benchling-sdk 1.15.0a1__py3-none-any.whl → 1.17.0__py3-none-any.whl

benchling_sdk/services/v2/stable/codon_usage_table_service.py

@@ -0,0 +1,73 @@
+from typing import Iterable, Optional
+
+from benchling_api_client.v2.stable.api.codon_usage_tables import list_codon_usage_tables
+from benchling_api_client.v2.types import Response
+
+from benchling_sdk.errors import raise_for_status
+from benchling_sdk.helpers.decorators import api_method
+from benchling_sdk.helpers.pagination_helpers import NextToken, PageIterator
+from benchling_sdk.helpers.serialization_helpers import none_as_unset, optional_array_query_param
+from benchling_sdk.models import CodonUsageTable, CodonUsageTablesPaginatedList, ListCodonUsageTablesSort
+from benchling_sdk.services.v2.base_service import BaseService
+
+
+class CodonUsageTableService(BaseService):
+    """
+    Codon Usage Tables.
+
+    Benchling curates codon usage data for a variety of organisms to support operations such as Codon
+    Optimization and Back Translation.
+
+    See https://benchling.com/api/reference#/Codon%20Usage%20Tables
+    """
+
+    @api_method
+    def _list_page(
+        self,
+        sort: Optional[ListCodonUsageTablesSort] = None,
+        ids: Optional[Iterable[str]] = None,
+        name: Optional[str] = None,
+        name_includes: Optional[str] = None,
+        names_any_of: Optional[Iterable[str]] = [],
+        page_size: Optional[int] = None,
+        next_token: NextToken = None,
+    ) -> Response[CodonUsageTablesPaginatedList]:
+        response = list_codon_usage_tables.sync_detailed(
+            client=self.client,
+            ids=none_as_unset(optional_array_query_param(ids)),
+            name=none_as_unset(name),
+            name_includes=none_as_unset(name_includes),
+            namesany_of=none_as_unset(optional_array_query_param(names_any_of)),
+            next_token=none_as_unset(next_token),
+            page_size=none_as_unset(page_size),
+            sort=none_as_unset(sort),
+        )
+        return raise_for_status(response)
+
+    def list(
+        self,
+        sort: Optional[ListCodonUsageTablesSort] = None,
+        ids: Optional[Iterable[str]] = None,
+        name: Optional[str] = None,
+        name_includes: Optional[str] = None,
+        names_any_of: Optional[Iterable[str]] = None,
+        page_size: Optional[int] = None,
+    ) -> PageIterator[CodonUsageTable]:
+        """
+        List codon usage tables.
+
+        See https://benchling.com/api/reference#/Codon%20Usage%20Tables/listCodonUsageTables
+        """
+
+        def api_call(next_token: NextToken) -> Response[CodonUsageTablesPaginatedList]:
+            return self._list_page(
+                sort=sort,
+                ids=ids,
+                name=name,
+                name_includes=name_includes,
+                names_any_of=names_any_of,
+                page_size=page_size,
+                next_token=next_token,
+            )
+
+        return PageIterator(api_call, lambda result: result.codon_usage_tables)

benchling_sdk/services/v2/stable/dna_sequence_service.py

@@ -15,6 +15,7 @@ from benchling_api_client.v2.stable.api.dna_sequences import (
     get_dna_sequence,
     list_dna_sequences,
     match_bases_dna_sequences,
+    optimize_codons,
     search_dna_sequences,
     unarchive_dna_sequences,
     update_dna_sequence,
@@ -54,6 +55,7 @@ from benchling_sdk.models import (
     EntityArchiveReason,
     ListDNASequencesSort,
     MatchBasesRequest,
+    OptimizeCodons,
     SearchBasesRequest,
 )
 from benchling_sdk.services.v2.base_service import BaseService
@@ -398,3 +400,13 @@ class DnaSequenceService(BaseService):
             client=self.client, json_body=find_matching_region
         )
         return model_from_detailed(response)
+
+    @api_method
+    def optimize_codons(self, optimize_request: OptimizeCodons) -> AsyncTaskLink:
+        """
+        Create codon-optimized DNA sequences.
+
+        See https://benchling.com/api/reference#/DNA%20Sequences/optimizeCodons
+        """
+        response = optimize_codons.sync_detailed(client=self.client, json_body=optimize_request)
+        return model_from_detailed(response)

