BiodbFactory: A class for constructing biodb objects.
In pkrog/biodb: biodb, a library and a development framework for connecting to chemical and biological databases
BiodbFactory R Documentation
A class for constructing biodb objects.
Description
A class for constructing biodb objects.
A class for constructing biodb objects.
Details
This class is responsible for the creation of database connectors and
database entries. You must go through the single instance of this class to
create and get connectors, as well as instantiate entries. To get the single
instance of this class, call the getFactory() method of class
BiodbMain.
Methods
Public methods
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Method new()
New instance initializer. The BiodbFactory class must not be instantiated
directly.
Instead, call the getFactory() method from the BiodbMain instance.
Usage
BiodbFactory$new(bdb)
Arguments
bdbThe BiodbMain instance.
Returns
Nothing.
Method getBiodb()
Returns the biodb main class instance to which this object is
attached.
Usage
BiodbFactory$getBiodb()
Returns
The main biodb instance.
Method createConn()
Creates a connector to a database.
Usage
BiodbFactory$createConn(
db.class,
url = NULL,
token = NA_character_,
fail.if.exists = TRUE,
get.existing.conn = TRUE,
conn.id = NULL,
cache.id = NULL
)
Arguments
db.classThe type of a database. The list of types can be
obtained from the class BiodbDbsInfo.
urlAn URL to the database for which to create a connection.
Each database connector is configured with a default URL, but some
allow you to change it.
tokenA security access token for the database. Some database
require such a token for all or some of their webservices. Usually you
obtain the token through your account on the database website.
fail.if.existsIf set to TRUE, the method will fail if a
connector for
get.existing.connThis argument will be used only if
fail.if.exists is set to FALSE and an identical connector already
exists. If it set to TRUE, the existing connector instance will be
returned, otherwise NULL will be returned.
conn.idIf set, this identifier will be used for the new
connector. An error will be raised in case another connector already
exists with this identifier.
cache.idIf set, this ID will be used as the cache ID for the
new connector. An error will be raised in case another connector
already exists with this cache identifier.
Returns
An instance of the requested connector class.
Method connExists()
Tests if a connector exists.
Usage
BiodbFactory$connExists(conn.id)
Arguments
conn.idA connector ID.
Returns
TRUE if a connector with this ID exists, FALSE otherwise.
Method deleteConn()
Deletes an existing connector.
Usage
BiodbFactory$deleteConn(conn)
Arguments
connA connector instance or a connector ID.
Returns
Nothing.
Method deleteConnByClass()
Deletes all existing connectors from a same class.
Usage
BiodbFactory$deleteConnByClass(db.class)
Arguments
db.classThe type of a database. All connectors of this
database type will be deleted.
Returns
Nothing.
Method getAllConnectors()
Gets all connectors.
Usage
BiodbFactory$getAllConnectors()
Returns
A list of all created connectors.
Method deleteAllConnectors()
Deletes all connectors.
Usage
BiodbFactory$deleteAllConnectors()
Returns
Nothing.
Method getConn()
Gets an instantiated connector instance, or create a new one.
Usage
BiodbFactory$getConn(conn.id, class = TRUE, create = TRUE)
Arguments
conn.idAn existing connector ID.
classIf set to TRUE, and \"conn.id\" does not correspond to
any instantiated connector, then interpret \"conn.id\" as a database
class and looks for the first instantiated connector of that class.
createIf set to TRUE, and \"class\" is also set to TRUE, and
no suitable instantiated connector was found, then creates a new
connector instance of the class specified by \"conn.id\".
Returns
The connector instance corresponding to the connector ID or to
the database ID submitted (if class \"parameter\" is set to TRUE).
Method getEntry()
Retrieves database entry objects from IDs (accession numbers), for the
specified connector.
Usage
BiodbFactory$getEntry(conn.id, id, drop = TRUE, no.null = FALSE, limit = 0)
Arguments
conn.idAn existing connector ID.
idA character vector containing database entry IDs (accession
numbers).
dropIf set to TRUE and the list of entries contains only one
element, then returns this element instead of the list. If set to
FALSE, then returns always a list.
no.nullSet to TRUE to remove NULL entries.
limitSet to a positive value to limit the number of entries
returned.
Returns
A list of BiodbEntry objects, the same length as id. A
NULL value is put into the list for each invalid ID of id.
