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Often, institutes need to pull data from OpenSpecimen into an external database like the institute's data warehouse, LIMS, or other clinical systems. This can be achieved in two ways:
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Is there an ability to provide authentication by tokens or certificates?
Yes, the APIs have a mechanism to authenticate the API invokers/callers based on the token included in every request. The auth token is included in the X-OS-API-TOKEN header. More details about authentication can be found here.
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Unlike other social media applications (notorious for compromising users' data), OpenSpecimen does not support persistent CP or user-based tokens.
Can we do read-only API credentialing per Collection Protocol?
Yes. APIs are accessed via a an OpenSpecimen user account. The CPs accessible to that user via the UI are the CPs that are accessible via the APIs. You can configure it by going to the Users→Roles tab.
Using the Query module
OpenSpecimen's Query module supports the automated export of data into a CSV file. This CSV file can then be picked by an external program and processed.
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- Via GUI, create a query with the required filters (e.g. filter by CP) and add the columns needed by the external system
- Save the query
- Schedule the query to run at required intervals (E.g. nightly, hourly, etc) (For details: Scheduling Queries)
- In every query run, the data satisfying the filters are exported to a CSV file. The exported CSV file is stored in the directory
$OS_DATA_DIR/query-exported-datausing the following name format -scheduled_query_<query_id>_<job_run_id>.csv. - Write an external program to monitor the query export directory and process the required CSV files (using the filename scheduled_query_<query_id>_*.csv).
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