opencloning 0.4.3__tar.gz → 0.4.5__tar.gz

{opencloning-0.4.3 → opencloning-0.4.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: opencloning
-Version: 0.4.3
+Version: 0.4.5
 Summary: Backend of OpenCloning, a web application to generate molecular cloning strategies in json format, and share them with others.
 License: MIT
 License-File: LICENSE
@@ -17,7 +17,7 @@ Requires-Dist: beautifulsoup4 (>=4.11.1,<5.0.0)
 Requires-Dist: biopython (>=1.85,<2.0)
 Requires-Dist: fastapi
 Requires-Dist: httpx (>=0.28.1,<0.29.0)
-Requires-Dist: opencloning-linkml (==0.4.3)
+Requires-Dist: opencloning-linkml (==0.4.4)
 Requires-Dist: openpyxl (>=3.1.5,<4.0.0)
 Requires-Dist: packaging (>=25.0,<26.0)
 Requires-Dist: pairwise-alignments-to-msa (>=0.1.1,<0.2.0)

{opencloning-0.4.3 → opencloning-0.4.5}/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 = "0.4.3"
+version = "0.4.5"
 package-mode = true
 readme = "README.md"
 repository = "https://github.com/manulera/OpenCloning_backend"
@@ -26,7 +26,7 @@ pydantic = "^2.7.1"
 pandas = "^2.2.3"
 openpyxl = "^3.1.5"
 pyyaml = "^6.0.2"
-opencloning-linkml = "0.4.3"
+opencloning-linkml = "0.4.4"
 primer3-py = "2.2.0"
 biopython = "^1.85"
 packaging = "^25.0"

{opencloning-0.4.3 → opencloning-0.4.5}/src/opencloning/app_settings.py

@@ -44,6 +44,7 @@ default_allowed_urls = [
     'http://www.euroscarf.de/',
     'https://wekwikgene.wllsb.edu.cn',
     'http://bahlerweb.cs.ucl.ac.uk',
+    'https://assets.opencloning.org/open-dna-collections',
 ]
 
 if os.environ.get('ALLOWED_EXTERNAL_URLS') is not None:

{opencloning-0.4.3 → opencloning-0.4.5}/src/opencloning/endpoints/external_import.py

@@ -24,6 +24,7 @@ from ..pydantic_models import (
     SequenceFileFormat,
     SEVASource,
     SequenceLocationStr,
+    OpenDNACollectionsSource,
 )
 from ..dna_functions import (
     format_sequence_genbank,
@@ -234,7 +235,8 @@ def repository_id_http_error_handler(exception: HTTPError, source: RepositoryIdS
             | list[BenchlingUrlSource]
             | list[EuroscarfSource]
             | list[WekWikGeneIdSource]
-            | list[SEVASource],
+            | list[SEVASource]
+            | list[OpenDNACollectionsSource],
             ...,
         ),
         sequences=(list[TextFileSequence], ...),
@@ -249,6 +251,7 @@ async def get_from_repository_id(
         | EuroscarfSource
         | WekWikGeneIdSource
         | SEVASource
+        | OpenDNACollectionsSource
     ),
 ):
     return RedirectResponse(f'/repository_id/{source.repository_name}', status_code=307)
@@ -384,6 +387,22 @@ async def get_from_repository_id_igem(source: IGEMSource):
         repository_id_http_error_handler(exception, source)
 
 
+@router.post(
+    '/repository_id/open_dna_collections',
+    response_model=create_model(
+        'OpenDNACollectionsResponse',
+        sources=(list[OpenDNACollectionsSource], ...),
+        sequences=(list[TextFileSequence], ...),
+    ),
+)
+async def get_from_repository_id_open_dna_collections(source: OpenDNACollectionsSource):
+    try:
+        dseq = (await get_sequences_from_file_url(source.sequence_file_url))[0]
+        return {'sequences': [format_sequence_genbank(dseq, source.output_name)], 'sources': [source]}
+    except HTTPError as exception:
+        repository_id_http_error_handler(exception, source)
+
+
 @router.post(
     '/genome_coordinates',
     response_model=create_model(

{opencloning-0.4.3 → opencloning-0.4.5}/src/opencloning/endpoints/other.py

@@ -3,6 +3,7 @@ from Bio.Restriction.Restriction_Dictionary import rest_dict
 from pydantic import ValidationError
 from opencloning_linkml.migrations import migrate
 from opencloning_linkml._version import __version__ as schema_version
+import os
 
 from ..bug_fixing.backend_v0_3 import fix_backend_v0_3
 
@@ -22,9 +23,27 @@ from .._version import __version__ as backend_version
 router = get_router()
 
 
+def version_to_int(version: str | None) -> int | None:
+    if version is None:
+        return None
+    try:
+        version = version.replace('v', '')
+        # Pad to 2 digits
+        int_vals = [val.zfill(2) for val in version.split('.')]
+        return int(''.join(int_vals))
+    except ValueError:
+        return None
+
+
 @router.get('/version')
 async def get_version():
-    return {'backend_version': backend_version, 'schema_version': schema_version}
+    opencloning_version = os.getenv('OPENCLONING_VERSION')
+    return {
+        'backend_version': backend_version,
+        'schema_version': schema_version,
+        'opencloning_version': opencloning_version,
+        'opencloning_version_int': version_to_int(opencloning_version),
+    }
 
 
 @router.get('/restriction_enzyme_list', response_model=dict[str, list[str]])

{opencloning-0.4.3 → opencloning-0.4.5}/src/opencloning/http_client.py

@@ -22,7 +22,7 @@ class AllowedExternalUrlsTransport(AsyncHTTPTransport):
     async def handle_async_request(self, request: Request) -> Response:
         if any(str(request.url).startswith(url) for url in allowed_external_urls):
             return await super().handle_async_request(request)
-
+        print('>>>', request.url)
         raise HTTPError(request.url, 403, f'Request to {request.url} is not allowed', None, None)
 
 

{opencloning-0.4.3 → opencloning-0.4.5}/src/opencloning/pydantic_models.py

@@ -50,6 +50,7 @@ from opencloning_linkml.datamodel import (
     CreLoxRecombinationSource as _CreLoxRecombinationSource,
     InVivoAssemblySource as _InVivoAssemblySource,
     SourceInput as _SourceInput,
+    OpenDNACollectionsSource as _OpenDNACollectionsSource,
 )
 from pydna.assembly2 import (
     edge_representation2subfragment_representation,
@@ -183,6 +184,10 @@ class IGEMSource(SourceCommonClass, _IGEMSource):
         return self
 
 
+class OpenDNACollectionsSource(SourceCommonClass, _OpenDNACollectionsSource):
+    pass
+
+
 class SEVASource(SourceCommonClass, _SEVASource):
     pass