hea-scripts 1.0.0b1__py3-none-any.whl

hea/scripts/encryption.py

@@ -0,0 +1,79 @@
+from cryptography.fernet import Fernet
+from argparse import ArgumentParser
+from hea.scripts.scriptlib import parse_hea_encryption_key, get_env_data_as_dict
+import sys
+
+ENCODING = 'utf-8'
+
+
+def main() -> None:
+    parser = ArgumentParser(description='Encrypt or decrypt data using a symmetric key. Writes to stdout. Input data is '
+                            'assumed to be UTF-8 encoded text, and output is also in UTF-8. An encryption key must be '
+                            'specified in the .env file using either the HEA_ENCRYPTION_KEY or HEA_ENCRYPTION_KEY_FILE '
+                            'properties.')
+    group = parser.add_mutually_exclusive_group(required=True)
+    group.add_argument('-e', '--encrypt', action='store_true', help='Encrypt the input data.')
+    group.add_argument('-d', '--decrypt', action='store_true', help='Decrypt the input data.')
+    parser.add_argument('-f', '--file', action='store_true', help='If provided, input is a file from which to read input.')
+    parser.add_argument('-p', '--property', help='Process a property from the .env file')
+    parser.add_argument('-o', '--output-file', help='If provided, output will be written to the specified file instead of stdout.')
+    parser.add_argument('input', help='The input data to encrypt or decrypt. If -, reads from stdin or the .env.')
+
+    args = parser.parse_args()
+
+    dot_env = get_env_data_as_dict('.env')
+
+    try:
+        key = parse_hea_encryption_key(dot_env)
+    except Exception as e:
+        print(f'Error parsing HEA encryption key: {e}', file=sys.stderr)
+        sys.exit(1)
+
+    fernet = Fernet(key)
+
+    def encrypt_data(data: str) -> str:
+        return fernet.encrypt(data.encode(ENCODING)).decode(ENCODING)
+
+    def decrypt_data(token: str) -> str:
+        return fernet.decrypt(token.encode(ENCODING)).decode(ENCODING)
+
+    if args.encrypt:
+        if args.file:
+            with open(args.input, 'r') as infile:
+                input_data = infile.read()
+        elif args.property:
+            if args.property not in dot_env:
+                print(f'Property {args.property} not found in .env file.', file=sys.stderr)
+                sys.exit(2)
+            input_data = dot_env[args.property].strip()
+        elif args.input == '-':
+            input_data = sys.stdin.readline().strip()
+        else:
+            input_data = args.input
+        result = encrypt_data(input_data)
+        if args.property:
+            result = '{crypt}' + result
+    elif args.decrypt:
+        if args.file:
+            with open(args.input, 'r') as infile:
+                token = infile.read().strip()
+        elif args.property:
+            if args.property not in dot_env:
+                print(f'Property {args.property} not found in .env file.', file=sys.stderr)
+                sys.exit(2)
+            token = dot_env[args.property].strip().removeprefix('{crypt}')
+        elif args.input == '-':
+            token = sys.stdin.readline().strip()
+        else:
+            token = args.input
+        result = decrypt_data(token)
+
+    if args.output_file:
+        with open(args.output_file, 'w') as outfile:
+            outfile.write(result)
+    else:
+        print(result)
+
+
+if __name__ == '__main__':
+    main()

hea/scripts/gen_encryption_key.py

@@ -0,0 +1,18 @@
+from cryptography.fernet import Fernet
+from argparse import ArgumentParser
+
+
+def generate_key() -> None:
+    parser = ArgumentParser(description='Generates a new symmetric key for encrypting secrets.')
+    _ = parser.parse_args()
+
+    print("Generating encryption key...")
+    print("Save this key in your .env file as HEA_ENCRYPTION_KEY to enable password encryption for stored credentials. "
+          "For better security, save the key in a file outside of the HEA directory tree called hea_encryption_key.txt. "
+          "Ensure it is only readable by the user running HEA -- for example, assuming you are the user running docker "
+          "compose, on Linux you can run 'chmod 600 <the file> after creating it.")
+    print("Key:", Fernet.generate_key().decode('utf-8'))
+
+
+if __name__ == '__main__':
+    generate_key()

hea/scripts/scriptlib.py

@@ -0,0 +1,39 @@
+from string import whitespace
+import os
+from cryptography.fernet import Fernet
+
+
+def get_env_data_as_dict(path: str) -> dict[str, str]:
+    with open(path, 'r') as f:
+        return dict((k, v.strip("'\" ")) for k, v in (line.strip().split('=', maxsplit=1) for line in f.readlines()
+                    if not line.startswith('#') and not line.startswith(tuple(w for w in whitespace))))
+
+
+def parse_hea_encryption_key(dot_env: dict[str, str]) -> bytes:
+    if 'HEA_ENCRYPTION_KEY_FILE' in os.environ:
+        path = os.path.expanduser(os.environ['HEA_ENCRYPTION_KEY_FILE'])
+        with open(path, 'rb') as key_file:
+            print('Using encryption key from file (environment variable)...')
+            return key_file.read().strip()
+    elif 'HEA_ENCRYPTION_KEY_FILE' in dot_env:
+        path = os.path.expanduser(dot_env['HEA_ENCRYPTION_KEY_FILE'])
+        with open(path, 'rb') as key_file:
+            print('Using encryption key from file...')
+            return key_file.read().strip()
+    elif result := os.environ.get('HEA_ENCRYPTION_KEY', '').encode('utf-8'):
+        print('Using encryption key from environment variable (environment variable)...')
+        return result
+    elif result := dot_env.get('HEA_ENCRYPTION_KEY', '').encode('utf-8'):
+        print('Using encryption key from environment variable...')
+        return result
+    else:
+        raise ValueError('HEA_ENCRYPTION_KEY is not set and HEA_ENCRYPTION_KEY_FILE does not exist or is empty.')
+
+
+def decrypt(encrypted_password: str, dot_env: dict[str, str]) -> str:
+    if encrypted_password.startswith('{crypt}'):
+        fernet = Fernet(parse_hea_encryption_key(dot_env))
+        print('Decrypting MongoDB password...')
+        return fernet.decrypt(encrypted_password[len('{crypt}'):]).decode('utf-8')
+    else:
+        return encrypted_password

