benchling-sdk 1.21.1__py3-none-any.whl → 1.22.0a0__py3-none-any.whl

benchling_sdk/models/webhooks/v0/__init__.py

@@ -350,8 +350,12 @@ 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
+    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
     )
@@ -484,7 +488,9 @@ if TYPE_CHECKING:
     V2WorkflowTaskUpdatedStatusEventEventType = (
         benchling_api_client.webhooks.v0.stable.models.v2_workflow_task_updated_status_event_event_type.V2WorkflowTaskUpdatedStatusEventEventType
     )
-    WebhookEnvelopeV0 = benchling_api_client.webhooks.v0.stable.models.webhook_envelope_v0.WebhookEnvelopeV0
+    WebhookEnvelopeV0 = (
+        benchling_api_client.webhooks.v0.stable.models.webhook_envelope_v0.WebhookEnvelopeV0
+    )
     WebhookEnvelopeV0App = (
         benchling_api_client.webhooks.v0.stable.models.webhook_envelope_v0_app.WebhookEnvelopeV0App
     )
@@ -494,7 +500,9 @@ if TYPE_CHECKING:
     WebhookEnvelopeV0Version = (
         benchling_api_client.webhooks.v0.stable.models.webhook_envelope_v0_version.WebhookEnvelopeV0Version
     )
-    WebhookMessageV0 = benchling_api_client.webhooks.v0.stable.models.webhook_message_v0.WebhookMessageV0
+    WebhookMessageV0 = (
+        benchling_api_client.webhooks.v0.stable.models.webhook_message_v0.WebhookMessageV0
+    )
     WorkflowOutputCreatedWebhookV2 = (
         benchling_api_client.webhooks.v0.stable.models.workflow_output_created_webhook_v2.WorkflowOutputCreatedWebhookV2
     )

benchling_sdk/services/v2/base_service.py

@@ -1,5 +1,5 @@
 from abc import ABC
-from typing import Type, TYPE_CHECKING
+from typing import Optional, Type, TYPE_CHECKING
 
 from benchling_api_client.v2.stable.client import Client
 from benchling_api_client.v2.types import Response
@@ -17,7 +17,7 @@ class BaseService(ABC):
     _client: Client
     _retry_strategy: RetryStrategy
 
-    def __init__(self, client: Client, retry_strategy: RetryStrategy = RetryStrategy()):
+    def __init__(self, client: Client, retry_strategy: Optional[RetryStrategy] = None):
         """
         Initialize a service.
 
@@ -25,7 +25,7 @@ class BaseService(ABC):
         :param retry_strategy: Retry strategy for failed HTTP calls
         """
         self._client = client
-        self._retry_strategy = retry_strategy
+        self._retry_strategy = retry_strategy or RetryStrategy()
 
     @property
     def client(self) -> Client:
@@ -38,7 +38,8 @@ class BaseService(ABC):
         return self._retry_strategy
 
     def _create_service(self, cls):
-        """Instantiate a service that derives from BaseService, with the same properties as this service.
+        """
+        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.
         """

benchling_sdk/services/v2/beta/v2_beta_data_frame_service.py

@@ -72,7 +72,8 @@ class V2BetaDataFrameService(BaseService):
         input_bytes: Union[BytesIO, bytes],
         timeout_seconds: float = _DEFAULT_HTTP_TIMEOUT_UPLOAD_DATA_FRAME,
     ) -> None:
-        """Upload bytes to an existing data frame.
+        """
+        Upload bytes to an existing data frame.
 
         :param url: The url provided by Benchling for uploading to the data frame
         :param input_bytes: Data to upload as bytes or BytesIO
@@ -90,7 +91,8 @@ class V2BetaDataFrameService(BaseService):
     def upload_file(
         self, url: str, file: Path, timeout_seconds: float = _DEFAULT_HTTP_TIMEOUT_UPLOAD_DATA_FRAME
     ) -> None:
-        """Upload a file to an existing data frame.
+        """
+        Upload a file to an existing data frame.
 
