sbol2.partshop

Module Contents

Classes

PartShop

A class which provides an API front-end for
class sbol2.partshop.PartShop(url, spoofed_url='')

A class which provides an API front-end for online bioparts repositories

_validate_url(self, url, url_name)

Function to validate url with type checking, urlparse and terminal forward slash’s as well as allowing spoofed url to pass as ‘’

property logger(self)
abstract count(self)

Return the count of objects contained in a PartShop

spoof(self, spoofed_url)
sparqlQuery(self, query)

Issue a SPARQL query :param query: the SPARQL query :return: the HTTP response object

pull(self, uris, doc, recursive=True)

Retrieve an object from an online resource :param uris: A list of SBOL objects you want to retrieve, or a single SBOL object URI :param doc: A document to add the data to :param recursive: Whether the GET request should be recursive :return: nothing (doc parameter is updated, or an exception is thrown)

submit(self, doc, collection='', overwrite=0)

Submit a SBOL Document to SynBioHub :param doc: The Document to submit :param collection: The URI of a SBOL Collection to which the Document contents will be uploaded :param overwrite: An integer code: 0 (default) - do not overwrite, 1 - overwrite, 2 - merge :return: the HTTP response object

_uri2url(self, uri)

Converts an SBOL URI to a URL for running queries to a SynBioHub endpoint.

remove(self, uri)
login(self, user_id, password='')

In order to submit to a PartShop, you must login first. Register on [SynBioHub](http://synbiohub.org) to obtain account credentials. :param user_id: User ID :param password: User password :return: the HTTP response object

getKey(self)
getURL(self)
getUser(self)
getSpoofedURL(self)
attachFile(self, top_level_uri, filepath)

Attach a file to an object in SynBioHub.

Returns None if successful.

Raises SBOLError with code SBOL_ERROR_HTTP_UNAUTHORIZED if it there is an HTTP Unauthorized response.

Raises SBOLError with code SBOL_ERROR_BAD_HTTP_REQUEST on any other HTTP error. The actual status code is embedded in the string message.

downloadAttachment(self, attachment_uri, filepath='.')

Download a file attachment from SynBioHub. :param attachment_uri: The URI of the file to download :param filepath: The local path or filename to which the file will be written Returns None if successful.

Raises EnvironmentError if the filepath is invalid

Raises SBOLError with code SBOL_ERROR_HTTP_UNAUTHORIZED if it there is an HTTP Unauthorized response.

Raises SBOLError with code SBOL_ERROR_BAD_HTTP_REQUEST on any other HTTP error. The actual status code is embedded in the string message.

_make_search_item(self, item: dict) → sbol2.identified.Identified

Given a URL, perform the search and parse the results. The URL is formed by one of the other search methods: search_exact, search_general, and search_advanced.

search_general(self, search_text: str, object_type: Optional[str] = SBOL_COMPONENT_DEFINITION, offset: int = 0, limit: int = 25) → List[sbol2.identified.Identified]
search_exact(self, search_text: str, object_type: Optional[str] = SBOL_COMPONENT_DEFINITION, property_uri: Optional[str] = None, offset: int = 0, limit: int = 25) → List[sbol2.identified.Identified]
search_advanced(self, search_query: sbol2.SearchQuery)
search(self, search_text: Union[str, sbol2.SearchQuery], object_type: Optional[str] = SBOL_COMPONENT_DEFINITION, property_uri: Optional[Union[str, int]] = None, offset: int = 0, limit: int = 25) → List[sbol2.identified.Identified]
_search_count(self, url)
search_count(self, search_text, object_type, property_uri)
search_count_advanced(self, search_query)
searchCount(self, search_text, object_type=None, property_uri=None)

Returns the number of records matching the given criteria.