benchling_sdk/services/v2/stable/enzyme_service.py

@@ -0,0 +1,72 @@
+from typing import Iterable, Optional
+
+from benchling_api_client.v2.stable.api.enzymes import list_enzymes
+from benchling_api_client.v2.types import Response
+
+from benchling_sdk.errors import raise_for_status
+from benchling_sdk.helpers.decorators import api_method
+from benchling_sdk.helpers.pagination_helpers import NextToken, PageIterator
+from benchling_sdk.helpers.serialization_helpers import none_as_unset, optional_array_query_param
+from benchling_sdk.models import Enzyme, EnzymesPaginatedList, ListEnzymesSort
+from benchling_sdk.services.v2.base_service import BaseService
+
+
+class EnzymeService(BaseService):
+    """
+    Enzymes.
+
+    Restriction enzymes are curated by Benchling for operations such as Digests and Codon Optimization.
+
+    See https://benchling.com/api/reference#/Enzymes
+    """
+
+    @api_method
+    def _list_page(
+        self,
+        sort: Optional[ListEnzymesSort] = None,
+        ids: Optional[Iterable[str]] = None,
+        name: Optional[str] = None,
+        name_includes: Optional[str] = None,
+        names_any_of: Optional[Iterable[str]] = [],
+        page_size: Optional[int] = None,
+        next_token: NextToken = None,
+    ) -> Response[EnzymesPaginatedList]:
+        response = list_enzymes.sync_detailed(
+            client=self.client,
+            ids=none_as_unset(optional_array_query_param(ids)),
+            name=none_as_unset(name),
+            name_includes=none_as_unset(name_includes),
+            namesany_of=none_as_unset(optional_array_query_param(names_any_of)),
+            next_token=none_as_unset(next_token),
+            page_size=none_as_unset(page_size),
+            sort=none_as_unset(sort),
+        )
+        return raise_for_status(response)
+
+    def list(
+        self,
+        sort: Optional[ListEnzymesSort] = None,
+        ids: Optional[Iterable[str]] = None,
+        name: Optional[str] = None,
+        name_includes: Optional[str] = None,
+        names_any_of: Optional[Iterable[str]] = None,
+        page_size: Optional[int] = None,
+    ) -> PageIterator[Enzyme]:
+        """
+        List enzymes.
+
+        See https://benchling.com/api/reference#/Enzymes/listEnzymes
+        """
+
+        def api_call(next_token: NextToken) -> Response[EnzymesPaginatedList]:
+            return self._list_page(
+                sort=sort,
+                ids=ids,
+                name=name,
+                name_includes=name_includes,
+                names_any_of=names_any_of,
+                page_size=page_size,
+                next_token=next_token,
+            )
+
+        return PageIterator(api_call, lambda result: result.enzymes)

