adding file obj upload function for s3

basepair/__init__.py

@@ -12,7 +12,7 @@
 # Exposing the storage wrapper
 
 __title__ = 'basepair'
-__version__ = '2.1.11'
+__version__ = '2.1.12'
 __copyright__ = 'Copyright [2017] - [2024] Basepair INC'
 
 

basepair/modules/aws/s3.py

@@ -415,6 +415,34 @@ def upload_file(self, file_name, full_path, extra_args=None, force=False, show_l
       'path': full_path,
       'url': self.get_self_signed(full_path),
     }
+
+  def upload_file_obj(self, file_obj, full_path, extra_args=None, force=False, show_log=True):
+    '''Upload a file to an S3 bucket'''
+    extra_args = extra_args or {}
+    mimetype, _ = mimetypes.guess_type(file_obj)
+    if mimetype:
+      extra_args['ContentType'] = mimetype
+
+    # Upload the file
+    try:
+      if force or not self.get_object_head(full_path, show_log=show_log):
+        self.client.upload_fileobj(file_obj, self.bucket, full_path, ExtraArgs=extra_args)
+      else:
+        print(f'Skipping file {full_path} because already exist in S3.')
+    except ClientError as error:
+      response = self.get_log_msg({
+        'exception': error,
+        'msg': f'Not able to upload file {file_obj}.',
+      })
+      if ExceptionHandler.is_throttled_error(exception=error):
+        raise error
+      return response
+
+    # get url by key
+    return {
+      'path': full_path,
+      'url': self.get_self_signed(full_path),
+    }
 
   @staticmethod
   def convert_to_v2(rules):

basepair/modules/storage/drivers/aws_s3.py

@@ -114,3 +114,7 @@ def set_lifecycle(self, **kwargs):
     def upload(self, file_name, full_path, **kwargs):
         """Upload file to storage"""
         return self.s3_service.upload_file(file_name, full_path, **kwargs)
+
+    def upload_file(self, fileobj, key, **kwargs):
+        """Upload file object to storage"""
+        return self.s3_service.upload_file_obj(fileobj, key, **kwargs)

basepair/modules/storage/main.py

@@ -79,3 +79,7 @@ def set_lifecycle(self, **kwargs):
     def upload(self, file_name, full_path, **kwargs):
         """Upload file to storage"""
         return self.driver.upload(file_name, full_path, **kwargs)
+
+    def upload_fileobj(self, fileobj, uri):
+        """Upload file object to storage"""
+        return self.driver.upload_fileobj(fileobj, uri)