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Job request: 2648

Organisation:
Workspace:
online-consultations-emis
ID:
lwtj3fgy6g5pe5ex
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 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

Pipeline

Show 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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 06:22:03

These timestamps are generated and stored using the UTC timezone on the EMIS backend.

Job information

Status
Succeeded
Backend
EMIS
Workspace
online-consultations-emis
Requested by
George Hickman
Branch
emis-branch
Force run dependencies
No
Git commit hash
dd14a64
Requested actions
  • run_model_bycode_emis

Code comparison

Compare the code used in this Job Request