using mock for runtime network calls

voseq/blast_local/utils.py

@@ -148,12 +148,11 @@ def create_blast_db(self):
 
     def save_query_to_file(self):
         b = Sequences.objects.get(code_id=self.voucher_code, gene_code=self.gene_code)
-        this_id = b.code_id + '|' + b.gene_code
+        this_id = '{0}|{1}'.format(b.code_id, b.gene_code)
         seq = self.strip_question_marks(b.sequences)
 
-        if seq != '':
-            seq_record = SeqRecord(Seq(seq),
-                                   id=this_id)
+        if seq:
+            seq_record = SeqRecord(Seq(seq), id=this_id)
             SeqIO.write(seq_record, self.query_file, "fasta")
 
     def do_blast(self):

voseq/blast_ncbi/tests/tests_blast_ncbi.py

@@ -1,4 +1,7 @@
+from io import StringIO
+import os
 import unittest
+from unittest.mock import patch
 
 from django.conf import settings
 from django.test import TestCase
@@ -7,20 +10,24 @@
 from blast_ncbi.utils import BLASTNcbi
 
 
+TEST_PATH = os.path.abspath(os.path.dirname(__file__))
+with open(os.path.join(TEST_PATH, "CP100-10_COI-begin.xml"), "r") as handle:
+    ncbi_return_handle = StringIO(handle.read())
+
+
 class TestNcbiBlast(TestCase):
     def setUp(self):
         args = []
-        opts = {'dumpfile': 'test_db_dump.xml', 'verbosity': 0}
+        opts = {'dumpfile': 'test_db_dump2.xml', 'verbosity': 0}
         cmd = 'migrate_db'
         call_command(cmd, *args, **opts)
 
         voucher_code = 'CP100-10'
-        gene_code = 'COI'
+        gene_code = 'COI-begin'
         self.blast = BLASTNcbi(voucher_code, gene_code)
 
-    @unittest.skipIf(settings.TRAVIS is True,
-                     'Testing using BLASTNcbi fails due to network problems')
-    def test_blast_with_accession_number_in_header(self):
+    @patch("Bio.Blast.NCBIWWW.qblast", return_value=ncbi_return_handle)
+    def test_blast_with_accession_number_in_header(self, mock_qblast):
         self.blast.save_query_to_file()
         self.blast.do_blast()
         result = self.blast.parse_blast_output()

voseq/blast_ncbi/utils.py

@@ -7,7 +7,8 @@
 
 
 class BLASTNcbi(BLAST):
-    """Handles duties related to blast against sequences in NCBI Genbank.
+    """Handles duties related to blast against sequences in NCBI GenBank.
+
     """
     def __init__(self, voucher_code, gene_code):
         self.voucher_code = voucher_code
@@ -22,7 +23,8 @@ def __init__(self, voucher_code, gene_code):
                                         "output_{0}.xml".format(uuid.uuid4().hex))
 
     def do_blast(self):
-        """Does a blast against NCBI and saves returned XML file to local disk.
+        """Blasts against NCBI and saves returned XML file to local disk.
+
         """
         with open(self.query_file) as handle:
             fasta_string = handle.read()