dcicutils 8.8.4.1b24__tar.gz → 8.8.4.1b26__tar.gz

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Files changed (80) hide show
  1. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/PKG-INFO +1 -1
  2. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/file_utils.py +15 -5
  3. dcicutils-8.8.4.1b26/dcicutils/http_utils.py +39 -0
  4. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/pyproject.toml +1 -1
  5. dcicutils-8.8.4.1b24/dcicutils/http_utils.py +0 -31
  6. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/LICENSE.txt +0 -0
  7. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/README.rst +0 -0
  8. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/__init__.py +0 -0
  9. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/base.py +0 -0
  10. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/beanstalk_utils.py +0 -0
  11. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/bundle_utils.py +0 -0
  12. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/captured_output.py +0 -0
  13. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/cloudformation_utils.py +0 -0
  14. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/codebuild_utils.py +0 -0
  15. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/command_utils.py +0 -0
  16. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/common.py +0 -0
  17. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/contribution_scripts.py +0 -0
  18. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/contribution_utils.py +0 -0
  19. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/creds_utils.py +0 -0
  20. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/data_readers.py +0 -0
  21. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/data_utils.py +0 -0
  22. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/datetime_utils.py +0 -0
  23. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/deployment_utils.py +0 -0
  24. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/diff_utils.py +0 -0
  25. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/docker_utils.py +0 -0
  26. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/ecr_scripts.py +0 -0
  27. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/ecr_utils.py +0 -0
  28. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/ecs_utils.py +0 -0
  29. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/env_base.py +0 -0
  30. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/env_manager.py +0 -0
  31. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/env_scripts.py +0 -0
  32. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/env_utils.py +0 -0
  33. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/env_utils_legacy.py +0 -0
  34. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/es_utils.py +0 -0
  35. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/exceptions.py +0 -0
  36. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/ff_mocks.py +0 -0
  37. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/ff_utils.py +0 -0
  38. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/function_cache_decorator.py +0 -0
  39. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/glacier_utils.py +0 -0
  40. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/jh_utils.py +0 -0
  41. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/kibana/dashboards.json +0 -0
  42. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/kibana/readme.md +0 -0
  43. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/lang_utils.py +0 -0
  44. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/license_policies/c4-infrastructure.jsonc +0 -0
  45. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/license_policies/c4-python-infrastructure.jsonc +0 -0
  46. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/license_policies/park-lab-common-server.jsonc +0 -0
  47. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/license_policies/park-lab-common.jsonc +0 -0
  48. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/license_policies/park-lab-gpl-pipeline.jsonc +0 -0
  49. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/license_policies/park-lab-pipeline.jsonc +0 -0
  50. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/license_utils.py +0 -0
  51. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/log_utils.py +0 -0
  52. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/misc_utils.py +0 -0
  53. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/obfuscation_utils.py +0 -0
  54. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/opensearch_utils.py +0 -0
  55. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/portal_object_utils.py +0 -0
  56. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/portal_utils.py +0 -0
  57. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/progress_bar.py +0 -0
  58. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/project_utils.py +0 -0
  59. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/qa_checkers.py +0 -0
  60. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/qa_utils.py +0 -0
  61. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/redis_tools.py +0 -0
  62. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/redis_utils.py +0 -0
  63. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/s3_utils.py +0 -0
  64. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/schema_utils.py +0 -0
  65. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/scripts/publish_to_pypi.py +0 -0
  66. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/scripts/run_license_checker.py +0 -0
  67. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/scripts/view_portal_object.py +0 -0
  68. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/secrets_utils.py +0 -0
  69. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/sheet_utils.py +0 -0
  70. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/snapshot_utils.py +0 -0
  71. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/ssl_certificate_utils.py +0 -0
  72. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/structured_data.py +0 -0
  73. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/submitr/progress_constants.py +0 -0
  74. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/submitr/ref_lookup_strategy.py +0 -0
  75. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/task_utils.py +0 -0
  76. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/tmpfile_utils.py +0 -0
  77. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/trace_utils.py +0 -0
  78. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/validation_utils.py +0 -0
  79. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/variant_utils.py +0 -0
  80. {dcicutils-8.8.4.1b24 → dcicutils-8.8.4.1b26}/dcicutils/zip_utils.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: dcicutils
3
- Version: 8.8.4.1b24
3
+ Version: 8.8.4.1b26
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
@@ -104,21 +104,25 @@ def normalize_path(value: Union[str, pathlib.Path], absolute: bool = False, expa
104
104
  return value
105
105
 
106
106
 
107
- def get_file_size(file: str) -> Optional[int]:
107
+ def get_file_size(file: str, raise_exception: bool = True) -> Optional[int]:
108
108
  try:
109
109
  return os.path.getsize(file) if isinstance(file, str) else None
110
110
  except Exception:
111
+ if raise_exception is True:
112
+ raise
111
113
  return None
112
114
 
113
115
 
114
- def get_file_modified_datetime(file: str) -> Optional[datetime]:
116
+ def get_file_modified_datetime(file: str, raise_exception: bool = True) -> Optional[datetime]:
115
117
  try:
116
118
  return datetime.fromtimestamp(os.path.getmtime(file)) if isinstance(file, str) else None
117
119
  except Exception:
120
+ if raise_exception is True:
121
+ raise
118
122
  return None
119
123
 
