pybiolib 1.1.1753__py3-none-any.whl → 1.1.1769__py3-none-any.whl

biolib/_internal/runtime/__init__.py

@@ -0,0 +1 @@
+from .job_data import RuntimeJobData

biolib/_internal/runtime/job_data.py

@@ -0,0 +1,29 @@
+import json
+from biolib.typing_utils import TypedDict, Optional, cast
+
+
+class RuntimeJobDataDict(TypedDict):
+    version: str
+    job_requested_machine: str
+    job_uuid: str
+    job_auth_token: str
+
+
+class RuntimeJobData:
+    _job_data: Optional[RuntimeJobDataDict] = None
+
+    @staticmethod
+    def get() -> Optional[RuntimeJobDataDict]:
+        if not RuntimeJobData._job_data:
+            try:
+                with open('/biolib/secrets/biolib_system_secret', mode='r') as file:
+                    job_data: RuntimeJobDataDict = json.load(file)
+            except BaseException:
+                return None
+
+            if not job_data['version'].startswith('1.'):
+                raise Exception(f"Unexpected system secret version {job_data['version']} expected 1.x.x")
+
+            RuntimeJobData._job_data = job_data
+
+        return cast(RuntimeJobDataDict, RuntimeJobData._job_data)

biolib/biolib_api_client/api_client.py

@@ -6,6 +6,7 @@ import os
 from datetime import datetime, timezone
 from json.decoder import JSONDecodeError
 
+from biolib._internal.runtime import RuntimeJobData
 from biolib._internal.http_client import HttpClient
 from biolib.typing_utils import Optional
 from biolib.biolib_errors import BioLibError
@@ -188,8 +189,9 @@ class BiolibApiClient:
 
     @staticmethod
     def assert_is_signed_in(authenticated_action_description: str) -> None:
+        runtime_job_data = RuntimeJobData.get()
         api_client = BiolibApiClient.get()
-        if not api_client.is_signed_in:
+        if not api_client.is_signed_in and not runtime_job_data:
             raise BioLibError(
                 f'You must be signed in to {authenticated_action_description}. '
                 f'Please set the environment variable "BIOLIB_TOKEN"'

biolib/biolib_api_client/biolib_app_api.py

@@ -35,7 +35,7 @@ def encode_multipart(data, files):
     line_array.append('')
 
     data_encoded = b'\r\n'.join([line.encode() if isinstance(line, str) else line for line in line_array])
-    return 'multipart/form-data; boundary={}'.format(boundary), data_encoded
+    return f'multipart/form-data; boundary={boundary}', data_encoded
 
 
 def _get_git_branch_name() -> str:

biolib/compute_node/cloud_utils/cloud_utils.py

@@ -81,8 +81,8 @@ class CloudUtils:
                         'error': error,
                     },
                 )
-            except BaseException as error:
-                logger_no_user_data.error(f'Failed to deregister got error: {error}')
+            except BaseException as error_object:
+                logger_no_user_data.error(f'Failed to deregister got error: {error_object}')
         else:
             logger_no_user_data.error("Not deregistering as environment is not cloud")
 

biolib/compute_node/job_worker/executors/docker_executor.py

@@ -18,6 +18,8 @@ from docker.errors import ImageNotFound, APIError  # type: ignore
 from docker.models.containers import Container  # type: ignore
 
 from biolib import utils
+
+from biolib._internal.runtime.job_data import RuntimeJobDataDict
 from biolib.biolib_binary_format import ModuleInput, ModuleOutputV2
 from biolib.biolib_docker_client import BiolibDockerClient
 from biolib.biolib_errors import DockerContainerNotFoundDuringExecutionException, BioLibError
@@ -267,12 +269,12 @@ class DockerExecutor:
             internal_network = self._options['internal_network']
             extra_hosts: Dict[str, str] = {}
 
-            biolib_system_secret = {
-                'version': '1.0.0',
-                'job_requested_machine': self._options['job']['requested_machine'],
-                'job_uuid': self._options['job']['public_id'],
-                'job_auth_token': self._options['job']['auth_token'],
-            }
+            biolib_system_secret = RuntimeJobDataDict(
+                version='1.0.0',
+                job_requested_machine=self._options['job']['requested_machine'],
+                job_uuid=self._options['job']['public_id'],
+                job_auth_token=self._options['job']['auth_token'],
+            )
             secrets: Dict[str, str] = dict(
                 **module.get('secrets', {}),
                 biolib_system_secret=json.dumps(biolib_system_secret, indent=4),

biolib/compute_node/job_worker/job_worker.py

@@ -97,7 +97,11 @@ class JobWorker:
         if socket_port:
             self._connect_to_parent()
 
