pybiolib 1.1.1747__py3-none-any.whl → 1.1.1881__py3-none-any.whl

biolib/lfs/utils.py

@@ -1,30 +1,15 @@
 import io
-import json
 import os
 import zipfile as zf
-from collections import namedtuple
 from pathlib import Path
-from struct import Struct
 
-from biolib import utils
-from biolib._internal.http_client import HttpClient
-from biolib.app import BioLibApp
-from biolib.biolib_api_client.biolib_account_api import BiolibAccountApi
-from biolib.biolib_api_client.biolib_large_file_system_api import BiolibLargeFileSystemApi
+from biolib import utils, api
 from biolib.biolib_api_client import BiolibApiClient
+from biolib.biolib_api_client.lfs_types import LargeFileSystem, LargeFileSystemVersion
 from biolib.biolib_logging import logger
 from biolib.biolib_errors import BioLibError
 from biolib.typing_utils import List, Tuple, Iterator, Optional
-from biolib.utils.zip.remote_zip import RemoteZip  # type:ignore
-
-
-def _get_lfs_info_from_uri(lfs_uri):
-    lfs_uri_parts = lfs_uri.split('/')
-    lfs_uri_parts = [uri_part for uri_part in lfs_uri_parts if '@' not in uri_part]  # Remove hostname
-    team_account_handle = lfs_uri_parts[0]
-    lfs_name = lfs_uri_parts[1]
-    account = BiolibAccountApi.fetch_by_handle(team_account_handle)
-    return account, lfs_name
+from biolib.utils.app_uri import parse_app_uri
 
 
 def get_files_and_size_of_directory(directory: str) -> Tuple[List[str], int]:
@@ -98,14 +83,23 @@ def get_iterable_zip_stream(files: List[str], chunk_size: int) -> Iterator[bytes
         yield chunk
 
 
-def create_large_file_system(lfs_uri: str):
+def create_large_file_system(lfs_uri: str) -> str:
     BiolibApiClient.assert_is_signed_in(authenticated_action_description='create a Large File System')
-    lfs_account, lfs_name = _get_lfs_info_from_uri(lfs_uri)
-    lfs_resource = BiolibLargeFileSystemApi.create(account_uuid=lfs_account['public_id'], name=lfs_name)
-    logger.info(f"Successfully created new Large File System '{lfs_resource['uri']}'")
+
+    uri_parsed = parse_app_uri(lfs_uri)
+    response = api.client.post(
+        path='/lfs/',
+        data={
+            'account_handle': uri_parsed['account_handle_normalized'],
+            'name': uri_parsed['app_name'],
+        },
+    )
+    lfs: LargeFileSystem = response.json()
+    logger.info(f"Successfully created new Large File System '{lfs['uri']}'")
+    return lfs['uri']
 
 
-def push_large_file_system(lfs_uri: str, input_dir: str, chunk_size_in_mb: Optional[int] = None) -> None:
+def push_large_file_system(lfs_uri: str, input_dir: str, chunk_size_in_mb: Optional[int] = None) -> str:
     BiolibApiClient.assert_is_signed_in(authenticated_action_description='push data to a Large File System')
 
     if not os.path.isdir(input_dir):
@@ -114,8 +108,6 @@ def push_large_file_system(lfs_uri: str, input_dir: str, chunk_size_in_mb: Optio
     if os.path.realpath(input_dir) == '/':
         raise BioLibError('Pushing your root directory is not possible')
 
-    lfs_resource = BioLibApp(lfs_uri)
-
     original_working_dir = os.getcwd()
     os.chdir(input_dir)
     files_to_zip, data_size_in_bytes = get_files_and_size_of_directory(directory=os.getcwd())
@@ -137,9 +129,8 @@ def push_large_file_system(lfs_uri: str, input_dir: str, chunk_size_in_mb: Optio
     data_size_in_mb = round(data_size_in_bytes / 10 ** 6)
     print(f'Zipping {len(files_to_zip)} files, in total ~{data_size_in_mb}mb of data')
 
-    lfs_resource_version = BiolibLargeFileSystemApi.create_version(resource_uuid=lfs_resource.uuid)
-    lfs_resource_version_uuid = lfs_resource_version['uuid']
-
+    response = api.client.post(path='/lfs/versions/', data={'resource_uri': lfs_uri})
+    lfs_version: LargeFileSystemVersion = response.json()
     iterable_zip_stream = get_iterable_zip_stream(files=files_to_zip, chunk_size=chunk_size_in_bytes)
 
