pybiolib 1.1.1007__tar.gz → 1.1.1011__tar.gz

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Files changed (111) hide show
  1. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/PKG-INFO +1 -1
  2. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/utils/cache_state.py +9 -9
  3. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/pyproject.toml +1 -1
  4. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/LICENSE +0 -0
  5. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/README.md +0 -0
  6. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/__init__.py +0 -0
  7. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/api/__init__.py +0 -0
  8. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/api/client.py +0 -0
  9. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/app/__init__.py +0 -0
  10. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/app/app.py +0 -0
  11. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/app/search_apps.py +0 -0
  12. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/app/utils.py +0 -0
  13. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_api_client/__init__.py +0 -0
  14. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_api_client/api_client.py +0 -0
  15. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_api_client/app_types.py +0 -0
  16. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_api_client/auth.py +0 -0
  17. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_api_client/biolib_account_api.py +0 -0
  18. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_api_client/biolib_app_api.py +0 -0
  19. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_api_client/biolib_job_api.py +0 -0
  20. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_api_client/biolib_large_file_system_api.py +0 -0
  21. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_api_client/common_types.py +0 -0
  22. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_api_client/job_types.py +0 -0
  23. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_api_client/lfs_types.py +0 -0
  24. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_api_client/user_state.py +0 -0
  25. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_binary_format/__init__.py +0 -0
  26. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_binary_format/base_bbf_package.py +0 -0
  27. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_binary_format/common_types.py +0 -0
  28. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_binary_format/encrypted_module_output.py +0 -0
  29. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_binary_format/module_input.py +0 -0
  30. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_binary_format/module_output.py +0 -0
  31. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_binary_format/remote_endpoints.py +0 -0
  32. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_binary_format/rsa_encrypted_aes_package.py +0 -0
  33. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_binary_format/saved_job.py +0 -0
  34. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_binary_format/stdout_and_stderr.py +0 -0
  35. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_binary_format/system_exception.py +0 -0
  36. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_binary_format/system_status_update.py +0 -0
  37. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_binary_format/unencrypted_module_output.py +0 -0
  38. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_binary_format/utils.py +0 -0
  39. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_docker_client/__init__.py +0 -0
  40. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_errors.py +0 -0
  41. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_logging.py +0 -0
  42. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/biolib_push.py +0 -0
  43. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/cli/__init__.py +0 -0
  44. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/cli/init.py +0 -0
  45. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/cli/lfs.py +0 -0
  46. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/cli/push.py +0 -0
  47. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/cli/run.py +0 -0
  48. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/cli/runtime.py +0 -0
  49. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/cli/start.py +0 -0
  50. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/cli_utils.py +0 -0
  51. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/.gitignore +0 -0
  52. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/__init__.py +0 -0
  53. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/cloud_utils/__init__.py +0 -0
  54. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/cloud_utils/cloud_utils.py +0 -0
  55. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/__init__.py +0 -0
  56. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/cache_state.py +0 -0
  57. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/cache_types.py +0 -0
  58. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/docker_image_cache.py +0 -0
  59. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/executors/__init__.py +0 -0
  60. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/executors/base_executor.py +0 -0
  61. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/executors/docker_executor.py +0 -0
  62. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/executors/docker_types.py +0 -0
  63. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/executors/remote/__init__.py +0 -0
  64. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/executors/remote/remote_executor.py +0 -0
  65. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/executors/tars/__init__.py +0 -0
  66. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/executors/types.py +0 -0
  67. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py +0 -0
  68. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/job_max_runtime_timer_thread.py +0 -0
  69. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/job_storage.py +0 -0
  70. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/job_worker.py +0 -0
  71. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/large_file_system.py +0 -0
  72. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/mappings.py +0 -0
  73. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/job_worker/utils.py +0 -0
  74. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/remote_host_proxy.py +0 -0
  75. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/socker_listener_thread.py +0 -0
  76. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/socket_sender_thread.py +0 -0
  77. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/utils.py +0 -0
  78. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/webserver/__init__.py +0 -0
  79. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/webserver/gunicorn_flask_application.py +0 -0
  80. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/webserver/webserver.py +0 -0
  81. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/webserver/webserver_types.py +0 -0
  82. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/webserver/webserver_utils.py +0 -0
  83. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/compute_node/webserver/worker_thread.py +0 -0
  84. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/experiments/__init__.py +0 -0
  85. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/experiments/experiment.py +0 -0
  86. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/experiments/types.py +0 -0
  87. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/jobs/__init__.py +0 -0
  88. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/jobs/job.py +0 -0
  89. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/jobs/job_result.py +0 -0
  90. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/jobs/types.py +0 -0
  91. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/lfs/__init__.py +0 -0
  92. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/lfs/cache.py +0 -0
  93. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/lfs/utils.py +0 -0
  94. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/runtime/__init__.py +0 -0
  95. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/runtime/results.py +0 -0
  96. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/start_cli.py +0 -0
  97. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/tables.py +0 -0
  98. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/templates/__init__.py +0 -0
  99. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/templates/example_app.py +0 -0
  100. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/typing_utils.py +0 -0
  101. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/user/__init__.py +0 -0
  102. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/user/sign_in.py +0 -0
  103. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/utils/__init__.py +0 -0
  104. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/utils/multipart_uploader.py +0 -0
  105. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/utils/seq_util.py +0 -0
  106. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/utils/zip/remote_zip.py +0 -0
  107. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/validators/validate_app_version.py +0 -0
  108. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/validators/validate_argument.py +0 -0
  109. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/validators/validate_module.py +0 -0
  110. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/validators/validate_zip_file.py +0 -0
  111. {pybiolib-1.1.1007 → pybiolib-1.1.1011}/biolib/validators/validator_utils.py +0 -0
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: pybiolib
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- Version: 1.1.1007
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+ Version: 1.1.1011
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  Summary: BioLib Python Client
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  Home-page: https://github.com/biolib
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  License: MIT
@@ -68,17 +68,17 @@ class CacheState(abc.ABC, Generic[StateType]):
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  logger_no_user_data.debug(f'CacheState: Exited state path: {self._state_path}')
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70
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  def _acquire_state_lock(self) -> None:
71
- timeout_seconds = 5.0
72
- seconds_to_sleep = 0.5
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+ for _ in range(10):
72
+ try:
73
+ lock_file = open(self._state_lock_path, mode='x')
74
+ lock_file.close()
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+ return
76
+ except BaseException as error: # pylint: disable=broad-except
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+ logger_no_user_data.debug(f'Failed to acquire lock file "{self._state_lock_path}". Got error: {error}')
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74
- while os.path.exists(self._state_lock_path):
75
- time.sleep(seconds_to_sleep)
76
- timeout_seconds -= seconds_to_sleep
77
- if timeout_seconds < 0:
78
- raise CacheStateError('Cache state timed out waiting for lock file')
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+ time.sleep(0.5)
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80
- lock_file = open(self._state_lock_path, mode='x')
81
- lock_file.close()
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+ raise CacheStateError(f'Cache state timed out waiting to acquire lock file "{self._state_lock_path}"')
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83
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  def _release_state_lock(self) -> None:
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  if os.path.exists(self._state_lock_path):
@@ -1,6 +1,6 @@
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  [tool.poetry]
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  name = "pybiolib"
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- version = "1.1.1007"
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+ version = "1.1.1011"
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  description = "BioLib Python Client"
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  readme = "README.md"
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  license = "MIT"
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