Extensions of ID3C for the Seattle Flu Study
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Workflow for prepping UW clinical datasets

This Snakefile captures what I was doing by hand to get the latest clinical data from UW (5.08.19,11.17.19.deduplicate.csv) ingested.

This workflow should either:

a. be replaced by direct usage of geocoding and location lookup functions in id3c clinical parse-uw, or

b. grow and take over more parts of id3c clinical parse-uw, eventually replacing it with a pipeline of geocode, location lookup, de-identify and other (not yet existing) core commands.

I think (a) is the more sensible option in the short and middle term. Option (b) might be called the "augur strategy", which might be better longer term.

Running

The workflow is written to be run on a single dataset at a time, which is automatically pulled from s3://fh-pi-bedford-t/seattleflu/uw/. The dataset filename must be specified as a configuration value when running snakemake, for example:

snakemake -C dataset=5.08.19,11.17.19.deduplicate.csv

Output files are also stored on S3 and named after the input dataset.

Various steps of the workflow require different environment variables. To run the entire thing against the production database, you'll need the following defined:

  • PostgreSQL connection variables, e.g. PGSERVICE=seattleflu-production

  • PARTICIPANT_DEIDENTIFICATION_SECRET that we've previously used (eventually to be replaced by ID3C_DEIDENTIFY_SECRET).

  • Fred Hutch AWS credentials either in the environment or in local config files. If you use a separate config profile for the Hutch, you can define AWS_PROFILE.

  • SmartyStreets API credentials in SMARTYSTREETS_AUTH_ID and SMARTYSTREETS_AUTH_TOKEN. These are technically only required the first time before the local geocoding cache is populated.

Additionally, snakemake must be able to run the id3c command. This is enabled by running it within an appropriate pipenv shell or using pipenv run. Make sure to use the deployed id3c-production environment from the backoffice repo unless you're doing development.