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"""Database definitions for retrieval of FASTA formatted sequences.
"""
from Bio.config.DBRegistry import DBGroup, EUtilsDB
from _support import *
from Martel import *
proxy_error_expr = has_expr(Alt(Str("500"), Str("502")) + Str(" Proxy Error"))
diagnostic_error_expr = has_str("WWW Error 500 Diagnostic")
error_expr = Str("ERROR")
ncbi_failures=[
(proxy_error_expr, "proxy error"),
(diagnostic_error_expr, "diagnostic error"),
(error_expr, "ERROR"),
(html_expr, "I got HTML and shouldn't have"),
(Str("Please try again later"), "Please try again later"),
(Str("The sequence has been intentionally withdrawn"),
"Sequence withdrawn"),
(blank_expr, "No data returned")
]
fasta_sequence_eutils = EUtilsDB(
name = "fasta-sequence-eutils",
doc = "Retrieve Fasta formatted sequence data from NCBI using EUtils",
delay = 5.0,
db = "sequences",
rettype = "fasta",
failure_cases = ncbi_failures
)
fasta = DBGroup(
name = "fasta",
behavior = "serial")
fasta.add(fasta_sequence_eutils)
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