benchling-sdk 1.17.0a0__py3-none-any.whl → 1.18.0__py3-none-any.whl

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/instrument_query_service.py

@@ -0,0 +1,28 @@
+from benchling_api_client.v2.stable.api.instrument_queries import get_instrument_query
+
+from benchling_sdk.helpers.decorators import api_method
+from benchling_sdk.helpers.response_helpers import model_from_detailed
+from benchling_sdk.models import InstrumentQuery
+from benchling_sdk.services.v2.base_service import BaseService
+
+
+class InstrumentQueryService(BaseService):
+    """
+    Instrument Queries.
+
+    Instrument Queries are used to query the instrument service.
+
+    See https://benchling.com/api/reference#/Instrument%20Queries
+    """
+
+    @api_method
+    def get_by_id(self, instrument_query_id: str) -> InstrumentQuery:
+        """
+        Get an instrument query.
+
+        See https://benchling.com/api/reference#/Instrument%20Queries/getInstrumentQuery
+        """
+        response = get_instrument_query.sync_detailed(
+            client=self.client, instrument_query_id=instrument_query_id
+        )
+        return model_from_detailed(response)

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_alpha_service.py

@@ -10,6 +10,7 @@ from benchling_sdk.helpers.retry_helpers import RetryStrategy
 
 if TYPE_CHECKING:
     from benchling_sdk.services.v2.alpha.v2_alpha_app_service import V2AlphaAppService
+    from benchling_sdk.services.v2.alpha.v2_alpha_assembly_service import V2AlphaAssemblyService
 
 from benchling_sdk.services.v2.base_service import BaseService
 
@@ -48,6 +49,20 @@ class V2AlphaService(BaseService):
 
         return self._create_service(V2AlphaAppService)
 
+    @cached_property
+    def assemblies(self) -> V2AlphaAssemblyService:
+        """
+        V2-Alpha Assemblies.
+
+        In Benchling, Assemblies are records of a process in which many fragment sequences are
+        assembled in silico to create new construct sequences.
+
+            https://benchling.com/api/v2-alpha/reference#/Assemblies
+        """
+        from .alpha.v2_alpha_assembly_service import V2AlphaAssemblyService
+
+        return self._create_service(V2AlphaAssemblyService)
+
     def _create_service(self, cls):
         """Instantiate a service using the alpha client."""
         return cls(self._alpha_client, self._retry_strategy)

benchling_sdk/services/v2/v2_beta_service.py

@@ -11,7 +11,10 @@ from benchling_sdk.services.v2.base_service import BaseService
 from benchling_sdk.services.v2.beta.v2_beta_data_frame_service import V2BetaDataFrameService
 
 if TYPE_CHECKING:
+    from benchling_sdk.services.v2.beta.v2_beta_analysis_service import V2BetaAnalysisService
+    from benchling_sdk.services.v2.beta.v2_beta_app_definition_service import V2BetaAppDefinitionService
     from benchling_sdk.services.v2.beta.v2_beta_app_service import V2BetaAppService
+    from benchling_sdk.services.v2.beta.v2_beta_audit_service import V2BetaAuditService
     from benchling_sdk.services.v2.beta.v2_beta_collaboration_service import V2BetaCollaborationService
     from benchling_sdk.services.v2.beta.v2_beta_entry_service import V2BetaEntryService
     from benchling_sdk.services.v2.beta.v2_beta_folder_service import V2BetaFolderService
@@ -40,6 +43,19 @@ class V2BetaService(BaseService):
         super().__init__(client, retry_strategy)
         self._beta_client = v2_beta_client(self.client)
 
+    @cached_property
+    def analyses(self) -> V2BetaAnalysisService:
+        """
+        V2-Beta Analyses.
+
+        Analyses allow experimental data to be viewed, analyzed, and visualized.
+
+        https://benchling.com/api/v2-beta/reference#/Analyses
+        """
+        from .beta.v2_beta_analysis_service import V2BetaAnalysisService
+
+        return self._create_service(V2BetaAnalysisService)
+
     @cached_property
     def apps(self) -> V2BetaAppService:
         """
@@ -47,12 +63,38 @@ class V2BetaService(BaseService):
 
         Create and manage Apps on your tenant.
 
-        https://benchling.com/api/v2-beta/reference?stability=not-available#/Apps
+        https://benchling.com/api/v2-beta/reference#/Apps
         """
         from .beta.v2_beta_app_service import V2BetaAppService
 
         return self._create_service(V2BetaAppService)
 
+    @cached_property
+    def app_definitions(self) -> V2BetaAppDefinitionService:
+        """
+        V2-Beta App Definitions.
+
+        Create and manage Benchling app definitions on your tenant.
+
+        https://benchling.com/api/v2-beta/reference#/App%20Definitions
+        """
+        from .beta.v2_beta_app_definition_service import V2BetaAppDefinitionService
+
+        return self._create_service(V2BetaAppDefinitionService)
+
+    @cached_property
+    def audit(self) -> V2BetaAuditService:
+        """
+        V2-Beta Audit.
+
+        Export audit log data for Benchling objects.
+
+        https://benchling.com/api/v2-beta/reference#/Audit
+        """
+        from .beta.v2_beta_audit_service import V2BetaAuditService
+
+        return self._create_service(V2BetaAuditService)
+
     @cached_property
     def collaborations(self) -> V2BetaCollaborationService:
         """