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benchling.utils.write_entity

class NamingStrategy​

Different options for handling naming when creating custom entities.
See: https://help.benchling.com/hc/en-us/articles/9684227098893-Choose-a-naming-option-for-your-Registry-schema

function register_entity​

Register custom entity to Benchling registry with retry logic

Parameters​

benchling_context : BenchlingContext
        Benchling context object to get connection
entity_id : str
        ID of the entity to register
registry_id : str
        ID of the registry to register the entity to

Raises​

RegistrationError
        Failure to register entity to registry

function create_custom_entity​

Creates and returns the id of the custom entity.

Parameters​

benchling_context : Benchling Context object
        Benchling context object to get connection
entity_name : str
        Name of new entity to be created
folder_id : str | Unset
        Folder ID containing Benchling entity to be created. This should be a string starting with
        "lib_"
input_schema_id : str | Unset
        Input schema ID Tag. schema associated with Benchling entity to be created This should be
        a string starting with "ts_"
registry_id : str | Unset
        Project associated with custom entity.    This identifies the registry that your run entity
        will be registered to.    This can be found by clicking on Avatar - Feature Settings -
        Registry Settings, and you will be able to find it in the URL.    This should be a string
        starting with "src_"
custom_entity_fields : dict | None
        Fields associated with Benchling entity
author_id : str | None
        Author ID to associate with custom entity. Should be a string starting with "ent_"
naming_strategy : NamingStrategy
        Strategy to use for naming the entity.    See NamingStrategy for more details.

Returns​

dict[str, str]
        Dictionary with custom entity name as key and custom entity ID as value

Raises​

BenchlingError
        Failure to create entity

function update_custom_entity​

Updates custom entity

Parameters​

benchling_context : BenchlingContext
        Benchling Context object
existing_entity : benchling_api_client.v2.stable.models.custom_entity.CustomEntity
        Existing custom entity to be updated
folder_id : str
        Folder ID containing Benchling entity to be created. This should be a string starting with
        "lib_"
input_schema_id : str
        Input schema ID Tag. schema associated with Benchling entity to be updated. This should be
        a string starting with "ts_"
registry_id : str
        Project associated with custom entity.    This identifies the registry that your run entity
        will be registered to.    This can be found by clicking on Avatar - Feature Settings -
        Registry Settings, and you will be able to find it in the URL.    This should be a string
        starting with "src_"
custom_entity_fields : dict | None
        Fields associated with Benchling entity

Returns​

dict[str, str]
        Dictionary of entity name, custom entity id pair

function create_benchling_ids_from_files​

Upload blob files to Benchling and return a dictionary where the keys are the file names and the
values are the benchling IDs

Parameters​

benchling_context : Benchling Context object
        Benchling context object to get connection
file_name : list[str]
        File names to associate to file content
file_content : list[bytes] | list[pd.DataFrame]
        Blob or data content to upload
keys_as_benchling_name : bool
        Use to process file_name for benchling by converting string to lowercase and removing
        periods. Default is False.

Returns​

dict[str, Unset | str]
        Returns a dictionary of IDs from benchling_sdk.models.Blob

function create_benchling_ids_from_file​

Get output file id for blob or data created from bytes.

Parameters​

benchling_context : Benchling Context object
        Benchling context object to get connection
file_name : str
        File name to associate with data
file_content : bytes
        Blob or data to upload as a file

Returns​

str
        Returns the id of benchling_sdk.models.Blob

function create_benchling_ids_from_data_file​

Get output file id for blob created from bytes.

Parameters​

benchling_context : Benchling Context object
        Benchling context object to get connection
file_name : str
        File name to associate with data
df : pd.DataFrame
        Data frame to upload as a file

Returns​

str
        Returns the id of benchling_sdk.models.Blob

function create_benchling_ids_from_blob_file​

Get output file id for blob created from bytes.

Parameters​

benchling_context : Benchling Context object
        Benchling context object to get connection
blob_name : str
        File name to associate with data
blob : bytes
        Blob to upload as a file.

