Fhir-pipe helps extracting data from SQL databases and converting it to the standardized health format FHIR, using given mapping rules provided by the pyrog project.
The mapping rules are provided through the pyrog graphql API. To each FHIR Resource (e.g. Patient) corresponds a rule file, and each attribute of the ressource (for example patient.name.firstname) has a mapping instruction which details which DATABASE/TABLE/COLUMN to select and which processing scripts to apply, as the data might need to be cleaned. A non-exhaustive list of scripts is available in arkhn/scripts.
fhirpipe is an ETL which is agnostic of the type of input SQL databases. It should be able to parse mapping rules, connect to arbitrary SQL databases, and populate processed FHIR objects using these databases and the processing rules given.
We have reported several issues with the label Good first issue which can be a good way to start! You can also join our Slack to contact us if you have trouble or questions :)
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