benchling-sdk 1.13.0a2__py3-none-any.whl → 1.14.0__py3-none-any.whl

benchling_sdk/models/webhooks/v0/__init__.py

@@ -50,6 +50,7 @@ __all__ = [
     "LifecycleDeactivateWebhookV0Beta",
     "LifecycleDeactivateWebhookV0BetaType",
     "LifecycleDeactivateWebhookV0Type",
+    "MessageBase",
     "MessageBaseV0",
     "RequestCreatedWebhookV2",
     "RequestCreatedWebhookV2Type",
@@ -162,6 +163,7 @@ if TYPE_CHECKING:
     import benchling_api_client.webhooks.v0.stable.models.lifecycle_deactivate_webhook_v0_beta
     import benchling_api_client.webhooks.v0.stable.models.lifecycle_deactivate_webhook_v0_beta_type
     import benchling_api_client.webhooks.v0.stable.models.lifecycle_deactivate_webhook_v0_type
+    import benchling_api_client.webhooks.v0.stable.models.message_base
     import benchling_api_client.webhooks.v0.stable.models.message_base_v0
     import benchling_api_client.webhooks.v0.stable.models.request_created_webhook_v2
     import benchling_api_client.webhooks.v0.stable.models.request_created_webhook_v2_type
@@ -354,6 +356,7 @@ if TYPE_CHECKING:
     LifecycleDeactivateWebhookV0Type = (
         benchling_api_client.webhooks.v0.stable.models.lifecycle_deactivate_webhook_v0_type.LifecycleDeactivateWebhookV0Type
     )
+    MessageBase = benchling_api_client.webhooks.v0.stable.models.message_base.MessageBase
     MessageBaseV0 = benchling_api_client.webhooks.v0.stable.models.message_base_v0.MessageBaseV0
     RequestCreatedWebhookV2 = (
         benchling_api_client.webhooks.v0.stable.models.request_created_webhook_v2.RequestCreatedWebhookV2
@@ -596,6 +599,7 @@ else:
         "LifecycleDeactivateWebhookV0Beta": "benchling_api_client.webhooks.v0.stable.models.lifecycle_deactivate_webhook_v0_beta",
         "LifecycleDeactivateWebhookV0BetaType": "benchling_api_client.webhooks.v0.stable.models.lifecycle_deactivate_webhook_v0_beta_type",
         "LifecycleDeactivateWebhookV0Type": "benchling_api_client.webhooks.v0.stable.models.lifecycle_deactivate_webhook_v0_type",
+        "MessageBase": "benchling_api_client.webhooks.v0.stable.models.message_base",
         "MessageBaseV0": "benchling_api_client.webhooks.v0.stable.models.message_base_v0",
         "RequestCreatedWebhookV2": "benchling_api_client.webhooks.v0.stable.models.request_created_webhook_v2",
         "RequestCreatedWebhookV2Type": "benchling_api_client.webhooks.v0.stable.models.request_created_webhook_v2_type",

benchling_sdk/services/v2/base_service.py

@@ -30,3 +30,10 @@ class BaseService(ABC):
     def retry_strategy(self) -> RetryStrategy:
         """Provide access to the underlying user-specified RetryStrategy."""
         return self._retry_strategy
+
+    def _create_service(self, cls):
+        """Instantiate a service that derives from BaseService, with the same properties as this service.
+
+        Override this in alpha and beta services that use a client other than self._client.
+        """
+        return cls(self._client, self._retry_strategy)

benchling_sdk/services/v2/stable/aa_sequence_service.py

@@ -8,6 +8,7 @@ from benchling_api_client.v2.stable.api.aa_sequences import (
     bulk_update_aa_sequences,
     bulk_upsert_aa_sequences,
     create_aa_sequence,
+    find_matching_regions_aa_sequences,
     get_aa_sequence,
     list_aa_sequences,
     unarchive_aa_sequences,
@@ -37,6 +38,7 @@ from benchling_sdk.models import (
     AaSequencesBulkCreateRequest,
     AaSequencesBulkUpdateRequest,
     AaSequencesBulkUpsertRequest,
+    AaSequencesFindMatchingRegion,
     AaSequencesPaginatedList,
     AaSequencesUnarchive,
     AaSequenceUpdate,
@@ -312,3 +314,15 @@ class AaSequenceService(BaseService):
             client=self.client, json_body=body, returning=none_as_unset(returning_string)
         )
         return model_from_detailed(response)
+
+    @api_method
+    def find_matching_regions(self, find_matching_region: AaSequencesFindMatchingRegion) -> AsyncTaskLink:
+        """
+        Find matching regions for AA sequences.
+
+        See https://benchling.com/api/v2/reference#/AA%20Sequences/findMatchingRegionsAaSequences
+        """
+        response = find_matching_regions_aa_sequences.sync_detailed(
+            client=self.client, json_body=find_matching_region
+        )
+        return model_from_detailed(response)