Returns​

str
        Returns the id of benchling_sdk.models.Blob

Notes​

The file type is necessary to upload to benchling which is guessed based on the blob_name using
the mimetypes package.

function create_assay_results_from_dataframe​

Processes input DataFrame for upload to Benchling.

Parameters​

data : pd.DataFrame
        Tabular result(s) of data to send to Benchling. Converted to list of dictionaries for each
        row.
schema_id : str
        ID should contain the Benchling schema ID to write to.    This should be a string starting
        with "assaysch_"
project_id : str
        ID that results will be recorded against.    This should be a string starting with "src_".

        The members of your organization that have access to this project will also have
        visibility to the results that this integration generates.    You can find this ID by
        right clicking on the Project that you have selected, and click on "Copy API ID".
        If you don't see "Copy API ID" as an option, click on your avatar, click Settings,
        and scroll to the bottom and verify that
        "Enable Copy API ID button" is checked.
replace_special_characters : bool
        Replace special characters in column names with underscores to mimic Benchling behavior.
        Default is True.
ignore_na : bool
        If True, drop columns with only nulls prior to upload. Default is True.
error_on_empty_result : bool
        If True, raise an error if the DataFrame is empty. Default is True.
**kwargs
        Keyword args to pass to create_assay_result_from_dict
        drop_na (bool | None)

Returns​

list[AssayResultCreate]
        List of AssayResultCreate's to be uploaded to Benchling

function create_assay_result_from_dict​

Set up AssayResultCreate from dictionary

Parameters​

result : dict
        Dictionary of values to send to Benchling
schema_id : str
        Benchling schema id
project_id : str
        Benchling project id
drop_na : bool
        Determine if you should remove na from benchling results dict

Returns​

AssayResultCreate
        Assay results to be uploaded to Benchling

function create_custom_entity_obj​

Create a custom entity object to create in Benchling

Parameters​

entity_name : str
        Name of the entity to create
folder_id : str
        ID of the folder to create the entity in
input_schema_id : str
        ID of the entity schema to use
registry_id : str
        ID of the registry to use
fields : dict | None
        Dictionary of fields to add to the entity
author_id : str | None
        ID of the author to assign to the entity
naming_strategy : NamingStrategy
        Naming strategy to use for the entity, by default NamingStrategy.NEW_IDS

Returns​

entity_item : CustomEntityBulkCreate
        Custom entity object to create in Benchling

function create_custom_entities_bulk​

Create custom entities in Benchling

Parameters​

benchling_context : BenchlingContext
        Benchling context object
custom_entities_objs : List
        List of custom entity objects to create
custom_entity_service : CustomEntityService
        Initiated custom entity service object
wait : bool
        Whether to wait for the task to complete. Defaults to True.
error_on_fail : bool
        Whether to raise an error if the task fails. Defaults to True.

Returns​

custom_entity_task_ids : List
        List of task ids for the custom entities created

function update_custom_entities_bulk​

Update custom entities in Benchling

Parameters​

benchling_context : BenchlingContext
        Benchling context object
custom_entities_objs : List
        List of custom entity objects to update
custom_entity_service : CustomEntityService
        Initiated custom entity service object
wait : bool
        Whether to wait for the task to complete. Defaults to True.
error_on_fail : bool
        Whether to raise an error if the task fails. Defaults to True.

Returns​

custom_entity_ids : List
        List of task ids for the custom entities updated

function update_custom_entity_obj​

Update a custom entity object to update in Benchling

Parameters​

existing_entity : CustomEntity
        Existing custom entity to update
folder_id : str | None
        ID of the folder to move the custom entity to (if specified)
input_schema_id : str
        ID of the entity schema to use
fields : dict | None
        Dictionary of fields to add to the entity
author_id : str | None
        ID of the author to assign to the entity

Returns​

new_entity_param : CustomEntityBulkUpdate
        Custom entity object to update in Benchling