     multipart_uploader = utils.MultiPartUploader(
@@ -147,91 +138,16 @@ def push_large_file_system(lfs_uri: str, input_dir: str, chunk_size_in_mb: Optio
         get_presigned_upload_url_request=dict(
             headers=None,
             requires_biolib_auth=True,
-            path=f'/lfs/versions/{lfs_resource_version_uuid}/presigned_upload_url/',
+            path=f"/lfs/versions/{lfs_version['uuid']}/presigned_upload_url/",
         ),
         complete_upload_request=dict(
             headers=None,
             requires_biolib_auth=True,
-            path=f'/lfs/versions/{lfs_resource_version_uuid}/complete_upload/',
+            path=f"/lfs/versions/{lfs_version['uuid']}/complete_upload/",
         ),
     )
 
     multipart_uploader.upload(payload_iterator=iterable_zip_stream, payload_size_in_bytes=data_size_in_bytes)
-    logger.info(f"Successfully pushed a new LFS version '{lfs_resource_version['uri']}'")
     os.chdir(original_working_dir)
-
-
-def describe_large_file_system(lfs_uri: str, output_as_json: bool = False) -> None:
-    BiolibApiClient.assert_is_signed_in(authenticated_action_description='describe a Large File System')
-    lfs_resource = BioLibApp(lfs_uri)
-    lfs_version = BiolibLargeFileSystemApi.fetch_version(lfs_version_uuid=lfs_resource.version['public_id'])
-
-    files = []
-    total_size = 0
-    with RemoteZip(url=lfs_version['presigned_download_url']) as remote_zip:
-        central_directory = remote_zip.get_central_directory()
-        for file in central_directory.values():
-            files.append(dict(path=file['filename'], size_bytes=file['file_size']))
-            total_size += file['file_size']
-
-    lfs_version_metadata = dict(files=files, **lfs_version)
-    lfs_version_metadata['size_bytes'] = total_size
-
-    if output_as_json:
-        print(json.dumps(lfs_version_metadata, indent=4))
-    else:
-        print(f"Large File System {lfs_version_metadata['uri']}\ntotal {lfs_version_metadata['size_bytes']} bytes\n")
-        print('size bytes    path')
-        for file in files:
-            size_string = str(file['size_bytes'])
-            leading_space_string = ' ' * (10 - len(size_string))
-            print(f"{leading_space_string}{size_string}    {file['path']}")
-
-
-def get_file_data_from_large_file_system(lfs_uri: str, file_path: str) -> bytes:
-    BiolibApiClient.assert_is_signed_in(authenticated_action_description='get file from a Large File System')
-    lfs_resource = BioLibApp(lfs_uri)
-    lfs_version = BiolibLargeFileSystemApi.fetch_version(lfs_version_uuid=lfs_resource.version['public_id'])
-    lfs_url = lfs_version['presigned_download_url']
-
-    with RemoteZip(lfs_url) as remote_zip:
-        central_directory = remote_zip.get_central_directory()
-        if file_path not in central_directory:
-            raise Exception('File not found in Large File System')
-
-        file_info = central_directory[file_path]
-
-        local_file_header_signature_bytes = b'\x50\x4b\x03\x04'
-        local_file_header_struct = Struct('<H2sHHHIIIHH')
-        LocalFileHeader = namedtuple('LocalFileHeader', (
-            'version',
-            'flags',
-            'compression_raw',
-            'mod_time',
-            'mod_date',
-            'crc_32_expected',
-            'compressed_size_raw',
-            'uncompressed_size_raw',
-            'file_name_len',
-            'extra_field_len',
-        ))
-
-        local_file_header_start = file_info['header_offset'] + len(local_file_header_signature_bytes)
-        local_file_header_end = local_file_header_start + local_file_header_struct.size
-
-        local_file_header_response = HttpClient.request(
-            url=lfs_url,
-            headers={'range': f'bytes={local_file_header_start}-{local_file_header_end - 1}'},
-            timeout_in_seconds=300,
-        )
-        local_file_header = LocalFileHeader._make(local_file_header_struct.unpack(local_file_header_response.content))
-
-        file_start = local_file_header_end + local_file_header.file_name_len + local_file_header.extra_field_len
-        file_end = file_start + file_info['file_size']
-
-        response = HttpClient.request(
-            url=lfs_url,
-            headers={'range': f'bytes={file_start}-{file_end - 1}'},
-            timeout_in_seconds=300,  # timeout after 5 min
-        )
-        return response.content
+    logger.info(f"Successfully pushed a new LFS version '{lfs_version['uri']}'")
+    return lfs_version['uri']

biolib/runtime/__init__.py

@@ -1 +1,13 @@
-from .results import set_main_result_prefix
+import warnings
+from biolib.sdk import Runtime as _Runtime
+
+
+def set_main_result_prefix(result_prefix: str) -> None:
+    warnings.warn(
+        'The "biolib.runtime.set_main_result_prefix" function is deprecated. '
+        'It will be removed in future releases from mid 2024. '
+        'Please use "from biolib.sdk import Runtime" and then "Runtime.set_main_result_prefix" instead.',
+        DeprecationWarning,
+        stacklevel=2,
+    )
+    _Runtime.set_main_result_prefix(result_prefix)