benchling_sdk/services/v2/stable/monomer_service.py

@@ -0,0 +1,144 @@
+from typing import Iterable, Optional
+
+from benchling_api_client.v2.stable.api.monomers import (
+    archive_monomers,
+    create_monomer,
+    list_monomers,
+    unarchive_monomers,
+    update_monomer,
+)
+from benchling_api_client.v2.types import Response
+
+from benchling_sdk.errors import raise_for_status
+from benchling_sdk.helpers.decorators import api_method
+from benchling_sdk.helpers.pagination_helpers import NextToken, PageIterator
+from benchling_sdk.helpers.response_helpers import model_from_detailed
+from benchling_sdk.helpers.serialization_helpers import none_as_unset, optional_array_query_param
+from benchling_sdk.models import (
+    Monomer,
+    MonomerCreate,
+    MonomersArchivalChange,
+    MonomersArchive,
+    MonomersArchiveReason,
+    MonomersPaginatedList,
+    MonomersUnarchive,
+    MonomerUpdate,
+)
+from benchling_sdk.services.v2.base_service import BaseService
+
+
+class MonomerService(BaseService):
+    """
+    Monomers.
+
+    Monomers are chemical building blocks with specified structures used to compose modified
+    nucleotides. Note that monomer write endpoints require tenant admin permissions.
+
+    See https://benchling.com/api/reference#/Monomers
+    """
+
+    @api_method
+    def _list_page(
+        self,
+        page_size: Optional[int] = None,
+        next_token: NextToken = None,
+        returning: Optional[Iterable[str]] = None,
+    ) -> Response[MonomersPaginatedList]:
+        response = list_monomers.sync_detailed(
+            client=self.client,
+            next_token=none_as_unset(next_token),
+            page_size=none_as_unset(page_size),
+            returning=none_as_unset(optional_array_query_param(returning)),
+        )
+        return raise_for_status(response)
+
+    def list(
+        self,
+        page_size: Optional[int] = None,
+        returning: Optional[Iterable[str]] = None,
+    ) -> PageIterator[Monomer]:
+        """
+        List monomers.
+
+        See https://benchling.com/api/reference#/Monomers/listMonomers
+        """
+
+        def api_call(next_token: NextToken) -> Response[MonomersPaginatedList]:
+            return self._list_page(
+                page_size=page_size,
+                next_token=next_token,
+                returning=returning,
+            )
+
+        return PageIterator(api_call, lambda result: result.monomers)
+
+    @api_method
+    def create(
+        self,
+        monomer: MonomerCreate,
+        returning: Optional[Iterable[str]] = None,
+    ) -> Monomer:
+        """
+        Create a monomer.
+
+        See https://benchling.com/api/reference#/Monomers/createMonomer
+        """
+        response = create_monomer.sync_detailed(
+            client=self.client,
+            json_body=monomer,
+            returning=none_as_unset(optional_array_query_param(returning)),
+        )
+        return model_from_detailed(response)
+
+    @api_method
+    def update(
+        self,
+        monomer_id: str,
+        monomer: MonomerUpdate,
+        returning: Optional[Iterable[str]] = None,
+    ) -> Monomer:
+        """
+        Update a Monomer.
+
+        See https://benchling.com/api/reference#/Monomers/updateMonomer
+        """
+        response = update_monomer.sync_detailed(
+            client=self.client,
+            monomer_id=monomer_id,
+            json_body=monomer,
+            returning=none_as_unset(optional_array_query_param(returning)),
+        )
+        return model_from_detailed(response)
+
+    @api_method
+    def archive(
+        self,
+        monomer_ids: Iterable[str],
+        reason: MonomersArchiveReason,
+    ) -> MonomersArchivalChange:
+        """
+        Archive Monomers.
+
+        See https://benchling.com/api/reference#/Monomers/archiveMonomers
+        """
+        response = archive_monomers.sync_detailed(
+            client=self.client,
+            json_body=MonomersArchive(monomer_ids=list(monomer_ids), reason=reason),
+        )
+        return model_from_detailed(response)
+
+    @api_method
+    def unarchive(
+        self,
+        monomer_ids: Iterable[str],
+    ) -> MonomersArchivalChange:
+        """
+        Unarchive Monomers.
+
+        See https://benchling.com/api/reference#/Monomers/unarchiveMonomers
+        """
+        response = unarchive_monomers.sync_detailed(
+            client=self.client,
+            json_body=MonomersUnarchive(monomer_ids=list(monomer_ids)),
+        )
+        return model_from_detailed(response)

benchling_sdk/services/v2/stable/organization_service.py

@@ -1,6 +1,14 @@
 from typing import Iterable, List, Optional, Union
 
-from benchling_api_client.v2.stable.api.organizations import get_organization, list_organizations
+from benchling_api_client.v2.stable.api.organizations import (
+    create_organization_membership,
+    delete_organization_membership,
+    get_organization,
+    get_organization_membership,
+    list_organization_memberships,
+    list_organizations,
+    update_organization_membership,
+)
 from benchling_api_client.v2.types import Response
 
 from benchling_sdk.errors import raise_for_status
@@ -10,7 +18,15 @@ from benchling_sdk.helpers.logging_helpers import log_not_implemented
 from benchling_sdk.helpers.pagination_helpers import NextToken, PageIterator
 from benchling_sdk.helpers.response_helpers import model_from_detailed
 from benchling_sdk.helpers.serialization_helpers import none_as_unset, optional_array_query_param
-from benchling_sdk.models import ListOrganizationsSort, Organization, OrganizationsPaginatedList
+from benchling_sdk.models import (
+    ListOrganizationsSort,
+    Membership,
+    MembershipCreate,
+    MembershipsPaginatedList,
+    MembershipUpdate,
+    Organization,
+    OrganizationsPaginatedList,
+)
 from benchling_sdk.services.v2.base_service import BaseService
 
