opencloning 0.4.4__py3-none-any.whl → 0.4.6__py3-none-any.whl

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/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/http_client.py

@@ -22,7 +22,6 @@ 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)
-
         raise HTTPError(request.url, 403, f'Request to {request.url} is not allowed', None, None)
 
 

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
 

{opencloning-0.4.4.dist-info → opencloning-0.4.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: opencloning
-Version: 0.4.4
+Version: 0.4.6
 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-0.4.4.dist-info → opencloning-0.4.6.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=FJFayBMLtE9gRC1e0ns5sVQRUb9DVXJ8o-ix4bTlPmI,2911
+opencloning/app_settings.py,sha256=6gtIgDIVA9FzfBCnv8IJrEkroTjg4qdAGI4lNdxoA9E,2970
 opencloning/batch_cloning/EBIC/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 opencloning/batch_cloning/EBIC/barcode.gb,sha256=G6kP6MuY23S-n3xg16LQaTasFtYFqik5eEgcooZ9ATM,815
 opencloning/batch_cloning/EBIC/common_plasmid.gb,sha256=At1HJjqJ2MsLMEx6W3MihJy7tgdtDu3fhwF4YGuw8Dk,13068
@@ -29,21 +29,21 @@ 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=xkvChfwspdh2lnCi9tQFfTQuEhJfNXNjDb4wRKymZV8,21727
-opencloning/endpoints/external_import.py,sha256=Z9zd94kzmnbLG_yEAjI-1HK7sIAMcLz3FSZZR66BV-U,18386
+opencloning/endpoints/external_import.py,sha256=Fdjj6zu0bdZg8vRi1f5bMejnKNBlt3So-BxaeD1CLxk,19115
 opencloning/endpoints/no_assembly.py,sha256=F6mRZFGUAASZ0v7EhPyBgmn_O-YLySMR1a_0aUH2U70,4806
 opencloning/endpoints/no_input.py,sha256=0wc5sTD6nL0SrsXmT__x0g-m6m45ID5hq-D8KDKy98Y,4170
 opencloning/endpoints/other.py,sha256=KvsrfaZXmZcfh3R7mCovuoe62O66EXKEb0pZaEAAYr8,3992
 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=coVesi_qJWea-VHBOd-V-Th6e4P9rzl-8ZILPGq2ne0,1262
+opencloning/http_client.py,sha256=m8LPCxT4b63XPOWGAMmecaNZ7Ho1uxzJm8z7bbhOMqY,1261
 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=N18tl8r6owDxTBRtrvB7DU3kmp59sBc8gYxujT9q6jE,19900
+opencloning/pydantic_models.py,sha256=SZDFrITTELkel3jOu9YlPC27RsJHzaAXTEYOMEZvvqs,20048
 opencloning/request_examples.py,sha256=_VvY4lNpgqhLTM6O_OUs1TujhL7RUbRFZ9ptyssbxLk,2934
 opencloning/utils.py,sha256=0Lvw1h1AsUJTK2b9mNzYVi_DBeWmWCFA5dIPl_gERcI,1479
-opencloning-0.4.4.dist-info/METADATA,sha256=NV3X1i61xwbv9VwKTpawPRjeFh-xv6W2vP-DmjycFqA,9211
-opencloning-0.4.4.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-opencloning-0.4.4.dist-info/licenses/LICENSE,sha256=VSdVE1f8axjIh6gvo9ZZygJdTVkRFMcwCW_hvjOHC_w,1058
-opencloning-0.4.4.dist-info/RECORD,,
+opencloning-0.4.6.dist-info/METADATA,sha256=0PsN9Ho48_stnFV5pX-qHjMqhTlrdE7dGl3pgRHZfpc,9211
+opencloning-0.4.6.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+opencloning-0.4.6.dist-info/licenses/LICENSE,sha256=VSdVE1f8axjIh6gvo9ZZygJdTVkRFMcwCW_hvjOHC_w,1058
+opencloning-0.4.6.dist-info/RECORD,,