opencloning 0.3.7__py3-none-any.whl → 0.4.2__py3-none-any.whl

opencloning/pydantic_models.py

@@ -1,5 +1,5 @@
-from pydantic import BaseModel, Field, model_validator, field_validator
-from typing import Optional, List
+from pydantic import BaseModel, Field, model_validator, field_validator, Discriminator, Tag
+from typing import Optional, List, Union, Annotated
 from pydantic_core import core_schema
 from ._version import __version__
 
@@ -49,8 +49,9 @@ from opencloning_linkml.datamodel import (
     SEVASource as _SEVASource,
     CreLoxRecombinationSource as _CreLoxRecombinationSource,
     InVivoAssemblySource as _InVivoAssemblySource,
+    SourceInput as _SourceInput,
 )
-from .assembly2 import (
+from pydna.assembly2 import (
     edge_representation2subfragment_representation,
     subfragment_representation2edge_representation,
 )
@@ -64,6 +65,10 @@ class TextFileSequence(_TextFileSequence):
     pass
 
 
+class SourceInput(_SourceInput):
+    pass
+
+
 class PrimerModel(_Primer):
     """Called PrimerModel not to be confused with the class from pydna."""
 
@@ -94,8 +99,23 @@ class SeqFeatureModel(BaseModel):
 # Sources =========================================
 
 
-class SourceCommonClass:
-    input: Optional[List[int]] = Field(
+def input_discriminator(v) -> str | None:
+    """
+    Discriminator that yields SourceInput by default
+    """
+    if isinstance(v, dict):
+        input_type = v.get('type', None)
+        if input_type is None:
+            return 'SourceInput'
+        else:
+            return input_type
+    elif isinstance(v, SourceInput):
+        return v.type
+    return None
+
+
+class SourceCommonClass(BaseModel):
+    input: Optional[List[SourceInput]] = Field(
         default_factory=list,
         description="""The sequences that are an input to this source. If the source represents external import of a sequence, it's empty.""",
         json_schema_extra={'linkml_meta': {'alias': 'input', 'domain_of': ['Source']}},
@@ -292,7 +312,7 @@ class SequenceLocationStr(str):
         return cls.field_validator(value)
 
 
-class AssemblyFragment(_AssemblyFragment):
+class AssemblyFragment(_AssemblyFragment, SourceInput):
     left_location: Optional[SequenceLocationStr] = None
     right_location: Optional[SequenceLocationStr] = None
 
@@ -322,14 +342,26 @@ class AssemblyFragment(_AssemblyFragment):
 class AssemblySourceCommonClass(SourceCommonClass):
     # TODO: This is different in the LinkML model, because there it is not required,
     # and here we make it default to list.
-    assembly: List[AssemblyFragment] = Field(
-        default_factory=list, description="""The joins between the fragments in the assembly"""
+    input: Optional[
+        List[
+            Annotated[
+                Union[
+                    Annotated[SourceInput, Tag('SourceInput')],
+                    Annotated['AssemblyFragment', Tag('AssemblyFragment')],
+                ],
+                Discriminator(input_discriminator),
+            ]
+        ]
+    ] = Field(
+        default_factory=list,
+        description="""The inputs to this source. If the source represents external import of a sequence, it's empty.""",
+        json_schema_extra={'linkml_meta': {'alias': 'input', 'domain_of': ['Source'], 'slot_uri': 'schema:object'}},
     )
 
     def minimal_overlap(self):
         """Returns the minimal overlap between the fragments in the assembly"""
         all_overlaps = list()
-        for f in self.assembly:
+        for f in self.input:
             if f.left_location is not None:
                 all_overlaps.append(f.left_location.end - f.left_location.start)
             if f.right_location is not None:
@@ -338,9 +370,13 @@ class AssemblySourceCommonClass(SourceCommonClass):
 
     def get_assembly_plan(self, fragments: list[_SeqRecord]) -> tuple:
         """Returns the assembly plan"""
-        subf = [f.to_fragment_tuple(fragments) for f in self.assembly]
+        subf = [f.to_fragment_tuple(fragments) for f in self.input if f.type == 'AssemblyFragment']
         return subfragment_representation2edge_representation(subf, self.circular)
 
