# Copyright 2007-2010 by Peter Cock.  All rights reserved.
# Revisions copyright 2007-2008 by Michiel de Hoon.  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.
 
"""Testing online code for fetching sequences, and parsing them
 
Uses Bio.SeqIO to parse files downloaded with Bio.GenBank, Bio.WWW.NCBI,
Bio.ExPASy etc.
 
Goals:
    Make sure that all retrieval is working as expected.
    May catch some format changes early too.
"""
import unittest
 
import requires_internet
requires_internet.check()
 
#We want to test these:
from Bio import Entrez
from Bio import ExPASy
 
#In order to check any sequences returned
from Bio import SeqIO
from Bio._py3k import StringIO
from Bio.SeqUtils.CheckSum import seguid
 
from Bio.File import UndoHandle
from Bio._py3k import _as_string
 
#This lets us set the email address to be sent to NCBI Entrez:
Entrez.email = "biopython-dev@biopython.org"
 
 
class ExPASyTests(unittest.TestCase):
    """Tests for Bio.ExPASy module."""
    def test_get_sprot_raw(self):
        """Bio.ExPASy.get_sprot_raw("O23729")"""
        identifier = "O23729"
        #This is to catch an error page from our proxy:
        handle = UndoHandle(ExPASy.get_sprot_raw(identifier))
        if _as_string(handle.peekline()).startswith("<!DOCTYPE HTML"):
            raise IOError
        record = SeqIO.read(handle, "swiss")
        handle.close()
        self.assertEqual(record.id, identifier)
        self.assertEqual(len(record), 394)
        self.assertEqual(seguid(record.seq), "5Y08l+HJRDIlhLKzFEfkcKd1dkM")
 
 
class EntrezTests(unittest.TestCase):
    def simple(self, database, formats, entry, length, checksum):
        for f in formats:
            handle = Entrez.efetch(db=database, id=entry, rettype=f, retmode="text")
            if f == "gbwithparts":
                f = "gb"
            record = SeqIO.read(handle, f)
            handle.close()
            self.assertTrue((entry in record.name) or
                         (entry in record.id) or
                         ("gi" in record.annotations
                          and record.annotations["gi"]==entry),
                         "%s got %s, %s" % (entry, record.name, record.id))
            self.assertEqual(len(record), length)
            self.assertEqual(seguid(record.seq), checksum)
 
for database, formats, entry, length, checksum in [
        ("nuccore", ["fasta", "gb"], "X52960", 248,
         "Ktxz0HgMlhQmrKTuZpOxPZJ6zGU"),
        ("nucleotide", ["fasta", "gb"], "6273291", 902,
         "bLhlq4mEFJOoS9PieOx4nhGnjAQ"),
        ("protein", ["fasta", "gbwithparts"], "16130152", 367,
         "fCjcjMFeGIrilHAn6h+yju267lg"),
        ]:
 
    def funct(d, f, e, l, c):
        method = lambda x : x.simple(d, f, e, l, c)
        method.__doc__ = "Bio.Entrez.efetch(%r, id=%r, ...)" % (d, e)
        return method
 
    setattr(EntrezTests, "test_%s_%s" % (database, entry),
            funct(database, formats, entry, length, checksum))
    del funct
del database, formats, entry, length, checksum
 
if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity = 2)
    unittest.main(testRunner=runner)