Method createNewEntry()
Creates a new empty entry object from scratch. This entry is not stored in
cache, and is directly attached to the factory instance instead of a
particular connector.
Usage
BiodbFactory$createNewEntry(db.class)
Arguments
db.classA database ID.
Returns
A new BiodbEntry object.
Method createEntryFromContent()
Creates an entry instance from a content.
Usage
BiodbFactory$createEntryFromContent(conn.id, content, drop = TRUE)
Arguments
conn.idA valid BiodbConn identifier.
contentA list or character vector of contents to parse to create the
entries.
dropIf set to TRUE
Returns
A list of new BiodbEntry objects.
Method getAllCacheEntries()
For a connector, gets all entries stored in the cache.
Usage
BiodbFactory$getAllCacheEntries(conn.id)
Arguments
conn.idA connector ID.
Returns
A list of BiodbEntry objects.
Method deleteAllEntriesFromVolatileCache()
Deletes all entries stored in the cache of the given connector. This
method is deprecated, please use deleteAllEntriesFromVolatileCache()
instead.
Usage
BiodbFactory$deleteAllEntriesFromVolatileCache(conn.id)
Arguments
conn.idA connector ID.
Returns
Nothing.
Method deleteAllCacheEntries()
Deletes all entries stored in the cache of the given connector.
Usage
BiodbFactory$deleteAllCacheEntries(conn.id)
Arguments
conn.idA connector ID.
Returns
Nothing.
Method print()
Prints information about this instance.
Usage
BiodbFactory$print()
Returns
Nothing.
Method clone()
The objects of this class are cloneable with this method.
Usage
BiodbFactory$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
See Also
BiodbMain, BiodbConn and
BiodbEntry.
Examples
# Create a BiodbMain instance with default settings:
mybiodb <- biodb::newInst()
# Obtain the factory instance:
factory <- mybiodb$getFactory()
# Get a compound CSV file database
chebi.tsv <- system.file("extdata", "chebi_extract.tsv", package='biodb')
# Create a connector:
conn <- mybiodb$getFactory()$createConn('comp.csv.file', url=chebi.tsv)
# Get a database entry:
entry <- conn$getEntry(conn$getEntryIds(1))
# Terminate instance.
mybiodb$terminate()
pkrog/biodb documentation built on Nov. 29, 2022, 4:24 a.m.
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| BiodbFactory | R Documentation |
A class for constructing biodb objects.
Description
A class for constructing biodb objects.
A class for constructing biodb objects.
Details
This class is responsible for the creation of database connectors and
database entries. You must go through the single instance of this class to
create and get connectors, as well as instantiate entries. To get the single
instance of this class, call the getFactory() method of class
BiodbMain.
Methods
Public methods
Method new()
New instance initializer. The BiodbFactory class must not be instantiated directly. Instead, call the getFactory() method from the BiodbMain instance.
Usage
BiodbFactory$new(bdb)
Arguments
bdbThe BiodbMain instance.
Returns
Nothing.
Method getBiodb()
Returns the biodb main class instance to which this object is attached.
Usage
BiodbFactory$getBiodb()
Returns
The main biodb instance.
Method createConn()
Creates a connector to a database.
Usage
BiodbFactory$createConn( db.class, url = NULL, token = NA_character_, fail.if.exists = TRUE, get.existing.conn = TRUE, conn.id = NULL, cache.id = NULL )
Arguments
db.classThe type of a database. The list of types can be obtained from the class BiodbDbsInfo.
urlAn URL to the database for which to create a connection. Each database connector is configured with a default URL, but some allow you to change it.
tokenA security access token for the database. Some database require such a token for all or some of their webservices. Usually you obtain the token through your account on the database website.
fail.if.existsIf set to TRUE, the method will fail if a connector for
get.existing.connThis argument will be used only if fail.if.exists is set to FALSE and an identical connector already exists. If it set to TRUE, the existing connector instance will be returned, otherwise NULL will be returned.
conn.idIf set, this identifier will be used for the new connector. An error will be raised in case another connector already exists with this identifier.
cache.idIf set, this ID will be used as the cache ID for the new connector. An error will be raised in case another connector already exists with this cache identifier.
Returns
An instance of the requested connector class.
Method connExists()
Tests if a connector exists.
Usage
BiodbFactory$connExists(conn.id)
Arguments
conn.idA connector ID.
