opencloning 0.2.6.1__tar.gz → 0.2.6.3__tar.gz

{opencloning-0.2.6.1 → opencloning-0.2.6.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: opencloning
-Version: 0.2.6.1
+Version: 0.2.6.3
 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
@@ -12,14 +12,15 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: beautifulsoup4 (>=4.11.1,<5.0.0)
+Requires-Dist: biopython (==1.84)
 Requires-Dist: fastapi
 Requires-Dist: httpx (>=0.25.0,<0.26.0)
-Requires-Dist: opencloning-linkml (==0.2.5.1a)
+Requires-Dist: opencloning-linkml (==0.2.5.2a0)
 Requires-Dist: openpyxl (>=3.1.5,<4.0.0)
 Requires-Dist: pandas (>=2.2.3,<3.0.0)
 Requires-Dist: primer3-py (>=2.0.3,<3.0.0)
 Requires-Dist: pydantic (>=2.7.1,<3.0.0)
-Requires-Dist: pydna (>=5.3,<6.0)
+Requires-Dist: pydna (==5.5.0)
 Requires-Dist: python-multipart
 Requires-Dist: pyyaml (>=6.0.2,<7.0.0)
 Requires-Dist: regex (>=2023.10.3,<2024.0.0)
@@ -41,7 +42,11 @@ This python API is built with [FastAPI](https://fastapi.tiangolo.com/) and is fo
 
 Read [main project readme](https://github.com/manulera/OpenCloning) first.
 
-This API provides a series of entry points. The API documentation can be accessed [here](https://OpenCloning.api.genestorian.org/docs). You can use the documentation page to try some request directly on the browser. Otherwise, the API is open for you to make requests from a python script or command line at: [https://opencloning.api.genestorian.org/](https://opencloning.api.genestorian.org/).
+This API provides a series of entry points. The API documentation can be accessed [here](https://api.opencloning.org/docs). You can use the documentation page to try some request directly on the browser. Otherwise, the API is open for you to make requests from a python script or command line at: [https://api.opencloning.org/](https://api.opencloning.org/).
+
+## Scripting
+
+The API functions can also be used to write python scripts to automate cloning. See the [scripting examples](examples/scripting) for more information.
 
 ## Getting started
 
@@ -103,7 +108,7 @@ docker run -d --name backendcontainer -p 8000:8000 manulera/opencloningbackend
 
 ```
 
-If you don't want to download the repository and build the image, you can fetch the latest image from dockerhub (same image that is used in [https://opencloning.api.genestorian.org/](https://opencloning.api.genestorian.org/))
+If you don't want to download the repository and build the image, you can fetch the latest image from dockerhub (same image that is used in [https://api.opencloning.org/](https://api.opencloning.org/))
 
 ```bash
 docker pull manulera/opencloningbackend

{opencloning-0.2.6.1 → opencloning-0.2.6.3}/README.md

@@ -11,7 +11,11 @@ This python API is built with [FastAPI](https://fastapi.tiangolo.com/) and is fo
 
 Read [main project readme](https://github.com/manulera/OpenCloning) first.
 
-This API provides a series of entry points. The API documentation can be accessed [here](https://OpenCloning.api.genestorian.org/docs). You can use the documentation page to try some request directly on the browser. Otherwise, the API is open for you to make requests from a python script or command line at: [https://opencloning.api.genestorian.org/](https://opencloning.api.genestorian.org/).
+This API provides a series of entry points. The API documentation can be accessed [here](https://api.opencloning.org/docs). You can use the documentation page to try some request directly on the browser. Otherwise, the API is open for you to make requests from a python script or command line at: [https://api.opencloning.org/](https://api.opencloning.org/).
+
+## Scripting
+
+The API functions can also be used to write python scripts to automate cloning. See the [scripting examples](examples/scripting) for more information.
 
