Class Adaptor

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Instance Methods

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__init__(self, conn, dbutils)

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last_id(self, table)

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autocommit(self, y=True)

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commit(self)

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rollback(self)

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close(self)

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fetch_dbid_by_dbname(self, dbname)

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fetch_seqid_by_display_id(self, dbid, name)

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fetch_seqid_by_accession(self, dbid, name)

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fetch_seqids_by_accession(self, dbid, name)

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fetch_seqid_by_version(self, dbid, name)

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fetch_seqid_by_identifier(self, dbid, identifier)

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list_biodatabase_names(self)

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list_bioentry_ids(self, dbid)

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list_bioentry_display_ids(self, dbid)

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list_any_ids(self, sql, args)
Return ids given a SQL statement to select for them.

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execute_one(self, sql, args=None)

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execute(self, sql, args=None)
Just execute an sql command.

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get_subseq_as_string(self, seqid, start, end)

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execute_and_fetch_col0(self, sql, args=None)

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execute_and_fetchall(self, sql, args=None)

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Method Details

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list_any_ids(self, sql, args)

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Return ids given a SQL statement to select for them.

This assumes that the given SQL does a SELECT statement that returns a list of items. This parses them out of the 2D list they come as and just returns them in a list.