opencloning 0.2.8.2__py3-none-any.whl → 0.3.0__py3-none-any.whl

opencloning/pydantic_models.py

@@ -1,11 +1,14 @@
-from pydantic import BaseModel, Field, model_validator
+from pydantic import BaseModel, Field, model_validator, field_validator
 from typing import Optional, List
+from pydantic_core import core_schema
+from ._version import __version__
 
 from Bio.SeqFeature import (
     SeqFeature,
     Location,
-    SimpleLocation as BioSimpleLocation,
+    SimpleLocation,
     FeatureLocation as BioFeatureLocation,
+    LocationParserError,
 )
 from Bio.SeqIO.InsdcIO import _insdc_location_string as format_feature_location
 from Bio.Restriction.Restriction import RestrictionType, RestrictionBatch
@@ -31,7 +34,6 @@ from opencloning_linkml.datamodel import (
     CRISPRSource as _CRISPRSource,
     Primer as _Primer,
     AssemblyFragment as _AssemblyFragment,
-    SimpleSequenceLocation as _SimpleSequenceLocation,
     AddgeneIdSource as _AddgeneIdSource,
     WekWikGeneIdSource as _WekWikGeneIdSource,
     BenchlingUrlSource as _BenchlingUrlSource,
@@ -48,8 +50,11 @@ from opencloning_linkml.datamodel import (
     CreLoxRecombinationSource as _CreLoxRecombinationSource,
     InVivoAssemblySource as _InVivoAssemblySource,
 )
-from pydna.utils import shift_location as _shift_location
-from .assembly2 import edge_representation2subfragment_representation, subfragment_representation2edge_representation
+from .assembly2 import (
+    edge_representation2subfragment_representation,
+    subfragment_representation2edge_representation,
+)
+from pydna.utils import location_boundaries, shift_location
 
 
 SequenceFileFormat = _SequenceFileFormat
@@ -110,7 +115,17 @@ class ManuallyTypedSource(SourceCommonClass, _ManuallyTypedSource):
 
 
 class UploadedFileSource(SourceCommonClass, _UploadedFileSource):
-    pass
+    coordinates: Optional['SequenceLocationStr'] = Field(
+        default=None,
+        description="""If provided, coordinates within the sequence of the file to extract a subsequence""",
+        json_schema_extra={'linkml_meta': {'alias': 'coordinates', 'domain_of': ['UploadedFileSource']}},
+    )
+
+    @field_validator('coordinates', mode='before')
+    def parse_coordinates(cls, v):
+        if v is None:
+            return None
+        return SequenceLocationStr.field_validator(v)
 
 
 class RepositoryIdSource(SourceCommonClass, _RepositoryIdSource):
@@ -218,36 +233,91 @@ class RestrictionEnzymeDigestionSource(SourceCommonClass, _RestrictionEnzymeDige
         return sorted(list(set(out)), key=out.index)
 
 
-class SimpleSequenceLocation(_SimpleSequenceLocation):
+class SequenceLocationStr(str):
+    """A string representation of a sequence location, genbank-like."""
+
     # TODO: this should handle origin-spanning simple locations (splitted)
     @classmethod
-    def from_simple_location(cls, location: BioSimpleLocation):
-        return cls(
-            start=location.start,
-            end=location.end,
-            strand=location.strand,
+    def from_biopython_location(cls, location: Location):
+        return cls(format_feature_location(location, None))
+
+    @classmethod
+    def from_start_and_end(cls, start: int, end: int, seq_len: int | None = None, strand: int | None = 1):
+        if end >= start:
+            return cls.from_biopython_location(SimpleLocation(start, end, strand=strand))
+        else:
+            if seq_len is None:
+                raise ValueError('Sequence length is required to handle origin-spanning simple locations')
+            unwrapped_location = SimpleLocation(start, end + seq_len, strand=strand)
+            wrapped_location = shift_location(unwrapped_location, 0, seq_len)
+            return cls.from_biopython_location(wrapped_location)
+
+    def to_biopython_location(self) -> BioFeatureLocation:
+        return Location.fromstring(self)
+
+    @classmethod
+    def field_validator(cls, v):
+        if isinstance(v, str):
+            value = cls(v)
+            try:
+                value.to_biopython_location()
+            except LocationParserError:
+                raise ValueError(f'Location "{v}" is not a valid location')
+            return value
+        raise ValueError(f'Location must be a string or a {cls.__name__}')
+
+    @property
+    def start(self) -> int:
+        return location_boundaries(self.to_biopython_location())[0]
+
+    @property
+    def end(self) -> int:
+        return location_boundaries(self.to_biopython_location())[1]
+
+    @classmethod
+    def __get_pydantic_core_schema__(
+        cls,
+        source_type,
+        handler,
+    ) -> core_schema.CoreSchema:
+        """Generate Pydantic core schema for SequenceLocationStr."""
+        return core_schema.with_info_after_validator_function(
+            cls._validate,
+            core_schema.str_schema(),
         )
 
