Unverified Commit 56d22baa authored by mvdbeek's avatar mvdbeek
Browse files

Use get_file_obj to render compressed data in mako 

We were mostly doing this already. Also raises an exception in
`text_data` if content is not decodable.

Fixes
https://sentry.galaxyproject.org/share/issue/b826c0be95a4424e8b1d63983255f23d/:
```
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
  File "galaxy/web/framework/middleware/error.py", line 167, in __call__
    app_iter = self.application(environ, sr_checker)
  File "galaxy/web/framework/middleware/statsd.py", line 29, in __call__
    req = self.application(environ, start_response)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.11/site-packages/paste/httpexceptions.py", line 635, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/base.py", line 174, in __call__
    return self.handle_request(request_id, path_info, environ, start_response)
  File "galaxy/web/framework/base.py", line 263, in handle_request
    body = method(trans, **kwargs)
  File "galaxy/webapps/galaxy/controllers/dataset.py", line 152, in display
    display_data, headers = data.datatype.display_data(
  File "galaxy/datatypes/tabular.py", line 199, in display_data
    truncated_data=open(dataset.get_file_name()).read(max_peek_size),
  File "<frozen codecs>", line 322, in decode
```
parent 18157159

lib/galaxy/datatypes/data.py

+22 −20
Original line number Diff line number Diff line
@@ -484,11 +484,12 @@ class Data(metaclass=DataMeta): 


    def _serve_binary_file_contents_as_text(self, trans, data, headers, file_size, max_peek_size):

        headers["content-type"] = "text/html"

        with open(data.get_file_name(), "rb") as fh:

            return (

                trans.fill_template_mako(

                    "/dataset/binary_file.mako",

                    data=data,

                file_contents=open(data.get_file_name(), "rb").read(max_peek_size),

                    file_contents=fh.read(max_peek_size),

                    file_size=util.nice_size(file_size),

                    truncated=file_size > max_peek_size,

                ),
@@ -502,12 +503,13 @@ class Data(metaclass=DataMeta): 
        if not preview or isinstance(data.datatype, images.Image) or file_size < max_peek_size:

            return self._yield_user_file_content(trans, data, data.get_file_name(), headers), headers



        with compression_utils.get_fileobj(data.get_file_name(), "rb") as fh:

            # preview large text file

            headers["content-type"] = "text/html"

            return (

                trans.fill_template_mako(

                    "/dataset/large_file.mako",

                truncated_data=open(data.get_file_name(), "rb").read(max_peek_size),

                    truncated_data=fh.read(max_peek_size),

                    data=data,

                ),

                headers,

lib/galaxy/datatypes/tabular.py

+9 −8
Original line number Diff line number Diff line
@@ -193,10 +193,11 @@ class TabularData(Text): 
                return open(dataset.get_file_name(), mode="rb"), headers

            else:

                headers["content-type"] = "text/html"

                with compression_utils.get_fileobj(dataset.get_file_name(), "rb") as fh:

                    return (

                        trans.fill_template_mako(

                            "/dataset/large_file.mako",

                        truncated_data=open(dataset.get_file_name()).read(max_peek_size),

                            truncated_data=fh.read(max_peek_size),

                            data=dataset,

                        ),

                        headers,

lib/galaxy/managers/hdas.py

+4 −1
Original line number Diff line number Diff line
@@ -311,7 +311,10 @@ class HDAManager( 


        truncated = preview and os.stat(file_path).st_size > MAX_PEEK_SIZE

        with get_fileobj(file_path) as fh:

            try:

                hda_data = fh.read(MAX_PEEK_SIZE)

            except UnicodeDecodeError:

                raise exceptions.RequestParameterInvalidException("Cannot generate text preview for dataset.")

        return truncated, hda_data



    # .... annotatable