opencloning 0.3.7__tar.gz → 0.3.8__tar.gz

{opencloning-0.3.7 → opencloning-0.3.8}/PKG-INFO

@@ -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 → opencloning-0.3.8}/README.md

@@ -55,8 +55,8 @@ 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 → opencloning-0.3.8}/pyproject.toml

@@ -8,7 +8,7 @@ authors = ["Manuel Lera-Ramirez <manulera14@gmail.com>"]
 description = "Backend of OpenCloning, a web application to generate molecular cloning strategies in json format, and share them with others."
 license = "MIT"
 name = "opencloning"
-version = "0.3.7"
+version = "0.3.8"
 package-mode = true
 readme = "README.md"
 repository = "https://github.com/manulera/OpenCloning_backend"
@@ -27,7 +27,7 @@ pandas = "^2.2.3"
 openpyxl = "^3.1.5"
 pyyaml = "^6.0.2"
 opencloning-linkml = "0.3.0a0"
-primer3-py = "2.0.3"
+primer3-py = "2.2.0"
 biopython = "1.84"
 packaging = "^25.0"
 

{opencloning-0.3.7 → opencloning-0.3.8}/src/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-0.3.7 → opencloning-0.3.8}/src/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-0.3.7 → opencloning-0.3.8}/src/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())