-    def to_biopython_location(self, circular: bool = False, seq_len: int = None) -> BioFeatureLocation:
-        if circular and self.start > self.end and seq_len is not None:
-            unwrapped_location = BioSimpleLocation(self.start, self.end + seq_len, self.strand)
-            return _shift_location(unwrapped_location, 0, seq_len)
-        return BioSimpleLocation(self.start, self.end, self.strand)
+    @classmethod
+    def _validate(cls, value: str, info):
+        """Validate and create SequenceLocationStr instance."""
+        return cls.field_validator(value)
 
 
 class AssemblyFragment(_AssemblyFragment):
-    left_location: Optional[SimpleSequenceLocation] = None
-    right_location: Optional[SimpleSequenceLocation] = None
+    left_location: Optional[SequenceLocationStr] = None
+    right_location: Optional[SequenceLocationStr] = None
 
-    def to_fragment_tuple(self, fragments) -> tuple[int, BioSimpleLocation, BioSimpleLocation]:
+    def to_fragment_tuple(self, fragments) -> tuple[int, Location, Location]:
         fragment_ids = [int(f.id) for f in fragments]
+        # By convention, these have no strand
+        left_loc = None if self.left_location is None else self.left_location.to_biopython_location()
+        right_loc = None if self.right_location is None else self.right_location.to_biopython_location()
+        if left_loc is not None:
+            left_loc.strand = None
+        if right_loc is not None:
+            right_loc.strand = None
 
         return (
             (fragment_ids.index(self.sequence) + 1) * (-1 if self.reverse_complemented else 1),
-            None if self.left_location is None else self.left_location.to_biopython_location(),
-            None if self.right_location is None else self.right_location.to_biopython_location(),
+            left_loc,
+            right_loc,
         )
 
+    @field_validator('left_location', 'right_location', mode='before')
+    def parse_location(cls, v):
+        if v is None:
+            return None
+        return SequenceLocationStr.field_validator(v)
+
 
 class AssemblySourceCommonClass(SourceCommonClass):
     # TODO: This is different in the LinkML model, because there it is not required,
@@ -290,8 +360,8 @@ class AssemblySourceCommonClass(SourceCommonClass):
         assembly_fragments = [
             AssemblyFragment(
                 sequence=fragment_ids[abs(pos) - 1],
-                left_location=None if left_loc is None else SimpleSequenceLocation.from_simple_location(left_loc),
-                right_location=None if right_loc is None else SimpleSequenceLocation.from_simple_location(right_loc),
+                left_location=None if left_loc is None else SequenceLocationStr.from_biopython_location(left_loc),
+                right_location=None if right_loc is None else SequenceLocationStr.from_biopython_location(right_loc),
                 reverse_complemented=pos < 0,
             )
             for pos, left_loc, right_loc in fragment_assembly_positions
@@ -410,6 +480,11 @@ class BaseCloningStrategy(_CloningStrategy):
         description="""The primers that are used in the cloning strategy""",
         json_schema_extra={'linkml_meta': {'alias': 'primers', 'domain_of': ['CloningStrategy']}},
     )
+    backend_version: Optional[str] = Field(
+        default=__version__,
+        description="""The version of the backend that was used to generate this cloning strategy""",
+        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
@@ -436,8 +511,27 @@ class BaseCloningStrategy(_CloningStrategy):
         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"""
+        source = next(s for s in self.sources if s.id == source_id)
+        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]
+        new_source_ids = [s.id for s in sources_that_take_output_as_input]
+
+        source_children.extend(new_source_ids)
+        for new_source_id in new_source_ids:
+            self.all_children_source_ids(new_source_id, source_children)
+        return source_children
+
 