benchling_sdk/services/v2/stable/dna_sequence_service.py

@@ -11,6 +11,7 @@ from benchling_api_client.v2.stable.api.dna_sequences import (
     bulk_update_dna_sequences,
     bulk_upsert_dna_sequences,
     create_dna_sequence,
+    find_matching_regions_dna_sequences,
     get_dna_sequence,
     list_dna_sequences,
     match_bases_dna_sequences,
@@ -45,6 +46,7 @@ from benchling_sdk.models import (
     DnaSequencesBulkCreateRequest,
     DnaSequencesBulkUpdateRequest,
     DnaSequencesBulkUpsertRequest,
+    DnaSequencesFindMatchingRegion,
     DnaSequencesPaginatedList,
     DnaSequencesUnarchive,
     DnaSequenceUpdate,
@@ -384,3 +386,15 @@ class DnaSequenceService(BaseService):
             json_body=search_bases_request,
         )
         return model_from_detailed(response)
+
+    @api_method
+    def find_matching_regions(self, find_matching_region: DnaSequencesFindMatchingRegion) -> AsyncTaskLink:
+        """
+        Find matching regions for DNA sequences.
+
+        See https://benchling.com/api/v2/reference#/DNA%20Sequences/findMatchingRegionsDnaSequences
+        """
+        response = find_matching_regions_dna_sequences.sync_detailed(
+            client=self.client, json_body=find_matching_region
+        )
+        return model_from_detailed(response)

benchling_sdk/services/v2/stable/entry_service.py

@@ -11,6 +11,7 @@ from benchling_api_client.v2.stable.api.entries import (
     list_entry_templates,
     unarchive_entries,
     update_entry,
+    update_entry_template,
 )
 from benchling_api_client.v2.types import Response
 
@@ -31,6 +32,7 @@ from benchling_sdk.models import (
     EntryExternalFile,
     EntryTemplate,
     EntryTemplatesPaginatedList,
+    EntryTemplateUpdate,
     EntryUpdate,
     ListEntriesReviewStatus,
     ListEntriesSort,
@@ -332,3 +334,24 @@ class EntryService(BaseService):
             client=self.client, entry_template_id=entry_template_id, returning=none_as_unset(returning_string)
         )
         return model_from_detailed(response)
+
+    @api_method
+    def update_entry_template(
+        self,
+        entry_template_id: str,
+        entry_template: EntryTemplateUpdate,
+        returning: Optional[Iterable[str]] = None,
+    ) -> EntryTemplate:
+        """
+        Update a notebook entry template's metadata.
+
+        See https://benchling.com/api/reference#/Entries/updateEntryTemplate
+        """
+        returning_string = optional_array_query_param(returning)
+        response = update_entry_template.sync_detailed(
+            client=self.client,
+            entry_template_id=entry_template_id,
+            json_body=entry_template,
+            returning=none_as_unset(returning_string),
+        )
+        return model_from_detailed(response)

benchling_sdk/services/v2/stable/workflow_flowchart_config_version_service.py

@@ -0,0 +1,32 @@
+from benchling_api_client.v2.stable.api.workflow_flowchart_config_versions import (
+    get_workflow_flowchart_config_version,
+)
+
+from benchling_sdk.helpers.decorators import api_method
+from benchling_sdk.helpers.response_helpers import model_from_detailed
+from benchling_sdk.models import WorkflowFlowchartConfigVersion
+from benchling_sdk.services.v2.base_service import BaseService
+
+
+class WorkflowFlowchartConfigVersionService(BaseService):
+    """
+    Workflow Flowchart Config Versions.
+
+    Workflow flowchart config versions are versioned graphs of flowchart configurations.
+
+    See https://benchling.com/api/reference#/Workflow%20Flowchart%20Config%20Versions
+    """
+
+    @api_method
+    def get_by_id(self, workflow_flowchart_config_version_id: str) -> WorkflowFlowchartConfigVersion:
+        """
+        Get a workflow flowchart config version.
+
+        If there is a template flowchart, serializes that flowchart in the same format as the workflow_flowcharts service.
+
+        See https://benchling.com/api/reference#/Workflow%20Flowcharts/getWorkflowConfigVersion
+        """
+        response = get_workflow_flowchart_config_version.sync_detailed(
+            client=self.client, workflow_flowchart_config_version_id=workflow_flowchart_config_version_id
+        )
+        return model_from_detailed(response)

