pybiolib 1.2.465.dev1__tar.gz → 1.2.497__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-1.2.465.dev1 → pybiolib-1.2.497}/PKG-INFO +1 -1
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/data_record/data_record.py +5 -2
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/jobs/job.py +13 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/pyproject.toml +1 -1
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/LICENSE +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/PYPI_README.md +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_data_record/data_record.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/data_record/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/data_record/push_data.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/data_record/remote_storage_endpoint.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/file_utils.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/fuse_mount/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/fuse_mount/experiment_fuse_mount.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/http_client.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/lfs/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/lfs/cache.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/libs/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/libs/fusepy/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/push_application.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/runtime.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/types/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/types/app.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/types/data_record.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/types/experiment.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/types/file_node.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/types/resource.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/types/resource_version.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/types/typing.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/utils/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/utils/multinode.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_runtime/runtime.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/api/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/api/client.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/app/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/app/app.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/app/search_apps.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_api_client/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_api_client/api_client.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_api_client/app_types.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_api_client/auth.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_api_client/biolib_app_api.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_api_client/biolib_job_api.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_api_client/common_types.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_api_client/job_types.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_api_client/lfs_types.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_api_client/user_state.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_binary_format/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_binary_format/base_bbf_package.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_binary_format/file_in_container.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_binary_format/module_input.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_binary_format/module_output_v2.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_binary_format/remote_endpoints.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_binary_format/remote_stream_seeker.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_binary_format/saved_job.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_binary_format/stdout_and_stderr.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_binary_format/system_exception.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_binary_format/system_status_update.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_binary_format/utils.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_docker_client/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_download_container.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_errors.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/biolib_logging.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/cli/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/cli/auth.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/cli/data_record.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/cli/download_container.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/cli/init.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/cli/lfs.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/cli/push.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/cli/run.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/cli/runtime.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/cli/start.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/.gitignore +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/cloud_utils/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/cloud_utils/cloud_utils.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/job_worker/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/job_worker/cache_state.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/job_worker/cache_types.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/job_worker/docker_image_cache.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/job_worker/executors/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/job_worker/executors/docker_executor.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/job_worker/executors/docker_types.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/job_worker/executors/tars/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/job_worker/executors/types.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/job_worker/job_max_runtime_timer_thread.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/job_worker/job_storage.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/job_worker/job_worker.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/job_worker/large_file_system.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/job_worker/mappings.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/job_worker/utilization_reporter_thread.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/job_worker/utils.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/remote_host_proxy.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/socker_listener_thread.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/socket_sender_thread.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/utils.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/webserver/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/webserver/gunicorn_flask_application.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/webserver/webserver.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/webserver/webserver_types.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/webserver/webserver_utils.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/compute_node/webserver/worker_thread.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/experiments/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/experiments/experiment.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/jobs/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/jobs/job_result.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/jobs/types.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/runtime/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/sdk/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/tables.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/templates/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/templates/example_app.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/typing_utils.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/user/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/user/sign_in.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/utils/__init__.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/utils/app_uri.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/utils/cache_state.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/utils/multipart_uploader.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/utils/seq_util.py +0 -0
- {pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/utils/zip/remote_zip.py +0 -0
@@ -4,6 +4,7 @@ from pathlib import Path
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from biolib._internal.types.data_record import SqliteV1DatabaseSchema
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from biolib.api import client as api_client
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from biolib.biolib_api_client import AppGetResponse
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from biolib.biolib_api_client.biolib_app_api import _get_app_uri_from_str
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from biolib.biolib_api_client.lfs_types import DataRecordVersionInfo
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@@ -82,9 +83,11 @@ def verify_schema(specification: SqliteV1DatabaseSchema, actual_schema: SqliteV1
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def get_data_record_state_from_uri(uri) -> 'DataRecordVersionInfo':
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normalized_uri = _get_app_uri_from_str(uri)
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app_response: AppGetResponse = api_client.get(path='/app/', params={'uri': normalized_uri}).json()
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resource_uri = app_response['app_version']['app_uri']
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if app_response['app']['type'] != 'data-record':
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raise Exception(f'Resource "{
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raise Exception(f'Resource "{resource_uri}" is not a Data Record')
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return DataRecordVersionInfo(
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resource_uri=app_response['app_version']['app_uri'],
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resource_uuid=app_response['app']['public_id'],
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@@ -217,6 +217,19 @@ class Job:
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except Exception as error:
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logger.error(f'Failed to cancel job {self._uuid} due to: {error}')
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def rename(self, name: str) -> None:
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try:
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api.client.patch(
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path=f'/jobs/{self._uuid}/main_result/',
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headers={'Job-Auth-Token': self._auth_token} if self._auth_token else None,
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data={'result_name_prefix': name},
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)
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self._refetch_job_dict(force_refetch=True)
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updated_name = self.get_name()
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logger.info(f'Job {self._uuid} renamed to "{updated_name}"')
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except Exception as error:
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raise BioLibError(f'Failed to rename job {self._uuid} due to: {error}') from error
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def recompute(self, app_uri: Optional[str] = None, machine: Optional[str] = None, blocking: bool = True) -> 'Job':
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app_response = BiolibAppApi.get_by_uri(uri=app_uri or self._job_dict['app_uri'])
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{pybiolib-1.2.465.dev1 → pybiolib-1.2.497}/biolib/_internal/data_record/remote_storage_endpoint.py
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