Skip to content

Job request: 15797

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

This page shows the technical details of what happened when the authorised researcher George Hickman 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_01GT227EDJYCTYGNET334PB70P:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_ethnicity 
      --param end_date="2023-02-15"
      --output-dir output/01GT227EDJYCTYGNET334PB70P --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GT227EDJYCTYGNET334PB70P/input_ethnicity.csv.gz


  generate_study_population_01GT227EDJYCTYGNET334PB70P:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --param codelist_1_path="codelists/codelist_1.csv"
      --param codelist_1_system="snomed"
      --param codelist_2_path="codelists/codelist_2.csv"
      --param codelist_2_system="snomed"
      --param codelist_1_frequency="monthly"
      --param time_value="5"
      --param time_scale="years"
      --param time_event="before"
      --param codelist_2_comparison_date="event_1_date"
      --param operator="AND"
      --param population="all"
      --param breakdowns="sex,age"
      --index-date-range="2019-09-01 to 2023-02-15 by month"
      --output-dir=output/01GT227EDJYCTYGNET334PB70P
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GT227EDJYCTYGNET334PB70P/input_*.csv.gz

  join_cohorts_01GT227EDJYCTYGNET334PB70P:
    run: >
      cohort-joiner:v0.0.38
        --lhs output/01GT227EDJYCTYGNET334PB70P/input_20*.csv.gz
        --rhs output/01GT227EDJYCTYGNET334PB70P/input_ethnicity.csv.gz
        --output-dir output/01GT227EDJYCTYGNET334PB70P/joined
    needs: [generate_study_population_01GT227EDJYCTYGNET334PB70P, generate_study_population_ethnicity_01GT227EDJYCTYGNET334PB70P]
    outputs:
      highly_sensitive:
        cohort: output/01GT227EDJYCTYGNET334PB70P/joined/input_20*.csv.gz

  generate_measures_01GT227EDJYCTYGNET334PB70P:
    run: >
      python:latest python analysis/measures.py
        --breakdowns="sex,age"
        --input_dir="output/01GT227EDJYCTYGNET334PB70P/joined"
        --measure="med_review"

    needs: [join_cohorts_01GT227EDJYCTYGNET334PB70P]
    outputs:
      moderately_sensitive:
        measure: output/01GT227EDJYCTYGNET334PB70P/joined/measure*rate.csv
        decile_measure: output/01GT227EDJYCTYGNET334PB70P/joined/measure*rate_deciles.csv

  top_5_table_01GT227EDJYCTYGNET334PB70P:
    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/01GT227EDJYCTYGNET334PB70P"
    needs: [generate_measures_01GT227EDJYCTYGNET334PB70P]
    outputs:
      moderately_sensitive:
        tables: output/01GT227EDJYCTYGNET334PB70P/joined/top_5*.csv

  deciles_chart_01GT227EDJYCTYGNET334PB70P:
    run: >
      deciles-charts:v0.0.33
        --input-files output/01GT227EDJYCTYGNET334PB70P/joined/measure_practice_rate_deciles.csv
        --output-dir output/01GT227EDJYCTYGNET334PB70P/joined
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures_01GT227EDJYCTYGNET334PB70P]
    outputs:
      moderately_sensitive:
        deciles_charts: output/01GT227EDJYCTYGNET334PB70P/joined/deciles_*.*

  plot_measure_01GT227EDJYCTYGNET334PB70P:
    run: >
      python:latest python analysis/plot_measures.py
        --breakdowns="sex,age"
        --output-dir output/01GT227EDJYCTYGNET334PB70P
    needs: [generate_measures_01GT227EDJYCTYGNET334PB70P]
    outputs:
      moderately_sensitive:
        measure: output/01GT227EDJYCTYGNET334PB70P/plot_measure*.png

  event_counts_01GT227EDJYCTYGNET334PB70P:
    run: >
      python:latest python analysis/event_counts.py --input_dir="output/01GT227EDJYCTYGNET334PB70P/joined" --output_dir="output/01GT227EDJYCTYGNET334PB70P"
    needs: [join_cohorts_01GT227EDJYCTYGNET334PB70P]
    outputs:
      moderately_sensitive:
        measure: output/01GT227EDJYCTYGNET334PB70P/event_counts.json

  create_notebook_01GT227EDJYCTYGNET334PB70P:
    run: >
      python:latest python analysis/create_notebook.py
      --output-dir "output/01GT227EDJYCTYGNET334PB70P"
      --codelist-1-description="None"
      --codelist-2-description="None"
      --codelist-1-link="https://codelists.opensafely.org/codelist/opensafely/dmards/2020-06-23"
      --codelist-2-link="https://codelists.opensafely.org/codelist/opensafely/medication-review-opensafely-service-restoration-observatory/24b50f64"
      --report-title="Medication Review Report"
      --measure-description="Medication Review"
      --population="all"
      --breakdowns="sex,age"
    outputs:
      moderately_sensitive:
        notebook: output/01GT227EDJYCTYGNET334PB70P/report.ipynb

  generate_notebook_01GT227EDJYCTYGNET334PB70P:
    run: jupyter:latest jupyter nbconvert /workspace/output/01GT227EDJYCTYGNET334PB70P/report.ipynb --execute --to html --output-dir=/workspace/output/01GT227EDJYCTYGNET334PB70P --ExecutePreprocessor.timeout=86400 --no-input
    needs: [create_notebook_01GT227EDJYCTYGNET334PB70P, event_counts_01GT227EDJYCTYGNET334PB70P, deciles_chart_01GT227EDJYCTYGNET334PB70P, top_5_table_01GT227EDJYCTYGNET334PB70P, plot_measure_01GT227EDJYCTYGNET334PB70P]
    outputs:
      moderately_sensitive:
        notebook: output/01GT227EDJYCTYGNET334PB70P/report.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:28:16

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

Job request

Status
Failed
Backend
TPP
Workspace
opensafely-internal-interactive
Requested by
George Hickman
Branch
main
Force run dependencies
Yes
Git commit hash
5c5f978
Requested actions
  • run_all

Code comparison

Compare the code used in this job request