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.
Files changed (100) hide show
  1. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/PKG-INFO +1 -1
  2. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/jobs/job.py +17 -26
  3. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/pyproject.toml +1 -1
  4. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/LICENSE +0 -0
  5. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/README.md +0 -0
  6. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/__init__.py +0 -0
  7. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/api/__init__.py +0 -0
  8. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/api/client.py +0 -0
  9. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/app/__init__.py +0 -0
  10. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/app/app.py +0 -0
  11. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/app/search_apps.py +0 -0
  12. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/__init__.py +0 -0
  13. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/api_client.py +0 -0
  14. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/app_types.py +0 -0
  15. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/auth.py +0 -0
  16. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/biolib_account_api.py +0 -0
  17. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/biolib_app_api.py +0 -0
  18. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/biolib_job_api.py +0 -0
  19. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/biolib_large_file_system_api.py +0 -0
  20. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/common_types.py +0 -0
  21. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/job_types.py +0 -0
  22. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/lfs_types.py +0 -0
  23. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_api_client/user_state.py +0 -0
  24. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/__init__.py +0 -0
  25. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/base_bbf_package.py +0 -0
  26. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/file_in_container.py +0 -0
  27. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/module_input.py +0 -0
  28. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/module_output_v2.py +0 -0
  29. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/remote_endpoints.py +0 -0
  30. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/remote_stream_seeker.py +0 -0
  31. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/saved_job.py +0 -0
  32. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/stdout_and_stderr.py +0 -0
  33. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/system_exception.py +0 -0
  34. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/system_status_update.py +0 -0
  35. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_binary_format/utils.py +0 -0
  36. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_docker_client/__init__.py +0 -0
  37. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_errors.py +0 -0
  38. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_logging.py +0 -0
  39. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/biolib_push.py +0 -0
  40. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/cli/__init__.py +0 -0
  41. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/cli/init.py +0 -0
  42. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/cli/lfs.py +0 -0
  43. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/cli/push.py +0 -0
  44. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/cli/run.py +0 -0
  45. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/cli/runtime.py +0 -0
  46. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/cli/start.py +0 -0
  47. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/.gitignore +0 -0
  48. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/__init__.py +0 -0
  49. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/cloud_utils/__init__.py +0 -0
  50. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/cloud_utils/cloud_utils.py +0 -0
  51. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/__init__.py +0 -0
  52. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/cache_state.py +0 -0
  53. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/cache_types.py +0 -0
  54. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/docker_image_cache.py +0 -0
  55. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/executors/__init__.py +0 -0
  56. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/executors/docker_executor.py +0 -0
  57. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/executors/docker_types.py +0 -0
  58. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/executors/tars/__init__.py +0 -0
  59. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/executors/types.py +0 -0
  60. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py +0 -0
  61. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/job_max_runtime_timer_thread.py +0 -0
  62. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/job_storage.py +0 -0
  63. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/job_worker.py +0 -0
  64. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/large_file_system.py +0 -0
  65. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/mappings.py +0 -0
  66. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/utilization_reporter_thread.py +0 -0
  67. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/job_worker/utils.py +0 -0
  68. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/remote_host_proxy.py +0 -0
  69. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/socker_listener_thread.py +0 -0
  70. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/socket_sender_thread.py +0 -0
  71. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/utils.py +0 -0
  72. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/webserver/__init__.py +0 -0
  73. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/webserver/gunicorn_flask_application.py +0 -0
  74. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/webserver/webserver.py +0 -0
  75. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/webserver/webserver_types.py +0 -0
  76. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/webserver/webserver_utils.py +0 -0
  77. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/compute_node/webserver/worker_thread.py +0 -0
  78. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/experiments/__init__.py +0 -0
  79. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/experiments/experiment.py +0 -0
  80. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/experiments/types.py +0 -0
  81. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/jobs/__init__.py +0 -0
  82. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/jobs/job_result.py +0 -0
  83. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/jobs/types.py +0 -0
  84. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/lfs/__init__.py +0 -0
  85. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/lfs/cache.py +0 -0
  86. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/lfs/utils.py +0 -0
  87. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/runtime/__init__.py +0 -0
  88. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/runtime/results.py +0 -0
  89. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/tables.py +0 -0
  90. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/templates/__init__.py +0 -0
  91. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/templates/example_app.py +0 -0
  92. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/typing_utils.py +0 -0
  93. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/user/__init__.py +0 -0
  94. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/user/sign_in.py +0 -0
  95. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/utils/__init__.py +0 -0
  96. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/utils/app_uri.py +0 -0
  97. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/utils/cache_state.py +0 -0
  98. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/utils/multipart_uploader.py +0 -0
  99. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/utils/seq_util.py +0 -0
  100. {pybiolib-1.1.1418 → pybiolib-1.1.1420}/biolib/utils/zip/remote_zip.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: pybiolib
3
- Version: 1.1.1418
3
+ Version: 1.1.1420
4
4
  Summary: BioLib Python Client
5
5
  Home-page: https://github.com/biolib
6
6
  License: MIT
@@ -37,7 +37,7 @@ class Job:
37
37
  self._job_dict: JobDict = job_dict
38
38
  self._job_dict_last_fetched_at: datetime = datetime.utcnow()
39
39
  self._result: Optional[JobResult] = None
40
- self._module_input_dict: Optional[ModuleInputDict] = None
40
+ self._cached_input_arguments: Optional[List[str]] = None
41
41
 