 class PrimerDesignQuery(BaseModel):
+    model_config = {'arbitrary_types_allowed': True}
     sequence: TextFileSequence
-    location: SimpleSequenceLocation
+    location: SequenceLocationStr
     forward_orientation: bool = True
+
+    @field_validator('location', mode='before')
+    def parse_location(cls, v):
+        return SequenceLocationStr.field_validator(v)

opencloning/utils.py

@@ -43,15 +43,3 @@ class TemporaryFolderOverride:
         if self.target_folder_exists:
             os.mkdir(self.target_folder)
             move_all_contents(self.backup_folder, self.target_folder)
-
-
-def api_version() -> dict[str, str | None]:
-    version = None
-    commit_sha = None
-    if os.path.exists('version.txt'):
-        with open('version.txt', 'r') as f:
-            version = f.read().strip()
-    if os.path.exists('commit_sha.txt'):
-        with open('commit_sha.txt', 'r') as f:
-            commit_sha = f.read().strip()
-    return {'version': version, 'commit_sha': commit_sha}

{opencloning-0.2.8.2.dist-info → opencloning-0.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: opencloning
-Version: 0.2.8.2
+Version: 0.3.0
 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
@@ -15,10 +15,11 @@ 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 (==0.2.6.1a0)
+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,<3.0.0)
+Requires-Dist: primer3-py (==2.0.3)
 Requires-Dist: pydantic (>=2.7.1,<3.0.0)
 Requires-Dist: pydna (==5.5.0)
 Requires-Dist: python-multipart
@@ -48,6 +49,12 @@ This API provides a series of entry points. The API documentation can be accesse
 
 The API functions can also be used to write python scripts to automate cloning. See the [scripting examples](examples/scripting) for more information.
 
+## Migrating between model versions and fixing model bugs
+
+* The data model changes, so the json files you created may not be compatible with the newest version of the library, which uses the latest data mode. You can easily fix this using `python -m opencloning_linkml.migrations.migrate file.json
+` see [full documentation](https://github.com/OpenCloning/OpenCloning_LinkML?tab=readme-ov-file#migration-from-previous-versions-of-the-schema).
+* Before version 0.3, there was a bug for assembly fields that included locations spanning the origin. See the details and how to fix it in the documentation of [this file](./src/opencloning/bug_fixing/README.md).
+
 ## Getting started
 
 If you want to quickly set up a local instance of the frontend and backend of the application, check [getting started in 5 minutes](https://github.com/manulera/OpenCloning#timer_clock-getting-started-in-5-minutes) in the main repository.
@@ -61,7 +68,7 @@ You can install this as a python package:
 python -m venv .venv
 # Activate the virtual environment
 source .venv/bin/activate
-# Install the package from github (will be in pypi at some point)
+# Install the package from pypi
 pip install opencloning
 # Run the API (uvicorn should be installed in the virtual environment)
 uvicorn opencloning.main:app