 ## Getting started
 
@@ -73,7 +77,7 @@ docker run -d --name backendcontainer -p 8000:8000 manulera/opencloningbackend
 
 ```
 
-If you don't want to download the repository and build the image, you can fetch the latest image from dockerhub (same image that is used in [https://opencloning.api.genestorian.org/](https://opencloning.api.genestorian.org/))
+If you don't want to download the repository and build the image, you can fetch the latest image from dockerhub (same image that is used in [https://api.opencloning.org/](https://api.opencloning.org/))
 
 ```bash
 docker pull manulera/opencloningbackend

{opencloning-0.2.6.1 → opencloning-0.2.6.3}/pyproject.toml

@@ -3,7 +3,7 @@ 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 = "v0.2.6.1"
+version = "v0.2.6.3"
 package-mode = true
 readme = "README.md"
 repository = "https://github.com/manulera/OpenCloning_backend"
@@ -15,15 +15,16 @@ httpx = "^0.25.0"
 python = "^3.11"
 python-multipart = "*"
 uvicorn = "*"
-pydna = "^5.3"
+pydna = "5.5.0"
 requests = "^2.31.0"
 regex = "^2023.10.3"
 pydantic = "^2.7.1"
 pandas = "^2.2.3"
 openpyxl = "^3.1.5"
 pyyaml = "^6.0.2"
-opencloning-linkml = "0.2.5.1a"
+opencloning-linkml = "0.2.5.2a0"
 primer3-py = "^2.0.3"
+biopython = "1.84"
 
 [tool.poetry.group.dev.dependencies]
 autopep8 = "^2.0.4"
@@ -31,6 +32,7 @@ flake8-bugbear = "^24.2.6"
 black = "^24.2.0"
 pre-commit = "^3.6.2"
 watchfiles = "^0.21.0"
+nbstripout = "^0.8.1"
 
 [tool.poetry.group.test.dependencies]
 pytest = "8.3.4"

{opencloning-0.2.6.1 → opencloning-0.2.6.3}/src/opencloning/batch_cloning/pombe/index.html

@@ -51,7 +51,7 @@ SPBC15D4.01c</textarea><br>
         <div>
             <input type="radio" id="plasmid_addgene" name="plasmid_option" value="addgene" checked
                 onchange="togglePlasmidInput()">
-            <label for="plasmid_addgene">Provide AddGene Identifier</label>
+            <label for="plasmid_addgene">Provide Addgene Identifier</label>
 
             <br>
             <input type="radio" id="plasmid_file" name="plasmid_option" value="file" onchange="togglePlasmidInput()">
@@ -67,7 +67,7 @@ SPBC15D4.01c</textarea><br>
         </div>
 
         <div id="addgene_input">
-            <label for="addgene_id">AddGene Identifier:</label><br>
+            <label for="addgene_id">Addgene Identifier:</label><br>
             <input value="19343" type="text" id="addgene_id" name="addgene_id"><br><br>
         </div>
 

{opencloning-0.2.6.1 → opencloning-0.2.6.3}/src/opencloning/batch_cloning/pombe/pombe_clone.py

@@ -4,7 +4,7 @@ from ...endpoints.assembly import pcr, homologous_recombination
 from ...pydantic_models import (
     GenomeCoordinatesSource,
     TextFileSequence,
-    AddGeneIdSource,
+    AddgeneIdSource,
     PCRSource,
     PrimerModel,
     HomologousRecombinationSource,
@@ -81,13 +81,13 @@ async def main(
         plasmid_source: UploadedFileSource = UploadedFileSource.model_validate(resp['sources'][0])
         plasmid_source.output = 4
     else:
-        addgene_source = AddGeneIdSource(
+        addgene_source = AddgeneIdSource(
             id=3,
             repository_id=plasmid,
             repository_name='addgene',
         )
         resp = await get_from_repository_id_addgene(addgene_source)
-        plasmid_source: AddGeneIdSource = AddGeneIdSource.model_validate(resp['sources'][0])
+        plasmid_source: AddgeneIdSource = AddgeneIdSource.model_validate(resp['sources'][0])
         plasmid_source.output = 4
 
     plasmid_seq: TextFileSequence = TextFileSequence.model_validate(resp['sequences'][0])
@@ -175,7 +175,7 @@ if __name__ == '__main__':
         '--plasmid',
         type=str,
         default='19343',
-        help='AddGene ID for the plasmid (default: 19343)',
+        help='Addgene ID for the plasmid (default: 19343)',
     )
 
     args = parser.parse_args()

