Skip to content

Job request: 9304

Organisation:
University of Bristol
Workspace:
lockdown-and-vulnerable-groups
ID:
fm6f4mumnl2neids
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Scott Walter 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.

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-09-02 to 2020-01-13 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv.gz

  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-01-20 to 2020-06-01 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input*.csv.gz

  generate_study_population_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-06-08 to 2020-10-19 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/inpu*.csv.gz

  generate_study_population_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-10-26 to 2021-03-01 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/inp*.csv.gz

  generate_study_population_5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-03-08 to 2021-06-14 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/in*.csv.gz

  generate_study_population_6:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-06-21 to 2021-09-27 by week" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/i*.csv.gz


  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition
    needs: [generate_study_population_1, generate_study_population_2, generate_study_population_3, generate_study_population_4, generate_study_population_5, generate_study_population_6]
    outputs:
      moderately_sensitive:
        measure_csv: output/measure_*_rate.csv


  run_subgroup_setup:
    run: stata-mp:latest analysis/subgroup_data_setup.do
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        subgroup1: output/dva_female.dta
        subgroup2: output/dva_male.dta
        subgroup3: output/dva_all.dta
        subgroup4: output/intdis_sub14.dta
        subgroup5: output/intdis_over14.dta
        subgroup6: output/intdis_all.dta
        subgroup7: output/RCGPsafeguard_sub18.dta
        subgroup8: output/CovidNewCaseCounts.dta

  run_model_dva_female:
    run: stata-mp:latest analysis/model_DVA_female.do
    needs: [run_subgroup_setup]
    outputs:
      moderately_sensitive:
        model_dva_female1: output/dva_female2.dta
        model_dva_female2: output/dva_female2_ld1.dta
        model_dva_female3: output/dva_ratioLoess_f1.svg
        model_dva_female4: output/diagnostics/dva_diagnostics_f1.svg
        model_dva_female5: output/dva_female_plot1.svg
        model_dva_female6: output/dva_female2_ld2.dta
        model_dva_female7: output/dva_ratioLoess_f2.svg
        model_dva_female8: output/diagnostics/dva_diagnostics_f2.svg
        model_dva_female9: output/dva_female_plot2.svg

  run_model_intdis:
    run: stata-mp:latest analysis/model_intdis.do
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        model_intdis1: output/intdis_plot1.pdf
        model_intdis2: output/intdis_plot2.pdf

  run_model_RCGPsafeguard:
    run: stata-mp:latest analysis/model_RCGPsafeguard.do
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        model_RCGPsafeguard1: output/RCGPsafeguard_plot1.pdf
        model_RCGPsafeguard2: output/RCGPsafeguard_plot2.pdf

  run_model_safeguard:
    run: stata-mp:latest analysis/model_safeguard.do
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        model_safeguard1: output/safeguard_plot1.pdf
        model_safeguard2: output/safeguard_plot2.pdf

  run_model_opioid:
    run: stata-mp:latest analysis/model_opioid.do
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        model_opioid1: output/opioid_plot1.pdf
        model_opioid2: output/opioid_plot2.pdf

  run_model_misuse:
    run: stata-mp:latest analysis/model_misuse.do
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        model_misuse1: output/misuse_plot1.pdf
        model_misuse2: output/misuse_plot2.pdf

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job information

Status
Failed 
GitRepoNotReachableError: Could not read from https://github.com/opensafely/lockdown-and-vulnerable-groups
Backend
TPP
Workspace
lockdown-and-vulnerable-groups
Requested by
Scott Walter
Branch
main
Force run dependencies
No
Git commit hash
04c37eb
Requested actions
  • run_model_dva_female

Code comparison

Compare the code used in this Job Request