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Job request: 4744

Workspace:
germdefence
ID:
qpmx5eh6z4w5qmij
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.

Jobs

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: 00:00:16

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

Job information

Status
Succeeded
Backend
TPP
Workspace
germdefence
Requested by
Scott Walter
Branch
main
Force run dependencies
No
Git commit hash
6c852cd
Requested actions
  • run_process_evaluation