Unverified Commit 9f463b6f authored by mvdbeek's avatar mvdbeek
Browse files

Adapt scripts/resumable_upload.py to fetch API 

Finding out that the `files` parameter is required took way more time
than I want to admit ... .
parent e0f4b86a

doc/source/admin/galaxy_options.rst

+6 −4
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@@ -292,8 +292,10 @@ 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~



:Description:

    Maximum size of uploadable files in gigabytes.

:Default: ``100``

    Maximum size of uploadable files, specified in bytes (default:

    100GB). This value is ignored if an external upload server is

    configured.

:Default: ``107374182400``

:Type: int
@@ -2337,8 +2339,8 @@ 
:Description:

    Galaxy can upload user files in chunks without using nginx. Enable

    the chunk uploader by specifying a chunk size larger than 0. The

    chunk size is specified in bytes (default: 100MB).

:Default: ``104857600``

    chunk size is specified in bytes (default: 10MB).

:Default: ``10485760``

:Type: int

lib/galaxy/config/sample/galaxy.yml.sample

+6 −4
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@@ -242,8 +242,10 @@ galaxy: 
  # <data_dir>.

  #new_file_path: tmp



  # Maximum size of uploadable files in gigabytes.

  #maximum_upload_file_size: 100

  # Maximum size of uploadable files, specified in bytes (default:

  # 100GB). This value is ignored if an external upload server is

  # configured.

  #maximum_upload_file_size: 107374182400



  # Tool config files, defines what tools are available in Galaxy. Tools

  # can be locally developed or installed from Galaxy tool sheds.
@@ -1185,8 +1187,8 @@ galaxy: 


  # Galaxy can upload user files in chunks without using nginx. Enable

  # the chunk uploader by specifying a chunk size larger than 0. The

  # chunk size is specified in bytes (default: 100MB).

  #chunk_upload_size: 104857600

  # chunk size is specified in bytes (default: 10MB).

  #chunk_upload_size: 10485760



  # Have Galaxy manage dynamic proxy component for routing requests to

  # other services based on Galaxy's session cookie.  It will attempt to

lib/galaxy/webapps/galaxy/buildapp.py

+1 −1
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@@ -1402,7 +1402,7 @@ def wrap_in_middleware(app, global_conf, application_stack, **local_conf): 
    app = wrap_if_allowed(app, stack, TusMiddleware, kwargs={

        'upload_path': '/api/upload/resumable_upload',

        'tmp_dir': application_stack.config.new_file_path,

        'max_size': application_stack.config.maximum_upload_file_size * 1024 ** 3

        'max_size': application_stack.config.maximum_upload_file_size

    })

    # api batch call processing middleware

    app = wrap_if_allowed(app, stack, BatchMiddleware, args=(webapp, {}))

lib/galaxy/webapps/galaxy/config_schema.yml

+3 −2
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@@ -227,10 +227,11 @@ mapping: 


      maximum_upload_file_size:

        type: int

        default: 100

        default: 107374182400

        required: false

        desc: |

          Maximum size of uploadable files in gigabytes.

          Maximum size of uploadable files, specified in bytes (default: 100GB).

          This value is ignored if an external upload server is configured.



      tool_config_file:

        type: any

lib/galaxy_test/api/test_tools_upload.py

+1 −1
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@@ -926,7 +926,7 @@ class ToolsUploadTestCase(ApiTestCase): 


        with self.dataset_populator.test_history() as history_id:

            session_id = upload_file(url=f"{self.url}/api/upload/resumable_upload", path=TestDataResolver().get_filename("1.fastqsanger.gz"), api_key=self.galaxy_interactor.api_key, history_id=history_id)

            hda = self._upload_and_get_details(content=json.dumps({'session_id': session_id, 'name': '1.fastqsanger.gz'}), api='fetch', ext='fastqsanger.gz')

            hda = self._upload_and_get_details(content=json.dumps({'session_id': session_id}), api='fetch', ext='fastqsanger.gz', name='1.fastqsanger.gz')

            assert hda['name'] == '1.fastqsanger.gz'

            assert hda['file_ext'] == 'fastqsanger.gz'

            assert hda['state'] == 'ok'