biolib/sdk/__init__.py

@@ -1,24 +1,33 @@
+# Imports to hide and use as private internal utils
+from biolib._internal.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.app import BioLibApp as _BioLibApp
+from biolib.typing_utils import Optional as _Optional
+
+# Imports to expose as public API
+from biolib._internal.runtime import Runtime
+
 
 def push_app_version(uri: str, path: str) -> _BioLibApp:
     push_data = _push_application(
         app_uri=uri,
         app_path=path,
         app_version_to_copy_images_from=None,
-        is_dev_version=True)
+        is_dev_version=True,
+    )
     uri = f'{push_data["app_uri"]}:{push_data["sematic_version"]}'
     return _BioLibApp(uri)
 
+
 def set_app_version_as_default(app_version: _BioLibApp) -> None:
     app_version_uuid = app_version.version['public_id']
     _set_app_version_as_active(app_version_uuid)
 
+
 def get_app_version_pytest_plugin(app_version: _BioLibApp):
     try:
-        import pytest # type: ignore # pylint: disable=import-outside-toplevel,import-error
+        import pytest  # type: ignore # pylint: disable=import-outside-toplevel,import-error
     except BaseException:
         raise Exception('Failed to import pytest; please make sure it is installed') from None
 
@@ -27,7 +36,11 @@ def get_app_version_pytest_plugin(app_version: _BioLibApp):
             self.app_version_ref = app_version_ref
 
         @pytest.fixture(scope='session')
-        def app_version(self, request): # pylint: disable=unused-argument
+        def app_version(self, request):  # pylint: disable=unused-argument
             return self.app_version_ref
 
     return AppVersionFixturePlugin(app_version)
+
+
+def create_data_record(destination: str, data_path: str, name: _Optional[str] = None) -> _DataRecord:
+    return _DataRecord.create(destination, data_path, name)

biolib/user/sign_in.py

@@ -1,19 +1,11 @@
 import time
-import uuid
+import webbrowser
 
 from biolib.biolib_api_client import BiolibApiClient
 from biolib.biolib_api_client.auth import BiolibAuthChallengeApi
 from biolib.biolib_logging import logger_no_user_data
 from biolib.utils import IS_RUNNING_IN_NOTEBOOK
-
-
-def _open_browser_window(url_to_open: str) -> None:
-    from IPython.display import display, Javascript, update_display  # type:ignore # pylint: disable=import-error, import-outside-toplevel
-
-    display_id = str(uuid.uuid4())
-    display(Javascript(f'window.open("{url_to_open}");'), display_id=display_id)
-    time.sleep(1)
-    update_display(Javascript(''), display_id=display_id)
+from biolib._internal.utils import open_browser_window_from_notebook
 
 
 def sign_out() -> None:
@@ -21,7 +13,7 @@ def sign_out() -> None:
     api_client.sign_out()
 
 
-def sign_in() -> None:
+def sign_in(open_in_default_browser: bool = False) -> None:
     api_client = BiolibApiClient.get()
     if api_client.is_signed_in:
         logger_no_user_data.info('Already signed in')
@@ -37,7 +29,11 @@ def sign_in() -> None:
     if IS_RUNNING_IN_NOTEBOOK:
         print(f'Opening authorization page at: {frontend_sign_in_url}')
         print('If your browser does not open automatically, click on the link above.')
-        _open_browser_window(frontend_sign_in_url)
+        open_browser_window_from_notebook(frontend_sign_in_url)
+    elif open_in_default_browser:
+        print(f'Opening authorization page at: {frontend_sign_in_url}')
+        print('If your browser does not open automatically, click on the link above.')
+        webbrowser.open(frontend_sign_in_url)
     else:
         print('Please copy and paste the following link into your browser:')
         print(frontend_sign_in_url)

biolib/utils/__init__.py

@@ -4,9 +4,9 @@ import os
 import socket
 import sys
 
-from typing import Optional
 from importlib_metadata import version, PackageNotFoundError
 
+from biolib.typing_utils import Optional
 from biolib.utils.seq_util import SeqUtil, SeqUtilRecord
 from biolib._internal.http_client import HttpClient
 from biolib.biolib_logging import logger_no_user_data, logger

biolib/utils/app_uri.py

@@ -12,17 +12,18 @@ class SemanticVersion(TypedDict):
 
 class AppUriParsed(TypedDict):
     account_handle_normalized: str
-    app_name_normalized: str
+    app_name_normalized: Optional[str]
+    app_name: Optional[str]
     resource_name_prefix: Optional[str]
     version: Optional[SemanticVersion]
 
 
-def normalize(string):
+def normalize(string: str) -> str:
     return string.replace('-', '_').lower()
 
