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src/b/c/bcbb-HEAD/gff/Scripts/gff/gff_to_biosql.py   bcbb(Download)
 
    print "Writing to BioSQL database..."
    server = BioSeqDatabase.open_database(driver="MySQLdb", user=user,
            passwd=passwd, host=host, db=db_name)
    try:

src/b/i/biopython-1.63/Scripts/Performance/biosql_performance_read.py   biopython(Download)
# set up the connection
from BioSQL import BioSeqDatabase
server = BioSeqDatabase.open_database(host="192.168.0.192", user="root",
                                       passwd="", db="test_biosql")
db = server["embl_rod"]

src/b/i/biopython-1.63/Scripts/Performance/biosql_performance_load.py   biopython(Download)
from Bio import GenBank
from BioSQL import BioSeqDatabase
server = BioSeqDatabase.open_database(host="192.168.0.192", user="root",
                                       passwd="", db="pythonloadtest")
 

src/b/i/biopython-HEAD/Scripts/Performance/biosql_performance_read.py   biopython(Download)
# set up the connection
from BioSQL import BioSeqDatabase
server = BioSeqDatabase.open_database(host="192.168.0.192", user="root",
                                       passwd="", db="test_biosql")
db = server["embl_rod"]

src/b/i/biopython-HEAD/Scripts/Performance/biosql_performance_load.py   biopython(Download)
from Bio import GenBank
from BioSQL import BioSeqDatabase
server = BioSeqDatabase.open_database(host="192.168.0.192", user="root",
                                       passwd="", db="pythonloadtest")
 

src/b/i/biopython-1.63/Tests/common_BioSQL.py   biopython(Download)
    try:
        if DBDRIVER in ["sqlite3"]:
            server = BioSeqDatabase.open_database(driver=DBDRIVER, db=TESTDB)
        else:
            server = BioSeqDatabase.open_database(driver=DBDRIVER,
def _do_db_create():
    """Do the actual work of database creation. Relevant for MySQL and PostgreSQL
    """
    # first open a connection to create the database
    server = BioSeqDatabase.open_database(driver = DBDRIVER,
 
    # now open a connection to load the database
    server = BioSeqDatabase.open_database(driver = DBDRIVER,
                                          user = DBUSER, passwd = DBPASSWD,
                                          host = DBHOST, db = TESTDB)
    # now open a connection to load the database
    db_name = "biosql-test"
    server = BioSeqDatabase.open_database(driver = DBDRIVER,
                                          user = DBUSER, passwd = DBPASSWD,
                                          host = DBHOST, db = TESTDB)

src/b/i/biopython-HEAD/Tests/common_BioSQL.py   biopython(Download)
    try:
        if DBDRIVER in ["sqlite3"]:
            server = BioSeqDatabase.open_database(driver=DBDRIVER, db=TESTDB)
        else:
            server = BioSeqDatabase.open_database(driver=DBDRIVER,
def _do_db_create():
    """Do the actual work of database creation. Relevant for MySQL and PostgreSQL
    """
    # first open a connection to create the database
    server = BioSeqDatabase.open_database(driver = DBDRIVER,
 
    # now open a connection to load the database
    server = BioSeqDatabase.open_database(driver = DBDRIVER,
                                          user = DBUSER, passwd = DBPASSWD,
                                          host = DBHOST, db = TESTDB)
    # now open a connection to load the database
    db_name = "biosql-test"
    server = BioSeqDatabase.open_database(driver = DBDRIVER,
                                          user = DBUSER, passwd = DBPASSWD,
                                          host = DBHOST, db = TESTDB)

src/b/i/biopython-1.63/Tests/test_BioSQL_sqlite3.py   biopython(Download)
    #the database.
    assert not os.path.isfile("BioSQL/cor6_6.db")
    server = BioSeqDatabase.open_database(driver=DBDRIVER,
                                          db="BioSQL/cor6_6.db")
    DBSCHEMA = "biosqldb-" + DBTYPE + ".sql"
    def test_backwards_compatibility(self):
        """Check can re-use an old BioSQL SQLite3 database."""
        original_records = list(SeqIO.parse("GenBank/cor6_6.gb", "gb"))
        # now open a connection to load the database
        server = BioSeqDatabase.open_database(driver=DBDRIVER,

src/b/i/biopython-HEAD/Tests/test_BioSQL_sqlite3.py   biopython(Download)
    #the database.
    assert not os.path.isfile("BioSQL/cor6_6.db")
    server = BioSeqDatabase.open_database(driver=DBDRIVER,
                                          db="BioSQL/cor6_6.db")
    DBSCHEMA = "biosqldb-" + DBTYPE + ".sql"
    def test_backwards_compatibility(self):
        """Check can re-use an old BioSQL SQLite3 database."""
        original_records = list(SeqIO.parse("GenBank/cor6_6.gb", "gb"))
        # now open a connection to load the database
        server = BioSeqDatabase.open_database(driver=DBDRIVER,