{opencloning-0.2.8.2.dist-info → opencloning-0.3.0.dist-info}/RECORD

@@ -1,7 +1,8 @@
 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=x5ddkaoyWE76fa4CdwIv-aDfg1eyZr6qTQwfKJB4mCo,1785
-opencloning/assembly2.py,sha256=WeNV0AK_MVzF_mdXaG3scNlNgwy-iJY63mvqBMfLAhI,56600
+opencloning/assembly2.py,sha256=_UdQCnjc2wmWoeVT9NKwXcYUAEBrBT0OSBNMbGYAIL8,57041
 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
@@ -9,7 +10,7 @@ opencloning/batch_cloning/EBIC/example.py,sha256=FWjROXWsgM-gz2oYnKiywUVKa9uoEe9
 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=nL4ZHdyEr_J0xzPFCYjujlwx81RcWYxeR_ax2V4-vuM,3532
+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
@@ -18,29 +19,32 @@ opencloning/batch_cloning/pombe/pombe_get_primers.py,sha256=1RbR_8YGhSrmeIVDOpUp
 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/ziqiang_et_al2024/index.html,sha256=EDncANDhhQkhi5FjnnAP6liHkG5srf4_Y46IrnMUG5g,4607
-opencloning/batch_cloning/ziqiang_et_al2024/ziqiang_et_al2024.json,sha256=mB81j2qWam7uRc-980YFjfqq2CiWTXJYfKFAoKuGtRw,157148
-opencloning/cre_lox.py,sha256=mb2ZddjrPIrUBT3xxMub5-c97WkKZ4Z-HkGFVzuR8pQ,2031
+opencloning/batch_cloning/ziqiang_et_al2024/ziqiang_et_al2024.json,sha256=d-7oXbxoKhMKLz4FJ2OGDdedWTisoaRqLAh1NZnScBg,157189
+opencloning/bug_fixing/README.md,sha256=9EMhP_ibl_HDt745dz1Cw_Pl2kTMVrNJQW5ysCBcJoE,4231
+opencloning/bug_fixing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+opencloning/bug_fixing/backend_v0_3.py,sha256=ubfDN-IEwj-dW1Qgy3ozrkXcUIXwXvZcxJHrVanR_Ws,4213
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 opencloning/dna_functions.py,sha256=ivepJM2wRTIW0ArSiQ5s-XuqBd69giEQijaWXXGT64E,16536
 opencloning/dna_utils.py,sha256=uv97aO04dbk3NnqbN6GlnwOu0MOpK88rl2np2QcEQ4Y,6301
 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=H1b7CRx1JZ5pcUGd3uyJG2syYugkXiIo8HRCA11TQfE,20704
-opencloning/endpoints/external_import.py,sha256=DG8WSvyvr-9xy-odEwLHHA4FWiIh8sw4DvTblw5NCYc,18179
+opencloning/endpoints/assembly.py,sha256=MMwvlyM2NHnT04Pp7LdKQRvahq0itdqTtZx3OQhOswc,20980
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 opencloning/endpoints/no_assembly.py,sha256=NY6rhEDCNoZVn6Xk81cen2n-FkMr7ierfxM8G0npbQs,4722
 opencloning/endpoints/no_input.py,sha256=DuqKD3Ph3a44ZxPMEzZv1nwD5xlxYsN7YyxXcfjSUFc,3844
-opencloning/endpoints/other.py,sha256=TzfCJLDmZFWeKYxKhEfXOvlQrWWyBIGJ5FR0yA7tuvI,1673
-opencloning/endpoints/primer_design.py,sha256=ItPUa7bBW9JOOfTuLj0yNnF9UmQ-I_0l3i8wHpnUc6k,12854
-opencloning/gateway.py,sha256=jzpLbB8UCSlks0S6Qe9PXJ7CdzHiH2ko_O7MzYQLR14,8435
+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/main.py,sha256=l9PrPBMtGMEWxAPiPWR15Qv2oDNnRoNd8H8E3bZW6Do,3750
 opencloning/ncbi_requests.py,sha256=JrFc-Ugr1r1F4LqsdpJZEiERj7ZemvZSgiIltl2Chx8,5547
 opencloning/primer_design.py,sha256=nqCmYIZ7UvU4CQwVGJwX7T5LTHwt3-51_ZcTZZAgT_Y,9175
-opencloning/pydantic_models.py,sha256=gsipVXhjQOXVz2NL-MiNpLuOZYDVo2Pli9F--bp6tjs,15345
+opencloning/pydantic_models.py,sha256=lMO78M4MwDgzTEGz9qzsaADwAFXagWK4qGsF1K1hLZw,18865
 opencloning/request_examples.py,sha256=QAsJxVaq5tHwlPB404IiJ9WC6SA7iNY7XnJm63BWT_E,2944
-opencloning/utils.py,sha256=wsdTJYliap-t3oa7yQE3pWDa1CR19mr5lUQfocp4hoM,1875
-opencloning-0.2.8.2.dist-info/LICENSE,sha256=VSdVE1f8axjIh6gvo9ZZygJdTVkRFMcwCW_hvjOHC_w,1058
-opencloning-0.2.8.2.dist-info/METADATA,sha256=OrcZ2VMjjkWI31tB4B1tEa6GgIxBFlOiGWxmA_8eK6A,8429
-opencloning-0.2.8.2.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-opencloning-0.2.8.2.dist-info/RECORD,,
+opencloning/utils.py,sha256=0Lvw1h1AsUJTK2b9mNzYVi_DBeWmWCFA5dIPl_gERcI,1479
+opencloning-0.3.0.dist-info/LICENSE,sha256=VSdVE1f8axjIh6gvo9ZZygJdTVkRFMcwCW_hvjOHC_w,1058
+opencloning-0.3.0.dist-info/METADATA,sha256=fqz_qzNi4Q4eHOzzx4B6iMUMf7WMLFOu5EY4x0vthek,9083
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