opencloning 0.3.7__py3-none-any.whl → 0.3.8__py3-none-any.whl

opencloning/app_settings.py

@@ -31,6 +31,25 @@ if PLANNOTATE_URL is not None and not PLANNOTATE_URL.endswith('/'):
 PROXY_URL = os.environ.get('PROXY_URL')
 PROXY_CERT_FILE = os.environ.get('PROXY_CERT_FILE')
 
+# Allowed external URLs ===========================================
+default_allowed_urls = [
+    'https://www.addgene.org/',
+    'https://media.addgene.org/',
+    'https://seva-plasmids.com/',
+    'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/',
+    'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/',
+    'https://www.snapgene.com/local/fetch.php',
+    'https://benchling.com/',
+    'https://assets.opencloning.org/annotated-igem-distribution',
+    'http://www.euroscarf.de/',
+    'https://wekwikgene.wllsb.edu.cn',
+]
+
+if os.environ.get('ALLOWED_EXTERNAL_URLS') is not None:
+    ALLOWED_EXTERNAL_URLS = os.environ['ALLOWED_EXTERNAL_URLS'].split(',')
+else:
+    ALLOWED_EXTERNAL_URLS = default_allowed_urls
+
 
 class Settings(BaseModel):
     SERVE_FRONTEND: bool
@@ -43,6 +62,8 @@ class Settings(BaseModel):
     PROXY_URL: str | None
     # Must be a full path to the proxy certificate file
     PROXY_CERT_FILE: str | None
+    # Allowed external URLs
+    ALLOWED_EXTERNAL_URLS: list[str]
 
 
 settings = Settings(
@@ -55,4 +76,5 @@ settings = Settings(
     PLANNOTATE_TIMEOUT=PLANNOTATE_TIMEOUT,
     PROXY_URL=PROXY_URL,
     PROXY_CERT_FILE=PROXY_CERT_FILE,
+    ALLOWED_EXTERNAL_URLS=ALLOWED_EXTERNAL_URLS,
 )

opencloning/endpoints/external_import.py

@@ -216,6 +216,11 @@ def repository_id_http_error_handler(exception: HTTPError, source: RepositoryIdS
             404,
             f'{source.repository_name} returned: {exception} - Likely you inserted a wrong {source.repository_name} id',
         )
+    elif exception.code == 403:
+        raise HTTPException(
+            403,
+            f'Request to {source.repository_name} is not allowed. Please check that the URL is whitelisted.',
+        )
 
 
 # Redirect to the right repository

opencloning/http_client.py

@@ -6,36 +6,24 @@ from httpx import (  # noqa: F401
     TimeoutException,
     AsyncHTTPTransport,
     Request,
-    RequestError,
 )
+from urllib.error import HTTPError
 import ssl
 import certifi
 from .app_settings import settings
-import re
-
-white_listed_urls = {
-    r'^https://www.addgene.org/',
-    r'^https://media.addgene.org/',
-    r'^https://wekwikgene.wllsb.edu.cn',
-    r'^https://seva-plasmids.com/',
-    r'^https://api.ncbi.nlm.nih.gov/datasets/v2alpha/',
-    r'^https://eutils.ncbi.nlm.nih.gov/entrez/eutils/',
-    r'^https://www.snapgene.com/local/fetch.php',
-    r'^https://benchling.com/',
-    r'^https://assets.opencloning.org/annotated-igem-distribution',
-    r'^http://www.euroscarf.de/',
-}
+
+allowed_external_urls = settings.ALLOWED_EXTERNAL_URLS
 
 if settings.PLANNOTATE_URL:
-    white_listed_urls.add(settings.PLANNOTATE_URL)
+    allowed_external_urls.append(settings.PLANNOTATE_URL)
 
 
-class WhiteListTransport(AsyncHTTPTransport):
+class AllowedExternalUrlsTransport(AsyncHTTPTransport):
     async def handle_async_request(self, request: Request) -> Response:
-        if any(re.match(url, str(request.url)) for url in white_listed_urls):
+        if any(str(request.url).startswith(url) for url in allowed_external_urls):
             return await super().handle_async_request(request)
 
-        raise RequestError(f'Request to {request.url} is not whitelisted')
+        raise HTTPError(request.url, 403, f'Request to {request.url} is not allowed', None, None)
 
 
 proxy = None
@@ -44,7 +32,7 @@ if settings.PROXY_URL:
 
 
 def get_http_client():
-    transport = WhiteListTransport()
+    transport = AllowedExternalUrlsTransport()
     client_ctx = None
     if proxy is not None:
         client_ctx = ssl.create_default_context(cafile=certifi.where())

{opencloning-0.3.7.dist-info → opencloning-0.3.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: opencloning
-Version: 0.3.7
+Version: 0.3.8
 Summary: Backend of OpenCloning, a web application to generate molecular cloning strategies in json format, and share them with others.
 License: MIT
 Author: Manuel Lera-Ramirez
@@ -19,7 +19,7 @@ Requires-Dist: opencloning-linkml (==0.3.0a0)
 Requires-Dist: openpyxl (>=3.1.5,<4.0.0)
 Requires-Dist: packaging (>=25.0,<26.0)
 Requires-Dist: pandas (>=2.2.3,<3.0.0)
-Requires-Dist: primer3-py (==2.0.3)
+Requires-Dist: primer3-py (==2.2.0)
 Requires-Dist: pydantic (>=2.7.1,<3.0.0)
 Requires-Dist: pydna (==5.5.0)
 Requires-Dist: python-multipart
@@ -86,8 +86,8 @@ poetry install
 # Install the pre-commit hooks
 pre-commit install
 