 
 # Mainly copied from backend
-def parse_app_uri(uri: str) -> AppUriParsed:
+def parse_app_uri(uri: str, use_account_as_name_default: bool = True) -> AppUriParsed:
     uri_regex = r'^(@(?P<resource_name_prefix>[\w._-]+)/)?(?P<account_handle>[\w-]+)(/(?P<app_name>[\w-]+))?' \
                 r'(:(?P<version>(?P<major>0|[1-9]\d*)\.(?P<minor>0|[1-9]\d*)\.(?P<patch>0|[1-9]\d*)))?$'
 
@@ -36,12 +37,18 @@ def parse_app_uri(uri: str) -> AppUriParsed:
     app_name: Optional[str] = matches.group('app_name')
 
     # Default to account_handle if app_name is not supplied
-    app_name_normalized = normalize(app_name) if app_name is not None else account_handle_normalized
+    if app_name:
+        app_name_normalized = normalize(app_name)
+    elif use_account_as_name_default:
+        app_name_normalized = account_handle_normalized
+    else:
+        app_name_normalized = None
 
     return AppUriParsed(
         resource_name_prefix=resource_name_prefix.lower() if resource_name_prefix is not None else 'biolib.com',
         account_handle_normalized=account_handle_normalized,
         app_name_normalized=app_name_normalized,
+        app_name=app_name if app_name is not None or not use_account_as_name_default else account_handle_normalized,
         version=None if not matches.group('version') else SemanticVersion(
             major=int(matches.group('major')),
             minor=int(matches.group('minor')),

biolib/utils/cache_state.py

@@ -10,7 +10,7 @@ from biolib.biolib_errors import BioLibError
 from biolib.biolib_logging import logger_no_user_data
 from biolib.typing_utils import Optional, Generic, TypeVar
 
-StateType = TypeVar('StateType')
+StateType = TypeVar('StateType')  # pylint: disable=invalid-name
 
 
 class CacheStateError(BioLibError):
@@ -37,7 +37,7 @@ class CacheState(abc.ABC, Generic[StateType]):
     def _state_lock_path(self) -> str:
         return f'{self._state_path}.lock'
 
-    def __init__(self):
+    def __init__(self) -> None:
         self._state: Optional[StateType] = None
 
     def __enter__(self) -> StateType:

biolib/utils/seq_util.py

@@ -3,16 +3,21 @@ from io import BufferedIOBase
 from biolib.typing_utils import List, Optional, Dict, Union
 
 allowed_sequence_chars = set("ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789-_.")
+
+
 def find_invalid_sequence_characters(sequence):
     invalid_chars = [char for char in sequence if char not in allowed_sequence_chars]
     return invalid_chars
 
+
 class SeqUtilRecord:
-    def __init__(self,
-                 sequence: str,
-                 sequence_id: str,
-                 description: Optional['str'],
-                 properties: Optional[Dict[str, str]] = None):
+    def __init__(
+            self,
+            sequence: str,
+            sequence_id: str,
+            description: Optional['str'],
+            properties: Optional[Dict[str, str]] = None,
+    ):
         self.sequence = sequence
         self.id = sequence_id  # pylint: disable=invalid-name
         self.description = description
@@ -33,11 +38,11 @@ class SeqUtilRecord:
 class SeqUtil:
     @staticmethod
     def parse_fasta(
-        input_file: Union[str, BufferedIOBase] = None,
-        default_header: Optional[str] = None,
-        allow_any_sequence_characters: bool = False,
-        allow_empty_sequence: bool = False,
-        file_name: Optional[str] = None,
+            input_file: Union[str, BufferedIOBase, None] = None,
+            default_header: Optional[str] = None,
+            allow_any_sequence_characters: bool = False,
+            allow_empty_sequence: bool = False,
+            file_name: Optional[str] = None,
     ) -> List[SeqUtilRecord]:
         if input_file is None:
             if file_name:

{pybiolib-1.1.1747.dist-info → pybiolib-1.1.1881.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1747
+Version: 1.1.1881
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.1747.dist-info → pybiolib-1.1.1881.dist-info}/RECORD