benchling_sdk/services/v2/stable/workflow_flowchart_service.py

@@ -0,0 +1,85 @@
+import datetime
+from typing import Iterable, List, Optional
+
+from benchling_api_client.v2.stable.api.workflow_flowcharts import (
+    get_workflow_flowchart,
+    list_workflow_flowcharts,
+)
+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 ListWorkflowFlowchartsSort, WorkflowFlowchart, WorkflowFlowchartPaginatedList
+from benchling_sdk.services.v2.base_service import BaseService
+
+
+class WorkflowFlowchartService(BaseService):
+    """
+    Workflow Flowcharts.
+
+    Workflow flowcharts represent the nodes and edges that a flowchart is comprised of.
+
+    See https://benchling.com/api/reference#/Workflow%20Flowcharts
+    """
+
+    @api_method
+    def get_by_id(self, workflow_flowchart_id: str) -> WorkflowFlowchart:
+        """
+        Get a workflow flowchart.
+
+        See https://benchling.com/api/reference#/Workflow%20Flowcharts/getWorkflowFlowchart
+        """
+        response = get_workflow_flowchart.sync_detailed(
+            client=self.client, workflow_flowchart_id=workflow_flowchart_id
+        )
+        return model_from_detailed(response)
+
+    @api_method
+    def _workflow_tasks_page(
+        self,
+        sort: Optional[ListWorkflowFlowchartsSort] = None,
+        ids: Optional[Iterable[str]] = None,
+        created_at: Optional[datetime.date] = None,
+        page_size: Optional[int] = None,
+        next_token: NextToken = None,
+    ) -> Response[WorkflowFlowchartPaginatedList]:
+        response = list_workflow_flowcharts.sync_detailed(
+            client=self.client,
+            ids=none_as_unset(optional_array_query_param(ids)),
+            created_at=none_as_unset(created_at),
+            next_token=none_as_unset(next_token),
+            page_size=none_as_unset(page_size),
+            sort=none_as_unset(sort),
+        )
+        raise_for_status(response)
+        return response  # type: ignore
+
+    def list(
+        self,
+        sort: Optional[ListWorkflowFlowchartsSort] = None,
+        ids: Optional[Iterable[str]] = None,
+        created_at: Optional[datetime.date] = None,
+        page_size: Optional[int] = None,
+    ) -> PageIterator[WorkflowFlowchart]:
+        """
+        List workflow flowcharts.
+
+        See https://benchling.com/api/reference#/Workflow%20Tasks/listWorkflowFlowcharts
+        """
+
+        def api_call(next_token: NextToken) -> Response[WorkflowFlowchartPaginatedList]:
+            return self._workflow_tasks_page(
+                sort=sort,
+                ids=ids,
+                created_at=created_at,
+                page_size=page_size,
+                next_token=next_token,
+            )
+
+        def results_extractor(body: WorkflowFlowchartPaginatedList) -> Optional[List[WorkflowFlowchart]]:
+            return body.workflow_flowcharts
+
+        return PageIterator(api_call, results_extractor)

benchling_sdk/services/v2/v2_alpha_service.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
-from typing import Optional, TYPE_CHECKING
+from functools import cached_property
+from typing import TYPE_CHECKING
 
 from benchling_api_client.v2.stable.client import Client
 
@@ -9,7 +10,6 @@ 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_dna_sequence_service import V2AlphaDnaSequenceService
 
 from benchling_sdk.services.v2.base_service import BaseService
 
@@ -23,8 +23,6 @@ class V2AlphaService(BaseService):
     See https://benchling.com/api/v2-alpha/reference
     """
 
-    _app_service: Optional[V2AlphaAppService]
-    _dna_sequence_service: Optional[V2AlphaDnaSequenceService]
     _alpha_client: Client
 
     def __init__(self, client: Client, retry_strategy: RetryStrategy = RetryStrategy()):
@@ -36,10 +34,8 @@ class V2AlphaService(BaseService):
         """
         super().__init__(client, retry_strategy)
         self._alpha_client = v2_alpha_client(self.client)
-        self._app_service = None
-        self._dna_sequence_service = None
 
