pybiolib 1.1.1418__tar.gz → 1.1.1420__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/PKG-INFO +1 -1
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/jobs/job.py +17 -26
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/pyproject.toml +1 -1
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/LICENSE +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/README.md +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/api/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/api/client.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/app/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/app/app.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/app/search_apps.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/api_client.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/app_types.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/auth.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/biolib_account_api.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/biolib_app_api.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/biolib_job_api.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/biolib_large_file_system_api.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/common_types.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/job_types.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/lfs_types.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/user_state.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/base_bbf_package.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/file_in_container.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/module_input.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/module_output_v2.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/remote_endpoints.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/remote_stream_seeker.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/saved_job.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/stdout_and_stderr.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/system_exception.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/system_status_update.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/utils.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_docker_client/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_errors.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_logging.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_push.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/cli/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/cli/init.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/cli/lfs.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/cli/push.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/cli/run.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/cli/runtime.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/cli/start.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/.gitignore +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/cloud_utils/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/cloud_utils/cloud_utils.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/cache_state.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/cache_types.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/docker_image_cache.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/executors/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/executors/docker_executor.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/executors/docker_types.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/executors/tars/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/executors/types.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/job_max_runtime_timer_thread.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/job_storage.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/job_worker.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/large_file_system.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/mappings.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/utilization_reporter_thread.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/utils.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/remote_host_proxy.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/socker_listener_thread.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/socket_sender_thread.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/utils.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/webserver/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/webserver/gunicorn_flask_application.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/webserver/webserver.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/webserver/webserver_types.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/webserver/webserver_utils.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/webserver/worker_thread.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/experiments/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/experiments/experiment.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/experiments/types.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/jobs/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/jobs/job_result.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/jobs/types.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/lfs/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/lfs/cache.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/lfs/utils.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/runtime/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/runtime/results.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/tables.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/templates/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/templates/example_app.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/typing_utils.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/user/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/user/sign_in.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/utils/__init__.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/utils/app_uri.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/utils/cache_state.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/utils/multipart_uploader.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/utils/seq_util.py +0 -0
- {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/utils/zip/remote_zip.py +0 -0
@@ -37,7 +37,7 @@ class Job:
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self._job_dict: JobDict = job_dict
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self._job_dict_last_fetched_at: datetime = datetime.utcnow()
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self._result: Optional[JobResult] = None
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self.
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self._cached_input_arguments: Optional[List[str]] = None
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def __str__(self):
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return f"Job for {self._job_dict['app_uri']} created at {self._job_dict['created_at']} ({self._uuid})"
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return self.result.get_exit_code()
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def _get_module_input(self) -> ModuleInputDict:
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module_input_serialized: bytes = response.content
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except Exception as error:
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# TODO: Improve error handling and messages
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raise error
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try:
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self._module_input_dict = ModuleInput(module_input_serialized).deserialize()
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except Exception as error:
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# TODO: Improve error handling and messages
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raise error
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return self._module_input_dict
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self._refetch_job_dict()
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presigned_download_url = BiolibJobApi.get_job_storage_download_url(
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job_uuid=self._job_dict['uuid'],
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job_auth_token=self._job_dict['auth_token'],
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storage_type='input',
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)
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response = requests.get(url=presigned_download_url)
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response.raise_for_status()
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module_input_serialized: bytes = response.content
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return ModuleInput(module_input_serialized).deserialize()
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def get_input_arguments(self) -> List[str]:
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if self._cached_input_arguments is None:
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logger.debug('Fetching input arguments...')
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module_input = self._get_module_input()
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self._cached_input_arguments = module_input['arguments']
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return self._cached_input_arguments
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def save_input_files(self, output_dir: str) -> None:
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logger.info('Downloading input files...')
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{pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/biolib_large_file_system_api.py
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