42
42
  def __str__(self):
43
43
  return f"Job for {self._job_dict['app_uri']} created at {self._job_dict['created_at']} ({self._uuid})"
@@ -116,33 +116,24 @@ class Job:
116
116
  return self.result.get_exit_code()
117
117
 
118
118
  def _get_module_input(self) -> ModuleInputDict:
119
- if not self._module_input_dict:
120
- self._refetch_job_dict()
121
- try:
122
- presigned_download_url = BiolibJobApi.get_job_storage_download_url(
123
- job_uuid=self._job_dict['uuid'],
124
- job_auth_token=self._job_dict['auth_token'],
125
- storage_type='input',
126
- )
127
- response = requests.get(url=presigned_download_url)
128
- response.raise_for_status()
129
- module_input_serialized: bytes = response.content
130
- except Exception as error:
131
- # TODO: Improve error handling and messages
132
- raise error
133
-
134
- try:
135
- self._module_input_dict = ModuleInput(module_input_serialized).deserialize()
136
- except Exception as error:
137
- # TODO: Improve error handling and messages
138
- raise error
139
-
140
- return self._module_input_dict
119
+ self._refetch_job_dict()
120
+ presigned_download_url = BiolibJobApi.get_job_storage_download_url(
121
+ job_uuid=self._job_dict['uuid'],
122
+ job_auth_token=self._job_dict['auth_token'],
123
+ storage_type='input',
124
+ )
125
+ response = requests.get(url=presigned_download_url)
126
+ response.raise_for_status()
127
+ module_input_serialized: bytes = response.content
128
+ return ModuleInput(module_input_serialized).deserialize()
141
129
 
142
130
  def get_input_arguments(self) -> List[str]:
143
- logger.debug('Getting input arguments...')
144
- module_input = self._get_module_input()
145
- return module_input['arguments']
131
+ if self._cached_input_arguments is None:
132
+ logger.debug('Fetching input arguments...')
133
+ module_input = self._get_module_input()
134
+ self._cached_input_arguments = module_input['arguments']
135
+
136
+ return self._cached_input_arguments
146
137
 
147
138
  def save_input_files(self, output_dir: str) -> None:
148
139
  logger.info('Downloading input files...')
@@ -1,6 +1,6 @@
1
1
  [tool.poetry]
2
2
  name = "pybiolib"
3
- version = "1.1.1418"
3
+ version = "1.1.1420"
4
4
  description = "BioLib Python Client"
5
5
  readme = "README.md"
6
6
  license = "MIT"
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