+    def is_assembly_complete(self) -> bool:
+        """Returns True if the assembly is complete"""
+        return any(f.type == 'AssemblyFragment' for f in self.input)
+
     @classmethod
     def from_assembly(
         cls,
@@ -353,7 +389,6 @@ class AssemblySourceCommonClass(SourceCommonClass):
 
         # Replace the positions with the actual ids
         fragment_ids = [int(f.id) for f in fragments]
-        input_ids = [int(f.id) for f in fragments if not isinstance(f, _PydnaPrimer)]
 
         # Here the ids are still the positions in the fragments list
         fragment_assembly_positions = edge_representation2subfragment_representation(assembly, circular)
@@ -368,8 +403,7 @@ class AssemblySourceCommonClass(SourceCommonClass):
         ]
         return cls(
             id=id,
-            input=input_ids,
-            assembly=assembly_fragments,
+            input=assembly_fragments,
             circular=circular,
             **kwargs,
         )
@@ -428,7 +462,9 @@ class CRISPRSource(AssemblySourceCommonClass, _CRISPRSource):
         fragments: list[_SeqRecord],
         guides: list[int],
     ):
-        return super().from_assembly(assembly, id, False, fragments, guides=guides)
+        source = super().from_assembly(assembly, id, False, fragments)
+        source.input += [SourceInput(sequence=guide) for guide in guides]
+        return source
 
 
 class RestrictionAndLigationSource(AssemblySourceCommonClass, _RestrictionAndLigationSource):
@@ -486,17 +522,14 @@ class BaseCloningStrategy(_CloningStrategy):
         json_schema_extra={'linkml_meta': {'alias': 'backend_version', 'domain_of': ['CloningStrategy']}},
     )
 
-    def next_primer_id(self):
-        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()
+        primer.id = self.next_id()
         self.primers.append(primer)
 
-    def next_node_id(self):
-        return max([s.id for s in self.sources + self.sequences], default=0) + 1
+    def next_id(self):
+        return max([s.id for s in self.sources + self.sequences + self.primers], default=0) + 1
 
     def add_source_and_sequence(self, source: SourceCommonClass, sequence: TextFileSequence):
         if source in self.sources:
@@ -505,11 +538,11 @@ class BaseCloningStrategy(_CloningStrategy):
                     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()
+        new_id = self.next_id()
+        source.id = new_id
         self.sources.append(source)
-        sequence.id = self.next_node_id()
+        sequence.id = new_id
         self.sequences.append(sequence)
-        source.output = sequence.id
 
     def all_children_source_ids(self, source_id: int, source_children: list | None = None) -> list[int]:
         """Returns the ids of all source children ids of a source"""
@@ -517,7 +550,7 @@ class BaseCloningStrategy(_CloningStrategy):
         if source_children is None:
             source_children = []
 
-        sources_that_take_output_as_input = [s for s in self.sources if source.output in s.input]
+        sources_that_take_output_as_input = [s for s in self.sources if source.id in [inp.sequence for inp in s.input]]
         new_source_ids = [s.id for s in sources_that_take_output_as_input]
 
         source_children.extend(new_source_ids)

opencloning/request_examples.py

@@ -66,10 +66,10 @@ oligonucleotide_hybridization_examples = {
         'value': {
             'source': {
                 'id': 1,
-                'input': [],
-                'output': 0,
-                'forward_oligo': 2,
-                'reverse_oligo': 3,
+                'input': [
+                    {'sequence': 2},
+                    {'sequence': 3},
+                ],
             },
             'primers': [
                 {'id': 2, 'name': 'primer1', 'sequence': 'aaGCGGCCGCgtagaactttatgtgcttccttacattggt'},