         :param url: The url provided by Benchling for uploading to the data frame
         :param file: A valid Path to an existing file containing the data to upload
@@ -115,7 +117,8 @@ class V2BetaDataFrameService(BaseService):
         input_bytes: Union[BytesIO, bytes],
         timeout_seconds: float = _DEFAULT_HTTP_TIMEOUT_UPLOAD_DATA_FRAME,
     ) -> TaskHelper[DataFrame]:
-        """Create a data frame from bytes or BytesIO data.
+        """
+        Create a data frame from bytes or BytesIO data.
 
         :param data_frame: The DataFrameCreate specification for the data. This must be provided, as it cannot be inferred from file names.
         :param input_bytes: Data to upload as bytes or BytesIO
@@ -151,7 +154,8 @@ class V2BetaDataFrameService(BaseService):
         data_frame: Optional[DataFrameCreate] = None,
         timeout_seconds: float = _DEFAULT_HTTP_TIMEOUT_UPLOAD_DATA_FRAME,
     ) -> TaskHelper[DataFrame]:
-        """Create a data frame from file data.
+        """
+        Create a data frame from file data.
 
         :param file: A valid Path to an existing file containing the data to upload
         :param data_frame: The DataFrameCreate specification for the data. If not provided, it will be inferred from the file name
@@ -178,7 +182,8 @@ class V2BetaDataFrameService(BaseService):
     def download_data_frame_bytes(
         self, data_frame: DataFrame, timeout_seconds: float = _DEFAULT_HTTP_TIMEOUT_UPLOAD_DATA_FRAME
     ) -> List[BytesIO]:
-        """Download data frame data to bytes.
+        """
+        Download data frame data to bytes.
 
         :param data_frame: The data frame to download
         :param timeout_seconds: Extends the normal HTTP timeout settings since DataFrame uploads can be large
@@ -211,7 +216,8 @@ class V2BetaDataFrameService(BaseService):
         destination_path: Optional[Path] = None,
         timeout_seconds: float = _DEFAULT_HTTP_TIMEOUT_UPLOAD_DATA_FRAME,
     ) -> List[Path]:
-        """Download data frame data to files.
+        """
+        Download data frame data to files.
 
         :param data_frame: The data frame to download
         :param destination_path: A target directory to place the files. File names will be created based on the manifest item file names.
@@ -252,7 +258,8 @@ class V2BetaDataFrameService(BaseService):
     def download_data_frame_bytes_by_id(
         self, data_frame_id: str, timeout_seconds: float = _DEFAULT_HTTP_TIMEOUT_UPLOAD_DATA_FRAME
     ) -> List[BytesIO]:
-        """Download data frame data to files by data_frame_id.
+        """
+        Download data frame data to files by data_frame_id.
 
         Fetches the data frame first, then downloads the files.
 
@@ -272,7 +279,8 @@ class V2BetaDataFrameService(BaseService):
         destination_path: Optional[Path] = None,
         timeout_seconds: float = _DEFAULT_HTTP_TIMEOUT_UPLOAD_DATA_FRAME,
     ) -> List[Path]:
-        """Download data frame data to files by data_frame_id.
+        """
+        Download data frame data to files by data_frame_id.
 
         Fetches the data frame first, then downloads the files.
 