{opencloning-0.2.6.1 → opencloning-0.2.6.3}/src/opencloning/batch_cloning/ziqiang_et_al2024/ziqiang_et_al2024.json

@@ -78,7 +78,7 @@
       "id": 1,
       "input": [],
       "output": 2,
-      "type": "AddGeneIdSource",
+      "type": "AddgeneIdSource",
       "output_name": null,
       "repository_id": "71287",
       "repository_name": "addgene",
@@ -89,7 +89,7 @@
       "id": 3,
       "input": [],
       "output": 4,
-      "type": "AddGeneIdSource",
+      "type": "AddgeneIdSource",
       "output_name": null,
       "repository_id": "71287",
       "repository_name": "addgene",
@@ -100,7 +100,7 @@
       "id": 5,
       "input": [],
       "output": 6,
-      "type": "AddGeneIdSource",
+      "type": "AddgeneIdSource",
       "output_name": null,
       "repository_id": "213912",
       "repository_name": "addgene",
@@ -111,7 +111,7 @@
       "id": 7,
       "input": [],
       "output": 8,
-      "type": "AddGeneIdSource",
+      "type": "AddgeneIdSource",
       "output_name": null,
       "repository_id": "213913",
       "repository_name": "addgene",
@@ -122,7 +122,7 @@
       "id": 9,
       "input": [],
       "output": 10,
-      "type": "AddGeneIdSource",
+      "type": "AddgeneIdSource",
       "output_name": null,
       "repository_id": "133748",
       "repository_name": "addgene",
@@ -236,7 +236,7 @@
       "id": 17,
       "input": [],
       "output": 18,
-      "type": "AddGeneIdSource",
+      "type": "AddgeneIdSource",
       "output_name": null,
       "repository_id": "63143",
       "repository_name": "addgene",

{opencloning-0.2.6.1 → opencloning-0.2.6.3}/src/opencloning/dna_functions.py

@@ -4,7 +4,7 @@ from Bio.Restriction.Restriction import RestrictionBatch
 from Bio.Seq import reverse_complement
 from pydna.dseqrecord import Dseqrecord
 from pydna.dseq import Dseq
-from .pydantic_models import TextFileSequence, AddGeneIdSource, SequenceFileFormat, WekWikGeneIdSource, SEVASource
+from .pydantic_models import TextFileSequence, AddgeneIdSource, SequenceFileFormat, WekWikGeneIdSource, SEVASource
 from opencloning_linkml.datamodel import PlannotateAnnotationReport
 from pydna.parsers import parse as pydna_parse
 import requests
@@ -93,7 +93,7 @@ def get_sequence_from_snagene_url(url: str) -> Dseqrecord:
     return Dseqrecord(parsed_seq, circular=circularize)
 
 
-async def request_from_addgene(source: AddGeneIdSource) -> tuple[Dseqrecord, AddGeneIdSource]:
+async def request_from_addgene(source: AddgeneIdSource) -> tuple[Dseqrecord, AddgeneIdSource]:
 
     url = f'https://www.addgene.org/{source.repository_id}/sequences/'
     async with httpx.AsyncClient() as client:

{opencloning-0.2.6.1 → opencloning-0.2.6.3}/src/opencloning/endpoints/external_import.py

