pybiolib 1.1.929__tar.gz → 1.1.940__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 (110) hide show
  1. {pybiolib-1.1.929 → pybiolib-1.1.940}/PKG-INFO +1 -1
  2. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/api/client.py +25 -8
  3. {pybiolib-1.1.929 → pybiolib-1.1.940}/pyproject.toml +1 -1
  4. {pybiolib-1.1.929 → pybiolib-1.1.940}/LICENSE +0 -0
  5. {pybiolib-1.1.929 → pybiolib-1.1.940}/README.md +0 -0
  6. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/__init__.py +0 -0
  7. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/api/__init__.py +0 -0
  8. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/app/__init__.py +0 -0
  9. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/app/app.py +0 -0
  10. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/app/search_apps.py +0 -0
  11. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/app/utils.py +0 -0
  12. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_api_client/__init__.py +0 -0
  13. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_api_client/api_client.py +0 -0
  14. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_api_client/app_types.py +0 -0
  15. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_api_client/auth.py +0 -0
  16. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_api_client/biolib_account_api.py +0 -0
  17. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_api_client/biolib_app_api.py +0 -0
  18. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_api_client/biolib_job_api.py +0 -0
  19. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_api_client/biolib_large_file_system_api.py +0 -0
  20. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_api_client/common_types.py +0 -0
  21. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_api_client/job_types.py +0 -0
  22. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_api_client/lfs_types.py +0 -0
  23. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_api_client/user_state.py +0 -0
  24. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_binary_format/__init__.py +0 -0
  25. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_binary_format/base_bbf_package.py +0 -0
  26. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_binary_format/common_types.py +0 -0
  27. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_binary_format/encrypted_module_output.py +0 -0
  28. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_binary_format/module_input.py +0 -0
  29. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_binary_format/module_output.py +0 -0
  30. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_binary_format/rsa_encrypted_aes_package.py +0 -0
  31. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_binary_format/saved_job.py +0 -0
  32. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_binary_format/stdout_and_stderr.py +0 -0
  33. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_binary_format/system_exception.py +0 -0
  34. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_binary_format/system_status_update.py +0 -0
  35. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_binary_format/unencrypted_module_output.py +0 -0
  36. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_binary_format/utils.py +0 -0
  37. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_docker_client/__init__.py +0 -0
  38. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_errors.py +0 -0
  39. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_logging.py +0 -0
  40. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/biolib_push.py +0 -0
  41. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/cli/__init__.py +0 -0
  42. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/cli/init.py +0 -0
  43. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/cli/lfs.py +0 -0
  44. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/cli/push.py +0 -0
  45. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/cli/run.py +0 -0
  46. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/cli/runtime.py +0 -0
  47. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/cli/start.py +0 -0
  48. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/cli_utils.py +0 -0
  49. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/.gitignore +0 -0
  50. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/__init__.py +0 -0
  51. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/cloud_utils/__init__.py +0 -0
  52. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/cloud_utils/cloud_utils.py +0 -0
  53. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/__init__.py +0 -0
  54. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/cache_state.py +0 -0
  55. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/cache_types.py +0 -0
  56. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/docker_image_cache.py +0 -0
  57. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/executors/__init__.py +0 -0
  58. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/executors/base_executor.py +0 -0
  59. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/executors/docker_executor.py +0 -0
  60. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/executors/docker_types.py +0 -0
  61. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/executors/remote/__init__.py +0 -0
  62. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/executors/remote/remote_executor.py +0 -0
  63. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/executors/tars/__init__.py +0 -0
  64. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/executors/types.py +0 -0
  65. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py +0 -0
  66. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/job_max_runtime_timer_thread.py +0 -0
  67. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/job_storage.py +0 -0
  68. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/job_worker.py +0 -0
  69. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/large_file_system.py +0 -0
  70. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/mappings.py +0 -0
  71. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/job_worker/utils.py +0 -0
  72. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/remote_host_proxy.py +0 -0
  73. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/socker_listener_thread.py +0 -0
  74. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/socket_sender_thread.py +0 -0
  75. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/utils.py +0 -0
  76. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/webserver/__init__.py +0 -0
  77. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/webserver/gunicorn_flask_application.py +0 -0
  78. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/webserver/webserver.py +0 -0
  79. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/webserver/webserver_types.py +0 -0
  80. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/webserver/webserver_utils.py +0 -0
  81. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/compute_node/webserver/worker_thread.py +0 -0
  82. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/experiments/__init__.py +0 -0
  83. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/experiments/experiment.py +0 -0
  84. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/experiments/types.py +0 -0
  85. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/jobs/__init__.py +0 -0
  86. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/jobs/job.py +0 -0
  87. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/jobs/job_result.py +0 -0
  88. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/jobs/types.py +0 -0
  89. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/lfs/__init__.py +0 -0
  90. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/lfs/cache.py +0 -0
  91. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/lfs/utils.py +0 -0
  92. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/runtime/__init__.py +0 -0
  93. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/runtime/results.py +0 -0
  94. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/start_cli.py +0 -0
  95. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/tables.py +0 -0
  96. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/templates/__init__.py +0 -0
  97. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/templates/example_app.py +0 -0
  98. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/typing_utils.py +0 -0
  99. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/user/__init__.py +0 -0
  100. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/user/sign_in.py +0 -0
  101. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/utils/__init__.py +0 -0
  102. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/utils/cache_state.py +0 -0
  103. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/utils/multipart_uploader.py +0 -0
  104. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/utils/seq_util.py +0 -0
  105. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/utils/zip/remote_zip.py +0 -0
  106. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/validators/validate_app_version.py +0 -0
  107. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/validators/validate_argument.py +0 -0
  108. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/validators/validate_module.py +0 -0
  109. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/validators/validate_zip_file.py +0 -0
  110. {pybiolib-1.1.929 → pybiolib-1.1.940}/biolib/validators/validator_utils.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: pybiolib
3
- Version: 1.1.929
3
+ Version: 1.1.940
4
4
  Summary: BioLib Python Client
5
5
  Home-page: https://github.com/biolib
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  License: MIT
@@ -1,8 +1,10 @@
1
+ import time
1
2
  from urllib.parse import urljoin
2
3
 