 
@@ -116,3 +132,89 @@ class OrganizationService(BaseService):
             return body.organizations
 
         return PageIterator(api_call, results_extractor)
+
+    @api_method
+    def _list_memberships_page(
+        self,
+        organization_id: str,
+        role: Optional[str],
+        page_size: Optional[int],
+        next_token: NextToken,
+    ) -> Response[MembershipsPaginatedList]:
+        response = list_organization_memberships.sync_detailed(
+            client=self.client,
+            organization_id=organization_id,
+            page_size=none_as_unset(page_size),
+            next_token=next_token,
+            role=none_as_unset(role),
+        )
+        raise_for_status(response)
+        return response  # type: ignore
+
+    def list_memberships(
+        self,
+        organization_id: str,
+        role: Optional[str] = None,
+        page_size: Optional[int] = None,
+    ) -> PageIterator[MembershipsPaginatedList]:
+        """Return all organization memberships in the given organization.
+
+        See https://benchling.com/api/reference#/Organizations/listOrganizationMemberships
+        """
+
+        def api_call(next_token: NextToken) -> Response[MembershipsPaginatedList]:
+            return self._list_memberships_page(organization_id, role, page_size, next_token)
+
+        return PageIterator(api_call, lambda body: body.memberships)
+
+    @api_method
+    def get_membership(self, organization_id: str, user_id: str) -> Membership:
+        """Get organization membership.
+
+        See https://benchling.com/api/reference#/Organizations/getOrganizationMembership
+        """
+        response = get_organization_membership.sync_detailed(
+            client=self.client, organization_id=organization_id, user_id=user_id
+        )
+        return model_from_detailed(response)
+
+    @api_method
+    def create_membership(self, organization_id: str, membership: MembershipCreate) -> Membership:
+        """Create organization membership.
+
+        See https://benchling.com/api/reference#/Organizations/createOrganizationMembership
+        """
+        response = create_organization_membership.sync_detailed(
+            client=self.client,
+            organization_id=organization_id,
+            json_body=membership,
+        )
+        return model_from_detailed(response)
+
+    @api_method
+    def update_membership(
+        self, organization_id: str, user_id: str, membership: MembershipUpdate
+    ) -> Membership:
+        """Update organization membership by user ID and organization ID.
+
+        See https://benchling.com/api/reference#/Organizations/updateOrganizationMembership
+        """
+        response = update_organization_membership.sync_detailed(
+            client=self.client,
+            organization_id=organization_id,
+            user_id=user_id,
+            json_body=membership,
+        )
+        return model_from_detailed(response)
+
+    @api_method
+    def delete_membership(self, organization_id: str, user_id: str) -> None:
+        """Delete a single team membership.
+
+        See https://benchling.com/api/reference#/Organizations/deleteOrganizationMembership
+        """
+        raise_for_status(
+            delete_organization_membership.sync_detailed(
+                client=self.client, organization_id=organization_id, user_id=user_id
+            )
+        )

benchling_sdk/services/v2/stable/team_service.py

@@ -1,6 +1,16 @@
 from typing import Iterable, List, Optional, Union
 
-from benchling_api_client.v2.stable.api.teams import get_team, list_teams
+from benchling_api_client.v2.stable.api.teams import (
+    create_team,
+    create_team_membership,
+    delete_team_membership,
+    get_team,
+    get_team_membership,
+    list_team_memberships,
+    list_teams,
+    update_team,
+    update_team_membership,
+)
 from benchling_api_client.v2.types import Response
 
 from benchling_sdk.errors import raise_for_status
@@ -9,7 +19,17 @@ from benchling_sdk.helpers.decorators import api_method
 from benchling_sdk.helpers.pagination_helpers import NextToken, PageIterator
 from benchling_sdk.helpers.response_helpers import model_from_detailed
 from benchling_sdk.helpers.serialization_helpers import none_as_unset, optional_array_query_param
-from benchling_sdk.models import ListTeamsSort, Team, TeamsPaginatedList
+from benchling_sdk.models import (
+    ListTeamsSort,
+    Membership,
+    MembershipCreate,
+    MembershipsPaginatedList,
+    MembershipUpdate,
+    Team,
+    TeamCreate,
+    TeamsPaginatedList,
+    TeamUpdate,
+)
 from benchling_sdk.services.v2.base_service import BaseService
 