-    @property
+    @cached_property
     def apps(self) -> V2AlphaAppService:
         """
         V2-Alpha Apps.
@@ -48,26 +44,10 @@ class V2AlphaService(BaseService):
 
         https://benchling.com/api/v2-alpha/reference?stability=not-available#/Apps
         """
-        if self._app_service is None:
-            from benchling_sdk.services.v2.alpha.v2_alpha_app_service import V2AlphaAppService
+        from .alpha.v2_alpha_app_service import V2AlphaAppService
 
-            self._app_service = V2AlphaAppService(self._alpha_client, self._retry_strategy)
-        return self._app_service
+        return self._create_service(V2AlphaAppService)
 
-    @property
-    def dna_sequences(self) -> V2AlphaDnaSequenceService:
-        """
-        V2-Alpha DNA Sequences.
-
-        DNA sequences are the bread and butter of the Benchling Molecular Biology suite. On Benchling, these are
-        comprised of a string of nucleotides and collections of other attributes, such as annotations and primers.
-
-        See https://benchling.com/api/v2-alpha/reference#/DNA%20Sequences
-        """
-        if self._dna_sequence_service is None:
-            from benchling_sdk.services.v2.alpha.v2_alpha_dna_sequence_service import (
-                V2AlphaDnaSequenceService,
-            )
-
-            self._dna_sequence_service = V2AlphaDnaSequenceService(self._alpha_client, self._retry_strategy)
-        return self._dna_sequence_service
+    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

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
-from typing import Optional, TYPE_CHECKING
+from functools import cached_property
+from typing import TYPE_CHECKING
 
 from benchling_api_client.v2.stable.client import Client
 
@@ -10,7 +11,6 @@ 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_aa_sequence_service import V2BetaAaSequenceService
     from benchling_sdk.services.v2.beta.v2_beta_app_service import V2BetaAppService
     from benchling_sdk.services.v2.beta.v2_beta_collaboration_service import V2BetaCollaborationService
     from benchling_sdk.services.v2.beta.v2_beta_entry_service import V2BetaEntryService
@@ -28,14 +28,6 @@ class V2BetaService(BaseService):
     See https://benchling.com/api/v2-beta/reference
     """
 
-    _aa_sequence_service: Optional[V2BetaAaSequenceService]
-    _app_service: Optional[V2BetaAppService]
-    _collaboration_service: Optional[V2BetaCollaborationService]
-    _data_frame_service: Optional[V2BetaDataFrameService]
-    _entry_service: Optional[V2BetaEntryService]
-    _folder_service: Optional[V2BetaFolderService]
-    _project_service: Optional[V2BetaProjectService]
-    _worklist_service: Optional[V2BetaWorklistService]
     _beta_client: Client
 
     def __init__(self, client: Client, retry_strategy: RetryStrategy = RetryStrategy()):
@@ -47,33 +39,8 @@ class V2BetaService(BaseService):
         """
         super().__init__(client, retry_strategy)
         self._beta_client = v2_beta_client(self.client)
-        self._aa_sequence_service = None
-        self._app_service = None
-        self._collaboration_service = None
-        self._data_frame_service = None
-        self._entry_service = None
-        self._folder_service = None
-        self._project_service = None
-        self._worklist_service = None
 
-    @property
-    def aa_sequences(self) -> V2BetaAaSequenceService:
-        """
-        V2-Beta AA Sequences.
-
-        AA Sequences are the working units of cells that make everything run (they help make structures, catalyze
-        reactions and allow for signaling - a kind of internal cell communication). On Benchling, these are comprised
-        of a string of amino acids and collections of other attributes, such as annotations.
-
-        See https://benchling.com/api/v2-beta/reference#/AA%20Sequences
-        """
-        if self._aa_sequence_service is None:
-            from benchling_sdk.services.v2.beta.v2_beta_aa_sequence_service import V2BetaAaSequenceService
-
-            self._aa_sequence_service = V2BetaAaSequenceService(self._beta_client, self.retry_strategy)
-        return self._aa_sequence_service
-
-    @property
+    @cached_property
     def apps(self) -> V2BetaAppService:
         """
         V2-Beta Apps.
@@ -82,13 +49,11 @@ class V2BetaService(BaseService):
 
         https://benchling.com/api/v2-beta/reference?stability=not-available#/Apps
         """
-        if self._app_service is None:
-            from benchling_sdk.services.v2.beta.v2_beta_app_service import V2BetaAppService
+        from .beta.v2_beta_app_service import V2BetaAppService
 
