dcicutils 8.8.4.1b19__tar.gz → 8.8.4.1b21__tar.gz

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Files changed (79) hide show
  1. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/PKG-INFO +1 -1
  2. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/file_utils.py +38 -17
  3. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/misc_utils.py +13 -0
  4. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/pyproject.toml +1 -1
  5. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/LICENSE.txt +0 -0
  6. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/README.rst +0 -0
  7. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/__init__.py +0 -0
  8. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/base.py +0 -0
  9. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/beanstalk_utils.py +0 -0
  10. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/bundle_utils.py +0 -0
  11. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/captured_output.py +0 -0
  12. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/cloudformation_utils.py +0 -0
  13. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/codebuild_utils.py +0 -0
  14. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/command_utils.py +0 -0
  15. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/common.py +0 -0
  16. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/contribution_scripts.py +0 -0
  17. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/contribution_utils.py +0 -0
  18. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/creds_utils.py +0 -0
  19. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/data_readers.py +0 -0
  20. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/data_utils.py +0 -0
  21. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/datetime_utils.py +0 -0
  22. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/deployment_utils.py +0 -0
  23. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/diff_utils.py +0 -0
  24. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/docker_utils.py +0 -0
  25. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/ecr_scripts.py +0 -0
  26. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/ecr_utils.py +0 -0
  27. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/ecs_utils.py +0 -0
  28. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/env_base.py +0 -0
  29. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/env_manager.py +0 -0
  30. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/env_scripts.py +0 -0
  31. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/env_utils.py +0 -0
  32. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/env_utils_legacy.py +0 -0
  33. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/es_utils.py +0 -0
  34. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/exceptions.py +0 -0
  35. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/ff_mocks.py +0 -0
  36. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/ff_utils.py +0 -0
  37. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/function_cache_decorator.py +0 -0
  38. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/glacier_utils.py +0 -0
  39. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/http_utils.py +0 -0
  40. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/jh_utils.py +0 -0
  41. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/kibana/dashboards.json +0 -0
  42. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/kibana/readme.md +0 -0
  43. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/lang_utils.py +0 -0
  44. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/license_policies/c4-infrastructure.jsonc +0 -0
  45. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/license_policies/c4-python-infrastructure.jsonc +0 -0
  46. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/license_policies/park-lab-common-server.jsonc +0 -0
  47. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/license_policies/park-lab-common.jsonc +0 -0
  48. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/license_policies/park-lab-gpl-pipeline.jsonc +0 -0
  49. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/license_policies/park-lab-pipeline.jsonc +0 -0
  50. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/license_utils.py +0 -0
  51. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/log_utils.py +0 -0
  52. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/obfuscation_utils.py +0 -0
  53. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/opensearch_utils.py +0 -0
  54. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/portal_object_utils.py +0 -0
  55. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/portal_utils.py +0 -0
  56. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/progress_bar.py +0 -0
  57. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/project_utils.py +0 -0
  58. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/qa_checkers.py +0 -0
  59. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/qa_utils.py +0 -0
  60. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/redis_tools.py +0 -0
  61. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/redis_utils.py +0 -0
  62. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/s3_utils.py +0 -0
  63. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/schema_utils.py +0 -0
  64. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/scripts/publish_to_pypi.py +0 -0
  65. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/scripts/run_license_checker.py +0 -0
  66. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/scripts/view_portal_object.py +0 -0
  67. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/secrets_utils.py +0 -0
  68. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/sheet_utils.py +0 -0
  69. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/snapshot_utils.py +0 -0
  70. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/ssl_certificate_utils.py +0 -0
  71. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/structured_data.py +0 -0
  72. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/submitr/progress_constants.py +0 -0
  73. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/submitr/ref_lookup_strategy.py +0 -0
  74. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/task_utils.py +0 -0
  75. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/tmpfile_utils.py +0 -0
  76. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/trace_utils.py +0 -0
  77. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/validation_utils.py +0 -0
  78. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/variant_utils.py +0 -0
  79. {dcicutils-8.8.4.1b19 → dcicutils-8.8.4.1b21}/dcicutils/zip_utils.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: dcicutils
3
- Version: 8.8.4.1b19
3
+ Version: 8.8.4.1b21
4
4
  Summary: Utility package for interacting with the 4DN Data Portal and other 4DN resources
5
5
  Home-page: https://github.com/4dn-dcic/utils
6
6
  License: MIT
@@ -10,6 +10,8 @@ from tempfile import gettempdir as get_temporary_directory
10
10
  from typing import List, Optional, Union
11
11
  from uuid import uuid4 as uuid
12
12
 