-    def _handle_exit_gracefully(self, signum: int, frame: FrameType) -> None:  # pylint: disable=unused-argument
+    def _handle_exit_gracefully(
+            self,
+            signum: int,
+            frame: Optional[FrameType],  # pylint: disable=unused-argument
+    ) -> None:
         job_id = self._root_job_wrapper["job"]["public_id"] if self._root_job_wrapper else None
         logger_no_user_data.debug(
             f'_JobWorker ({job_id}) got exit signal {signal.Signals(signum).name}'  # pylint: disable=no-member

biolib/compute_node/remote_host_proxy.py

@@ -281,9 +281,8 @@ http {{
             proxy_ssl_server_name    on;
         }}
 
-        location ~* "^/api/lfs/.*$" {{
-            # Note: Using $1 here as URI part from regex must be used for proxy_pass
-            proxy_pass               {base_url}/api/lfs/$1;
+        location /api/lfs/ {{
+            proxy_pass               {base_url}/api/lfs/;
             proxy_set_header         authorization {'$bearer_token_on_post' if self._can_push_data_record_for_user else '""'};
             proxy_set_header         cookie "";
             proxy_ssl_server_name    on;

biolib/jobs/job.py

@@ -310,7 +310,7 @@ class Job:
             ).json()
         except Exception as error:
             logger.error(f'Could not get full streamed logs due to: {error}')
-            raise BioLibError from error
+            raise BioLibError('Could not get full streamed logs') from error
 
         for status_update in response_json.get('previous_status_updates', []):
             logger.info(f'Cloud: {status_update["log_message"]}')

biolib/lfs/utils.py

@@ -6,15 +6,18 @@ from collections import namedtuple
 from pathlib import Path
 from struct import Struct
 
-from biolib import utils
+from biolib import utils, api
+from biolib._internal.runtime import RuntimeJobData as _RuntimeJobData
 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.biolib_api_client import BiolibApiClient
+from biolib.biolib_api_client.lfs_types import LargeFileSystem
 from biolib.biolib_logging import logger
 from biolib.biolib_errors import BioLibError
 from biolib.typing_utils import List, Tuple, Iterator, Optional
+from biolib.utils.app_uri import parse_app_uri
 from biolib.utils.zip.remote_zip import RemoteZip  # type:ignore
 
 
@@ -98,11 +101,26 @@ 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) -> None:
     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']}'")
+
+    runtime_job_data = _RuntimeJobData.get()
+    if runtime_job_data:
+        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_normalized'],
+            },
+        )
+        lfs: LargeFileSystem = response.json()
+    else:
+        # TODO: Also use account_handle directly in POST request when backends are updated
+        lfs_account, lfs_name = _get_lfs_info_from_uri(lfs_uri)
+        lfs = BiolibLargeFileSystemApi.create(account_uuid=lfs_account['public_id'], name=lfs_name)
+
+    logger.info(f"Successfully created new Large File System '{lfs['uri']}'")
 
 
 def push_large_file_system(lfs_uri: str, input_dir: str, chunk_size_in_mb: Optional[int] = None) -> None:

biolib/runtime/results.py

@@ -1,20 +1,14 @@
-import json
-
 from biolib import api
+from biolib._internal.runtime import RuntimeJobData as _RuntimeJobData
 
 
 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")
+    runtime_job_data = _RuntimeJobData.get()
+    if not runtime_job_data:
+        raise Exception('Unable to load BioLib runtime job data') from None
 
     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/",
+        headers={'Job-Auth-Token': runtime_job_data['job_auth_token']},
+        path=f"/jobs/{runtime_job_data['job_uuid']}/main_result/",
     )

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/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):

{pybiolib-1.1.1753.dist-info → pybiolib-1.1.1769.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1753
+Version: 1.1.1769
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.1753.dist-info → pybiolib-1.1.1769.dist-info}/RECORD