-            self._app_service = V2BetaAppService(self._beta_client, self.retry_strategy)
-        return self._app_service
+        return self._create_service(V2BetaAppService)
 
-    @property
+    @cached_property
     def collaborations(self) -> V2BetaCollaborationService:
         """
         V2-Beta Collaborations.
@@ -97,15 +62,11 @@ class V2BetaService(BaseService):
 
         See https://benchling.com/api/v2-beta/reference?showLA=true#/Collaborations
         """
-        if self._collaboration_service is None:
-            from benchling_sdk.services.v2.beta.v2_beta_collaboration_service import (
-                V2BetaCollaborationService,
-            )
+        from .beta.v2_beta_collaboration_service import V2BetaCollaborationService
 
-            self._collaboration_service = V2BetaCollaborationService(self._beta_client, self.retry_strategy)
-        return self._collaboration_service
+        return self._create_service(V2BetaCollaborationService)
 
-    @property
+    @cached_property
     def data_frames(self) -> V2BetaDataFrameService:
         """
         V2-Beta DataFrames.
@@ -114,13 +75,11 @@ class V2BetaService(BaseService):
 
         See https://benchling.com/api/v2-beta/reference#/Data%20Frames
         """
-        if self._data_frame_service is None:
-            from benchling_sdk.services.v2.beta.v2_beta_data_frame_service import V2BetaDataFrameService
+        from .beta.v2_beta_data_frame_service import V2BetaDataFrameService
 
-            self._data_frame_service = V2BetaDataFrameService(self._beta_client, self.retry_strategy)
-        return self._data_frame_service
+        return self._create_service(V2BetaDataFrameService)
 
-    @property
+    @cached_property
     def entries(self) -> V2BetaEntryService:
         """
         V2-Beta Entries.
@@ -129,13 +88,11 @@ class V2BetaService(BaseService):
 
         https://benchling.com/api/v2-beta/reference#/Entries
         """
-        if self._entry_service is None:
-            from benchling_sdk.services.v2.beta.v2_beta_entry_service import V2BetaEntryService
+        from .beta.v2_beta_entry_service import V2BetaEntryService
 
-            self._entry_service = V2BetaEntryService(self._beta_client, self.retry_strategy)
-        return self._entry_service
+        return self._create_service(V2BetaEntryService)
 
-    @property
+    @cached_property
     def folders(self) -> V2BetaFolderService:
         """
         V2-Beta Folders.
@@ -144,13 +101,11 @@ class V2BetaService(BaseService):
 
         https://benchling.com/api/v2-beta/reference?showLA=true#/Folders
         """
-        if self._folder_service is None:
-            from benchling_sdk.services.v2.beta.v2_beta_folder_service import V2BetaFolderService
+        from .beta.v2_beta_folder_service import V2BetaFolderService
 
-            self._folder_service = V2BetaFolderService(self._beta_client, self.retry_strategy)
-        return self._folder_service
+        return self._create_service(V2BetaFolderService)
 
-    @property
+    @cached_property
     def projects(self) -> V2BetaProjectService:
         """
         V2-Beta Projects.
@@ -159,13 +114,11 @@ class V2BetaService(BaseService):
 
         See https://benchling.com/api/v2-beta/reference?#/Projects
         """
-        if self._project_service is None:
-            from benchling_sdk.services.v2.beta.v2_beta_project_service import V2BetaProjectService
+        from .beta.v2_beta_project_service import V2BetaProjectService
 
-            self._project_service = V2BetaProjectService(self._beta_client, self.retry_strategy)
-        return self._project_service
+        return self._create_service(V2BetaProjectService)
 
-    @property
+    @cached_property
     def worklists(self) -> V2BetaWorklistService:
         """
         V2-Beta Worklists.
@@ -175,8 +128,10 @@ class V2BetaService(BaseService):
 
         See https://benchling.com/api/v2-beta/reference#/Worklists
         """
-        if self._worklist_service is None:
-            from benchling_sdk.services.v2.beta.v2_beta_worklist_service import V2BetaWorklistService
+        from .beta.v2_beta_worklist_service import V2BetaWorklistService
+
+        return self._create_service(V2BetaWorklistService)
 
-            self._worklist_service = V2BetaWorklistService(self._beta_client, self.retry_strategy)
-        return self._worklist_service
+    def _create_service(self, cls):
+        """Instantiate a service using the beta client."""
+        return cls(self._beta_client, self._retry_strategy)