benchling_sdk/services/v2/stable/aa_sequence_service.py

@@ -93,6 +93,7 @@ class AaSequenceService(BaseService):
     def _aa_sequences_page(
         self,
         modified_at: Optional[str] = None,
+        created_at: Optional[str] = None,
         name: Optional[str] = None,
         amino_acids: Optional[str] = None,
         folder_id: Optional[str] = None,
@@ -118,6 +119,7 @@ class AaSequenceService(BaseService):
         response = list_aa_sequences.sync_detailed(
             client=self.client,
             modified_at=none_as_unset(modified_at),
+            created_at=none_as_unset(created_at),
             name=none_as_unset(name),
             amino_acids=none_as_unset(amino_acids),
             folder_id=none_as_unset(folder_id),
@@ -145,6 +147,7 @@ class AaSequenceService(BaseService):
     def list(
         self,
         modified_at: Optional[str] = None,
+        created_at: Optional[str] = None,
         name: Optional[str] = None,
         amino_acids: Optional[str] = None,
         folder_id: Optional[str] = None,
@@ -177,6 +180,7 @@ class AaSequenceService(BaseService):
         def api_call(next_token: NextToken) -> Response[AaSequencesPaginatedList]:
             return self._aa_sequences_page(
                 modified_at=modified_at,
+                created_at=created_at,
                 name=name,
                 amino_acids=amino_acids,
                 folder_id=folder_id,

benchling_sdk/services/v2/{beta/v2_beta_audit_service.py → stable/audit_service.py}

@@ -1,5 +1,5 @@
-from benchling_api_client.v2.beta.api.audit import audit_log
-from benchling_api_client.v2.beta.models.audit_log_export import AuditLogExport
+from benchling_api_client.v2.stable.api.audit import audit_log
+from benchling_api_client.v2.stable.models.audit_log_export import AuditLogExport
 
 from benchling_sdk.helpers.decorators import api_method
 from benchling_sdk.helpers.task_helpers import TaskHelper
@@ -7,13 +7,13 @@ from benchling_sdk.models import ExportAuditLogAsyncTaskResponse
 from benchling_sdk.services.v2.base_service import BaseService
 
 
-class V2BetaAuditService(BaseService):
+class AuditService(BaseService):
     """
-    V2-Beta Audit Service.
+    Audit Service.
 
     Export audit log data for Benchling objects.
 
-    https://benchling.com/api/v2-beta/reference#/Audit
+    https://benchling.com/api/reference#/Audit
     """
 
     @api_method
@@ -36,7 +36,7 @@ class V2BetaAuditService(BaseService):
         Example of submitting an export request and then getting the download URL from
         the completed task:
 
-            task = benchling.v2.beta.audit.get_audit_log(object_id, export)
+            task = benchling.v2.stable.audit.get_audit_log(object_id, export)
             task_result = task.wait_for_response()
             url = task_result.download_url
 

benchling_sdk/services/v2/stable/blob_service.py

@@ -46,7 +46,8 @@ DEFAULT_CHUNK_SIZE_BYTES: int = MINIMUM_CHUNK_SIZE_BYTES
 
 
 def _write_blob_file(file_contents: BytesIO, file_path: Optional[Path] = None) -> Path:
-    """Write bytes to a file. Will create a temp file if file_path isn't specified.
+    """
+    Write bytes to a file. Will create a temp file if file_path isn't specified.
 
     Returns the Path of the file written to, whether created or used.
     """
@@ -114,7 +115,8 @@ class BlobService(BaseService):
         timeout_seconds: float = DEFAULT_HTTP_TIMEOUT,
         chunk_size_bytes: int = DEFAULT_CHUNK_SIZE_BYTES,
     ) -> Blob:
-        """Create a Benchling Blob from bytes or a BytesIO stream.
+        """
+        Create a Benchling Blob from bytes or a BytesIO stream.
 
         Will automatically attempt a multi-part upload if the stream appears larger
         than the API's maximum size for single Blobs.
@@ -172,7 +174,8 @@ class BlobService(BaseService):
         timeout_seconds: float = DEFAULT_HTTP_TIMEOUT,
         chunk_size_bytes: int = DEFAULT_CHUNK_SIZE_BYTES,
     ) -> Blob:
-        """Create a Benchling Blob from a file.
+        """
+        Create a Benchling Blob from a file.
 