-# Activate the virtual environment
-poetry shell
+# Activate the virtual environment (used to be `poetry shell`)
+poetry env activate
 
 ```
 

{opencloning-0.3.7.dist-info → opencloning-0.3.8.dist-info}/RECORD

@@ -1,7 +1,7 @@
 opencloning/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 opencloning/_version.py,sha256=6QbWXLSZypjtWL_CwJFHH4dzMRK3AUH4B0YudzvGz9s,200
 opencloning/api_config_utils.py,sha256=inAXPGYNDz-DuEoSqitImj0Vv5TpQSbMZH9D3dQb5P0,4319
-opencloning/app_settings.py,sha256=MScy0le1Dn00rxqDkpeoBLWwjWQTyzHBQ-MqSDdmoe4,2054
+opencloning/app_settings.py,sha256=1GFD0_DcKTlhwAcbXRXGWY6d_7LrKbtbHd5NPVasKb8,2874
 opencloning/assembly2.py,sha256=M-Als7mrEdHc8Ee3Zr_pgQ5WiN7Uqd37BMxr9Q-1myw,61743
 opencloning/batch_cloning/EBIC/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 opencloning/batch_cloning/EBIC/barcode.gb,sha256=G6kP6MuY23S-n3xg16LQaTasFtYFqik5eEgcooZ9ATM,815
@@ -31,21 +31,21 @@ opencloning/ebic/primer_design.py,sha256=gPZTF9w5SV7WGgnefp_HBM831y0z73M1Kb0QUPn
 opencloning/ebic/primer_design_settings.py,sha256=OnFsuh0QCvplUEPXLZouzRo9R7rm4nLbcd2LkDCiIDM,1896
 opencloning/endpoints/annotation.py,sha256=3rlIXeNQzoqPD9lJUEBGLGxvlhUCTcfkqno814A8P0U,2283
 opencloning/endpoints/assembly.py,sha256=XBv2Vg0MrBl4WjKlclyJ4QTgydqda9P3LRl_25y3TOo,21307
-opencloning/endpoints/external_import.py,sha256=i2hAKSYi2IIdglmDhDhWmBzHbhn6A9A8ybbj4nmhROM,18188
+opencloning/endpoints/external_import.py,sha256=Z9zd94kzmnbLG_yEAjI-1HK7sIAMcLz3FSZZR66BV-U,18386
 opencloning/endpoints/no_assembly.py,sha256=NY6rhEDCNoZVn6Xk81cen2n-FkMr7ierfxM8G0npbQs,4722
 opencloning/endpoints/no_input.py,sha256=DuqKD3Ph3a44ZxPMEzZv1nwD5xlxYsN7YyxXcfjSUFc,3844
 opencloning/endpoints/other.py,sha256=7YBXU5UrVCjEjOjdYWw-0sASXn3MhWVZYwDYSZD4C9E,3452
 opencloning/endpoints/primer_design.py,sha256=3eiQ7MwgeLoAuXFUMNF-DzjzwH_eJGCjd4s32CjxIic,12717
 opencloning/gateway.py,sha256=pFB3gsCQL715kOFOP1NQOOsQqrkWuQe5qXk4IunF5SA,8486
 opencloning/get_router.py,sha256=l2DXaTbeL2tDqlnVMlcewutzt1sjaHlxku1X9HVUwJk,252
-opencloning/http_client.py,sha256=Ndxuoknrit5glKehvWLfKjqp0miLAfVsfLh4q57gEM4,1612
+opencloning/http_client.py,sha256=coVesi_qJWea-VHBOd-V-Th6e4P9rzl-8ZILPGq2ne0,1262
 opencloning/main.py,sha256=l9PrPBMtGMEWxAPiPWR15Qv2oDNnRoNd8H8E3bZW6Do,3750
 opencloning/ncbi_requests.py,sha256=b8ow9TDpXbyYk_0HeK-7RXWwwZGrhH-MylSNc3_tH0I,5557
 opencloning/primer_design.py,sha256=nqCmYIZ7UvU4CQwVGJwX7T5LTHwt3-51_ZcTZZAgT_Y,9175
 opencloning/pydantic_models.py,sha256=lMO78M4MwDgzTEGz9qzsaADwAFXagWK4qGsF1K1hLZw,18865
 opencloning/request_examples.py,sha256=QAsJxVaq5tHwlPB404IiJ9WC6SA7iNY7XnJm63BWT_E,2944
 opencloning/utils.py,sha256=0Lvw1h1AsUJTK2b9mNzYVi_DBeWmWCFA5dIPl_gERcI,1479
-opencloning-0.3.7.dist-info/LICENSE,sha256=VSdVE1f8axjIh6gvo9ZZygJdTVkRFMcwCW_hvjOHC_w,1058
-opencloning-0.3.7.dist-info/METADATA,sha256=yuwNExxPXtTWO-Xiur4esQhroyB85O6oo_BtQUQvnzw,9041
-opencloning-0.3.7.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-opencloning-0.3.7.dist-info/RECORD,,
+opencloning-0.3.8.dist-info/LICENSE,sha256=VSdVE1f8axjIh6gvo9ZZygJdTVkRFMcwCW_hvjOHC_w,1058
+opencloning-0.3.8.dist-info/METADATA,sha256=PUYYRDa7KjQKMswUYWykI9uj15NM-yt7qZ_ik-Hvt4w,9076
+opencloning-0.3.8.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+opencloning-0.3.8.dist-info/RECORD,,