benchling-api-client 2.0.415__py3-none-any.whl → 2.0.417__py3-none-any.whl

benchling_api_client/v2/beta/models/rna_sequence_with_entity_type_entity_type.py

@@ -0,0 +1,22 @@
+from enum import Enum
+from functools import lru_cache
+from typing import cast
+
+from ..extensions import Enums
+
+
+class RnaSequenceWithEntityTypeEntityType(Enums.KnownString):
+    RNA_SEQUENCE = "rna_sequence"
+
+    def __str__(self) -> str:
+        return str(self.value)
+
+    @staticmethod
+    @lru_cache(maxsize=None)
+    def of_unknown(val: str) -> "RnaSequenceWithEntityTypeEntityType":
+        if not isinstance(val, str):
+            raise ValueError(
+                f"Value of RnaSequenceWithEntityTypeEntityType must be a string (encountered: {val})"
+            )
+        newcls = Enum("RnaSequenceWithEntityTypeEntityType", {"_UNKNOWN": val}, type=Enums.UnknownString)  # type: ignore
+        return cast(RnaSequenceWithEntityTypeEntityType, getattr(newcls, "_UNKNOWN"))

benchling_api_client/v2/beta/openapi.yaml

@@ -2839,7 +2839,7 @@ components:
           description: The path of the web URL, omitting the tenant domain
           type: string
         webURL:
-          description: URL of the protein.
+          description: URL of the AA sequence.
           example: https://benchling.com/benchling/f/lib_55UxcIps-registry/prtn_7nMBOMm0-kedchain11/edit"
           format: uri
           readOnly: true
@@ -2926,6 +2926,16 @@ components:
           deprecated: true
           type: string
       type: object
+    AaSequenceWithEntityType:
+      allOf:
+      - $ref: '#/components/schemas/AaSequence'
+      - properties:
+          entityType:
+            enum:
+            - aa_sequence
+            type: string
+        type: object
+      type: object
     AccessPoliciesPaginatedList:
       additionalProperties: false
       properties:
@@ -3872,6 +3882,16 @@ components:
       allOf:
       - $ref: '#/components/schemas/EntityUpsertBaseRequest'
       - $ref: '#/components/schemas/CustomEntityBaseRequestForCreate'
+    CustomEntityWithEntityType:
+      allOf:
+      - $ref: '#/components/schemas/CustomEntity'
+      - properties:
+          entityType:
+            enum:
+            - custom_entity
+            type: string
+        type: object
+      type: object
     CustomField:
       properties:
         value:
@@ -4408,6 +4428,16 @@ components:
               chemical modifications
             example: RNA1{d(A)p.d(C)[Ssp].d(T)p.d(T)p.d(T)p.d(T)p.d(T)p}$$$$V2.0
             type: string
+    DnaOligoWithEntityType:
+      allOf:
+      - $ref: '#/components/schemas/DnaOligo'
+      - properties:
+          entityType:
+            enum:
+            - dna_oligo
+            type: string
+        type: object
+      type: object
     DnaSequence:
       properties:
         aliases:
@@ -4637,6 +4667,16 @@ components:
           minimum: -1
           type: integer
       type: object
+    DnaSequenceWithEntityType:
+      allOf:
+      - $ref: '#/components/schemas/DnaSequence'
+      - properties:
+          entityType:
+            enum:
+            - dna_sequence
+            type: string
+        type: object
+      type: object
     DropdownDependency:
       additionalProperties: false
       allOf:
@@ -4685,13 +4725,26 @@ components:
           type: array
       type: object
     Entity:
+      discriminator:
+        mapping:
+          aa_sequence: '#/components/schemas/AaSequenceWithEntityType'
+          custom_entity: '#/components/schemas/CustomEntityWithEntityType'
+          dna_oligo: '#/components/schemas/DnaOligoWithEntityType'
+          dna_sequence: '#/components/schemas/DnaSequenceWithEntityType'
+          mixture: '#/components/schemas/MixtureWithEntityType'
+          molecule: '#/components/schemas/MoleculeWithEntityType'
+          rna_oligo: '#/components/schemas/RnaOligoWithEntityType'
+          rna_sequence: '#/components/schemas/RnaSequenceWithEntityType'
+        propertyName: entityType
       oneOf:
-      - $ref: '#/components/schemas/DnaSequence'
-      - $ref: '#/components/schemas/AaSequence'
-      - $ref: '#/components/schemas/Mixture'
-      - $ref: '#/components/schemas/DnaOligo'
-      - $ref: '#/components/schemas/RnaOligo'
-      - $ref: '#/components/schemas/CustomEntity'
+      - $ref: '#/components/schemas/DnaSequenceWithEntityType'
+      - $ref: '#/components/schemas/RnaSequenceWithEntityType'
+      - $ref: '#/components/schemas/AaSequenceWithEntityType'
+      - $ref: '#/components/schemas/MixtureWithEntityType'
+      - $ref: '#/components/schemas/DnaOligoWithEntityType'
+      - $ref: '#/components/schemas/RnaOligoWithEntityType'
+      - $ref: '#/components/schemas/MoleculeWithEntityType'
+      - $ref: '#/components/schemas/CustomEntityWithEntityType'
       type: object
     EntityBulkUpsertBaseRequest:
       allOf:
@@ -6268,6 +6321,16 @@ components:
             - mixture_prep_table
             type: string
         type: object
+    MixtureWithEntityType:
+      allOf:
+      - $ref: '#/components/schemas/Mixture'
+      - properties:
+          entityType:
+            enum:
+            - mixture
+            type: string
+        type: object
