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Job request: 22753

Organisation:
Bennett Institute
Workspace:
the-impact-of-covid-19-on-prescribing-of-antimicrobials-interactive
ID:
noeaotausqtljndl
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Chris Wood 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_01HW38MAP18PWK35KP7T46DST1:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_ethnicity
      --output-dir output/01HW38MAP18PWK35KP7T46DST1 --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/01HW38MAP18PWK35KP7T46DST1/input_ethnicity.feather

  generate_study_population_weekly_01HW38MAP18PWK35KP7T46DST1:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --param codelist_1_frequency="weekly"
      --param breakdowns=""
      --index-date_range="2024-04-01 to 2024-04-01 by week"
      --output-dir=output/01HW38MAP18PWK35KP7T46DST1
      --output-format=feather
      --output-file=output/01HW38MAP18PWK35KP7T46DST1/input_weekly_2024-04-01.feather
    outputs:
      highly_sensitive:
        cohort: output/01HW38MAP18PWK35KP7T46DST1/input_weekly_2024-04-01.feather

  generate_study_population_01HW38MAP18PWK35KP7T46DST1:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range="2019-09-01 to 2024-03-31 by month"
      --output-dir=output/01HW38MAP18PWK35KP7T46DST1
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/01HW38MAP18PWK35KP7T46DST1/input_*.feather

  join_cohorts_01HW38MAP18PWK35KP7T46DST1:
    run: >
      cohort-joiner:v0.0.38
        --lhs output/01HW38MAP18PWK35KP7T46DST1/input_20*.feather
        --rhs output/01HW38MAP18PWK35KP7T46DST1/input_ethnicity.feather
        --output-dir output/01HW38MAP18PWK35KP7T46DST1/joined
    needs: [generate_study_population_01HW38MAP18PWK35KP7T46DST1, generate_study_population_ethnicity_01HW38MAP18PWK35KP7T46DST1]
    outputs:
      highly_sensitive:
        cohort: output/01HW38MAP18PWK35KP7T46DST1/joined/input_20*.feather

  generate_measures_01HW38MAP18PWK35KP7T46DST1:
    run: >
      python:latest -m analysis.measures
        --breakdowns=sex
        --breakdowns=age
        --breakdowns=ethnicity
        --breakdowns=imd
        --breakdowns=region
        --input-dir="output/01HW38MAP18PWK35KP7T46DST1/joined"
        --output-dir="output/01HW38MAP18PWK35KP7T46DST1"

    needs: [join_cohorts_01HW38MAP18PWK35KP7T46DST1]
    outputs:
      moderately_sensitive:
        measure: output/01HW38MAP18PWK35KP7T46DST1/measure_all.csv
        decile_measure: output/01HW38MAP18PWK35KP7T46DST1/measure_practice_rate_deciles.csv

  top_5_table_01HW38MAP18PWK35KP7T46DST1:
    run: >
      python:latest python analysis/top_5.py
      --codelist-1-path="interactive_codelists/codelist_1.csv"
      --codelist-2-path="interactive_codelists/codelist_2.csv"
      --output-dir="output/01HW38MAP18PWK35KP7T46DST1"
    needs: [generate_measures_01HW38MAP18PWK35KP7T46DST1]
    outputs:
      moderately_sensitive:
        table_1: output/01HW38MAP18PWK35KP7T46DST1/top_5_code_table_1.csv
        table_2: output/01HW38MAP18PWK35KP7T46DST1/top_5_code_table_2.csv
        tables_for_checking: output/01HW38MAP18PWK35KP7T46DST1/for_checking/top_5*.csv

  plot_measure_01HW38MAP18PWK35KP7T46DST1:
    run: >
      python:latest python analysis/plot_measures.py
        --breakdowns=sex
        --breakdowns=age
        --breakdowns=ethnicity
        --breakdowns=imd
        --breakdowns=region
        --input-dir output/01HW38MAP18PWK35KP7T46DST1
        --output-dir output/01HW38MAP18PWK35KP7T46DST1
    needs: [generate_measures_01HW38MAP18PWK35KP7T46DST1]
    outputs:
      moderately_sensitive:
        measure: output/01HW38MAP18PWK35KP7T46DST1/plot_measure*.png
        data: output/01HW38MAP18PWK35KP7T46DST1/for_checking/plot_measure_for_checking.csv
        deciles: output/01HW38MAP18PWK35KP7T46DST1/deciles_chart.png

  event_counts_01HW38MAP18PWK35KP7T46DST1:
    run: >
      python:latest -m analysis.event_counts --input-dir="output/01HW38MAP18PWK35KP7T46DST1" --output-dir="output/01HW38MAP18PWK35KP7T46DST1"
    needs: [join_cohorts_01HW38MAP18PWK35KP7T46DST1, generate_study_population_weekly_01HW38MAP18PWK35KP7T46DST1]
    outputs:
      moderately_sensitive:
        measure: output/01HW38MAP18PWK35KP7T46DST1/event_counts.json

  generate_report_01HW38MAP18PWK35KP7T46DST1:
    run: >
      python:latest python analysis/render_report.py
      --output-dir="output/01HW38MAP18PWK35KP7T46DST1"
    needs: [event_counts_01HW38MAP18PWK35KP7T46DST1, top_5_table_01HW38MAP18PWK35KP7T46DST1, plot_measure_01HW38MAP18PWK35KP7T46DST1]
    outputs:
      moderately_sensitive:
        notebook: output/01HW38MAP18PWK35KP7T46DST1/report.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 16:12:38

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

Job request

Status
Succeeded
Backend
TPP
Workspace
the-impact-of-covid-19-on-prescribing-of-antimicrobials-interactive
Requested by
Chris Wood
Branch
main
Force run dependencies
Yes
Git commit hash
95b70f8
Requested actions
  • run_all

Code comparison

Compare the code used in this job request