fix test in byteMzml pull request

pymzml · Apr 1, 2019 · 21b999a · 21b999a
1 parent 94f8385
commit 21b999a
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Showing 2 changed files with 20 additions and 15 deletions.
diff --git a/pymzml/run.py b/pymzml/run.py
@@ -226,9 +226,14 @@ def _determine_file_encoding(self, path):
         Returns:
             mzml_encoding (str): encoding type of the file
         """
-        mzml_encoding = 'utf-8'
         if os.path.exists(path):
-            with open(path, 'rb') as sniffer:
+            print(path)
+            if path.endswith('.gz') or path.endswith('.igz'):
+                import gzip
+                _open = gzip.open
+            else:
+                _open = open
+            with _open(path, 'rb') as sniffer:
                 return self._guess_encoding(sniffer)
 
     def _init_obo_translator(self):

diff --git a/tests/main_reader_test.py b/tests/main_reader_test.py
@@ -16,12 +16,12 @@ class runTest(unittest.TestCase):
     def setUp(self):
         """
         """
-        paths = test_file_paths.paths
+        self.paths = test_file_paths.paths
 
-        file_compressed_indexed     = paths[2]
-        file_compressed_unindexed   = paths[1]
-        file_uncompressed_indexed   = paths[0]
-        file_uncompressed_unindexed = paths[0]
+        file_compressed_indexed     = self.paths[2]
+        file_compressed_unindexed   = self.paths[1]
+        file_uncompressed_indexed   = self.paths[0]
+        file_uncompressed_unindexed = self.paths[0]
         self.reader_compressed_indexed     = run.Reader(file_compressed_indexed)
         self.reader_compressed_unindexed   = run.Reader(file_compressed_unindexed)
         self.reader_uncompressed_indexed   = run.Reader(file_uncompressed_indexed)
@@ -30,14 +30,14 @@ def setUp(self):
     def test_determine_file_encoding(self):
         """
         """
-        encoding = self.reader_compressed_indexed._determine_file_encoding(self.reader_compressed_indexed.info['encoding'])
-        self.assertEqual(encoding, 'utf-8')
-        encoding = self.reader_compressed_unindexed._determine_file_encoding(self.reader_compressed_unindexed.info['encoding'])
-        self.assertEqual(encoding, 'utf-8')
-        encoding = self.reader_uncompressed_indexed._determine_file_encoding(self.reader_uncompressed_indexed.info['encoding'])
-        self.assertEqual(encoding, 'utf-8')
-        encoding = self.reader_uncompressed_unindexed._determine_file_encoding(self.reader_uncompressed_unindexed.info['encoding'])
-        self.assertEqual(encoding, 'utf-8')
+        encoding = self.reader_compressed_indexed._determine_file_encoding(self.paths[2])
+        self.assertEqual(encoding, 'ISO-8859-1')
+        encoding = self.reader_compressed_unindexed._determine_file_encoding(self.paths[1])
+        self.assertEqual(encoding, 'ISO-8859-1')
+        encoding = self.reader_uncompressed_indexed._determine_file_encoding(self.paths[3])
+        self.assertEqual(encoding, 'ISO-8859-1')
+        encoding = self.reader_uncompressed_unindexed._determine_file_encoding(self.paths[0])
+        self.assertEqual(encoding, 'ISO-8859-1')
 
     def test_init_iter(self):
         """