrics/position.py#L95-L110

train

finklabs/metrics

metrics/position.py

PosMetric.process_token

def process_token(self, tok): """count lines and track position of classes and functions""" if tok[0] == Token.Text: count = tok[1].count('\n') if count: self._line += count # adjust linecount if self._detector.process(tok): pass # works been completed in the detector elif tok[0] == Token.Punctuation: if tok[0] == Token.Punctuation and tok[1] == '{': self._scope += 1 if tok[0] == Token.Punctuation and tok[1] == '}': self._scope += -1 if self._scope == 0 and self._curr is not None: self._curr['end'] = self._line # close last scope self._curr = None elif tok[0] == Token.Name.Class and self._scope == 0: self.add_scope('Class', tok[1], self._line) elif tok[0] == Token.Name.Function and self._scope in [0, 1]: self.add_scope('Function', tok[1], self._line, self._scope == 1)

python

def process_token(self, tok): """count lines and track position of classes and functions""" if tok[0] == Token.Text: count = tok[1].count('\n') if count: self._line += count # adjust linecount if self._detector.process(tok): pass # works been completed in the detector elif tok[0] == Token.Punctuation: if tok[0] == Token.Punctuation and tok[1] == '{': self._scope += 1 if tok[0] == Token.Punctuation and tok[1] == '}': self._scope += -1 if self._scope == 0 and self._curr is not None: self._curr['end'] = self._line # close last scope self._curr = None elif tok[0] == Token.Name.Class and self._scope == 0: self.add_scope('Class', tok[1], self._line) elif tok[0] == Token.Name.Function and self._scope in [0, 1]: self.add_scope('Function', tok[1], self._line, self._scope == 1)

count lines and track position of classes and functions

fd9974af498831664b9ae8e8f3834e1ec2e8a699

https://github.com/finklabs/metrics/blob/fd9974af498831664b9ae8e8f3834e1ec2e8a699/metrics/position.py#L112-L132

train

rwl/pylon

pylon/solver.py

_Solver._unpack_model

def _unpack_model(self, om): """ Returns data from the OPF model. """ buses = om.case.connected_buses branches = om.case.online_branches gens = om.case.online_generators cp = om.get_cost_params() # Bf = om._Bf # Pfinj = om._Pfinj return buses, branches, gens, cp

python

def _unpack_model(self, om): """ Returns data from the OPF model. """ buses = om.case.connected_buses branches = om.case.online_branches gens = om.case.online_generators cp = om.get_cost_params() # Bf = om._Bf # Pfinj = om._Pfinj return buses, branches, gens, cp

Returns data from the OPF model.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/pylon/solver.py#L78-L90

train

rwl/pylon

pylon/solver.py

_Solver._dimension_data

def _dimension_data(self, buses, branches, generators): """ Returns the problem dimensions. """ ipol = [i for i, g in enumerate(generators) if g.pcost_model == POLYNOMIAL] ipwl = [i for i, g in enumerate(generators) if g.pcost_model == PW_LINEAR] nb = len(buses) nl = len(branches) # Number of general cost vars, w. nw = self.om.cost_N # Number of piece-wise linear costs. if "y" in [v.name for v in self.om.vars]: ny = self.om.get_var_N("y") else: ny = 0 # Total number of control variables of all types. nxyz = self.om.var_N return ipol, ipwl, nb, nl, nw, ny, nxyz

python

def _dimension_data(self, buses, branches, generators): """ Returns the problem dimensions. """ ipol = [i for i, g in enumerate(generators) if g.pcost_model == POLYNOMIAL] ipwl = [i for i, g in enumerate(generators) if g.pcost_model == PW_LINEAR] nb = len(buses) nl = len(branches) # Number of general cost vars, w. nw = self.om.cost_N # Number of piece-wise linear costs. if "y" in [v.name for v in self.om.vars]: ny = self.om.get_var_N("y") else: ny = 0 # Total number of control variables of all types. nxyz = self.om.var_N return ipol, ipwl, nb, nl, nw, ny, nxyz

Returns the problem dimensions.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/pylon/solver.py#L93-L112

train

rwl/pylon

pylon/solver.py

_Solver._linear_constraints

def _linear_constraints(self, om): """ Returns the linear problem constraints. """ A, l, u = om.linear_constraints() # l <= A*x <= u # Indexes for equality, greater than (unbounded above), less than # (unbounded below) and doubly-bounded box constraints. # ieq = flatnonzero( abs(u - l) <= EPS ) # igt = flatnonzero( (u >= 1e10) & (l > -1e10) ) # ilt = flatnonzero( (l <= -1e10) & (u < 1e10) ) # ibx = flatnonzero( (abs(u - l) > EPS) & (u < 1e10) & (l > -1e10) ) # Zero-sized sparse matrices not supported. Assume equality # constraints exist. ## AA = A[ieq, :] ## if len(ilt) > 0: ## AA = vstack([AA, A[ilt, :]], "csr") ## if len(igt) > 0: ## AA = vstack([AA, -A[igt, :]], "csr") ## if len(ibx) > 0: ## AA = vstack([AA, A[ibx, :], -A[ibx, :]], "csr") # # if len(ieq) or len(igt) or len(ilt) or len(ibx): # sig_idx = [(1, ieq), (1, ilt), (-1, igt), (1, ibx), (-1, ibx)] # AA = vstack([sig * A[idx, :] for sig, idx in sig_idx if len(idx)]) # else: # AA = None # # bb = r_[u[ieq, :], u[ilt], -l[igt], u[ibx], -l[ibx]] # # self._nieq = ieq.shape[0] # # return AA, bb return A, l, u

python

def _linear_constraints(self, om): """ Returns the linear problem constraints. """ A, l, u = om.linear_constraints() # l <= A*x <= u # Indexes for equality, greater than (unbounded above), less than # (unbounded below) and doubly-bounded box constraints. # ieq = flatnonzero( abs(u - l) <= EPS ) # igt = flatnonzero( (u >= 1e10) & (l > -1e10) ) # ilt = flatnonzero( (l <= -1e10) & (u < 1e10) ) # ibx = flatnonzero( (abs(u - l) > EPS) & (u < 1e10) & (l > -1e10) ) # Zero-sized sparse matrices not supported. Assume equality # constraints exist. ## AA = A[ieq, :] ## if len(ilt) > 0: ## AA = vstack([AA, A[ilt, :]], "csr") ## if len(igt) > 0: ## AA = vstack([AA, -A[igt, :]], "csr") ## if len(ibx) > 0: ## AA = vstack([AA, A[ibx, :], -A[ibx, :]], "csr") # # if len(ieq) or len(igt) or len(ilt) or len(ibx): # sig_idx = [(1, ieq), (1, ilt), (-1, igt), (1, ibx), (-1, ibx)] # AA = vstack([sig * A[idx, :] for sig, idx in sig_idx if len(idx)]) # else: # AA = None # # bb = r_[u[ieq, :], u[ilt], -l[igt], u[ibx], -l[ibx]] # # self._nieq = ieq.shape[0] # # return AA, bb return A, l, u

Returns the linear problem constraints.

916514255db1ae1661406f0283df756baf960d14

https://github.com/rwl/pylon/blob/916514255db1ae1661406f0283df756baf960d14/pylon/solver.py#L115-L149

train