pybiolib 1.1.2184__tar.gz → 1.1.2191__tar.gz

{pybiolib-1.1.2184 → pybiolib-1.1.2191}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.2184
+Version: 1.1.2191
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.2184 → pybiolib-1.1.2191}/biolib/_data_record/data_record.py

@@ -156,7 +156,7 @@ class DataRecord:
         return DataRecord(_internal_state=get_data_record_state_from_uri(uri))
 
     @staticmethod
-    def create(destination: str, data_path: Optional[str] = None) -> 'DataRecord':
+    def create(destination: str, data_path: Optional[str] = None, record_type: Optional[str] = None) -> 'DataRecord':
         BiolibApiClient.assert_is_signed_in(authenticated_action_description='create a Data Record')
         if data_path is not None:
             assert os.path.isdir(data_path), f'The path "{data_path}" is not a directory.'
@@ -167,12 +167,11 @@ class DataRecord:
             record_name = 'data-record-' + datetime.now().isoformat().split('.')[0].replace(':', '-')
             data_record_uri = f'{destination}/{record_name}'
 
-        uri_parsed = parse_app_uri(data_record_uri)
         response = api.client.post(
-            path='/lfs/',
+            path='/resources/data-records/',
             data={
-                'account_handle': uri_parsed['account_handle_normalized'],
-                'name': uri_parsed['app_name'],
+                'uri': data_record_uri,
+                'type': record_type,
             },
         )
         data_record_info: DataRecordInfo = response.json()

{pybiolib-1.1.2184 → pybiolib-1.1.2191}/biolib/cli/data_record.py

@@ -19,8 +19,9 @@ def data_record() -> None:
 @data_record.command(help='Create a Data Record')
 @click.argument('uri', required=True)
 @click.option('--data-path', required=True, type=click.Path(exists=True))
-def create(uri: str, data_path: str) -> None:
-    DataRecord.create(destination=uri, data_path=data_path)
+@click.option('--record-type', required=False, type=str, default=None)
+def create(uri: str, data_path: str, record_type: Optional[str]) -> None:
+    DataRecord.create(destination=uri, data_path=data_path, record_type=record_type)
 
 
 @data_record.command(help='Update a Data Record')

{pybiolib-1.1.2184 → pybiolib-1.1.2191}/biolib/sdk/__init__.py

@@ -1,12 +1,14 @@
+from typing import Optional
+
 # Imports to hide and use as private internal utils
 from biolib._data_record.data_record import DataRecord as _DataRecord
 from biolib._internal.push_application import push_application as _push_application
 from biolib._internal.push_application import set_app_version_as_active as _set_app_version_as_active
+from biolib._runtime.runtime import Runtime as _Runtime
 from biolib.app import BioLibApp as _BioLibApp
-from biolib.typing_utils import Optional as _Optional
 
 # Classes to expose as public API
-from biolib._runtime.runtime import Runtime
+Runtime = _Runtime
 
 
 def push_app_version(uri: str, path: str) -> _BioLibApp:
@@ -31,7 +33,7 @@ def get_app_version_pytest_plugin(app_version: _BioLibApp):
     except BaseException:
         raise Exception('Failed to import pytest; please make sure it is installed') from None
 
-    class AppVersionFixturePlugin(object):
+    class AppVersionFixturePlugin:
         def __init__(self, app_version_ref):
             self.app_version_ref = app_version_ref
 
@@ -42,9 +44,14 @@ def get_app_version_pytest_plugin(app_version: _BioLibApp):
     return AppVersionFixturePlugin(app_version)
 
 
-def create_data_record(destination: str, data_path: str, name: _Optional[str] = None) -> _DataRecord:
-    if name:
-        destination_with_name = f"{destination}/{name}"
-    else:
-        destination_with_name = destination
-    return _DataRecord.create(destination_with_name, data_path)
+def create_data_record(
+    destination: str,
+    data_path: str,
+    name: Optional[str] = None,
+    record_type: Optional[str] = None,
+) -> _DataRecord:
+    return _DataRecord.create(
+        destination=f'{destination}/{name}' if name else destination,
+        data_path=data_path,
+        record_type=record_type,
+    )

{pybiolib-1.1.2184 → pybiolib-1.1.2191}/biolib/utils/seq_util.py

@@ -35,7 +35,7 @@ class SeqUtil:
         input_file: Union[str, BufferedIOBase, None] = None,
         default_header: Optional[str] = None,
         allow_any_sequence_characters: bool = False,
-        allow_empty_sequence: bool = False,
+        allow_empty_sequence: bool = True,
         file_name: Optional[str] = None,
     ) -> List[SeqUtilRecord]:
         if input_file is None:

{pybiolib-1.1.2184 → pybiolib-1.1.2191}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.1.2184"
+version = "1.1.2191"
 description = "BioLib Python Client"
 readme = "README.md"
 license = "MIT"