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Job request: 15899

Organisation:
Bennett Institute
Workspace:
opensafely-internal-interactive
ID:
canz7vdti365egse
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Lucy Bridges 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_01GTEF1K6BQMHC2DK0FD8GND9Q:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_ethnicity
      --param end_date="2023-02-22"
      --output-dir output/01GTEF1K6BQMHC2DK0FD8GND9Q --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GTEF1K6BQMHC2DK0FD8GND9Q/input_ethnicity.csv.gz


  generate_study_population_01GTEF1K6BQMHC2DK0FD8GND9Q:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --param codelist_1_path="codelists/codelist_1.csv"
      --param codelist_1_type="medication"
      --param codelist_2_path="codelists/codelist_2.csv"
      --param codelist_2_type="event"
      --param codelist_1_frequency="monthly"
      --param time_value="1"
      --param time_scale="years"
      --param time_event="before"
      --param codelist_2_comparison_date="event_1_date"
      --param operator="AND"
      --param population="adults"
      --param breakdowns="sex"
      --index-date-range="2019-09-01 to 2023-02-22 by month"
      --output-dir=output/01GTEF1K6BQMHC2DK0FD8GND9Q
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GTEF1K6BQMHC2DK0FD8GND9Q/input_*.csv.gz

  join_cohorts_01GTEF1K6BQMHC2DK0FD8GND9Q:
    run: >
      cohort-joiner:v0.0.38
        --lhs output/01GTEF1K6BQMHC2DK0FD8GND9Q/input_20*.csv.gz
        --rhs output/01GTEF1K6BQMHC2DK0FD8GND9Q/input_ethnicity.csv.gz
        --output-dir output/01GTEF1K6BQMHC2DK0FD8GND9Q/joined
    needs: [generate_study_population_01GTEF1K6BQMHC2DK0FD8GND9Q, generate_study_population_ethnicity_01GTEF1K6BQMHC2DK0FD8GND9Q]
    outputs:
      highly_sensitive:
        cohort: output/01GTEF1K6BQMHC2DK0FD8GND9Q/joined/input_20*.csv.gz

  generate_measures_01GTEF1K6BQMHC2DK0FD8GND9Q:
    run: >
      python:latest python analysis/measures.py
        --breakdowns="sex"
        --input_dir="output/01GTEF1K6BQMHC2DK0FD8GND9Q/joined"
        --measure="med_review"

    needs: [join_cohorts_01GTEF1K6BQMHC2DK0FD8GND9Q]
    outputs:
      moderately_sensitive:
        measure: output/01GTEF1K6BQMHC2DK0FD8GND9Q/joined/measure*rate.csv
        decile_measure: output/01GTEF1K6BQMHC2DK0FD8GND9Q/joined/measure*rate_deciles.csv

  top_5_table_01GTEF1K6BQMHC2DK0FD8GND9Q:
    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/01GTEF1K6BQMHC2DK0FD8GND9Q"
    needs: [generate_measures_01GTEF1K6BQMHC2DK0FD8GND9Q]
    outputs:
      moderately_sensitive:
        tables: output/01GTEF1K6BQMHC2DK0FD8GND9Q/joined/top_5*.csv

  deciles_chart_01GTEF1K6BQMHC2DK0FD8GND9Q:
    run: >
      deciles-charts:v0.0.33
        --input-files output/01GTEF1K6BQMHC2DK0FD8GND9Q/joined/measure_practice_rate_deciles.csv
        --output-dir output/01GTEF1K6BQMHC2DK0FD8GND9Q/joined
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures_01GTEF1K6BQMHC2DK0FD8GND9Q]
    outputs:
      moderately_sensitive:
        deciles_charts: output/01GTEF1K6BQMHC2DK0FD8GND9Q/joined/deciles_*.*

  plot_measure_01GTEF1K6BQMHC2DK0FD8GND9Q:
    run: >
      python:latest python analysis/plot_measures.py
        --breakdowns="sex"
        --output-dir output/01GTEF1K6BQMHC2DK0FD8GND9Q
    needs: [generate_measures_01GTEF1K6BQMHC2DK0FD8GND9Q]
    outputs:
      moderately_sensitive:
        measure: output/01GTEF1K6BQMHC2DK0FD8GND9Q/plot_measure*.png

  event_counts_01GTEF1K6BQMHC2DK0FD8GND9Q:
    run: >
      python:latest python analysis/event_counts.py --input_dir="output/01GTEF1K6BQMHC2DK0FD8GND9Q/joined" --output_dir="output/01GTEF1K6BQMHC2DK0FD8GND9Q"
    needs: [join_cohorts_01GTEF1K6BQMHC2DK0FD8GND9Q]
    outputs:
      moderately_sensitive:
        measure: output/01GTEF1K6BQMHC2DK0FD8GND9Q/event_counts.json

  create_notebook_01GTEF1K6BQMHC2DK0FD8GND9Q:
    run: >
      python:latest python analysis/create_notebook.py
      --output-dir "output/01GTEF1K6BQMHC2DK0FD8GND9Q"
      --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="DMARDs & Medication Review - OpenSAFELY Service Restoration Observatory"
      --measure-description="Medication Review"
      --population="adults"
      --breakdowns="sex"
    outputs:
      moderately_sensitive:
        notebook: output/01GTEF1K6BQMHC2DK0FD8GND9Q/report.ipynb

  generate_notebook_01GTEF1K6BQMHC2DK0FD8GND9Q:
    run: jupyter:latest jupyter nbconvert /workspace/output/01GTEF1K6BQMHC2DK0FD8GND9Q/report.ipynb --execute --to html --output-dir=/workspace/output/01GTEF1K6BQMHC2DK0FD8GND9Q --ExecutePreprocessor.timeout=86400 --no-input
    needs: [create_notebook_01GTEF1K6BQMHC2DK0FD8GND9Q, event_counts_01GTEF1K6BQMHC2DK0FD8GND9Q, deciles_chart_01GTEF1K6BQMHC2DK0FD8GND9Q, top_5_table_01GTEF1K6BQMHC2DK0FD8GND9Q, plot_measure_01GTEF1K6BQMHC2DK0FD8GND9Q]
    outputs:
      moderately_sensitive:
        notebook: output/01GTEF1K6BQMHC2DK0FD8GND9Q/report.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:51:05

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
Lucy Bridges
Branch
main
Force run dependencies
Yes
Git commit hash
fb006b0
Requested actions
  • run_all

Code comparison

Compare the code used in this job request