+      type: object
     Molecule:
       additionalProperties: false
       properties:
@@ -6437,6 +6500,16 @@ components:
       allOf:
       - $ref: '#/components/schemas/EntityUpsertBaseRequest'
       - $ref: '#/components/schemas/MoleculeBaseRequestForCreate'
+    MoleculeWithEntityType:
+      allOf:
+      - $ref: '#/components/schemas/Molecule'
+      - properties:
+          entityType:
+            enum:
+            - molecule
+            type: string
+        type: object
+      type: object
     NotFoundError:
       properties:
         error:
@@ -6973,6 +7046,143 @@ components:
           nucleotideType:
             example: RNA
             type: string
+    RnaOligoWithEntityType:
+      allOf:
+      - $ref: '#/components/schemas/RnaOligo'
+      - properties:
+          entityType:
+            enum:
+            - rna_oligo
+            type: string
+        type: object
+      type: object
+    RnaSequence:
+      properties:
+        aliases:
+          items:
+            type: string
+          type: array
+        alignmentIds:
+          description: API IDs of Nucleotide Alignments involving the RNA sequence
+          items:
+            type: string
+          type: array
+        annotations:
+          items:
+            $ref: '#/components/schemas/RnaAnnotation'
+          type: array
+        apiURL:
+          description: The canonical url of the RNA Sequence in the API.
+          example: https://benchling.com/api/v2/rna-sequences/seq_asZya4lk
+          format: uri
+          readOnly: true
+          type: string
+        archiveRecord:
+          allOf:
+          - $ref: '#/components/schemas/ArchiveRecord'
+          nullable: true
+        authors:
+          items:
+            $ref: '#/components/schemas/UserSummary'
+          type: array
+        bases:
+          type: string
+        createdAt:
+          format: date-time
+          readOnly: true
+          type: string
+        creator:
+          $ref: '#/components/schemas/UserSummary'
+        customFields:
+          $ref: '#/components/schemas/CustomFields'
+        customNotation:
+          description: Representation of the RNA Sequence in the custom notation specified
+            in the request. Null if no notation was specified.
+          nullable: true
+          type: string
+        customNotationName:
+          description: Name of the custom notation specified in the request. Null
+            if no notation was specified.
+          nullable: true
+          type: string
+        entityRegistryId:
+          nullable: true
+          type: string
+        fields:
+          $ref: '#/components/schemas/Fields'
+        folderId:
+          nullable: true
+          type: string
+        helm:
+          description: Representation of the RNA Sequence in HELM syntax, including
+            any chemical modifications.
+          example: RNA1{r(A)p.r(C)[Ssp].r(U)p.r(U)p.r(U)p.r(U)p.r(U)p}$$$$V2.0
+          nullable: true
+          type: string
+        id:
+          type: string
+        isCircular:
+          example: false
+          type: boolean
+        length:
+          type: integer
+        modifiedAt:
+          format: date-time
+          readOnly: true
+          type: string
+        name:
+          type: string
+        parts:
+          items:
+            $ref: '#/components/schemas/RnaSequencePart'
+          type: array
+        primers:
+          items:
+            $ref: '#/components/schemas/Primer'
+          type: array
+        registrationOrigin:
+          allOf:
+          - $ref: '#/components/schemas/RegistrationOrigin'
+          nullable: true
+          readOnly: true
+        registryId:
+          nullable: true
+          type: string
+        schema:
+          allOf:
+          - $ref: '#/components/schemas/SchemaSummary'
+          nullable: true
+        translations:
+          items:
+            $ref: '#/components/schemas/Translation'
+          type: array
+        url:
+          description: The path of the web URL, omitting the tenant domain
+          type: string
+        webURL:
+          readOnly: true
+          type: string
+      type: object
+    RnaSequencePart:
+      allOf:
+      - $ref: '#/components/schemas/NucleotideSequencePart'
+      - properties:
+          strand:
+            example: 1
+            maximum: 1
+            minimum: 1
+            type: integer
+        type: object
+    RnaSequenceWithEntityType:
+      allOf:
+      - $ref: '#/components/schemas/RnaSequence'
+      - properties:
+          entityType:
+            enum:
+            - rna_sequence
+            type: string
+        type: object
+      type: object
     SampleRestrictionStatus:
       enum:
       - RESTRICTED
@@ -7684,8 +7894,8 @@ tags:
     assigned to access an item.
   name: Collaborations
 - description: 'Benchling supports custom entities for biological entities that are
-    neither sequences or proteins. Custom entities must have an entity schema set
-    and can have both schema fields and custom fields.
+    neither DNA, RNA, nor AA sequences. Custom entities must have an entity schema
+    set and can have both schema fields and custom fields.
 