@@ -13,7 +13,7 @@ from ..pydantic_models import (
     TextFileSequence,
     UploadedFileSource,
     RepositoryIdSource,
-    AddGeneIdSource,
+    AddgeneIdSource,
     WekWikGeneIdSource,
     BenchlingUrlSource,
     SnapGenePlasmidSource,
@@ -179,7 +179,7 @@ def repository_id_http_error_handler(exception: HTTPError, source: RepositoryIdS
         'RepositoryIdResponse',
         sources=(
             list[RepositoryIdSource]
-            | list[AddGeneIdSource]
+            | list[AddgeneIdSource]
             | list[BenchlingUrlSource]
             | list[EuroscarfSource]
             | list[WekWikGeneIdSource]
@@ -192,7 +192,7 @@ def repository_id_http_error_handler(exception: HTTPError, source: RepositoryIdS
 async def get_from_repository_id(
     source: (
         RepositoryIdSource
-        | AddGeneIdSource
+        | AddgeneIdSource
         | BenchlingUrlSource
         | SnapGenePlasmidSource
         | EuroscarfSource
@@ -225,16 +225,16 @@ async def get_from_repository_id_genbank(source: RepositoryIdSource):
 @router.post(
     '/repository_id/addgene',
     response_model=create_model(
-        'AddgeneIdResponse', sources=(list[AddGeneIdSource], ...), sequences=(list[TextFileSequence], ...)
+        'AddgeneIdResponse', sources=(list[AddgeneIdSource], ...), sequences=(list[TextFileSequence], ...)
     ),
 )
-async def get_from_repository_id_addgene(source: AddGeneIdSource):
+async def get_from_repository_id_addgene(source: AddgeneIdSource):
     try:
         dseq, out_source = await request_from_addgene(source)
     except HTTPError as exception:
         repository_id_http_error_handler(exception, source)
     except httpx.ConnectError:
-        raise HTTPException(504, 'unable to connect to AddGene')
+        raise HTTPException(504, 'unable to connect to Addgene')
 
     return {'sequences': [format_sequence_genbank(dseq, source.output_name)], 'sources': [out_source]}
 

{opencloning-0.2.6.1 → opencloning-0.2.6.3}/src/opencloning/pydantic_models.py

@@ -1,5 +1,5 @@
 from pydantic import BaseModel, Field, model_validator
-from typing import Optional, List, Any
+from typing import Optional, List
 
 from Bio.SeqFeature import (
     SeqFeature,
@@ -32,7 +32,7 @@ from opencloning_linkml.datamodel import (
     Primer as _Primer,
     AssemblyFragment as _AssemblyFragment,
     SimpleSequenceLocation as _SimpleSequenceLocation,
-    AddGeneIdSource as _AddGeneIdSource,
+    AddgeneIdSource as _AddgeneIdSource,
     WekWikGeneIdSource as _WekWikGeneIdSource,
     BenchlingUrlSource as _BenchlingUrlSource,
     CloningStrategy as _CloningStrategy,
@@ -115,7 +115,7 @@ class RepositoryIdSource(SourceCommonClass, _RepositoryIdSource):
     pass
 
 
-class AddGeneIdSource(SourceCommonClass, _AddGeneIdSource):
+class AddgeneIdSource(SourceCommonClass, _AddgeneIdSource):
     # TODO: add this to LinkML
     # repository_name: RepositoryName = RepositoryName('addgene')
     pass
@@ -405,6 +405,8 @@ class BaseCloningStrategy(_CloningStrategy):
         return max([p.id for p in self.primers], default=0) + 1
 
     def add_primer(self, primer: PrimerModel):
+        if primer in self.primers:
+            return
         primer.id = self.next_primer_id()
         self.primers.append(primer)
 
@@ -412,6 +414,12 @@ class BaseCloningStrategy(_CloningStrategy):
         return max([s.id for s in self.sources + self.sequences], default=0) + 1
 
     def add_source_and_sequence(self, source: SourceCommonClass, sequence: TextFileSequence):
+        if source in self.sources:
+            if sequence not in self.sequences:
+                raise ValueError(
+                    f"Source {source.id} already exists in the cloning strategy, but sequence {sequence.id} it's not its output."
+                )
+            return
         source.id = self.next_node_id()
         self.sources.append(source)
         sequence.id = self.next_node_id()