{opencloning-0.3.7.dist-info → opencloning-0.4.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: opencloning
-Version: 0.3.7
+Version: 0.4.2
 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
@@ -12,19 +12,20 @@ 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: biopython (>=1.85,<2.0)
 Requires-Dist: fastapi
 Requires-Dist: httpx (>=0.28.1,<0.29.0)
-Requires-Dist: opencloning-linkml (==0.3.0a0)
+Requires-Dist: opencloning-linkml (==0.4.3)
 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)
 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: pydna (==5.5.2)
 Requires-Dist: python-multipart
 Requires-Dist: pyyaml (>=6.0.2,<7.0.0)
-Requires-Dist: regex (>=2023.10.3,<2024.0.0)
+Requires-Dist: regex (>=2024.11.6,<2025.0.0)
 Requires-Dist: uvicorn
 Project-URL: Repository, https://github.com/manulera/OpenCloning_backend
 Description-Content-Type: text/markdown
@@ -86,8 +87,8 @@ 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-0.4.2.dist-info}/RECORD

@@ -1,51 +1,49 @@
 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/assembly2.py,sha256=M-Als7mrEdHc8Ee3Zr_pgQ5WiN7Uqd37BMxr9Q-1myw,61743
+opencloning/app_settings.py,sha256=FJFayBMLtE9gRC1e0ns5sVQRUb9DVXJ8o-ix4bTlPmI,2911
 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
-opencloning/batch_cloning/EBIC/example.py,sha256=FWjROXWsgM-gz2oYnKiywUVKa9uoEe964FlFRle_hYI,6870
+opencloning/batch_cloning/EBIC/example.py,sha256=1OENMoPVn5lhTall_DvD7qx7t021a2HMV11kpStVs88,6851
 opencloning/batch_cloning/EBIC/primer_design_settings.py,sha256=MVML1r1ciJYMFUJoqZVcGLoPM-f28oBN1wSDzlD0y64,1896
 opencloning/batch_cloning/__init__.py,sha256=uDxAa45g30_S6dJScNMlIxubQXlLRUsWoLX4S4y-l88,244
 opencloning/batch_cloning/index.html,sha256=HDqPHrJxrrKfGmy_dwYHhOsdUgZHHIch7Z0ey8qyvZI,1332
 opencloning/batch_cloning/pombe/__init__.py,sha256=Fq7SroO0Fer5CtFBRWdduIvzp1_dTUZwBb8IjBtRQO0,3332
 opencloning/batch_cloning/pombe/index.html,sha256=3YchoKGpcKDfvTOW1Rdih4PkbZIkMjKIQ0PaVXfV3e8,8348
-opencloning/batch_cloning/pombe/pombe_all.sh,sha256=0yvDdBaIdt2RsIrvnjgn5L3KtYBToq3Rl8-X8RFHibE,364
-opencloning/batch_cloning/pombe/pombe_clone.py,sha256=OY6yOlBK-9OAmHu3HUhP50mIXvyR0HJg1_2OjBFifV8,8123
+opencloning/batch_cloning/pombe/pombe_clone.py,sha256=3Z51NA0rhU-e4SxuLnlV5iDWeQrqECJTfe8IfiDoiow,7996
 opencloning/batch_cloning/pombe/pombe_gather.py,sha256=qI-biMZGLxVDV-vOf3sT6bS1BawtTihZNcSYNlnnEi8,2432
 opencloning/batch_cloning/pombe/pombe_get_primers.py,sha256=nrn6V4_l8FWWfqS4WU3qPt95KwzvCXxETh8E-zWbRhM,3968
-opencloning/batch_cloning/pombe/pombe_summary.py,sha256=W9DLpnCuwK7w2DhHLu60N7L6jquuYubD3ZRFwdhNPVw,4033
-opencloning/batch_cloning/ziqiang_et_al2024/__init__.py,sha256=zZUbj3uMzd9rKMXi5s9LQ1yUg7sccdS0f_4kpw7SQlk,7584