@@ -4,17 +4,19 @@ biolib/__init__.py,sha256=ImZ0G02v6kpvzfyz8lPrLp2TdTKobhbaHZXvf8LV8Bg,3819
 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/runtime/__init__.py,sha256=T8o9Ha320O5k024Z93kWxUnGMi80NVZRyw4wdOSNA0s,37
+biolib/_internal/runtime/job_data.py,sha256=t-fN9i0tK3B6ly9PL7WQm6JxK8yC_hJ6xx65qcTyfLg,892
 biolib/api/__init__.py,sha256=iIO8ZRdn7YDhY5cR47-Wo1YsNOK8H6RN6jn8yor5WJI,137
 biolib/api/client.py,sha256=MtDkH2Amr2Fko-bCR5DdookJu0yZ1q-6K_PPg4KK_Ek,2941
 biolib/app/__init__.py,sha256=cdPtcfb_U-bxb9iSL4fCEq2rpD9OjkyY4W-Zw60B0LI,37
 biolib/app/app.py,sha256=r63gDoH1s8uQOGITmiKOVIrYDYdMrB5nwXHNRt2Da2M,10197
 biolib/app/search_apps.py,sha256=CIanvDebNpMtWck0w4IoR_tRZ6LpSWC8DPxXW2e6Ww4,1495
 biolib/biolib_api_client/__init__.py,sha256=E5EMa19wJoblwSdQPYrxc_BtIeRsAuO0L_jQweWw-Yk,182
-biolib/biolib_api_client/api_client.py,sha256=oaLqTb208TLRVW4-h_va734TrVDRD3kLpFJ93cwQTxk,7130
+biolib/biolib_api_client/api_client.py,sha256=AtD4ZA1onPFt00PpmDsC1yLjShuNhmCciXFwPrYsvI8,7255
 biolib/biolib_api_client/app_types.py,sha256=rEw4HICV7ujdmlzM3BjRcMNMbiYItliivpH0rkeJx4s,2465
 biolib/biolib_api_client/auth.py,sha256=kjm0ZHnH3I8so3su2sZbBxNHYp-ZUdrZ5lwQ0K36RSw,949
 biolib/biolib_api_client/biolib_account_api.py,sha256=sHng5jDvSktv6tOLKU8wJRieidY2kLxRU8hI_6ZauXE,210
-biolib/biolib_api_client/biolib_app_api.py,sha256=vPFoONWh-i-Bg7pm_x50EQqbN9qQFLgNDTkkWKqDUTY,4248
+biolib/biolib_api_client/biolib_app_api.py,sha256=DndlVxrNTes6DOaWyMINLGZQCRMWVvR7gwt5HVlyf5Y,4240
 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
@@ -48,25 +50,25 @@ biolib/cli/start.py,sha256=TpZq1VHVkLTW1_PyjIGkJg44E3PzxSaGrN2D_rNJL0c,1736
 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_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=yeNTw28XGuz1RRDqHWY1tXlbWKJ8G6oP_d34j6OsZkk,26420
 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=QwerjRPETxPa4DrI9_u2ZI89rBGtf6_w-KtIDvBI1Bw,28094
+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=GbqAnVju0fsEYQr3I4Voq_vdDM5p88vLFVV7Cl79n5g,14616
+biolib/compute_node/remote_host_proxy.py,sha256=SAp8H-mlNLF5njISF6LTXhSnO9-l5KATiABk-06lS8k,14520
 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
@@ -80,14 +82,14 @@ 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=8ro2DRBB0gGe6D-tDFQRDSACDbhUOyttUqS5fgJNPt8,15217
 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/cache.py,sha256=pQS2np21rdJ6I3DpoOutnzPHpLOZgUIS8TMltUJk_k4,2226
-biolib/lfs/utils.py,sha256=dVDNoXXfXFt9Sbf68tJ6BPv_cNAHMcqbrY2wLj-lLUA,9773
+biolib/lfs/utils.py,sha256=YUFZlGABMfuOA0BwZ8JGOd-OKNGQVUElLP_4CHe4zyw,10461
 biolib/runtime/__init__.py,sha256=WyuNnkzj1r-Sx4J-xWzp3US2oo9m5aIuCOYRmjlZ3ug,44
-biolib/runtime/results.py,sha256=7Fzrddb319dLMgTS1AVvz-RaTxAWOr7Qt75ftfSci9E,778
+biolib/runtime/results.py,sha256=OEtDFb5Auiubh6EClT9L_wMzfRpehIfRwj-8MSVDoz4,522
 biolib/sdk/__init__.py,sha256=vqqE2Sf3gLySkaJv8VgWtPRkYMi9hOf66y9Ay2waYVE,1339
 biolib/tables.py,sha256=acH7VjwAbadLo8P84FSnKEZxCTVsF5rEg9VPuxElNs8,872
 biolib/templates/__init__.py,sha256=Yx62sSyDCDesRQDQgmbDsLpfgEh93fWE8r9u4g2azXk,36
@@ -95,14 +97,14 @@ biolib/templates/example_app.py,sha256=EB3E3RT4SeO_ii5nVQqJpi5KDGNE_huF1ub-e5ZFv
 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/__init__.py,sha256=fwjciJyJicvYyZcVTzfDBgD0SKY13DeXqvTeG4qZIy8,5548
 biolib/utils/app_uri.py,sha256=hOFsTQfA7QbyQyg9ItGdD8VDWBJw0vYMqzLdSiJXmqQ,1857
-biolib/utils/cache_state.py,sha256=BFrZlV4XZIueIFzAFiPidX4hmwADKY5Y5ZuqlerF5l0,3060
+biolib/utils/cache_state.py,sha256=GaGPxQ1GfrBL6Mzo_HJPpmZCd_CbUDN_l_C5frQ5Sfs,3092
 biolib/utils/multipart_uploader.py,sha256=XvGP1I8tQuKhAH-QugPRoEsCi9qvbRk-DVBs5PNwwJo,8452
 biolib/utils/seq_util.py,sha256=3BGUppEaR8asFBxktHCrIW0cMmF23b06PsbDQOoeCDQ,4879
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
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