def load(self, record_iterator, fetch_NCBI_taxonomy=False):
"""Load a set of SeqRecords into the BioSQL database.
record_iterator is either a list of SeqRecord objects, or an
Iterator object that returns SeqRecord objects (such as the
output from the Bio.SeqIO.parse() function), which will be
used to populate the database.
fetch_NCBI_taxonomy is boolean flag allowing or preventing
connection to the taxonomic database on the NCBI server
(via Bio.Entrez) to fetch a detailed taxonomy for each
SeqRecord.
Example:
from Bio import SeqIO
count = db.load(SeqIO.parse(open(filename), format))
Returns the number of records loaded.
"""
db_loader = Loader.DatabaseLoader(self.adaptor, self.dbid, \
fetch_NCBI_taxonomy)
num_records = 0
for cur_record in record_iterator:
num_records += 1
db_loader.load_seqrecord(cur_record)
return num_records
def load(self, record_iterator, fetch_NCBI_taxonomy=False):
"""Load a set of SeqRecords into the BioSQL database.
record_iterator is either a list of SeqRecord objects, or an
Iterator object that returns SeqRecord objects (such as the
output from the Bio.SeqIO.parse() function), which will be
used to populate the database.
fetch_NCBI_taxonomy is boolean flag allowing or preventing
connection to the taxonomic database on the NCBI server
(via Bio.Entrez) to fetch a detailed taxonomy for each
SeqRecord.
Example:
from Bio import SeqIO
count = db.load(SeqIO.parse(open(filename), format))
Returns the number of records loaded.
"""
db_loader = Loader.DatabaseLoader(self.adaptor, self.dbid, \
fetch_NCBI_taxonomy)
num_records = 0
global _POSTGRES_RULES_PRESENT
for cur_record in record_iterator:
num_records += 1
#Hack to work arround BioSQL Bug 2839 - If using PostgreSQL and
#the RULES are present check for a duplicate record before loading
if _POSTGRES_RULES_PRESENT:
#Recreate what the Loader's _load_bioentry_table will do:
if cur_record.id.count(".") == 1:
accession, version = cur_record.id.split('.')
try:
version = int(version)
except ValueError:
accession = cur_record.id
version = 0
else:
accession = cur_record.id
version = 0
gi = cur_record.annotations.get("gi", None)
sql = "SELECT bioentry_id FROM bioentry WHERE (identifier " + \
"= '%s' AND biodatabase_id = '%s') OR (accession = " + \
"'%s' AND version = '%s' AND biodatabase_id = '%s')"
self.adaptor.execute(
sql % (gi, self.dbid, accession, version, self.dbid))
if self.adaptor.cursor.fetchone():
try:
raise self.adaptor.conn.IntegrityError(
"Duplicate record "
"detected: record has not been inserted")
except AttributeError: #psycopg version 1
import psycopg
raise psycopg.IntegrityError(
"Psycopg1: Duplicate record "
"detected: record has not been inserted")
#End of hack
db_loader.load_seqrecord(cur_record)
return num_records
