pybiolib 1.2.205__tar.gz → 1.2.211__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-1.2.205 → pybiolib-1.2.211}/PKG-INFO +1 -1
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/executors/docker_executor.py +4 -3
- {pybiolib-1.2.205 → pybiolib-1.2.211}/pyproject.toml +1 -1
- {pybiolib-1.2.205 → pybiolib-1.2.211}/LICENSE +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/PYPI_README.md +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_data_record/data_record.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/data_record/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/data_record/data_record.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/data_record/push_data.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/data_record/remote_storage_endpoint.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/file_utils.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/fuse_mount/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/fuse_mount/experiment_fuse_mount.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/http_client.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/lfs/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/lfs/cache.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/libs/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/libs/fusepy/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/push_application.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/runtime.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/types/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/types/app.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/types/data_record.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/types/experiment.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/types/file_node.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/types/resource.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/types/resource_version.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/types/typing.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/utils/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/utils/multinode.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_runtime/runtime.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/api/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/api/client.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/app/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/app/app.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/app/search_apps.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_api_client/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_api_client/api_client.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_api_client/app_types.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_api_client/auth.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_api_client/biolib_app_api.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_api_client/biolib_job_api.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_api_client/common_types.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_api_client/job_types.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_api_client/lfs_types.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_api_client/user_state.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_binary_format/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_binary_format/base_bbf_package.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_binary_format/file_in_container.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_binary_format/module_input.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_binary_format/module_output_v2.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_binary_format/remote_endpoints.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_binary_format/remote_stream_seeker.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_binary_format/saved_job.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_binary_format/stdout_and_stderr.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_binary_format/system_exception.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_binary_format/system_status_update.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_binary_format/utils.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_docker_client/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_download_container.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_errors.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/biolib_logging.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/cli/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/cli/auth.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/cli/data_record.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/cli/download_container.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/cli/init.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/cli/lfs.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/cli/push.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/cli/run.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/cli/runtime.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/cli/start.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/.gitignore +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/cloud_utils/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/cloud_utils/cloud_utils.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/cache_state.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/cache_types.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/docker_image_cache.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/executors/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/executors/docker_types.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/executors/tars/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/executors/types.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/job_max_runtime_timer_thread.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/job_storage.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/job_worker.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/large_file_system.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/mappings.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/utilization_reporter_thread.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/utils.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/remote_host_proxy.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/socker_listener_thread.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/socket_sender_thread.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/utils.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/webserver/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/webserver/gunicorn_flask_application.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/webserver/webserver.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/webserver/webserver_types.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/webserver/webserver_utils.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/webserver/worker_thread.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/experiments/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/experiments/experiment.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/jobs/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/jobs/job.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/jobs/job_result.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/jobs/types.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/runtime/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/sdk/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/tables.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/templates/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/templates/example_app.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/typing_utils.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/user/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/user/sign_in.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/utils/__init__.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/utils/app_uri.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/utils/cache_state.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/utils/multipart_uploader.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/utils/seq_util.py +0 -0
- {pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/utils/zip/remote_zip.py +0 -0
{pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/executors/docker_executor.py
RENAMED
@@ -41,9 +41,6 @@ class DockerExecutor:
|
|
41
41
|
self._is_cleaning_up = False
|
42
42
|
|
43
43
|
self._absolute_image_uri = f"{utils.BIOLIB_SITE_HOSTNAME}/{self._options['module']['image_uri']}"
|
44
|
-
if self._options['job'].get('federated_job_uuid'):
|
45
|
-
self._absolute_image_uri = self._options['module']['absolute_image_uri']
|
46
|
-
|
47
44
|
self._send_system_exception = options['send_system_exception']
|
48
45
|
self._send_stdout_and_stderr = options['send_stdout_and_stderr']
|
49
46
|
self._random_docker_id = compute_node_utils.random_string(15)
|
@@ -501,6 +498,10 @@ class DockerExecutor:
|
|
501
498
|
stdout=stdout,
|
502
499
|
)
|
503
500
|
except Exception as exception:
|
501
|
+
logger.error("Hit Error 23")
|
502
|
+
logger.exception("Error")
|
503
|
+
logger.error(str(exception))
|
504
|
+
time.sleep(3)
|
504
505
|
raise ComputeProcessException(
|
505
506
|
exception,
|
506
507
|
SystemExceptionCodes.FAILED_TO_SERIALIZE_AND_SEND_MODULE_OUTPUT.value,
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
{pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/_internal/data_record/remote_storage_endpoint.py
RENAMED
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
{pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/executors/docker_types.py
RENAMED
File without changes
|
{pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/executors/tars/__init__.py
RENAMED
File without changes
|
File without changes
|
File without changes
|
{pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/job_max_runtime_timer_thread.py
RENAMED
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
{pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/job_worker/utilization_reporter_thread.py
RENAMED
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
{pybiolib-1.2.205 → pybiolib-1.2.211}/biolib/compute_node/webserver/gunicorn_flask_application.py
RENAMED
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|
File without changes
|