     '
   name: Custom Entities

benchling_api_client/v2/stable/models/aa_sequence.py

@@ -809,7 +809,7 @@ class AaSequence:
 
     @property
     def web_url(self) -> str:
-        """ URL of the protein. """
+        """ URL of the AA sequence. """
         if isinstance(self._web_url, Unset):
             raise NotPresentError(self, "web_url")
         return self._web_url

benchling_api_client/v2/stable/models/aa_sequence_with_entity_type.py

@@ -851,7 +851,7 @@ class AaSequenceWithEntityType:
 
     @property
     def web_url(self) -> str:
-        """ URL of the protein. """
+        """ URL of the AA sequence. """
         if isinstance(self._web_url, Unset):
             raise NotPresentError(self, "web_url")
         return self._web_url

benchling_api_client/v2/stable/models/container_content.py

@@ -3,15 +3,17 @@ from typing import Any, cast, Dict, List, Optional, Type, TypeVar, Union
 import attr
 
 from ..extensions import NotPresentError, UnknownType
-from ..models.aa_sequence import AaSequence
+from ..models.aa_sequence_with_entity_type import AaSequenceWithEntityType
 from ..models.batch import Batch
-from ..models.custom_entity import CustomEntity
-from ..models.dna_oligo import DnaOligo
-from ..models.dna_sequence import DnaSequence
+from ..models.custom_entity_with_entity_type import CustomEntityWithEntityType
+from ..models.dna_oligo_with_entity_type import DnaOligoWithEntityType
+from ..models.dna_sequence_with_entity_type import DnaSequenceWithEntityType
 from ..models.inaccessible_resource import InaccessibleResource
 from ..models.measurement import Measurement
-from ..models.mixture import Mixture
-from ..models.rna_oligo import RnaOligo
+from ..models.mixture_with_entity_type import MixtureWithEntityType
+from ..models.molecule_with_entity_type import MoleculeWithEntityType
+from ..models.rna_oligo_with_entity_type import RnaOligoWithEntityType
+from ..models.rna_sequence_with_entity_type import RnaSequenceWithEntityType
 from ..types import UNSET, Unset
 