hea_scripts-1.0.0b1.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: hea-scripts
+Version: 1.0.0b1
+Summary: A collection of scripts for the HEA project.
+Author-email: "Comprehensive Oncology Data and Engineering Shared Resource (CODE), Huntsman Cancer Institute, Salt Lake City, UT" <Andrew.Post@hci.utah.edu>
+License-Expression: Apache-2.0
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: System Administrators
+Classifier: Natural Language :: English
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Topic :: Security :: Cryptography
+Classifier: Topic :: System :: Systems Administration
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: cryptography~=44.0.0
+Provides-Extra: dev
+Requires-Dist: pytest~=8.0; extra == "dev"
+Requires-Dist: mypy~=2.1; extra == "dev"
+Requires-Dist: build~=1.5; extra == "dev"
+Requires-Dist: coverage~=7.14.1; extra == "dev"
+Requires-Dist: twine~=6.2.0; extra == "dev"
+Requires-Dist: tox~=4.55.0; extra == "dev"
+Dynamic: license-file
+
+# HEA Scripts
+
+Contains scripts for configuring a Health Enterprise Analytics (HEA) deployment. The primary scripts handle Fernet symmetric encryption of secrets stored in `.env` files.
+
+## Setup
+
+Install the package in editable mode (the dev container does this automatically):
+
+```sh
+pip install --user -e .
+```
+
+Requires Python 3.10 - 3.12.
+
+## Usage
+
+### Generate an encryption key
+
+```sh
+hea-gen-encryption-key
+```
+
+Save the printed key in your `.env` file as `HEA_ENCRYPTION_KEY`, or in a dedicated file (recommended) referenced by `HEA_ENCRYPTION_KEY_FILE`. If using a file, restrict its permissions:
+
+```sh
+chmod 600 hea_encryption_key.txt
+```
+
+### Encrypt / decrypt a value
+
+```sh
+# Encrypt a literal value
+hea-encryption --encrypt <value>
+
+# Encrypt a property already in .env (result is written to stdout with {crypt} prefix)
+hea-encryption --encrypt -p <PROPERTY_NAME>
+
+# Decrypt a token
+hea-encryption --decrypt <token>
+
+# Read input from a file
+hea-encryption --encrypt -f <file>
+hea-encryption --decrypt -f <file>
+
+# Write output to a file instead of stdout
+hea-encryption --encrypt <value> -o <output_file>
+```
+
+## Configuration
+
+Scripts expect a `.env` file in the working directory. The encryption key is resolved in this order:
+
+1. `HEA_ENCRYPTION_KEY_FILE` environment variable (path to key file)
+2. `HEA_ENCRYPTION_KEY_FILE` in `.env` (path to key file)
+3. `HEA_ENCRYPTION_KEY` environment variable (inline key)
+4. `HEA_ENCRYPTION_KEY` in `.env` (inline key)
+
+Encrypted values stored in `.env` use the format:
+
+```
+PROPERTY={crypt}<fernet-token>
+```
+
+## Contributing
+
+Install the package with the `dev` optional dependencies to get pytest:
+
+```sh
+pip install --user -e ".[dev]"
+```
+
+Run the tests:
+
+```sh
+python -m pytest tests/
+```

hea_scripts-1.0.0b1.dist-info/RECORD

@@ -0,0 +1,10 @@
+hea/scripts/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+hea/scripts/encryption.py,sha256=QfAoQIHjMutX_bIG9NzRCIZmZG9zJIZz7g066sImlTY,3220
+hea/scripts/gen_encryption_key.py,sha256=hFy9xYcYRqyjquTkVXLE-33V550gUHQLFfMMrkFomDc,826
+hea/scripts/scriptlib.py,sha256=_bgA6ttH73QOvXtoNkA5xvpjmWkbI5rP_3h___kUmDg,1827
+hea_scripts-1.0.0b1.dist-info/licenses/LICENSE,sha256=5s0P5Dl6emNknE-b82MCJdEmfRHDNk-ujPK-Hzox5ro,9630
+hea_scripts-1.0.0b1.dist-info/METADATA,sha256=cYYWn8CLuQ6Abmism6s3qWLykwclXMhd25L2UWVoSrE,3372
+hea_scripts-1.0.0b1.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+hea_scripts-1.0.0b1.dist-info/entry_points.txt,sha256=yofuRzDAsfhNR7rh5VlsTaLRCHebddxPls8H-uKE0t8,132
+hea_scripts-1.0.0b1.dist-info/top_level.txt,sha256=4wql3sEup2EE1Ix8Awo-pwQOY7jjPTACRnnm95RAw2o,4
+hea_scripts-1.0.0b1.dist-info/RECORD,,

hea_scripts-1.0.0b1.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

hea_scripts-1.0.0b1.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+hea-encryption = hea.scripts.encryption:main
+hea-gen-encryption-key = hea.scripts.gen_encryption_key:generate_key

hea_scripts-1.0.0b1.dist-info/licenses/LICENSE

@@ -0,0 +1,169 @@
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hea_scripts-1.0.0b1.dist-info/top_level.txt

@@ -0,0 +1 @@
+hea