@@ -1,22 +1,25 @@
 LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
 README.md,sha256=_IH7pxFiqy2bIAmaVeA-iVTyUwWRjMIlfgtUbYTtmls,368
-biolib/__init__.py,sha256=ImZ0G02v6kpvzfyz8lPrLp2TdTKobhbaHZXvf8LV8Bg,3819
+biolib/__init__.py,sha256=nfZvVkrHZLvjvvlAvFzhvem9NMfqgmw8NWaCH9HGzew,4045
 biolib/_internal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biolib/_internal/http_client.py,sha256=HgKv559gVjeR-pgxhP0mqhd9a7Seuy9AJl57TxNwjJ8,4098
-biolib/_internal/push_application.py,sha256=NXQNLPucqkq7eKbNCJQA8OYx4CXYHRJ1CG1ViPAJJH4,10680
+biolib/_internal/data_record/__init__.py,sha256=1Bk303i3rFet9veS56fIsrBYtT5X3n9vcsYMA6T6c5o,36
+biolib/_internal/data_record/data_record.py,sha256=oQ2R7bD1on5aPC3jXP7OOSPeuXkWEqRUR8GV4a6hsJA,6539
+biolib/_internal/data_record/remote_storage_endpoint.py,sha256=LPq8Lr5FhKF9_o5K-bUdT7TeLe5XFUD0AAeTkNEVZug,1133
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 biolib/api/client.py,sha256=MtDkH2Amr2Fko-bCR5DdookJu0yZ1q-6K_PPg4KK_Ek,2941
 biolib/app/__init__.py,sha256=cdPtcfb_U-bxb9iSL4fCEq2rpD9OjkyY4W-Zw60B0LI,37
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 biolib/biolib_api_client/__init__.py,sha256=E5EMa19wJoblwSdQPYrxc_BtIeRsAuO0L_jQweWw-Yk,182
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 biolib/biolib_api_client/auth.py,sha256=kjm0ZHnH3I8so3su2sZbBxNHYp-ZUdrZ5lwQ0K36RSw,949
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 biolib/biolib_api_client/biolib_job_api.py,sha256=IpFahcRzm7GNy8DJ-XHYe-x7r4Voba8o22IXw5puHn8,6782
-biolib/biolib_api_client/biolib_large_file_system_api.py,sha256=p8QhvQ0aI0NJgyRm7duqDVtPx0zrVaSLKS22ocOafFQ,1038
 biolib/biolib_api_client/common_types.py,sha256=RH-1KNHqUF-EkTpfPOSTt5Mq1GPdfju_cqXDesscO1I,123
 biolib/biolib_api_client/job_types.py,sha256=XlDIxijxymLoJcClXhl91h1E4b2fT3pszO9wjlssD4A,1284
 biolib/biolib_api_client/lfs_types.py,sha256=xaGjE-yUyNVM3LyKdslJn5ZXWp6_kVCd4o-ch8Czfm4,227
@@ -32,41 +35,43 @@ biolib/biolib_binary_format/saved_job.py,sha256=nFHVFRNTNcAFGODLSiBntCtMk55QKwre
 biolib/biolib_binary_format/stdout_and_stderr.py,sha256=WfUUJFFCBrtfXjuWIaRPiWCpuBLxfko68oxoTKhrwx8,1023
 biolib/biolib_binary_format/system_exception.py,sha256=T3iL4_cSHAHim3RSDPS8Xyb1mfteaJBZonSXuRltc28,853
 biolib/biolib_binary_format/system_status_update.py,sha256=aOELuQ0k-GtpaZTUxYd0GFomP_OInmrK585y6fuQuKE,1191
-biolib/biolib_binary_format/utils.py,sha256=0MDEGsyShkiIAHNWXuHfmhrKYVvVhn21Yl9BNWqHIiw,3693
+biolib/biolib_binary_format/utils.py,sha256=1mZFX6KtbhvAXnzxnMJC_rYkiAjh9zhV31l68wVpA4A,4150
 biolib/biolib_docker_client/__init__.py,sha256=aBfA6mtWSI5dBEfNNMD6bIZzCPloW4ghKm0wqQiljdo,1481
 biolib/biolib_download_container.py,sha256=8TmBV8iv3bCvkNlHa1SSsc4zl0wX_eaxhfnW5rvFIh8,1779
 biolib/biolib_errors.py,sha256=5m4lK2l39DafpoXBImEBD4EPH3ayXBX0JgtPzmGClow,689
 biolib/biolib_logging.py,sha256=J3E5H_LL5k6ZUim2C8gqN7E6lCBZMTpO4tnMpOPwG9U,2854
-biolib/cli/__init__.py,sha256=EC_mFPV-eFzz4ViGBmFtetQiS78gxLeYVkf9UeFyvPE,1140
-biolib/cli/download_container.py,sha256=0X109ZRtThfbEqsXBPU_ocGjxuRVLilNA9pjRMueTqI,466
-biolib/cli/init.py,sha256=Rd6_zpQxQbB0UaSEBFxfsL2j64YuINilNzhDydDDBig,820
-biolib/cli/lfs.py,sha256=S7S4vNF77ptzddU0Jg5U3TipN9nUyW-9WmiqGRyXHsM,2630
-biolib/cli/push.py,sha256=HVSrfqmd3NxER-DBhoK5wYQN-LavpuDZxe4CtKKSFak,813
-biolib/cli/run.py,sha256=04T1Ez7hp42BiX7DoDc0m2nJmrSUarVz4sPA3avY5yM,1647
+biolib/cli/__init__.py,sha256=0v3c_J-U0k46c5ZWeQjLG_kTaKDJm81LBxQpDO2B_aI,1286
+biolib/cli/auth.py,sha256=wp-JQRzDgiEbxeUTxwlHfugk-9u6PiOtZiHl9brAgcA,2050