 T = TypeVar("T", bound="ContainerContent")
@@ -26,7 +28,17 @@ class ContainerContent:
     _entity: Union[
         Unset,
         None,
-        Union[DnaSequence, AaSequence, Mixture, DnaOligo, RnaOligo, CustomEntity, UnknownType],
+        Union[
+            DnaSequenceWithEntityType,
+            RnaSequenceWithEntityType,
+            AaSequenceWithEntityType,
+            MixtureWithEntityType,
+            DnaOligoWithEntityType,
+            RnaOligoWithEntityType,
+            MoleculeWithEntityType,
+            CustomEntityWithEntityType,
+            UnknownType,
+        ],
         InaccessibleResource,
         UnknownType,
     ] = UNSET
@@ -68,19 +80,25 @@ class ContainerContent:
         elif isinstance(self._entity, object):
             if isinstance(self._entity, UnknownType):
                 entity = self._entity.value
-            elif isinstance(self._entity, DnaSequence):
+            elif isinstance(self._entity, DnaSequenceWithEntityType):
+                entity = self._entity.to_dict()
+
+            elif isinstance(self._entity, RnaSequenceWithEntityType):
+                entity = self._entity.to_dict()
+
+            elif isinstance(self._entity, AaSequenceWithEntityType):
                 entity = self._entity.to_dict()
 
-            elif isinstance(self._entity, AaSequence):
+            elif isinstance(self._entity, MixtureWithEntityType):
                 entity = self._entity.to_dict()
 
-            elif isinstance(self._entity, Mixture):
+            elif isinstance(self._entity, DnaOligoWithEntityType):
                 entity = self._entity.to_dict()
 
-            elif isinstance(self._entity, DnaOligo):
+            elif isinstance(self._entity, RnaOligoWithEntityType):
                 entity = self._entity.to_dict()
 
-            elif isinstance(self._entity, RnaOligo):
+            elif isinstance(self._entity, MoleculeWithEntityType):
                 entity = self._entity.to_dict()
 