13
+ HOME_DIRECTORY = str(pathlib.Path().home())
14
+
13
15
 
14
16
  def search_for_file(file: str,
15
17
  location: Union[str, Optional[List[str]]] = None,
@@ -44,7 +46,7 @@ def search_for_file(file: str,
44
46
  directory = str(directory)
45
47
  if not (directory := directory.strip()):
46
48
  continue
47
- if os.path.isfile(directory := os.path.normpath(directory)):
49
+ if os.path.isfile(directory := os.path.abspath(os.path.normpath(directory))):
48
50
  # Allow a file; assume its parent directory was intended.
49
51
  if not (directory := os.path.dirname(directory)):
50
52
  continue
@@ -77,24 +79,43 @@ def search_for_file(file: str,
77
79
  return None if single is True else []
78
80
 
79
81
 
80
- def normalize_file_path(path: str, home_directory: bool = True) -> str:
82
+ def normalize_path(value: Union[str, pathlib.Path], absolute: bool = False, home: Optional[bool] = None) -> str:
81
83
  """
82
- Normalizes the given file path name and returns. Does things like remove multiple
83
- consecutive slashes and redundant/unnecessary parent paths; if the home_directory
84
- argument is True (the default) then also handles the special tilde home directory
85
- component/convention and uses this in the result if applicable.
84
+ Normalizes the given path value and returns the result; does things like remove redundant
85
+ consecutive directory separators and redundant parent paths. If the given absolute argument
86
+ is True than converts the path to an absolute path. If the given home argument is True and
87
+ if the path can reasonably be represented with a home directory indicator (i.e. "~"), then
88
+ converts it to such. If the home argument is False and path starts with the home directory
89
+ indicator then expands it to the actual (absolute) home path. If the given value is not
90
+ actually even a string (or pathlib.Path) then returns an empty string.
86
91
  """
87
- if not isinstance(path, str) or not path:
88
- path = os.getcwd()
89
- path = os.path.normpath(path)
90
- home_directory = os.path.expanduser("~") if home_directory is True else None
91
- if home_directory and path.startswith("~"):
92
- path = os.path.join(home_directory, path[2 if path.startswith("~/") else 1:])
93
- path = os.path.abspath(path)
94
- if home_directory and (os.name == "posix"):
95
- if path.startswith(home_directory) and path != home_directory:
96
- path = "~/" + pathlib.Path(path).relative_to(home_directory).as_posix()
97
- return path
92
+ if isinstance(value, pathlib.Path):
93
+ value = str(value)
94
+ elif not isinstance(value, str):
95
+ return ""
96
+ if not (value := value.strip()) or not (value := os.path.normpath(value)):
97
+ return ""
98
+ if home is False:
99
+ value = os.path.expanduser(value)
100
+ elif (home is True) and (os.name == "posix") and value.startswith(home := HOME_DIRECTORY + os.sep):
101
+ value = "~/" + value[len(home):]
102
+ if absolute is True:
103
+ value = os.path.abspath(value)
104
+ return value
105
+
106
+
107
+ def get_file_size(file: str) -> Optional[int]:
108
+ try:
109
+ return os.path.getsize(file) if isinstance(file, str) else None
110
+ except Exception:
111
+ return None
112
+
113
+
114
+ def get_file_modified_datetime(file: str) -> Optional[datetime]:
115
+ try:
116
+ return datetime.fromtimestamp(os.path.getmtime(file)) if isinstance(file, str) else None
117
+ except Exception:
118
+ return None
98
119
 
99
120
 
100
121
  def are_files_equal(filea: str, fileb: str) -> bool:
@@ -2551,6 +2551,19 @@ def normalize_spaces(value: str) -> str:
2551
2551
  return re.sub(r"\s+", " ", value).strip()
2552
2552
 
2553
2553
 
2554
+ def normalize_string(value: Optional[str]) -> Optional[str]:
2555
+ """
2556
+ Strips leading/trailing spaces, and converts multiple consecutive spaces to a single space
2557
+ in the given string value and returns the result. If the given value is None returns an
2558
+ empty string. If the given value is not actually even a string then return None.
2559
+ """
2560
+ if value is None:
2561
+ return ""
2562
+ elif isinstance(value, str):
2563
+ return value.strip()
2564
+ return None
2565
+
2566
+
2554
2567
  def find_nth_from_end(string: str, substring: str, nth: int) -> int:
2555
2568
  """
2556
2569
  Returns the index of the nth occurrence of the given substring within
@@ -1,6 +1,6 @@
1
1
  [tool.poetry]
2
2
  name = "dcicutils"
3
- version = "8.8.4.1b19" # TODO: To become 8.8.5
3
+ version = "8.8.4.1b21" # TODO: To become 8.8.5
4
4
  description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
5
5
  authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
6
6
  license = "MIT"