         Will automatically attempt a multi-part upload if the file appears larger
         than the API's maximum size for single Blobs.

benchling_sdk/services/v2/stable/box_service.py

@@ -71,6 +71,7 @@ class BoxService(BaseService):
         sort: Optional[ListBoxesSort] = None,
         schema_id: Optional[str] = None,
         modified_at: Optional[str] = None,
+        created_at: Optional[str] = None,
         name: Optional[str] = None,
         name_includes: Optional[str] = None,
         ancestor_storage_id: Optional[str] = None,
@@ -99,6 +100,7 @@ class BoxService(BaseService):
             sort=none_as_unset(sort),
             schema_id=none_as_unset(schema_id),
             modified_at=none_as_unset(modified_at),
+            created_at=none_as_unset(created_at),
             name=none_as_unset(name),
             name_includes=none_as_unset(name_includes),
             ancestor_storage_id=none_as_unset(ancestor_storage_id),
@@ -133,6 +135,7 @@ class BoxService(BaseService):
         sort: Optional[Union[str, ListBoxesSort]] = None,
         schema_id: Optional[str] = None,
         modified_at: Optional[str] = None,
+        created_at: Optional[str] = None,
         name: Optional[str] = None,
         name_includes: Optional[str] = None,
         ancestor_storage_id: Optional[str] = None,
@@ -169,6 +172,7 @@ class BoxService(BaseService):
                 sort=_translate_to_string_enum(ListBoxesSort, sort),
                 schema_id=schema_id,
                 modified_at=modified_at,
+                created_at=created_at,
                 name=name,
                 name_includes=name_includes,
                 ancestor_storage_id=ancestor_storage_id,

benchling_sdk/services/v2/stable/connect_service.py

@@ -0,0 +1,79 @@
+from typing import List
+
+from benchling_api_client.v2.stable.api.connect import (
+    convert_to_asm as api_client_convert_to_asm,
+    convert_to_csv as api_client_convert_to_csv,
+    list_allotropy_vendors as api_client_list_allotropy_vendors,
+)
+from benchling_api_client.v2.stable.models.convert_to_asm import ConvertToASM
+from benchling_api_client.v2.stable.models.convert_to_asm_response_200 import ConvertToASMResponse_200
+from benchling_api_client.v2.stable.models.convert_to_csv import ConvertToCSV
+from benchling_api_client.v2.stable.models.convert_to_csv_response_200_item import (
+    ConvertToCSVResponse_200Item,
+)
+
+from benchling_sdk.errors import raise_for_status
+from benchling_sdk.helpers.decorators import api_method
+from benchling_sdk.helpers.response_helpers import model_from_detailed
+from benchling_sdk.services.v2.base_service import BaseService
+
+
+class ConnectService(BaseService):
+    """
+    Connect.
+
+    Connect endpoints support Benchling Connect actions, like instrument data conversion.
+
+    See https://benchling.com/api/reference#/Connect
+    """
+
+    @api_method
+    def convert_to_asm(self, file_info: ConvertToASM) -> ConvertToASMResponse_200:
+        """
+        Convert an input blob or file containing instrument data to ASM (Allotrope Simple Model) JSON.
+
+        May provide the name of the instrument vendor (see /connect/list-allotropy-vendors) or the ID of a
+        connection associated with an instrument vendor.
+
+        See https://benchling.com/api/reference#/Connect/convertToASM
+        """
+        response = api_client_convert_to_asm.sync_detailed(client=self.client, json_body=file_info)
+        response = raise_for_status(response)
+        return model_from_detailed(response)
+
+    @api_method
+    def convert_to_csv(self, file_info: ConvertToCSV) -> List[ConvertToCSVResponse_200Item]:
+        """
+        Convert a blob or file containing ASM, JSON, or instrument data to CSV.
+
+        If the file is ASM JSON, specify either no transform type (in which case all transform types will be
+        returned), a matching transform type for the ASM schema, or a custom JSON mapper config.
+
+        If the file non-ASM JSON, must provide a JSON mapper config argument, which specifies how to map the
+        JSON to CSV. Reach out to Benchling Support for more information about how to create a JSON mapper
+        config.
+
+        If the file is an instrument file, must also specify an instrument vendor. The file will be converted
+        first to ASM JSON and then to CSV. Only the CSV output will be returned.
+
+        May provide an AutomationOutputFile with CSV transform arguments configured to read the transform type
+        or mapper config from.
+
+        May provide a connection ID associated with an instrument to read the vendor from.
+
+        See https://benchling.com/api/reference#/Connect/convertToCSV
+        """
+        response = api_client_convert_to_csv.sync_detailed(client=self.client, json_body=file_info)
+        response = raise_for_status(response)
+        return model_from_detailed(response)
+
+    @api_method
+    def list_allotropy_vendors(self) -> List[None]:
+        """
+        Return the list of available allotropy instrument vendor types.
+
+        See https://benchling.com/api/reference#/Connect/listAllotropyVendors
+        """
+        response = api_client_list_allotropy_vendors.sync_detailed(client=self.client)
+        response = raise_for_status(response)
+        return model_from_detailed(response)