3
4
  import requests
4
5
  from requests import Response, HTTPError
5
6
 
7
+ from biolib.biolib_logging import logger_no_user_data
6
8
  from biolib.typing_utils import Dict, Optional, Union
7
9
  from biolib.biolib_api_client import BiolibApiClient as DeprecatedApiClient
8
10
 
@@ -16,14 +18,29 @@ class ApiClient:
16
18
  headers: Optional[Dict[str, str]] = None,
17
19
  authenticate: bool = True,
18
20
  ) -> Response:
19
- response = requests.get(
20
- headers=self._get_headers(headers, authenticate),
21
- params=params,
22
- timeout=10,
23
- url=self._get_absolute_url(url),
24
- )
25
- ApiClient.raise_for_status(response)
26
- return response
21
+ retries = 5
22
+ for retry_count in range(retries):
23
+ if retry_count > 0:
24
+ time.sleep(1 * retry_count)
25
+ logger_no_user_data.debug('Retrying HTTP GET request...')
26
+ try:
27
+ response = requests.get(
28
+ headers=self._get_headers(headers, authenticate),
29
+ params=params,
30
+ timeout=10,
31
+ url=self._get_absolute_url(url),
32
+ )
33
+ if response.status_code == 502:
34
+ logger_no_user_data.debug('Got 502 status for HTTP GET')
35
+ continue
36
+
37
+ ApiClient.raise_for_status(response)
38
+ return response
39
+ except requests.exceptions.ReadTimeout:
40
+ logger_no_user_data.debug('Got read timeout of HTTP GET request')
41
+ continue
42
+
43
+ raise Exception(f'Failed to complete HTTP GET request for "{url}" after {retries} retries')
27
44
 
28
45
  def post(self, path: str, data: Dict, headers: Optional[Dict[str, str]] = None) -> Response:
29
46
  response = requests.post(
@@ -1,6 +1,6 @@
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1
  [tool.poetry]
2
2
  name = "pybiolib"
3
- version = "1.1.929"
3
+ version = "1.1.940"
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4
  description = "BioLib Python Client"
5
5
  readme = "README.md"
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6
  license = "MIT"
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