Fix tests for preprocessor

juliema · Feb 15, 2019 · 5b50a85 · 5b50a85
1 parent 816c25a
commit 5b50a85
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Showing 2 changed files with 12 additions and 12 deletions.
diff --git a/lib/util.py b/lib/util.py
@@ -58,9 +58,9 @@ def make_temp_dir(where=None, prefix=None, keep=False):
 @contextmanager
 def open_file(args, file_name):
     """Handle creation and deletion of temporary directory."""
-    if args['gzip']:
+    if args.get('gzip'):
         stream = gzip.open(file_name, 'rt')
-    elif args['bzip']:
+    elif args.get('bzip'):
         stream = bz2.open(file_name, 'rt')
     else:
         stream = open(file_name)

diff --git a/tests/lib/test_core_preprocessor.py b/tests/lib/test_core_preprocessor.py
@@ -67,11 +67,11 @@ def test_preprocess_01(
 @patch('lib.db.insert_sequences_batch')
 def test_load_one_file_01(insert_sequences_batch, info):
     """Load mixed sequences from a file into the atram database."""
-    cxn, _ = set_up()
+    cxn, args = set_up()
     db.BATCH_SIZE = 5
 
     file_1 = join('tests', 'data', 'load_seq1.txt')
-    core_preprocessor.load_one_file(cxn, file_1, 'mixed_ends')
+    core_preprocessor.load_one_file(args, cxn, file_1, 'mixed_ends')
 
     msg = 'Loading "{}" into sqlite database'.format(file_1)
     info.assert_called_once_with(msg)
@@ -94,11 +94,11 @@ def test_load_one_file_01(insert_sequences_batch, info):
 @patch('lib.db.insert_sequences_batch')
 def test_load_one_file_02(insert_sequences_batch, info):
     """Load end 1 sequences from a file into the atram database."""
-    cxn, _ = set_up()
+    cxn, args = set_up()
     db.BATCH_SIZE = 5
 
     file_1 = join('tests', 'data', 'load_seq1.txt')
-    core_preprocessor.load_one_file(cxn, file_1, 'end_1', '1')
+    core_preprocessor.load_one_file(args, cxn, file_1, 'end_1', '1')
 
     msg = 'Loading "{}" into sqlite database'.format(file_1)
     info.assert_called_once_with(msg)
@@ -121,11 +121,11 @@ def test_load_one_file_02(insert_sequences_batch, info):
 @patch('lib.db.insert_sequences_batch')
 def test_load_one_file_03(insert_sequences_batch, info):
     """Load end 2 sequences from a file into the atram database."""
-    cxn, _ = set_up()
+    cxn, args = set_up()
     db.BATCH_SIZE = 5
 
     file_1 = join('tests', 'data', 'load_seq1.txt')
-    core_preprocessor.load_one_file(cxn, file_1, 'end_2', '2')
+    core_preprocessor.load_one_file(args, cxn, file_1, 'end_2', '2')
 
     msg = 'Loading "{}" into sqlite database'.format(file_1)
     info.assert_called_once_with(msg)
@@ -148,12 +148,12 @@ def test_load_one_file_03(insert_sequences_batch, info):
 @patch('lib.db.insert_sequences_batch')
 def test_load_one_file_04(insert_sequences_batch, info):
     """Load single end sequences from a file into the atram database."""
-    cxn, _ = set_up()
+    cxn, args = set_up()
     db.BATCH_SIZE = 5
 
     file_1 = join('tests', 'data', 'load_seq1.txt')
     core_preprocessor.load_one_file(
-        cxn, file_1, 'single_ends', '')
+        args, cxn, file_1, 'single_ends', '')
 
     msg = 'Loading "{}" into sqlite database'.format(file_1)
     info.assert_called_once_with(msg)
@@ -176,11 +176,11 @@ def test_load_one_file_04(insert_sequences_batch, info):
 @patch('lib.db.insert_sequences_batch')
 def test_load_one_file_05(insert_sequences_batch, info):
     """Load single end sequences from a file into the atram database."""
-    cxn, _ = set_up()
+    cxn, args = set_up()
     db.BATCH_SIZE = 5
 
     file_1 = join('tests', 'data', 'load_seq2.txt')
-    core_preprocessor.load_one_file(cxn, file_1, 'mixed_ends')
+    core_preprocessor.load_one_file(args, cxn, file_1, 'mixed_ends')
 
     msg = 'Loading "{}" into sqlite database'.format(file_1)
     info.assert_called_once_with(msg)