benchling_sdk/services/v2/stable/container_service.py

@@ -104,6 +104,7 @@ class ContainerService(BaseService):
         sort: Optional[ListContainersSort] = None,
         schema_id: Optional[str] = None,
         modified_at: Optional[str] = None,
+        created_at: Optional[str] = None,
         name: Optional[str] = None,
         name_includes: Optional[str] = None,
         ancestor_storage_id: Optional[str] = None,
@@ -132,6 +133,7 @@ class ContainerService(BaseService):
             sort=none_as_unset(sort),
             schema_id=none_as_unset(schema_id),
             modified_at=none_as_unset(modified_at),
+            created_at=none_as_unset(created_at),
             name=none_as_unset(name),
             name_includes=none_as_unset(name_includes),
             ancestor_storage_id=none_as_unset(ancestor_storage_id),
@@ -174,6 +176,7 @@ class ContainerService(BaseService):
         sort: Optional[Union[str, ListContainersSort]] = None,
         schema_id: Optional[str] = None,
         modified_at: Optional[str] = None,
+        created_at: Optional[str] = None,
         name: Optional[str] = None,
         name_includes: Optional[str] = None,
         ancestor_storage_id: Optional[str] = None,
@@ -210,6 +213,7 @@ class ContainerService(BaseService):
                 sort=_translate_to_string_enum(ListContainersSort, sort),
                 schema_id=schema_id,
                 modified_at=modified_at,
+                created_at=created_at,
                 name=name,
                 name_includes=name_includes,
                 ancestor_storage_id=ancestor_storage_id,

benchling_sdk/services/v2/stable/custom_entity_service.py

@@ -77,6 +77,7 @@ class CustomEntityService(BaseService):
         self,
         schema_id: Optional[str] = None,
         modified_at: Optional[str] = None,
+        created_at: Optional[str] = None,
         name: Optional[str] = None,
         name_includes: Optional[str] = None,
         folder_id: Optional[str] = None,
@@ -101,6 +102,7 @@ class CustomEntityService(BaseService):
             client=self.client,
             schema_id=none_as_unset(schema_id),
             modified_at=none_as_unset(modified_at),
+            created_at=none_as_unset(created_at),
             name=none_as_unset(name),
             name_includes=none_as_unset(name_includes),
             folder_id=none_as_unset(folder_id),
@@ -128,6 +130,7 @@ class CustomEntityService(BaseService):
         self,
         schema_id: Optional[str] = None,
         modified_at: Optional[str] = None,
+        created_at: Optional[str] = None,
         name: Optional[str] = None,
         name_includes: Optional[str] = None,
         folder_id: Optional[str] = None,
@@ -162,6 +165,7 @@ class CustomEntityService(BaseService):
             return self._custom_entities_page(
                 schema_id=schema_id,
                 modified_at=modified_at,
+                created_at=created_at,
                 name=name,
                 name_includes=name_includes,
                 folder_id=folder_id,