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Job request: 8137

Organisation:
University of Bristol
Workspace:
lockdown-and-vulnerable-groups
ID:
6elw2ymira5gfpqt
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.

Jobs

  • Action:
    run_model_dva
    Status:
    Status: Succeeded
    Job identifier:
    vri3fbwsysyezeko

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 2021-07-19 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 "2021-07-26 to 2021-12-27 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_model_dva:
    run: stata-mp:latest analysis/model_DVA.do
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        model_dva1: output/dva_plot1.pdf
        model_dva2: output/dva_plot2.pdf

  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: 00:00:44

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

Job request

Status
Succeeded
Backend
TPP
Workspace
lockdown-and-vulnerable-groups
Requested by
Scott Walter
Branch
main
Force run dependencies
No
Git commit hash
3b235b6
Requested actions
  • run_model_dva

Code comparison

Compare the code used in this job request