Returns
TRUE if a connector with this ID exists, FALSE otherwise.
Method deleteConn()
Deletes an existing connector.
Usage
BiodbFactory$deleteConn(conn)
Arguments
connA connector instance or a connector ID.
Returns
Nothing.
Method deleteConnByClass()
Deletes all existing connectors from a same class.
Usage
BiodbFactory$deleteConnByClass(db.class)
Arguments
db.classThe type of a database. All connectors of this database type will be deleted.
Returns
Nothing.
Method getAllConnectors()
Gets all connectors.
Usage
BiodbFactory$getAllConnectors()
Returns
A list of all created connectors.
Method deleteAllConnectors()
Deletes all connectors.
Usage
BiodbFactory$deleteAllConnectors()
Returns
Nothing.
Method getConn()
Gets an instantiated connector instance, or create a new one.
Usage
BiodbFactory$getConn(conn.id, class = TRUE, create = TRUE)
Arguments
conn.idAn existing connector ID.
classIf set to TRUE, and \"conn.id\" does not correspond to any instantiated connector, then interpret \"conn.id\" as a database class and looks for the first instantiated connector of that class.
createIf set to TRUE, and \"class\" is also set to TRUE, and no suitable instantiated connector was found, then creates a new connector instance of the class specified by \"conn.id\".
Returns
The connector instance corresponding to the connector ID or to the database ID submitted (if class \"parameter\" is set to TRUE).
Method getEntry()
Retrieves database entry objects from IDs (accession numbers), for the specified connector.
Usage
BiodbFactory$getEntry(conn.id, id, drop = TRUE, no.null = FALSE, limit = 0)
Arguments
conn.idAn existing connector ID.
idA character vector containing database entry IDs (accession numbers).
dropIf set to TRUE and the list of entries contains only one element, then returns this element instead of the list. If set to FALSE, then returns always a list.
no.nullSet to TRUE to remove NULL entries.
limitSet to a positive value to limit the number of entries returned.
Returns
A list of BiodbEntry objects, the same length as id. A
NULL value is put into the list for each invalid ID of id.
Method createNewEntry()
Creates a new empty entry object from scratch. This entry is not stored in cache, and is directly attached to the factory instance instead of a particular connector.
Usage
BiodbFactory$createNewEntry(db.class)
Arguments
db.classA database ID.
Returns
A new BiodbEntry object.
Method createEntryFromContent()
Creates an entry instance from a content.
Usage
BiodbFactory$createEntryFromContent(conn.id, content, drop = TRUE)
Arguments
conn.idA valid BiodbConn identifier.
contentA list or character vector of contents to parse to create the entries.
dropIf set to TRUE
Returns
A list of new BiodbEntry objects.
Method getAllCacheEntries()
For a connector, gets all entries stored in the cache.
Usage
BiodbFactory$getAllCacheEntries(conn.id)
Arguments
conn.idA connector ID.
Returns
A list of BiodbEntry objects.
Method deleteAllEntriesFromVolatileCache()
Deletes all entries stored in the cache of the given connector. This method is deprecated, please use deleteAllEntriesFromVolatileCache() instead.
Usage
BiodbFactory$deleteAllEntriesFromVolatileCache(conn.id)
Arguments
conn.idA connector ID.
Returns
Nothing.
Method deleteAllCacheEntries()
Deletes all entries stored in the cache of the given connector.
Usage
BiodbFactory$deleteAllCacheEntries(conn.id)
Arguments
conn.idA connector ID.
Returns
Nothing.
Method print()
Prints information about this instance.
Usage
BiodbFactory$print()
Returns
Nothing.
Method clone()
The objects of this class are cloneable with this method.
Usage
BiodbFactory$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
See Also
BiodbMain, BiodbConn and
BiodbEntry.
Examples
# Create a BiodbMain instance with default settings:
mybiodb <- biodb::newInst()
# Obtain the factory instance:
factory <- mybiodb$getFactory()
# Get a compound CSV file database
chebi.tsv <- system.file("extdata", "chebi_extract.tsv", package='biodb')
# Create a connector:
conn <- mybiodb$getFactory()$createConn('comp.csv.file', url=chebi.tsv)
# Get a database entry:
entry <- conn$getEntry(conn$getEntryIds(1))
# Terminate instance.
mybiodb$terminate()
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