 
@@ -116,3 +136,101 @@ class TeamService(BaseService):
             return body.teams
 
         return PageIterator(api_call, results_extractor)
+
+    @api_method
+    def create(self, team: TeamCreate) -> Team:
+        """Create team.
+
+        See https://benchling.com/api/reference#/Teams/createTeam
+        """
+        response = create_team.sync_detailed(client=self.client, json_body=team)
+        return model_from_detailed(response)
+
+    @api_method
+    def update(self, team_id: str, team: TeamUpdate) -> Team:
+        """Update team.
+
+        See https://benchling.com/api/reference#/Teams/updateTeam
+        """
+        response = update_team.sync_detailed(client=self.client, team_id=team_id, json_body=team)
+        return model_from_detailed(response)
+
+    @api_method
+    def _list_memberships_page(
+        self,
+        team_id: str,
+        role: Optional[str],
+        page_size: Optional[int],
+        next_token: NextToken,
+    ) -> Response[MembershipsPaginatedList]:
+        response = list_team_memberships.sync_detailed(
+            client=self.client,
+            team_id=team_id,
+            page_size=none_as_unset(page_size),
+            next_token=next_token,
+            role=none_as_unset(role),
+        )
+        raise_for_status(response)
+        return response  # type: ignore
+
+    def list_memberships(
+        self,
+        team_id: str,
+        role: Optional[str] = None,
+        page_size: Optional[int] = None,
+    ) -> PageIterator[MembershipsPaginatedList]:
+        """Return all team memberships in the given team.
+
+        See https://benchling.com/api/reference#/Teams/listTeamMemberships
+        """
+
+        def api_call(next_token: NextToken) -> Response[MembershipsPaginatedList]:
+            return self._list_memberships_page(team_id, role, page_size, next_token)
+
+        return PageIterator(api_call, lambda body: body.memberships)
+
+    @api_method
+    def get_membership(self, team_id: str, user_id: str) -> Membership:
+        """Get team membership.
+
+        See https://benchling.com/api/reference#/Teams/getTeamMembership
+        """
+        response = get_team_membership.sync_detailed(client=self.client, team_id=team_id, user_id=user_id)
+        return model_from_detailed(response)
+
+    @api_method
+    def create_membership(self, team_id: str, membership: MembershipCreate) -> Membership:
+        """Create team membership for the given user, role, and team.
+
+        See https://benchling.com/api/reference#/Teams/createTeamMembership
+        """
+        response = create_team_membership.sync_detailed(
+            client=self.client,
+            team_id=team_id,
+            json_body=membership,
+        )
+        return model_from_detailed(response)
+
+    @api_method
+    def update_membership(self, team_id: str, user_id: str, membership: MembershipUpdate) -> Membership:
+        """Update a single team membership.
+
+        See https://benchling.com/api/reference#/Teams/updateTeamMembership
+        """
+        response = update_team_membership.sync_detailed(
+            client=self.client,
+            team_id=team_id,
+            user_id=user_id,
+            json_body=membership,
+        )
+        return model_from_detailed(response)
+
+    @api_method
+    def delete_membership(self, team_id: str, user_id: str) -> None:
+        """Delete a single team membership.
+
+        See https://benchling.com/api/reference#/Teams/deleteTeamMembership
+        """
+        raise_for_status(
+            delete_team_membership.sync_detailed(client=self.client, team_id=team_id, user_id=user_id)
+        )