+biolib/cli/data_record.py,sha256=piN3QUbRAkMi4wpayghN4unFfuiNE5VCjI1gag4d8qg,1725
+biolib/cli/download_container.py,sha256=HIZVHOPmslGE5M2Dsp9r2cCkAEJx__vcsDz5Wt5LRos,483
+biolib/cli/init.py,sha256=wQOfii_au-d30Hp7DdH-WVw-WVraKvA_zY4za1w7DE8,821
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+biolib/cli/push.py,sha256=TFi7O9tJ3zFe0VmtVTV3Vh9_xIMHnrc41xxcaBKU46g,813
+biolib/cli/run.py,sha256=BbvXLQ-XibjQ71Y2d4URMH_8dflNVwM0i3TIWhw_u_c,1634
 biolib/cli/runtime.py,sha256=Xv-nrma5xX8NidWcvbUKcUvuN5TCarZa4A8mPVmF-z0,361
-biolib/cli/start.py,sha256=TpZq1VHVkLTW1_PyjIGkJg44E3PzxSaGrN2D_rNJL0c,1736
+biolib/cli/start.py,sha256=rg8VVY8rboFhf1iQo3zE3WA5oh_R1VWWfYJEO1gMReY,1737
 biolib/compute_node/.gitignore,sha256=GZdZ4g7HftqfOfasFpBC5zV1YQAbht1a7EzcXD6f3zg,45
 biolib/compute_node/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/compute_node/cloud_utils/__init__.py,sha256=VZSScLqaz5tg_gpMvWgwkAu9Qf-vgW_QHRoDOaAmU44,67
-biolib/compute_node/cloud_utils/cloud_utils.py,sha256=OSnFEFzpNEnEBCGkFtUvw_V6Qhqo2TQMohKjYRQdzDM,7607
+biolib/compute_node/cloud_utils/cloud_utils.py,sha256=KIZjBnZPBtHParrR_KnRl7N343sHXMQugH9lkwAwTFk,7621
 biolib/compute_node/job_worker/__init__.py,sha256=ipdPWaABKYrltxny15e2kK8PWdEE7VzXbkKK6wM_zDk,71
-biolib/compute_node/job_worker/cache_state.py,sha256=N2AxvvgfizKx9P_ysM0GDCmueMUlgcveA4xSdz_Z2IQ,4822
+biolib/compute_node/job_worker/cache_state.py,sha256=MwjSRzcJJ_4jybqvBL4xdgnDYSIiw4s90pNn83Netoo,4830
 biolib/compute_node/job_worker/cache_types.py,sha256=ajpLy8i09QeQS9dEqTn3T6NVNMY_YsHQkSD5nvIHccQ,818
 biolib/compute_node/job_worker/docker_image_cache.py,sha256=ansHIkJIq_EMW1nZNlW-RRLVVeKWTbzNICYaOHpKiRE,7460
 biolib/compute_node/job_worker/executors/__init__.py,sha256=bW6t1qi3PZTlHM4quaTLa8EI4ALTCk83cqcVJfJfJfE,145
-biolib/compute_node/job_worker/executors/docker_executor.py,sha256=vXL2Y7bemwjcICbq78m3K8DsNHkImYl1fgQhnWMYQOs,26348
+biolib/compute_node/job_worker/executors/docker_executor.py,sha256=ezXRhVBW5dYpLJjM2m5Qf-I6PrrNeBdEYjApjo7XVso,26419
 biolib/compute_node/job_worker/executors/docker_types.py,sha256=VhsU1DKtJjx_BbCkVmiPZPH4ROiL1ygW1Y_s1Kbpa2o,216
 biolib/compute_node/job_worker/executors/tars/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/compute_node/job_worker/executors/types.py,sha256=yP5gG39hr-DLnw9bOE--VHi-1arDbIYiGuV1rlTbbHI,1466
 biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py,sha256=_cvEiZbOwfkv6fYmfrvdi_FVviIEYr_dSClQcOQaUWM,1198
 biolib/compute_node/job_worker/job_max_runtime_timer_thread.py,sha256=K_xgz7IhiIjpLlXRk8sqaMyLoApcidJkgu29sJX0gb8,1174
 biolib/compute_node/job_worker/job_storage.py,sha256=Ol43f43W6aD2EUkA6G2i9-WxdREr5JPSjo1xFylddOQ,4030
-biolib/compute_node/job_worker/job_worker.py,sha256=98-3ksp-mfTKge9yoUw7_ab08buBnC40dVe5rT_3Ncw,27949
+biolib/compute_node/job_worker/job_worker.py,sha256=QifGpDBn1ojJ5b43--XyXmz8YqsgNlGskh-z8mkYQqg,28147
 biolib/compute_node/job_worker/large_file_system.py,sha256=XXqRlVtYhs-Ji9zQGIk5KQPXFO_Q5jJH0nnlw4GkeMY,10461
 biolib/compute_node/job_worker/mappings.py,sha256=Z48Kg4nbcOvsT2-9o3RRikBkqflgO4XeaWxTGz-CNvI,2499
 biolib/compute_node/job_worker/utilization_reporter_thread.py,sha256=7tm5Yk9coqJ9VbEdnO86tSXI0iM0omwIyKENxdxiVXk,8575
 biolib/compute_node/job_worker/utils.py,sha256=wgxcIA8yAhUPdCwyvuuJ0JmreyWmmUoBO33vWtG60xg,1282
-biolib/compute_node/remote_host_proxy.py,sha256=9b_JILgeJ4lz0Vcv4KrHaTC7MnokShTASKQj1o9z908,14072
+biolib/compute_node/remote_host_proxy.py,sha256=spjYghbqwX3dFrmedGvXZGXEsnwop1IbbyrXTv1PWz0,15080