             else:
@@ -162,7 +180,17 @@ class ContainerContent:
         def get_entity() -> Union[
             Unset,
             None,
-            Union[DnaSequence, AaSequence, Mixture, DnaOligo, RnaOligo, CustomEntity, UnknownType],
+            Union[
+                DnaSequenceWithEntityType,
+                RnaSequenceWithEntityType,
+                AaSequenceWithEntityType,
+                MixtureWithEntityType,
+                DnaOligoWithEntityType,
+                RnaOligoWithEntityType,
+                MoleculeWithEntityType,
+                CustomEntityWithEntityType,
+                UnknownType,
+            ],
             InaccessibleResource,
             UnknownType,
         ]:
@@ -171,14 +199,34 @@ class ContainerContent:
             ) -> Union[
                 Unset,
                 None,
-                Union[DnaSequence, AaSequence, Mixture, DnaOligo, RnaOligo, CustomEntity, UnknownType],
+                Union[
+                    DnaSequenceWithEntityType,
+                    RnaSequenceWithEntityType,
+                    AaSequenceWithEntityType,
+                    MixtureWithEntityType,
+                    DnaOligoWithEntityType,
+                    RnaOligoWithEntityType,
+                    MoleculeWithEntityType,
+                    CustomEntityWithEntityType,
+                    UnknownType,
+                ],
                 InaccessibleResource,
                 UnknownType,
             ]:
                 entity: Union[
                     Unset,
                     None,
-                    Union[DnaSequence, AaSequence, Mixture, DnaOligo, RnaOligo, CustomEntity, UnknownType],
+                    Union[
+                        DnaSequenceWithEntityType,
+                        RnaSequenceWithEntityType,
+                        AaSequenceWithEntityType,
+                        MixtureWithEntityType,
+                        DnaOligoWithEntityType,
+                        RnaOligoWithEntityType,
+                        MoleculeWithEntityType,
+                        CustomEntityWithEntityType,
+                        UnknownType,
+                    ],
                     InaccessibleResource,
                     UnknownType,
                 ]
@@ -191,15 +239,78 @@ class ContainerContent:
                     def _parse_entity_or_inaccessible_resource(
                         data: Union[Dict[str, Any]]
                     ) -> Union[
-                        DnaSequence, AaSequence, Mixture, DnaOligo, RnaOligo, CustomEntity, UnknownType
+                        DnaSequenceWithEntityType,
+                        RnaSequenceWithEntityType,
+                        AaSequenceWithEntityType,
+                        MixtureWithEntityType,
+                        DnaOligoWithEntityType,
+                        RnaOligoWithEntityType,
+                        MoleculeWithEntityType,
+                        CustomEntityWithEntityType,
+                        UnknownType,
                     ]:
                         entity_or_inaccessible_resource: Union[
-                            DnaSequence, AaSequence, Mixture, DnaOligo, RnaOligo, CustomEntity, UnknownType
+                            DnaSequenceWithEntityType,
+                            RnaSequenceWithEntityType,
+                            AaSequenceWithEntityType,
+                            MixtureWithEntityType,
+                            DnaOligoWithEntityType,
+                            RnaOligoWithEntityType,
+                            MoleculeWithEntityType,
+                            CustomEntityWithEntityType,
+                            UnknownType,
                         ]
+                        discriminator_value: str = cast(str, data.get("entityType"))
+                        if discriminator_value is not None:
+                            entity: Union[
+                                DnaSequenceWithEntityType,
+                                RnaSequenceWithEntityType,
+                                AaSequenceWithEntityType,
+                                MixtureWithEntityType,
+                                DnaOligoWithEntityType,
+                                RnaOligoWithEntityType,
+                                MoleculeWithEntityType,
+                                CustomEntityWithEntityType,
+                                UnknownType,
+                            ]
+                            if discriminator_value == "aa_sequence":
+                                entity = AaSequenceWithEntityType.from_dict(data, strict=False)
+
+                                return entity
+                            if discriminator_value == "custom_entity":
+                                entity = CustomEntityWithEntityType.from_dict(data, strict=False)
+
+                                return entity
+                            if discriminator_value == "dna_oligo":
+                                entity = DnaOligoWithEntityType.from_dict(data, strict=False)
+
+                                return entity
+                            if discriminator_value == "dna_sequence":
+                                entity = DnaSequenceWithEntityType.from_dict(data, strict=False)
+
+                                return entity
+                            if discriminator_value == "mixture":
+                                entity = MixtureWithEntityType.from_dict(data, strict=False)
+
+                                return entity
+                            if discriminator_value == "molecule":
+                                entity = MoleculeWithEntityType.from_dict(data, strict=False)
+
+                                return entity
+                            if discriminator_value == "rna_oligo":
+                                entity = RnaOligoWithEntityType.from_dict(data, strict=False)
+
+                                return entity
+                            if discriminator_value == "rna_sequence":
+                                entity = RnaSequenceWithEntityType.from_dict(data, strict=False)
+
+                                return entity
+
+                            return UnknownType(value=data)
                         try:
                             if not isinstance(data, dict):
                                 raise TypeError()
-                            entity = DnaSequence.from_dict(data, strict=True)
+                            entity = DnaSequenceWithEntityType.from_dict(data, strict=True)
 
                             return entity
                         except:  # noqa: E722
@@ -207,7 +318,7 @@ class ContainerContent:
                         try:
                             if not isinstance(data, dict):
                                 raise TypeError()
-                            entity = AaSequence.from_dict(data, strict=True)
+                            entity = RnaSequenceWithEntityType.from_dict(data, strict=True)
 
