BIOVIA ELN Data Source
BIOVIA ELN
Create a New Data Flow
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To create a new data flow, navigate to the Integrate section, and click the New Data Flow button. Then, select the desired flow type from the list, and click the Create button.
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Select the BIOVIA ELN connector tile from the list of available connectors. Then, select the credential that will be used to connect to the BIOVIA ELN instance, and click Next; or, create a new BIOVIA ELN credential for use in this flow.
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In Nexla, BIOVIA ELN data sources can be created using pre-built endpoint templates, which expedite source setup for common BIOVIA ELN endpoints.
Configure Using a Template
Nexla provides pre-built templates that can be used to rapidly configure data sources to ingest data from common BIOVIA ELN endpoints. Each template is designed specifically for the corresponding BIOVIA ELN endpoint, making data source setup easy and efficient.
Endpoint Settings
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Select the endpoint from which this source will fetch data from the Endpoint pulldown menu. Available endpoint templates are listed in the expandable boxes below. Click on an endpoint to see more information about it and how to configure your data source for this endpoint.
Endpoint Testing
Once the selected endpoint template has been configured, Nexla can retrieve a sample of the data that will be fetched according to the current settings. This allows users to verify that the source is configured correctly before saving.
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To test the current endpoint configuration, click the Test button to the right of the endpoint selection menu. Sample data will be fetched & displayed in the Endpoint Test Result panel on the right.
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If the sample data is not as expected, review the selected endpoint and associated settings, and make any necessary adjustments. Then, click the Test button again, and check the sample data to ensure that the correct information is displayed.
Configure Manually
BIOVIA ELN sources can be manually configured to ingest data from any valid BIOVIA ELN API endpoint. Configuration options available for BIOVIA ELN sources allow them to be fully customized to suit any use case—including using chained API calls to fetch data from multiple endpoints or sources that require custom authentication headers or request parameters.
First, select the method that will be used for calls to the BIOVIA ELN API from the Method pulldown menu. The most common methods are:
- GET: For retrieving data from the API
- POST: For sending data to the API or triggering actions
- PUT: For updating existing data
- PATCH: For partial updates to existing data
- DELETE: For removing data
API Endpoint URL
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Enter the URL of the BIOVIA ELN API endpoint from which this source will fetch data in the Set API URL field. This should be the complete URL including the protocol (
https://) and any required path parameters.Common BIOVIA ELN API endpoints include paths such as:
/api/notebooks— to retrieve a list of notebooks/api/experiments— to retrieve experiment records/api/experiments/{'{experimentId}'}— to retrieve a specific experiment by ID/api/templates— to retrieve experiment templates/api/materials— to retrieve materials and inventory records
The exact API endpoint paths available in your BIOVIA ELN instance depend on your version and configuration. Consult your BIOVIA ELN system administrator or the API reference documentation included with your BIOVIA ELN deployment for a complete list of available endpoints.
Date/Time Macros (API URL)
Optionally, the API URL can be customized using macros—all macros added to the API URL will be converted into values when Nexla executes the API call. Macros are dynamic placeholders that allow you to create flexible API endpoints that can adapt to different time periods or data requirements.
Date/time macros are particularly useful when querying BIOVIA ELN for experiments or notebook entries created or modified within a specific time window, enabling incremental data ingestion to capture only new or updated records.
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To add a macro, type
{at the appropriate position in the API URL (within the Set API URL field), and select the desired macro from the dropdown list.{now}– The current datetime{now-1}– The datetime one time unit before the current datetime{now+1}– The datetime one time unit after the current datetimecustom– Datetime macros can reference any number of time units before or after the current datetime—for example, enter(now-4)to indicate the datetime four time units before the current datetime
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Select the format that will be applied to datetime macros from the Date Format for Date/Time Macro pulldown menu. This format will be applied to the base datetime value of the macro—i.e., the value of
{now}in{now-1}. -
Select the datetime unit that will be used to perform mathematical operations in the included macro(s) from the Time Unit for Operations pulldown menu—for example, for the macro
{now-1}, whenDayis selected,{now-1}will be converted to the datetime one day before the current datetime.
Lookup-Based Macros (API URL)
Column values from existing lookups can also be included as macros in the API URL. Lookup-based macros allow you to reference data from previously configured data sources or lookups, enabling dynamic API endpoints that can adapt based on existing data.