120
124
 
121
- def are_files_equal(filea: str, fileb: str) -> bool:
125
+ def are_files_equal(filea: str, fileb: str, raise_exception: bool = True) -> bool:
122
126
  """
123
127
  Returns True iff the contents of the two given files are exactly the same.
124
128
  """
@@ -135,10 +139,12 @@ def are_files_equal(filea: str, fileb: str) -> bool:
135
139
  break
136
140
  return True
137
141
  except Exception:
142
+ if raise_exception is True:
143
+ raise
138
144
  return False
139
145
 
140
146
 
141
- def compute_file_md5(file: str) -> str:
147
+ def compute_file_md5(file: str, raise_exception: bool = True) -> str:
142
148
  """
143
149
  Returns the md5 checksum for the given file.
144
150
  """
@@ -151,10 +157,12 @@ def compute_file_md5(file: str) -> str:
151
157
  md5.update(chunk)
152
158
  return md5.hexdigest()
153
159
  except Exception:
160
+ if raise_exception is True:
161
+ raise
154
162
  return ""
155
163
 
156
164
 
157
- def compute_file_etag(file: str) -> Optional[str]:
165
+ def compute_file_etag(file: str, raise_exception: bool = True) -> Optional[str]:
158
166
  """
159
167
  Returns the AWS S3 "etag" for the given file; this value is md5-like but
160
168
  not the same as a normal md5. We use this to compare that a file in S3
@@ -164,6 +172,8 @@ def compute_file_etag(file: str) -> Optional[str]:
164
172
  with io.open(file, "rb") as f:
165
173
  return _compute_file_etag(f)
166
174
  except Exception:
175
+ if raise_exception is True:
176
+ raise
167
177
  return None
168
178
 
169
179
 
@@ -0,0 +1,39 @@
1
+ from contextlib import contextmanager
2
+ import requests
3
+ from typing import Callable, Optional
4
+ from dcicutils.tmpfile_utils import temporary_file
5
+
6
+
7
+ @contextmanager
8
+ def download(url: str, suffix: Optional[str] = None, binary: bool = True,
9
+ progress: Optional[Callable] = None) -> Optional[str]:
10
+ """
11
+ Context manager to download the given URL into a temporary file and yields the file
12
+ path to it. An optional file suffix may be specified for this temporary file name.
13
+ Defaults to binary file mode; if not desired then pass False as the binary argument.
14
+ """
15
+ with temporary_file(suffix=suffix) as file:
16
+ download_to(url, file, binary=binary, progress=progress)
17
+ yield file
18
+
19
+
20
+ def download_to(url: str, file: str, binary: bool = True, progress: Optional[Callable] = None) -> None:
21
+ """
22
+ Download the given URL into the given file. Defaults to binary
23
+ file mode; if not desired then pass False as the binary argument.
24
+ """
25
+ if not callable(progress):
26
+ progress = None
27
+ response = requests.get(url, stream=True)
28
+ if progress:
29
+ nbytes = 0
30
+ nbytes_total = None
31
+ if isinstance(content_length := response.headers.get("Content-Length"), str) and content_length.isdigit():
32
+ nbytes_total = int(content_length)
33
+ with open(file, "wb" if binary is True else "w") as f:
34
+ for chunk in response.iter_content(chunk_size=8192):
35
+ if chunk:
36
+ f.write(chunk)
37
+ if progress:
38
+ nbytes += len(chunk)
39
+ progress(nbytes, nbytes_total)
@@ -1,6 +1,6 @@
1
1
  [tool.poetry]
2
2
  name = "dcicutils"
3
- version = "8.8.4.1b24" # TODO: To become 8.8.5
3
+ version = "8.8.4.1b26" # 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"
@@ -1,31 +0,0 @@
1
- from contextlib import contextmanager
2
- import requests
3
- from typing import Callable, Optional
4
- from dcicutils.tmpfile_utils import temporary_file
5
-
6
-
7
- @contextmanager
8
- def download(url: str, suffix: Optional[str] = None, binary: bool = True,
9
- progress: Optional[Callable] = None) -> Optional[str]:
10
- """
11
- Context manager to ownload the given URL into a temporary file and yields the file
12
- path to it. An optional file suffix may be specified. Defaults to binary file mode;
13
- if this is not desired then pass False as the binary argument.
14
- """
15
- if not callable(progress):
16
- progress = None
17
- with temporary_file(suffix=suffix) as file:
18
- response = requests.get(url, stream=True)
19
- if progress:
20
- nbytes = 0
21
- nbytes_total = None
22
- if isinstance(content_length := response.headers.get("Content-Length"), str) and content_length.isdigit():
23
- nbytes_total = int(content_length)
24
- with open(file, "wb" if binary is True else "w") as f:
25
- for chunk in response.iter_content(chunk_size=8192):
26
- if chunk:
27
- f.write(chunk)
28
- if progress:
29
- nbytes += len(chunk)
30
- progress(nbytes, nbytes_total)
31
- yield file