Detailed Description

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

Public Member Functions
	PartShop (std::string url, std::string spoofed_url="")
	Construct an interface to an instance of SynBioHub or other parts repository. More...

template<class SBOLClass >
int	count ()
	Return the count of objects contained in a PartShop. More...

std::string	sparqlQuery (std::string query)
	Issue a SPARQL query.

void	spoof (std::string spoofed_url)
	Specify the URL of a resource that is simulated or spoofed by this PartShop.

void	pull (std::string uri, Document &doc, bool recursive=true)
	Retrieve an object from an online resource. More...

void	pull (std::vector< std::string > uris, Document &doc, bool recursive=true)
	Retrieve an object from an online resource. More...

std::string	searchRootCollections ()
	Returns all Collections that are not members of any other Collections. More...

std::string	searchSubCollections (std::string uri)
	Returns all Collections that are members of the Collection specified by its URI. More...

SearchResponse &	search (std::string search_text, std::string object_type, std::string property_uri, int offset=0, int limit=25)
	An EXACT search. More...

SearchResponse &	search (std::string search_text, std::string object_type=SBOL_COMPONENT_DEFINITION, int offset=0, int limit=25)
	A GENERAL search. More...

SearchResponse &	search (SearchQuery &q)
	Perform an ADVANCED search using a SearchQuery object. More...

int	searchCount (std::string search_text, std::string object_type, std::string property_uri)
	Returns the number of search records for an EXACT search matching the given criteria. More...

int	searchCount (std::string search_text, std::string object_type=SBOL_COMPONENT_DEFINITION)
	Returns the number of search records for a general search matching the given criteria. More...

int	searchCount (SearchQuery &q)
	Returns the number of search records matching the given criteria for an ADVANCED search. More...

std::string	submit (Document &doc, std::string collection="", int overwrite=0)
	Submit an SBOL Document to SynBioHub. More...

void	login (std::string user_id, std::string password="")
	In order to submit to a PartShop, you must login first. More...

std::string	getURL ()
	Returns the network address of the PartShop. More...

void	attachFile (std::string topleveluri, std::string filename)
	Upload and attach a file to a TopLevel object in a PartShop. More...

void	downloadAttachment (std::string attachment_uri, std::string path=".")
	Download a file attached to a TopLevel object in an online repository. More...

Constructor & Destructor Documentation

◆ PartShop()

PartShop	(	std::string	url,
		std::string	spoofed_url = `""`
	)

inline

Construct an interface to an instance of SynBioHub or other parts repository.

Parameters

The	URL of the online repository

Member Function Documentation

◆ attachFile()

void attachFile	(	std::string	topleveluri,
		std::string	filename
	)

Upload and attach a file to a TopLevel object in a PartShop.

Parameters

top_level_uri	The identity of the object to which the file will be attached
file_name	A path to the file attachment

◆ count()

int count ( )

Return the count of objects contained in a PartShop.

Template Parameters

SBOLClass The type of SBOL object, usually a ComponentDefinition

◆ downloadAttachment()

void downloadAttachment	(	std::string	attachment_uri,
		std::string	path = `"."`
	)

Download a file attached to a TopLevel object in an online repository.

Parameters

attachment_uri	The full URI of the attached object
path	The target path to which the file will be downloaded

◆ getURL()

string getURL ( )

Returns the network address of the PartShop.

Returns: The URL of the online repository

◆ login()

void login	(	std::string	user_id,
		std::string	password = `""`
	)

In order to submit to a PartShop, you must login first.

Register on SynBioHub to obtain account credentials.

Parameters

email	The email associated with the user's SynBioHub account
password	The user's password

◆ pull() [1/2]

void pull	(	std::string	uri,
		Document &	doc,
		bool	recursive = `true`
	)

Retrieve an object from an online resource.

Parameters

uri	The identity of the SBOL object you want to retrieve
doc	A document to add the data to

◆ pull() [2/2]

void pull	(	std::vector< std::string >	uris,
		Document &	doc,
		bool	recursive = `true`
	)

Retrieve an object from an online resource.

Parameters

uris	A vector of URIs for multiple SBOL objects you want to retrieve
doc	A document to add the data to

◆ search() [1/3]

SearchResponse & search	(	std::string	search_text,
		std::string	object_type,
		std::string	property_uri,
		int	offset = `0`,
		int	limit = `25`
	)

An EXACT search.