Lookup-based macros are useful in BIOVIA ELN workflows when you need to construct API endpoints that reference specific experiment IDs, notebook IDs, or other identifiers retrieved from a prior step or a separate data source in your Nexla environment.
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To include a lookup column value macro, select the relevant lookup from the Add Lookups to Supported Macros pulldown menu.
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Type
{at the appropriate position in the API URL, and select the lookup column-based macro from the dropdown list. Lookup-based macros are automatically populated into the macro list when a lookup is selected in the Add Lookups to Supported Macros pulldown menu.
Path to Data
If only a subset of the data that will be returned by an API endpoint is needed, you can designate the part(s) of the response that should be included in the Nexset(s) produced from this source by specifying the path to the relevant data within the response. This is particularly useful when BIOVIA ELN API responses contain metadata, pagination information, or other data that you don't need for your analysis.
For example, when a request call is used to fetch a list of experiments, the BIOVIA ELN API will typically return an array of experiment records along with metadata in the response. By entering the path to the relevant data, you can configure Nexla to treat each element of the returned array as a record.
Path to Data is essential when BIOVIA ELN API responses have nested structures. Without specifying the correct path, Nexla might not be able to properly parse and organize your data into usable records.
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To specify which data should be treated as relevant in responses from this source, enter the path to the relevant data in the Set Path to Data in Response field.
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For responses in JSON format enter the JSON path that points to the object or array that should be treated as relevant data. JSON paths use dot notation (e.g.,
$.data.items[*]to access an array of items within a data object). -
For responses in XML format, enter the XPath that points to the object/array containing relevant data. XPath uses slash notation (e.g.,
/response/data/itemto access item elements within a data element).
Path to Data Example:If the BIOVIA ELN API response is in JSON format and includes a top-level array named
datathat contains the relevant experiment records, the path to the response would be entered as$.data[*]. -
Autogenerate Path Suggestions
Nexla can also autogenerate data path suggestions based on the response from the API endpoint. These suggested paths can be used as-is or modified to exactly suit your needs.
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To use this feature, click the Test button next to the Set API URL field to fetch a sample response from the API endpoint. Suggested data paths generated based on the content & format of the response will be displayed in the Suggestions box below the Set Path to Data in Response field.
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Click on a suggestion to automatically populate the Set Path to Data in Response field with the corresponding path. The populated path can be modified directly within the field if further customization is needed.
Metadata
If metadata is included in the response but is located outside of the defined path to relevant data, you can configure Nexla to include this data as common metadata in each record. This is useful when you want to preserve important contextual information that applies to all records but isn't part of the main data array.
For example, when a request call is used to fetch a list of BIOVIA ELN experiments, the API response will typically include the experiment records along with metadata such as total count, pagination information, or request timestamps. If you have specified the path to the relevant data but metadata of interest is located in a different part of the response, you can specify a path to this metadata to include it with each record in the generated Nexset(s).
Metadata paths are particularly useful for preserving API response context like request IDs, timestamps, or summary statistics that apply to all records in the response.
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To specify the location of metadata that should be included with each record, enter the path to the relevant metadata in the Path to Metadata in Response field.
- For responses in JSON format, enter the JSON path to the object or array that contains the metadata, and for responses in XML format, enter the XPath.
Request Headers
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If Nexla should include any additional request headers in API calls to this source, enter the headers & corresponding values as comma-separated pairs in the Request Headers field (e.g.,
header1:value1,header2:value2). Additional headers may be required for BIOVIA ELN API versioning, content type specifications, or custom authentication requirements specific to your deployment.You do not need to include any headers already present in the credentials. Common headers like Authorization, Content-Type, and Accept are typically handled automatically by Nexla based on your credential configuration.
Endpoint Testing
After configuring all settings for the selected endpoint, Nexla can retrieve a sample of the data that will be fetched according to the current configuration. This allows users to verify that the source is configured correctly before saving.
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To test the current endpoint configuration, click the Test button to the right of the endpoint selection menu. Sample data will be fetched & displayed in the Endpoint Test Result panel on the right.
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If the sample data is not as expected, review the selected endpoint and associated settings, and make any necessary adjustments. Then, click the Test button again, and check the sample data to ensure that the correct information is displayed.
Save & Activate the Source
- Once all of the relevant steps in the above sections have been completed, click the Create button in the upper right corner of the screen to save and create the new BIOVIA ELN data source. Nexla will now begin ingesting data from the configured endpoint and will organize any data that it finds into one or more Nexsets.