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OHNLP / Backbone

Provides backbone infrastructure elements for OHNLP toolsets.
Apache License 2.0
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COVID example configuration #1

Closed ymnliu closed 4 years ago

ymnliu commented 4 years ago

Can we have an example configuration file provided for a pre-defined user scenario?

qqndrew commented 4 years ago

We do already, please see

https://github.com/OHNLP/Backbone/blob/master/Example-Backbone-Configs/src/main/resources/%5Brun_nlp%5D_%5Bohdsi_cdm%5D_%5Bohdsi_cdm%5D.json

unless you mean something else?

ymnliu commented 4 years ago

That should be doing mostly it. Is is possible to ship a working example as well, maybe from a few test documents?

qqndrew commented 4 years ago

Not really - reason why is the pipeline we have set up is assuming you are reading from an OMOP CDM database you have already populated using the other example config, which uses Epic Clarity as a data faucet.

Would have to write a local file system data faucet to supply a shippeable example - which would naturally break gcp/spark support because they can't read from local file systems.... (will revisit this tomorrow)

As far as downloadable packages go, all the binary executables are already packaged in the appropriate structure and is downloadable from releases.