pybiolib 1.1.2184__py3-none-any.whl → 1.1.2191__py3-none-any.whl

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()

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')

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,
+    )

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.dist-info → pybiolib-1.1.2191.dist-info}/METADATA

@@ -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.dist-info → pybiolib-1.1.2191.dist-info}/RECORD

@@ -1,7 +1,7 @@
 LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
 README.md,sha256=_IH7pxFiqy2bIAmaVeA-iVTyUwWRjMIlfgtUbYTtmls,368
 biolib/__init__.py,sha256=_tThyzISH81yS9KXP_X3qEiKXmsIp5XOBcJIODfLVnc,4338
-biolib/_data_record/data_record.py,sha256=6PD-jBgWU2Cc4PwT-hLNPTFZygb4r0LBL617U-1eijE,12633
+biolib/_data_record/data_record.py,sha256=CoyYRse5VdUBhQzzPfR9BkytgOsM-IZxkfMX1kyRnPk,12589
 biolib/_internal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/_internal/data_record/__init__.py,sha256=fGdME6JGRU_2VxpJbYpGXYndjN-feUkmKY4fuMyq3cg,76
 biolib/_internal/data_record/data_record.py,sha256=YmaAABR57goDCE8-rKb2j0FPMSbDtRPCm_HhT3mM074,4299
@@ -57,7 +57,7 @@ biolib/biolib_errors.py,sha256=5m4lK2l39DafpoXBImEBD4EPH3ayXBX0JgtPzmGClow,689
 biolib/biolib_logging.py,sha256=J3E5H_LL5k6ZUim2C8gqN7E6lCBZMTpO4tnMpOPwG9U,2854
 biolib/cli/__init__.py,sha256=0v3c_J-U0k46c5ZWeQjLG_kTaKDJm81LBxQpDO2B_aI,1286
 biolib/cli/auth.py,sha256=rpWGmXs6Fz6CGrO9K8ibPRszOdXG78Vig_boKaVCD9A,2082
-biolib/cli/data_record.py,sha256=oDy8U6mv-h-hbeMihXRzVEvM-WrGQq6oBiBl3xDRaXs,3220
+biolib/cli/data_record.py,sha256=08JbZkFWKMo0PrnhhG0jQEKnNW7pPLti9cOw8s1TWfI,3344
 biolib/cli/download_container.py,sha256=HIZVHOPmslGE5M2Dsp9r2cCkAEJx__vcsDz5Wt5LRos,483
 biolib/cli/init.py,sha256=wQOfii_au-d30Hp7DdH-WVw-WVraKvA_zY4za1w7DE8,821
 biolib/cli/lfs.py,sha256=z2qHUwink85mv9yDgifbVKkVwuyknGhMDTfly_gLKJM,4151
@@ -103,7 +103,7 @@ biolib/jobs/job.py,sha256=OfG8cLd3AjGjiMWRlJRZdVVbLsRWSX-OM5nxJhR6mPQ,19136
 biolib/jobs/job_result.py,sha256=rALHiKYNaC9lHi_JJqBob1RubzNLwG9Z386kwRJjd2M,5885
 biolib/jobs/types.py,sha256=qhadtH2KDC2WUOOqPiwke0YgtQY4FtuB71Stekq1k48,970
 biolib/runtime/__init__.py,sha256=MlRepA11n2H-3plB5rzWyyHK2JmP6PiaP3i6x3vt0mg,506
-biolib/sdk/__init__.py,sha256=qJ_V_Edxolzi4VBQCrvem5lYIkJ0FVH3VZepSDuXjTc,1895
+biolib/sdk/__init__.py,sha256=amVp_jMxi2nqCcTsmL2aKUNGCAH3Yk4EzAnps9d1VH8,1928
 biolib/tables.py,sha256=acH7VjwAbadLo8P84FSnKEZxCTVsF5rEg9VPuxElNs8,872
 biolib/templates/__init__.py,sha256=Yx62sSyDCDesRQDQgmbDsLpfgEh93fWE8r9u4g2azXk,36
 biolib/templates/example_app.py,sha256=EB3E3RT4SeO_ii5nVQqJpi5KDGNE_huF1ub-e5ZFveE,715
@@ -114,10 +114,10 @@ biolib/utils/__init__.py,sha256=fwjciJyJicvYyZcVTzfDBgD0SKY13DeXqvTeG4qZIy8,5548
 biolib/utils/app_uri.py,sha256=Yq_-_VGugQhMMo6mM5f0G9yNlLkr0WK4j0Nrf3FE4xQ,2171
 biolib/utils/cache_state.py,sha256=u256F37QSRIVwqKlbnCyzAX4EMI-kl6Dwu6qwj-Qmag,3100
 biolib/utils/multipart_uploader.py,sha256=XvGP1I8tQuKhAH-QugPRoEsCi9qvbRk-DVBs5PNwwJo,8452
-biolib/utils/seq_util.py,sha256=WieuQ2RvV4QSJFUAMRVyvKXFs3YanFAmjh-CFIaQmQk,5184
+biolib/utils/seq_util.py,sha256=ZQFcaE37B2dtucN2zDjOmdya_X0ITc1zBFZJNQY13XA,5183
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.1.2184.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.2184.dist-info/METADATA,sha256=oiLPHe9yf3WdQZ9ChOjRqqPki4p_e3jZL_V5jtjoXOM,1508
-pybiolib-1.1.2184.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pybiolib-1.1.2184.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.2184.dist-info/RECORD,,
+pybiolib-1.1.2191.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.2191.dist-info/METADATA,sha256=rKlCDAj0A1ygrKqBGIyZKZy_fy723ESDGg79nYwGoOg,1508
+pybiolib-1.1.2191.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.1.2191.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.2191.dist-info/RECORD,,