biana.BianaObjects.ExternalDatabase'.ExternalDatabase

Class ExternalDatabase

Class to represent an external database (any database giving biologic relevant information)

Instance Methods

__init__(self, databaseName, databaseVersion, databaseFile, databaseDescription, defaultExternalEntityAttribute, databaseDate=None, externalDatabaseID=None, isPromiscuous=False)
Initializes a ExternalDatabase Object

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__str__(self)
str(x)

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add_valid_external_entity_attribute_type(self, attribute_identifier)

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add_valid_external_entity_relation_attribute_type(self, attribute_identifier)

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add_valid_external_entity_relation_type(self, eEr_type)

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add_valid_external_entity_type(self, eE_type)

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get_default_eE_attribute(self)

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get_description(self)

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get_id(self)

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get_name(self)

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get_parsed_file(self)

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get_parsing_date(self)

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get_parsing_time(self)

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get_promiscuity(self)

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get_valid_external_entity_attribute_type(self)

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get_valid_external_entity_relation_attribute_type(self)

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get_valid_external_entity_relation_type(self)

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get_valid_external_entity_type(self)

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get_version(self)

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has_external_entity_type(self, eE_type)
Checks if this external database contains external entities of the type "eE_type"

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set_id(self, externalDatabaseID)

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set_parsing_time(self, time)

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Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__

Properties

[hide private]

Inherited from object: __class__

init(self, databaseName, databaseVersion, databaseFile, databaseDescription, defaultExternalEntityAttribute, databaseDate=None, externalDatabaseID=None, isPromiscuous=False)
(Constructor)

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Initializes a ExternalDatabase Object

"databaseName" is the name for the external database (i.e. swissprot, IntAct, Reactome...)

"datavaseVersion" is the version of the database. The combination of databaseName and databaseVersion must be unique!

"databaseFile" is the parsed database file. If there are multiple files, it is an empty string

"databaseDescription" is a longer description of the database (for example, "public repository of interactions of ncbi", etc.)

"externalDatabaseID" is a unique identifier for the database. When parsing it should not be added, only when this information is persistent in the database

"defaultExternalEntityAttribute" is the default attribute type of the data an external database is providing

"databaseDate" Parsing date. If it is None, automatically assigns to current date to it "isPromiscuous" Flag deciding whether database gives information that is going to be added to more than one user entiries

Overrides: object.__init__

str(self)
(Informal representation operator)

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str(x)

Overrides: object.__str__: (inherited documentation)

Class ExternalDatabase

__init__(self, databaseName, databaseVersion, databaseFile, databaseDescription, defaultExternalEntityAttribute, databaseDate=None, externalDatabaseID=None, isPromiscuous=False) (Constructor)

__str__(self) (Informal representation operator)

init(self, databaseName, databaseVersion, databaseFile, databaseDescription, defaultExternalEntityAttribute, databaseDate=None, externalDatabaseID=None, isPromiscuous=False)
(Constructor)

str(self)
(Informal representation operator)