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# Copyright 2002 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from Bio.config.DBRegistry import CGIDB, DBGroup
from _support import *
embl_xembl_cgi = CGIDB(
name="embl-xembl-cgi",
doc="Query XEMBL for EMBL sequence data in XML format.",
cgi="http://www.ebi.ac.uk/cgi-bin/xembl/XEMBL.pl",
url="http://www.ebi.ac.uk/xembl/",
delay=5.0,
params=[("format", "Bsml")],
key="id",
failure_cases=[(has_str("NOT EXIST"), "id does not exist")],
)
embl_dbfetch_cgi = CGIDB(
name="embl-dbfetch-cgi",
cgi="http://www.ebi.ac.uk/cgi-bin/dbfetch",
url="http://www.ebi.ac.uk/cgi-bin/dbfetch",
doc="dbfetch provides EMBL, Genbank, and SWALL sequences",
delay=5.0,
params=[("db", "embl"),
("style", "raw"),
("format", "embl"),
],
key="id",
failure_cases=[(has_str("not found in database"), "id does not exist")]
)
embl_ebi_cgi = CGIDB(
name="embl-ebi-cgi",
cgi="http://www.ebi.ac.uk/cgi-bin/emblfetch",
url="http://www.ebi.ac.uk/cgi-bin/emblfetch",
doc="Retrieve many kinds of sequences from EBI",
delay=5.0,
params=[("db", "EMBL"),
("format", "default"), # also Fasta, bsml, agave available
("style", "raw")
],
key="id",
failure_cases=[(blank_expr, "No results returned")]
)
embl = DBGroup(
name="embl",
behavior="serial",
## cache="XXX"
)
embl.add(embl_dbfetch_cgi)
embl.add(embl_ebi_cgi)
embl_xml = DBGroup(
name = "embl-xml",
behavior = "serial")
embl_fast = DBGroup(
name="embl-fast",
behavior="concurrent",
)
embl_fast.add(embl_dbfetch_cgi)
embl_fast.add(embl_ebi_cgi)
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