+opencloning/batch_cloning/pombe/pombe_summary.py,sha256=DBpoSEV1xPFm8TFDhrxS4tjqxJVrfH-ttM_0ELjQqok,4350
+opencloning/batch_cloning/ziqiang_et_al2024/__init__.py,sha256=9-aG8JfZx8Y91qUAchTqRL2Rq5lSrZ34O_VkD8WNyiY,7083
 opencloning/batch_cloning/ziqiang_et_al2024/index.html,sha256=EDncANDhhQkhi5FjnnAP6liHkG5srf4_Y46IrnMUG5g,4607
-opencloning/batch_cloning/ziqiang_et_al2024/ziqiang_et_al2024.json,sha256=d-7oXbxoKhMKLz4FJ2OGDdedWTisoaRqLAh1NZnScBg,157189
-opencloning/bug_fixing/README.md,sha256=fGf_4HPTZ2TjGfIOZzw8IAD78-N-RnBrX8mz14wjXEQ,4237
+opencloning/batch_cloning/ziqiang_et_al2024/ziqiang_et_al2024.json,sha256=JAOe35VPeG3QF1CnDzZxOzqpBTSpeCCtAo2W1mVOFEo,157159
+opencloning/bug_fixing/README.md,sha256=eak5x1NTyTxsklaZ1BzB3RYH26MC_2gNuH-gHvuNpKY,4441
 opencloning/bug_fixing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-opencloning/bug_fixing/backend_v0_3.py,sha256=BTnqCXYIcOShut0WfwH6tDjJ1fecAHFHVSDTOKJgUZw,4119
+opencloning/bug_fixing/backend_v0_3.py,sha256=GfuDRvlmcSBv9emXZSWqW-SktOeI1xH-tl2UET-BSoY,4145
 opencloning/cre_lox.py,sha256=x_OVYzfaLJH5eVyp05_I9YNycT606UL683AswhQ-gjU,4294
-opencloning/dna_functions.py,sha256=WvEiKuZEzy3mXjIkOMv4Ymej6xQ3gm4mymM8JCgvE_o,16611
-opencloning/dna_utils.py,sha256=LmkIScIlogpWxprQfsIdjqtLDpqDmTZp45pcZwWFpZM,6683
+opencloning/dna_functions.py,sha256=O5H5DilNUOIzH8gVFiOuG8SVlrenrbwyo9lKwfxIHnY,16663
+opencloning/dna_utils.py,sha256=NSS_b5q8u8XNzVqCwzCQaxj4I2xHf_Inmw7iBWS9gc8,6746
 opencloning/ebic/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 opencloning/ebic/primer_design.py,sha256=gPZTF9w5SV7WGgnefp_HBM831y0z73M1Kb0QUPnbfIM,2270
 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/no_assembly.py,sha256=NY6rhEDCNoZVn6Xk81cen2n-FkMr7ierfxM8G0npbQs,4722
-opencloning/endpoints/no_input.py,sha256=DuqKD3Ph3a44ZxPMEzZv1nwD5xlxYsN7YyxXcfjSUFc,3844
+opencloning/endpoints/assembly.py,sha256=KdVi63Bjmb7qwCQrwMUkRK6lAhlAJvBcHLqj1VJtuAQ,21584
+opencloning/endpoints/external_import.py,sha256=Z9zd94kzmnbLG_yEAjI-1HK7sIAMcLz3FSZZR66BV-U,18386
+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=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/pydantic_models.py,sha256=N18tl8r6owDxTBRtrvB7DU3kmp59sBc8gYxujT9q6jE,19900
+opencloning/request_examples.py,sha256=_VvY4lNpgqhLTM6O_OUs1TujhL7RUbRFZ9ptyssbxLk,2934
 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-0.4.2.dist-info/LICENSE,sha256=VSdVE1f8axjIh6gvo9ZZygJdTVkRFMcwCW_hvjOHC_w,1058
+opencloning-0.4.2.dist-info/METADATA,sha256=jdAjLsb539U782FhTf2O7jV3UdQ-07mlCvu4LnFyd-c,9138
+opencloning-0.4.2.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+opencloning-0.4.2.dist-info/RECORD,,