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Job request: 16057

Organisation:
Bennett Institute
Workspace:
opensafely-internal-interactive
ID:
fvhdqrnaltsylrpo
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Brian Mackenna (Gmail) 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_study_population_ethnicity_01GTXZYD69QT48K89NT8Y96Z2H:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_ethnicity
      --param end_date="2023-02-22"
      --output-dir output/01GTXZYD69QT48K89NT8Y96Z2H --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GTXZYD69QT48K89NT8Y96Z2H/input_ethnicity.csv.gz


  generate_study_population_01GTXZYD69QT48K89NT8Y96Z2H:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --param codelist_1_path="codelists/codelist_1.csv"
      --param codelist_1_type="event"
      --param codelist_2_path="codelists/codelist_2.csv"
      --param codelist_2_type="medication"
      --param codelist_1_frequency="monthly"
      --param time_value="3"
      --param time_scale="months"
      --param time_event="before"
      --param codelist_2_comparison_date="event_1_date"
      --param operator="AND"
      --param population="all"
      --param breakdowns="age"
      --index-date-range="2022-08-26 to 2023-02-22 by month"
      --output-dir=output/01GTXZYD69QT48K89NT8Y96Z2H
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GTXZYD69QT48K89NT8Y96Z2H/input_*.csv.gz

  join_cohorts_01GTXZYD69QT48K89NT8Y96Z2H:
    run: >
      cohort-joiner:v0.0.38
        --lhs output/01GTXZYD69QT48K89NT8Y96Z2H/input_20*.csv.gz
        --rhs output/01GTXZYD69QT48K89NT8Y96Z2H/input_ethnicity.csv.gz
        --output-dir output/01GTXZYD69QT48K89NT8Y96Z2H/joined
    needs: [generate_study_population_01GTXZYD69QT48K89NT8Y96Z2H, generate_study_population_ethnicity_01GTXZYD69QT48K89NT8Y96Z2H]
    outputs:
      highly_sensitive:
        cohort: output/01GTXZYD69QT48K89NT8Y96Z2H/joined/input_20*.csv.gz

  generate_measures_01GTXZYD69QT48K89NT8Y96Z2H:
    run: >
      python:latest python analysis/measures.py
        --breakdowns="age"
        --input_dir="output/01GTXZYD69QT48K89NT8Y96Z2H/joined"
        --measure="med_review"

    needs: [join_cohorts_01GTXZYD69QT48K89NT8Y96Z2H]
    outputs:
      moderately_sensitive:
        measure: output/01GTXZYD69QT48K89NT8Y96Z2H/joined/measure*rate.csv
        decile_measure: output/01GTXZYD69QT48K89NT8Y96Z2H/joined/measure*rate_deciles.csv

  top_5_table_01GTXZYD69QT48K89NT8Y96Z2H:
    run: >
      python:latest python analysis/top_5.py
      --codelist-1-path="codelists/codelist_1.csv"
      --codelist-2-path="codelists/codelist_2.csv"
      --output-dir="output/01GTXZYD69QT48K89NT8Y96Z2H"
    needs: [generate_measures_01GTXZYD69QT48K89NT8Y96Z2H]
    outputs:
      moderately_sensitive:
        tables: output/01GTXZYD69QT48K89NT8Y96Z2H/joined/top_5*.csv

  deciles_chart_01GTXZYD69QT48K89NT8Y96Z2H:
    run: >
      deciles-charts:v0.0.33
        --input-files output/01GTXZYD69QT48K89NT8Y96Z2H/joined/measure_practice_rate_deciles.csv
        --output-dir output/01GTXZYD69QT48K89NT8Y96Z2H/joined
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures_01GTXZYD69QT48K89NT8Y96Z2H]
    outputs:
      moderately_sensitive:
        deciles_charts: output/01GTXZYD69QT48K89NT8Y96Z2H/joined/deciles_*.*

  plot_measure_01GTXZYD69QT48K89NT8Y96Z2H:
    run: >
      python:latest python analysis/plot_measures.py
        --breakdowns="age"
        --output-dir output/01GTXZYD69QT48K89NT8Y96Z2H
    needs: [generate_measures_01GTXZYD69QT48K89NT8Y96Z2H]
    outputs:
      moderately_sensitive:
        measure: output/01GTXZYD69QT48K89NT8Y96Z2H/plot_measure*.png

  event_counts_01GTXZYD69QT48K89NT8Y96Z2H:
    run: >
      python:latest python analysis/event_counts.py --input_dir="output/01GTXZYD69QT48K89NT8Y96Z2H/joined" --output_dir="output/01GTXZYD69QT48K89NT8Y96Z2H"
    needs: [join_cohorts_01GTXZYD69QT48K89NT8Y96Z2H]
    outputs:
      moderately_sensitive:
        measure: output/01GTXZYD69QT48K89NT8Y96Z2H/event_counts.json

  generate_report_01GTXZYD69QT48K89NT8Y96Z2H:
    run: >
      python:latest python analysis/render_report.py
      --report-title="Asthma Admission codes & Asthma Inhaler Salbutamol Medication"
      --population="all"
      --breakdowns="age"
      --codelist-1-name="Asthma Admission codes"
      --codelist-2-name="Asthma Inhaler Salbutamol Medication"
      --codelist-1-link="primis-covid19-vacc-uptake/astadm/v.1.5.3"
      --codelist-2-link="opensafely/asthma-inhaler-salbutamol-medication/2020-04-15"
      --time-value="3"
      --time-scale="months"
      --time-event="before"
      --start-date="2022-08-26"
      --end-date="2023-02-22"
      --num-practices=1000
      --request-id="01GTXZYD69QT48K89NT8Y96Z2H"
    needs: [event_counts_01GTXZYD69QT48K89NT8Y96Z2H, deciles_chart_01GTXZYD69QT48K89NT8Y96Z2H, top_5_table_01GTXZYD69QT48K89NT8Y96Z2H, plot_measure_01GTXZYD69QT48K89NT8Y96Z2H]
    outputs:
      moderately_sensitive:
        notebook: output/01GTXZYD69QT48K89NT8Y96Z2H/report.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 04:07:12

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

Job request

Status
Succeeded
Backend
TPP
Workspace
opensafely-internal-interactive
Requested by
Brian Mackenna (Gmail)
Branch
main
Force run dependencies
Yes
Git commit hash
f6b6df5
Requested actions
  • run_all

Code comparison

Compare the code used in this job request