Job request: 2648

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher George Hickman 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
fatpig4kireb2bun succeeded generate_cohorts_bycode_emis
7zi3wapeczwwcok5 succeeded run_model_bycode_emis

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 1000

actions:


### Single 2-year activity query - compromise to cope with RAM. (no trendline)
  generate_cohorts_bycode_emis:
      run: cohortextractor:latest generate_cohort --study-definition study_definition_EMIS_bycode
      outputs:
        highly_sensitive:
          cohort: output/input_EMIS_bycode.csv

  run_model_bycode_emis:
    run: r:latest analysis/EMIS06-bycode.R
    needs: [generate_cohorts_bycode_emis]
    outputs:
      moderately_sensitive:
        log: logs/log-EMIS06-bycode.txt
        tb01: output/tables/EMISsc06_tb01_nat.csv
        fig03: output/plots/EMISsc06_fig03_pracnatcoverage.svg


### Monthly tallies.
  generate_cohorts_long_emis:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_EMISmeasures_bycode --index-date-range "2019-01-01 to 2020-12-01 by month" --output-dir=output/emismeasures
    outputs:
      highly_sensitive:
        cohort: output/emismeasures/input_EMISmeasures_bycode_*.csv

  generate_measures_emis:
    run: cohortextractor:latest generate_measures --study-definition study_definition_EMISmeasures_bycode --output-dir=output/emismeasures
    needs: [generate_cohorts_long_emis]
    outputs:
      moderately_sensitive:
        measure_csv: output/emismeasures/measure_*.csv

  run_model_long_emis:
    run: r:latest analysis/EMIS03-createnattrends_codes.R
    needs: [generate_cohorts_long_emis]
    outputs:
      moderately_sensitive:
        log: logs/log-EMIS03-createnattrends.txt
        tb01: output/tables/EMISsc03_tb01_nattrends.csv
        fig01: output/plots/EMISsc03_fig01_nattrends.svg
        fig02: output/plots/EMISsc03_fig02_absnattrends.svg
        fig03: output/plots/EMISsc03_fig03_pracnatcoverage.svg

  run_model_measures_emis:
    run: r:latest analysis/EMIS02-createtemporal.R
    needs: [generate_cohorts_long_emis,generate_measures_emis]
    outputs:
      moderately_sensitive:
        log: logs/log-EMIS02-createtemporal.txt
        red_measures: output/tables/redacted_*.csv
        figquant: output/plots/emisplot_quantiles_*_practice.svg
        figlogquant: output/plots/emisplot_logquantiles_*_practice.svg

### Weekly tallies to compare with OC/VC supplier data. https://docs.opensafely.org/en/latest/measures/
  generate_cohorts_weekly2021_emis:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_EMISmeasures_weekly --index-date-range "2020-01-06 to 2021-05-31 by week" --output-dir=output/emismeasures-weekly
    outputs:
      highly_sensitive:
        cohort: output/emismeasures-weekly/input_EMISmeasures_weekly_*.csv

  generate_measures_weekly2021_emis:
    run: cohortextractor:latest generate_measures --study-definition study_definition_EMISmeasures_weekly --output-dir=output/emismeasures-weekly
    needs: [generate_cohorts_weekly2021_emis]
    outputs:
      moderately_sensitive:
        measure_csv: output/emismeasures-weekly/measure_*.csv

  run_model_weekly2021_emis:
    run: r:latest analysis/EMIS04-weekly2021.R
    needs: [generate_cohorts_weekly2021_emis,generate_measures_weekly2021_emis]
    outputs:
      moderately_sensitive:
        log: logs/log-EMIS04-weekly2021.txt
        tab1: output/tables/EMISsc04-weeklynattrend.csv

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 06:22:03

Config

  • Backend:
    EMIS
  • Workspace:
    online-consultations-emis
  • Branch:
    emis-branch
  • Creator:
    ghickman
  • Force run dependencies:
    False
  • Git Commit Hash:
    dd14a64
  • Requested actions:
    • run_model_bycode_emis