[Fixes #41692207] Added UNKNOWN as a catch-all file type for unknown …

…file types. Modified set_filetype() to accept any file types.

refinery/file_store/models.py

@@ -136,6 +136,7 @@ def file_path(instance, filename):
 WIG = 'wig'
 XML = 'xml'
 ZIP = 'zip'
+UNKNOWN = ''    # special catch-all type with no corresponding extension
 
 # file types with descriptions used by FileStoreItem.filetype choice field
 FILE_TYPES = (
@@ -166,6 +167,7 @@ def file_path(instance, filename):
     (WIG, 'Wiggle Track Format'),
     (XML, 'XML file'),
     (ZIP, 'Zip compressed archive'),
+    (UNKNOWN, 'Unknown file type'),
 )
 
 # mapping of file extensions to file types
@@ -352,7 +354,8 @@ def set_filetype(self, filetype=''):
         try:
             self.filetype = FILE_EXTENSIONS[filetype]
         except KeyError:
-            logger.error("'%s' is an invalid file type", filetype)
+            logger.info("'%s' is an unknown file type", filetype)
+            self.filetype = UNKNOWN
             return False
 
         self.save()
@@ -373,7 +376,7 @@ def is_symlinked(self):
 
     def is_local(self):
         '''Check if the datafile can be used as a file object.
-        
+
         :returns: bool -- True if the datafile can be used as a file object, False otherwise.
 
         '''
@@ -389,7 +392,7 @@ def is_local(self):
 
     def delete_datafile(self):
         '''Delete datafile if it exists on disk.
-        
+
         :returns: bool -- True if deletion succeeded, False otherwise.
 
         '''

refinery/file_store/tests.py

@@ -110,7 +110,7 @@ def test_get_file_type(self):
         '''Check that the correct file type is returned
 
         '''
-        filetype = 'bb'
+        filetype = models.BIGBED
         item_from_path = models.FileStoreItem.objects.create(source=self.url_source,
                                                              sharename=self.sharename,
                                                              filetype=filetype)
@@ -128,23 +128,25 @@ def test_set_valid_file_type(self):
                                                              sharename=self.sharename)
         item_from_url = models.FileStoreItem.objects.create(source=self.path_source,
                                                             sharename=self.sharename)
-        filetype = 'wig'
+        filetype = models.WIG
         self.assertTrue(item_from_path.set_filetype(filetype))
         self.assertEqual(item_from_path.filetype, filetype)
         self.assertTrue(item_from_url.set_filetype(filetype))
         self.assertEqual(item_from_url.filetype, filetype)
 
-    def test_set_invalid_file_type(self):
-        '''Check that an invalid file type is not set
+    def test_set_unkown_file_type(self):
+        '''Check that an unknown file type is not set
 
         '''
         item_from_url = models.FileStoreItem.objects.create(source=self.path_source,
                                                             sharename=self.sharename)
         item_from_path = models.FileStoreItem.objects.create(source=self.url_source,
                                                              sharename=self.sharename)
-        filetype = 'invalidtype'
+        filetype = 'unknowntype'
         self.assertFalse(item_from_path.set_filetype(filetype))
+        self.assertEqual(item_from_path.filetype, models.UNKNOWN)
         self.assertFalse(item_from_url.set_filetype(filetype))
+        self.assertEqual(item_from_url.filetype, models.UNKNOWN)
 
     def test_set_file_type_automatically(self):
         '''Check that a file type is set automatically