 biolib/compute_node/socker_listener_thread.py,sha256=T5_UikA3MB9bD5W_dckYLPTgixh72vKUlgbBvj9dbM0,1601
 biolib/compute_node/socket_sender_thread.py,sha256=YgamPHeUm2GjMFGx8qk-99WlZhEs-kAb3q_2O6qByig,971
 biolib/compute_node/utils.py,sha256=M7i_WTyxbFM3Lri9RWZ_8FeQNYrQIWpKGLfp2I55oeY,4677
@@ -80,29 +85,28 @@ biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuF
 biolib/experiments/experiment.py,sha256=xUd3LkV5ztFIjTx_ehBu8e-flvfuQnYimFtPj1upzb0,5942
 biolib/experiments/types.py,sha256=n9GxdFA7cLMfHvLLqLmZzX31ELeSSkMXFoEEdFsdWGY,171
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
-biolib/jobs/job.py,sha256=mrRQd0aI8VElYgwd7BtXE-mjB0c4xbyRh8Ngpd2gZ7Q,15181
+biolib/jobs/job.py,sha256=_lYtqaTrtq3ayDvnaB9RuUMBTxCRKYGKVADUd473pWQ,15718
 biolib/jobs/job_result.py,sha256=8GasUmUXD8SjUYrE2N-HrDx7-AI6TEkFONH8H91t01Q,4913
 biolib/jobs/types.py,sha256=4OAvlhOKANzFMrZDd-mhXpEd8RaKcx8sPneZUoWhJ2U,970
-biolib/lfs/__init__.py,sha256=wspftSqe_x7xPMZbeW8mcIBuxbHFCiFI3V4TuZU4nZ4,193
+biolib/lfs/__init__.py,sha256=Qv8vdYeK43JecT4SsE93ZYE2VmNiZENdNpW8P9-omxs,115
 biolib/lfs/cache.py,sha256=pQS2np21rdJ6I3DpoOutnzPHpLOZgUIS8TMltUJk_k4,2226
-biolib/lfs/utils.py,sha256=dVDNoXXfXFt9Sbf68tJ6BPv_cNAHMcqbrY2wLj-lLUA,9773
-biolib/runtime/__init__.py,sha256=WyuNnkzj1r-Sx4J-xWzp3US2oo9m5aIuCOYRmjlZ3ug,44
-biolib/runtime/results.py,sha256=7Fzrddb319dLMgTS1AVvz-RaTxAWOr7Qt75ftfSci9E,778
-biolib/sdk/__init__.py,sha256=vqqE2Sf3gLySkaJv8VgWtPRkYMi9hOf66y9Ay2waYVE,1339
+biolib/lfs/utils.py,sha256=HSs7F2wXklYhhv5tabfaeC5noXJyxRjbGD5IhWOVdxs,5918
+biolib/runtime/__init__.py,sha256=x1Ivydtu9TFTaX-Cofg_kGA-TI0zLon-ccrFiiVgBok,492
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 biolib/tables.py,sha256=acH7VjwAbadLo8P84FSnKEZxCTVsF5rEg9VPuxElNs8,872
 biolib/templates/__init__.py,sha256=Yx62sSyDCDesRQDQgmbDsLpfgEh93fWE8r9u4g2azXk,36
 biolib/templates/example_app.py,sha256=EB3E3RT4SeO_ii5nVQqJpi5KDGNE_huF1ub-e5ZFveE,715
 biolib/typing_utils.py,sha256=krMhxB3SedVQA3HXIrC7DBXWpHKWN5JNmXGcSrrysOc,263
 biolib/user/__init__.py,sha256=Db5wtxLfFz3ID9TULSSTo77csw9tO6RtxMRvV5cqKEE,39
-biolib/user/sign_in.py,sha256=CvHBgoYjg5d5CL9etVopns_g1pImgW8mQH3zAjpe1Ik,2061
-biolib/utils/__init__.py,sha256=AuBhxgZV8-3LWPnewhhYw4isQhPmVs-k55umk8t-r7U,5535
-biolib/utils/app_uri.py,sha256=hOFsTQfA7QbyQyg9ItGdD8VDWBJw0vYMqzLdSiJXmqQ,1857
-biolib/utils/cache_state.py,sha256=BFrZlV4XZIueIFzAFiPidX4hmwADKY5Y5ZuqlerF5l0,3060
+biolib/user/sign_in.py,sha256=q-E2B3wLVwPU5plbITJXP4GDWWUzUcDpYu_y8BShNQ8,2039
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 biolib/utils/multipart_uploader.py,sha256=XvGP1I8tQuKhAH-QugPRoEsCi9qvbRk-DVBs5PNwwJo,8452
-biolib/utils/seq_util.py,sha256=3BGUppEaR8asFBxktHCrIW0cMmF23b06PsbDQOoeCDQ,4879
+biolib/utils/seq_util.py,sha256=jC5WhH63FTD7SLFJbxQGA2hOt9NTwq9zHl_BEec1Z0c,4907
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.1.1747.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.1747.dist-info/METADATA,sha256=l0Xv2iALOshL_L-q7k7EzOq5QBWOlc-lm1SG2a5_41E,1508
-pybiolib-1.1.1747.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-pybiolib-1.1.1747.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.1747.dist-info/RECORD,,
+pybiolib-1.1.1881.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.1881.dist-info/METADATA,sha256=oanwAPIfyI5nATML26HjNK4sjPb2ciuoyP2jLxg8Kbs,1508
+pybiolib-1.1.1881.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.1.1881.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.1881.dist-info/RECORD,,

