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Job request: 2590

Organisation:
Workspace:
online-consultations-emis
ID:
g6oako6ef53mkccu
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Peter Inglesby requested one or more actions to be run against real patient data within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

### 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:

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

Job request

Status
Failed 
JobRequestError: generate_cohorts_long_emis failed on a previous run and must be re-run
Backend
EMIS
Workspace
online-consultations-emis
Requested by
Peter Inglesby
Branch
emis-branch
Force run dependencies
No
Git commit hash
cda778b
Requested actions
  • run_all

Code comparison

Compare the code used in this job request