                             return entity
                         except:  # noqa: E722
@@ -215,7 +326,7 @@ class ContainerContent:
                         try:
                             if not isinstance(data, dict):
                                 raise TypeError()
-                            entity = Mixture.from_dict(data, strict=True)
+                            entity = AaSequenceWithEntityType.from_dict(data, strict=True)
 
                             return entity
                         except:  # noqa: E722
@@ -223,7 +334,7 @@ class ContainerContent:
                         try:
                             if not isinstance(data, dict):
                                 raise TypeError()
-                            entity = DnaOligo.from_dict(data, strict=True)
+                            entity = MixtureWithEntityType.from_dict(data, strict=True)
 
                             return entity
                         except:  # noqa: E722
@@ -231,7 +342,7 @@ class ContainerContent:
                         try:
                             if not isinstance(data, dict):
                                 raise TypeError()
-                            entity = RnaOligo.from_dict(data, strict=True)
+                            entity = DnaOligoWithEntityType.from_dict(data, strict=True)
 
                             return entity
                         except:  # noqa: E722
@@ -239,7 +350,23 @@ class ContainerContent:
                         try:
                             if not isinstance(data, dict):
                                 raise TypeError()
-                            entity = CustomEntity.from_dict(data, strict=True)
+                            entity = RnaOligoWithEntityType.from_dict(data, strict=True)
+
+                            return entity
+                        except:  # noqa: E722
+                            pass
+                        try:
+                            if not isinstance(data, dict):
+                                raise TypeError()
+                            entity = MoleculeWithEntityType.from_dict(data, strict=True)
+
+                            return entity
+                        except:  # noqa: E722
+                            pass
+                        try:
+                            if not isinstance(data, dict):
+                                raise TypeError()
+                            entity = CustomEntityWithEntityType.from_dict(data, strict=True)
 
                             return entity
                         except:  # noqa: E722
@@ -274,7 +401,17 @@ class ContainerContent:
                 Union[
                     Unset,
                     None,
-                    Union[DnaSequence, AaSequence, Mixture, DnaOligo, RnaOligo, CustomEntity, UnknownType],
+                    Union[
+                        DnaSequenceWithEntityType,
+                        RnaSequenceWithEntityType,
+                        AaSequenceWithEntityType,
+                        MixtureWithEntityType,
+                        DnaOligoWithEntityType,
+                        RnaOligoWithEntityType,
+                        MoleculeWithEntityType,
+                        CustomEntityWithEntityType,
+                        UnknownType,
+                    ],
                     InaccessibleResource,
                     UnknownType,
                 ],
@@ -342,7 +479,17 @@ class ContainerContent:
         self,
     ) -> Optional[
         Union[
-            Union[DnaSequence, AaSequence, Mixture, DnaOligo, RnaOligo, CustomEntity, UnknownType],
+            Union[
+                DnaSequenceWithEntityType,
+                RnaSequenceWithEntityType,
+                AaSequenceWithEntityType,
+                MixtureWithEntityType,
+                DnaOligoWithEntityType,
+                RnaOligoWithEntityType,
+                MoleculeWithEntityType,
+                CustomEntityWithEntityType,
+                UnknownType,
+            ],
             InaccessibleResource,
             UnknownType,
         ]
@@ -356,7 +503,17 @@ class ContainerContent:
         self,
         value: Optional[
             Union[
-                Union[DnaSequence, AaSequence, Mixture, DnaOligo, RnaOligo, CustomEntity, UnknownType],
+                Union[
+                    DnaSequenceWithEntityType,
+                    RnaSequenceWithEntityType,
+                    AaSequenceWithEntityType,
+                    MixtureWithEntityType,
+                    DnaOligoWithEntityType,
+                    RnaOligoWithEntityType,
+                    MoleculeWithEntityType,
+                    CustomEntityWithEntityType,
+                    UnknownType,
+                ],
                 InaccessibleResource,
                 UnknownType,
             ]