Scan the parts repository for objects that exactly match the specified criteria. In most uses of this function, LibSBOL's built-in RDF type constants (see constants.h) will come in handy. For instance, searching for all SBOL_COMPONENT_DEFINITION of type BIOPAX_DNA. (These constants follow a fairly systematic and consistent naming scheme (see constants.h). The number of records returned in the search is specified by offset and limit parameters.

Parameters

search_text	This may be a literal text value or it may be a URI.
object_type	The RDF type of an SBOL object. See constants.h. For example, SBOL_COMPONENT_DEFINITION
property_uri	The RDF type of an SBOL property. Specifies which field of an SBOL object to search. For example, SBOL_ROLES. Refer to constants.h
offset	The index of the first record to return. This parameter is indexed starting from zero.
limit	The total count number of records to return

Returns: Metadata formatted as a string encoding JSON.

◆ search() [2/3]

SearchResponse & search	(	std::string	search_text,
		std::string	object_type = `SBOL_COMPONENT_DEFINITION`,
		int	offset = `0`,
		int	limit = `25`
	)

A GENERAL search.

Search name, description, and displayId properties for a match to the search text, including matches to substrings of the property value. The type of object to search for can be further restricted by use of the second parameter, though this is set to SBOL_COMPONENT_DEFINITION by default. See constants.h for more of libSBOL's built-in RDF type constants. These constants follow a fairly predictable and consistent naming scheme. The number of records returned in the search is specified by offset and limit parameters.

Parameters

search_text	A snippet of text to search for in a property's value.
object_type	The RDF type of an SBOL object. See constants.h. For example, SBOL_COMPONENT_DEFINITION by default.
offset	The index of the first record to return. This parameter is indexed starting from zero.
limit	The total count number of records to return

Returns: Metadata formatted as a string encoding JSON.

◆ search() [3/3]

SearchResponse & search ( SearchQuery & q )

Perform an ADVANCED search using a SearchQuery object.

Parameters

search_query A map of string key-value pairs. Keys are objectType, sbolTag, collection, dcterms:tag, namespace/tag, offset, limit.

Returns: Search metadata A vector of maps with key-value pairs.

◆ searchCount() [1/3]

int searchCount	(	std::string	search_text,
		std::string	object_type,
		std::string	property_uri
	)

Returns the number of search records for an EXACT search matching the given criteria.

Returns: An integer count.

◆ searchCount() [2/3]

int searchCount	(	std::string	search_text,
		std::string	object_type = `SBOL_COMPONENT_DEFINITION`
	)

Returns the number of search records for a general search matching the given criteria.

Returns: An integer count.

◆ searchCount() [3/3]

int searchCount ( SearchQuery & q )

Returns the number of search records matching the given criteria for an ADVANCED search.

Parameters

search_query A map of string key-value pairs. See SearchQuery for required and optional criteria.

Returns: An integer count.

◆ searchRootCollections()

std::string searchRootCollections ( )

Returns all Collections that are not members of any other Collections.

Parameters

doc	A Document to add the Collections to

◆ searchSubCollections()

std::string searchSubCollections ( std::string uri )

Returns all Collections that are members of the Collection specified by its URI.

Parameters

uri	The URI of a Collection of Collections
doc	A Document to add the subcollections to

◆ submit()

std::string submit	(	Document &	doc,
		std::string	collection = `""`,
		int	overwrite = `0`
	)

Submit an SBOL Document to SynBioHub.

Parameters

doc	The Document to submit
collection	The URI of an SBOL Collection to which the Document contents will be uploaded
overwrite	An integer code: '0' prevent, '1' overwrite, '2' merge and prevent, '3' merge and overwrite

The documentation for this class was generated from the following files:

/Users/bbartley/Dev/git/libSBOL/source/partshop.h
/Users/bbartley/Dev/git/libSBOL/source/partshop.cpp

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

◆ PartShop()

Member Function Documentation

◆ attachFile()

◆ count()

◆ downloadAttachment()

◆ getURL()

◆ login()

◆ pull() [1/2]

◆ pull() [2/2]

◆ search() [1/3]

◆ search() [2/3]

◆ search() [3/3]

◆ searchCount() [1/3]

◆ searchCount() [2/3]

◆ searchCount() [3/3]

◆ searchRootCollections()

◆ searchSubCollections()

◆ submit()