benchling_sdk/services/v2/v2_stable_service.py

@@ -16,6 +16,7 @@ if TYPE_CHECKING:
     from benchling_sdk.services.v2.stable.assay_run_service import AssayRunService
     from benchling_sdk.services.v2.stable.blob_service import BlobService
     from benchling_sdk.services.v2.stable.box_service import BoxService
+    from benchling_sdk.services.v2.stable.codon_usage_table_service import CodonUsageTableService
     from benchling_sdk.services.v2.stable.container_service import ContainerService
     from benchling_sdk.services.v2.stable.custom_entity_service import CustomEntityService
     from benchling_sdk.services.v2.stable.custom_notation_service import CustomNotationService
@@ -25,6 +26,7 @@ if TYPE_CHECKING:
     from benchling_sdk.services.v2.stable.dropdown_service import DropdownService
     from benchling_sdk.services.v2.stable.entity_service import EntityService
     from benchling_sdk.services.v2.stable.entry_service import EntryService
+    from benchling_sdk.services.v2.stable.enzyme_service import EnzymeService
     from benchling_sdk.services.v2.stable.event_service import EventService
     from benchling_sdk.services.v2.stable.export_service import ExportService
     from benchling_sdk.services.v2.stable.feature_library_service import FeatureLibraryService
@@ -35,6 +37,7 @@ if TYPE_CHECKING:
     from benchling_sdk.services.v2.stable.location_service import LocationService
     from benchling_sdk.services.v2.stable.mixture_service import MixtureService
     from benchling_sdk.services.v2.stable.molecule_service import MoleculeService
+    from benchling_sdk.services.v2.stable.monomer_service import MonomerService
     from benchling_sdk.services.v2.stable.nucleotide_alignments_service import NucleotideAlignmentsService
     from benchling_sdk.services.v2.stable.oligo_service import OligoService
     from benchling_sdk.services.v2.stable.organization_service import OrganizationService
@@ -179,6 +182,20 @@ class V2StableService(BaseService):
 
         return self._create_service(BoxService)
 
+    @cached_property
+    def codon_usage_tables(self) -> CodonUsageTableService:
+        """
+        Codon Usage Tables.
+
+        Benchling curates codon usage data for a variety of organisms to support operations such as Codon
+        Optimization and Back Translation.
+
+        See https://benchling.com/api/reference#/Codon%20Usage%20Tables
+        """
+        from .stable.codon_usage_table_service import CodonUsageTableService
+
+        return self._create_service(CodonUsageTableService)
+
     @cached_property
     def containers(self) -> ContainerService:
         """
@@ -323,6 +340,19 @@ class V2StableService(BaseService):
 
         return self._create_service(EntryService)
 
+    @cached_property
+    def enzymes(self) -> EnzymeService:
+        """
+        Enzymes.
+
+        Restriction enzymes are curated by Benchling for operations such as Digests and Codon Optimization.
+
+        See https://benchling.com/api/reference#/Enzymes
+        """
+        from .stable.enzyme_service import EnzymeService
+
+        return self._create_service(EnzymeService)
+
     @cached_property
     def events(self) -> EventService:
         """
@@ -444,6 +474,20 @@ class V2StableService(BaseService):
 
         return self._create_service(MixtureService)
 
+    @cached_property
+    def monomers(self) -> MonomerService:
+        """
+        Monomers.
+
+        Monomers are chemical building blocks with specified structures used to compose modified
+        nucleotides. Note that monomer write endpoints require tenant admin permissions.
+
+        See https://benchling.com/api/reference#/Monomers
+        """
+        from .stable.monomer_service import MonomerService
+
+        return self._create_service(MonomerService)
+
     @cached_property
     def molecules(self) -> MoleculeService:
         """

{benchling_sdk-1.15.0a1.dist-info → benchling_sdk-1.17.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: benchling-sdk
-Version: 1.15.0a1
+Version: 1.17.0
 Summary: SDK for interacting with the Benchling Platform.
 License: Apache-2.0
 Author: Benchling Support
@@ -15,9 +15,9 @@ Classifier: Programming Language :: Python :: 3.11
 Provides-Extra: cryptography
 Provides-Extra: python-jose
 Requires-Dist: PyYAML (>=6.0,<7.0)
-Requires-Dist: attrs (>=20.1.0,<24)
+Requires-Dist: attrs (>=20.1.0)
 Requires-Dist: backoff (>=1.10.0,<3)
-Requires-Dist: benchling-api-client (==2.0.309)
+Requires-Dist: benchling-api-client (==2.0.317)
 Requires-Dist: certifi (>=2022.12.7)
 Requires-Dist: cryptography (>=42.0.0) ; extra == "cryptography"
 Requires-Dist: dataclasses-json (>=0.5.2,<0.6.0)