add gzip mime

uclahs-cds · Nov 12, 2024 · a5a4257 · a5a4257
1 parent e1ea633
commit a5a4257
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Showing 3 changed files with 5 additions and 3 deletions.
diff --git a/pipeval/validate/files.py b/pipeval/validate/files.py
@@ -11,7 +11,7 @@ def _identify_compression(path:Path):
     ''' Identify compression type and returns appropriate file handler '''
     compression_handlers = {
         'application/x-gzip': gzip.open,
-        # 'application/gzip': gzip.open,
+        'application/gzip': gzip.open,
         'application/x-bzip2': bz2.open
     }
 

diff --git a/pipeval/validate/validators/fastq.py b/pipeval/validate/validators/fastq.py
@@ -86,7 +86,7 @@ def _get_file_handler(self):
         '''Detect file format and return approriate handler to read file'''
         _handler_map = {
             'application/x-gzip': gzip.open,
-#            'application/gzip': gzip.open,
+            'application/gzip': gzip.open,
             'application/x-bzip2': bz2.open,
             'text/plain': open
         }

diff --git a/test/unit/test_validate.py b/test/unit/test_validate.py
@@ -125,6 +125,7 @@ def test__check_compressed__raises_warning_for_uncompressed_path(mock_path, mock
     'compression_mime',
     [
         ('application/x-gzip'),
+        ('application/gzip'),
         ('application/x-bzip2')
     ]
 )
@@ -491,7 +492,7 @@ def test__validate_record__passes_valid_read():
     'test_file_type, test_handler',
     [
         ('application/x-gzip', gzip.open),
-        # ('application/gzip', gzip.open),
+        ('application/gzip', gzip.open),
         ('application/x-bzip2', bz2.open),
         ('text/plain', open)
     ]
@@ -581,6 +582,7 @@ def test__validate_fastq__passes_valid_fastq(
     'test_file_type, test_handler',
     [
         ('application/x-gzip', gzip.open),
+        ('application/gzip', gzip.open),
         ('application/x-bzip2', bz2.open),
         ('any/other', None)
     ]