This page shows the technical details of what happened when authorised researcher Kev Wing requested one or more actions to be run against real patient data in the long-covid-symptoms project, within a secure environment.
By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what
security level various outputs were written to. Outputs
highly_sensitive can never be viewed directly by a
researcher; they can only request that code runs against them. Outputs marked as
moderately_sensitive can be
viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as
moderately_sensitive can be requested for release to the public, via a controlled output review service.
Show Hide project.yaml
version: '3.0' expectations: population_size: 20000 actions: # 1. EXTRACT DATA FOR EXPOSED AND POTENTIAL CONTROLS generate_community_cases_cohort: run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_community outputs: highly_sensitive: cohort: output/input_covid_community.csv # 2. EXTRACT DATA FOR POTENTIAL COMPARATORS # new extract potential comparators code... I guess I'll have to this twice for each control group # or potentially 3 times: 2018 matches, 2019 matches, contemporary matches? # *** contemporary potential comparators generate_potential_controls_contemporary: run: cohortextractor:latest generate_cohort --study-definition study_definition_potential_controls_contemporary outputs: highly_sensitive: cohort: output/input_potential_controls_contemporary.csv # 3. MATCH CASES TO COMPARATORS # *** contemporary potential comparators match_contemporary: run: python:latest python analysis/match_contemporary.py needs: [generate_community_cases_cohort, generate_potential_controls_contemporary] outputs: moderately_sensitive: matching_report: output/matching_report_contemporary.txt highly_sensitive: matched_cases: output/matched_cases_contemporary.csv matched_matches: output/matched_matches_contemporary.csv matched_all: output/matched_combined_contemporary.csv
State is inferred from the related Jobs.
Timings set to UTC timezone.
- Runtime: 103:38:10