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Job request: 4747

Organisation:
University of Bristol
Workspace:
germdefence
ID:
6mghc6zkn2ol2oax
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Scott Walter 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: 10000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-07-14 to 2021-03-15 by week" --skip-existing --output-format=csv.gz --output-dir=output/measures
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv.gz

  generate_practice_variables:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_practice --skip-existing --output-format=dta --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_practice.dta

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        measure_csv: output/measures/measure_*.csv

  run_practice_variables:
    run: stata-mp:latest analysis/practice_variables.do
    needs: [generate_practice_variables]
    outputs:
      moderately_sensitive:
        model: output/practice_variables.dta
        model2: output/practice_variables.xlsx

  run_model:
    run: stata-mp:latest analysis/model.do
    needs: [generate_measures, run_practice_variables]
    outputs:
      moderately_sensitive:
        model1: output/PerProtocol.xlsx
        model2: output/DiD_weekly.xlsx
        data: output/process_eval.dta
        check: output/weekly_check.xlsx
        check2: output/practice_weekly_glmm.xlsx
        model3: output/CITS_weekly.xlsx
        model4: output/CITS_RandInt.xlsx
        plot1: output/rti_plot.pdf
        plot2: output/arti_plot.pdf
        plot3: output/gastro_plot.pdf
        plot4: output/coviddiag_plot.pdf
        plot5: output/covidsympsens_plot.pdf
        plot6: output/covidsympspec_plot.pdf
        plot7: output/antibio_plot.pdf
        plot8: output/adm_plot.pdf

  run_process_evaluation:
    run: stata-mp:latest analysis/process_eval.do
    needs: [run_model]
    outputs:
      moderately_sensitive:
        model1: output/process_eval.xlsx
        model2: output/process_eval_cat.xlsx
        model3: output/process_eval2.xlsx
        model4: output/process_eval_cat2.xlsx
        data: output/process_eval_check.xlsx

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job request

Status
Failed 
GitRepoNotReachableError: Could not read from https://github.com/opensafely/GermDefence
Backend
TPP
Workspace
germdefence
Requested by
Scott Walter
Branch
main
Force run dependencies
No
Git commit hash
16f610b
Requested actions
  • run_process_evaluation

Code comparison

Compare the code used in this job request