Job request: 1441

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher mbfons requested one or more actions to be run against real patient data in the Online Consultations 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 marked as 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.

Jobs

ID Status Action
3sru4lc4rbnezrs5 succeeded generate_cohorts_main
r4mjc4chsoevtfwd succeeded run_model
hih46j2o3oq7ilho succeeded generate_cohorts_long
7iouynnx5k62in6q succeeded generate_measures
qizfyfe3vo7gmqfn succeeded run_model_long
scxzyt6latpts6ud succeeded run_model_measures
m7r4f5xk526efoui succeeded run_model_measuresDEBUG
2k6easqbtxiqqyh3 succeeded run_model_redactedmeasures

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_cohorts_main:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ori
    outputs:
      highly_sensitive:
        cohort: output/input_ori.csv

  run_model:
    run: r:latest analysis/01-createSDtables.R
    needs: [generate_cohorts_main]
    outputs:
      moderately_sensitive:
        log: logs/log-01-createSDtables.txt
        #gtpng1: output/tables/gt_ocpop.png
        #gtpng2: output/tables/gt_gpcpop.png
        rdata1: output/tables/gt_ocpop.RData
        rdata2: output/tables/gt_gpcpop.RData
        #tb01: output/tables/tb01_gpcr_region.csv
        #tb02: output/tables/tb02_gpcr_stp.csv # guidance says to not output identifiable regions
        tb04: output/tables/tb04_gpcr_agesex.csv
        tb05: output/tables/tb05_gpcr_ethnicity.csv
        tb06: output/tables/tb06_gpcr_ruc.csv
        tb07: output/tables/tb07_gpcr_care.csv
        tb08: output/tables/tb08_gpcr_dis.csv
        tb09: output/tables/tb09_gpcr_imd.csv

  # https://docs.opensafely.org/en/latest/measures/
  generate_cohorts_long:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures_bycode --index-date-range "2019-01-01 to 2020-12-01 by month" --output-dir=output/measures
    outputs:
      highly_sensitive:
        cohort: output/measures/input_measures_bycode_*.csv

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_measures_bycode --output-dir=output/measures
    needs: [generate_cohorts_long]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_*.csv

  run_model_long:
    run: r:latest analysis/03-createnattrends_codes.R
    needs: [generate_cohorts_long]
    outputs:
      moderately_sensitive:
        log: logs/log-03-createnattrends.txt
        tb01: output/tables/sc03_tb01_nattrends.csv
        fig01: output/plots/sc03_fig01_nattrends.svg
        fig02: output/plots/sc03_fig02_nattrends.svg
        fig03: output/plots/sc03_fig03_pracnatcoverage.svg
        fig04: output/plots/sc03_fig04_pracbyregcoverage.svg

  run_model_measures:
    run: r:latest analysis/02-createtemporal.R
    needs: [generate_cohorts_long,generate_measures]
    outputs:
      moderately_sensitive:
        log: logs/log-02-createtemporal.txt
        red_measures: output/tables/redacted_*.csv
        #tb01: output/measures_gpc_pop.csv # redundant into. omit output
        fig01: output/plots/plot_overall_gpc_pop.svg
        #figall: output/plots/plot_each_OC_*_practice.svg
        figquant: output/plots/plot_quantiles_OC_*_practice.svg


  run_model_measuresDEBUG:
    run: r:latest analysis/02-createtemporal_debug.R
    needs: [generate_cohorts_long,generate_measures]
    outputs:
      moderately_sensitive:
        log: logs/log-02-createtemporal-debug.txt
        #tb01: output/measures_gpc_pop_debug.csv
        #fig01: output/plots/plot_overall_gpc_pop_debug.svg
        #figall: output/plots/plot_each_debug_*_practice.svg
        #figquant: output/plots/plot_quantiles_debug_*_practice.svg
        #figquant2: output/plots/plot_quantiles2_debug_*_practice.svg

  run_model_redactedmeasures:
    run: r:latest analysis/02a-createredactedmeasure.R
    needs: [generate_cohorts_long,generate_measures]
    outputs:
      moderately_sensitive:
        log: logs/log-02a-createredactedmeasure.txt
        red_measures: output/tables/redacted2a_*.csv

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 00:54:39

Config