{pybiolib-1.1.1747.dist-info → pybiolib-1.1.1881.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.8.1
+Generator: poetry-core 1.9.0
 Root-Is-Purelib: true
 Tag: py3-none-any

biolib/biolib_api_client/biolib_account_api.py

@@ -1,8 +0,0 @@
-import biolib.api
-
-class BiolibAccountApi:
-
-    @staticmethod
-    def fetch_by_handle(account_handle):
-        response = biolib.api.client.get(path=f'/account/{account_handle}')
-        return response.json()

biolib/biolib_api_client/biolib_large_file_system_api.py

@@ -1,34 +0,0 @@
-import biolib.api
-from biolib.biolib_api_client.lfs_types import LargeFileSystemVersion, LargeFileSystem
-
-
-class BiolibLargeFileSystemApi:
-
-    @staticmethod
-    def create(account_uuid: str, name: str) -> LargeFileSystem:
-        response = biolib.api.client.post(
-            path='/lfs/',
-            data={'account_uuid': account_uuid, 'name': name},
-        )
-
-        lfs: LargeFileSystem = response.json()
-        return lfs
-
-    @staticmethod
-    def fetch_version(lfs_version_uuid: str) -> LargeFileSystemVersion:
-        response = biolib.api.client.get(
-            path=f'/lfs/versions/{lfs_version_uuid}/',
-        )
-
-        lfs_version: LargeFileSystemVersion = response.json()
-        return lfs_version
-
-    @staticmethod
-    def create_version(resource_uuid: str) -> LargeFileSystemVersion:
-        response = biolib.api.client.post(
-            path='/lfs/versions/',
-            data={'resource_uuid': resource_uuid},
-        )
-
-        lfs_version: LargeFileSystemVersion = response.json()
-        return lfs_version

biolib/runtime/results.py

@@ -1,20 +0,0 @@
-import json
-
-from biolib import api
-
-
-def set_main_result_prefix(result_prefix: str) -> None:
-    try:
-        with open('/biolib/secrets/biolib_system_secret', mode='r') as system_secrets_file:
-            system_secrets = json.loads(system_secrets_file.read())
-    except Exception:  # pylint: disable=broad-except
-        raise Exception('Unable to load the BioLib runtime system secret') from None
-
-    if not system_secrets['version'].startswith('1.'):
-        raise Exception(f"Unexpected system secret version {system_secrets['version']} expected 1.x.x")
-
-    api.client.patch(
-        data={'result_name_prefix': result_prefix},
-        headers={'Job-Auth-Token': system_secrets['job_auth_token']},
-        path=f"/jobs/{system_secrets['job_uuid']}/main_result/",
-    )