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Job request: 17229

Organisation:
Bennett Institute
Workspace:
the-impact-of-covid-19-on-prescribing-of-antimicrobials-interactive
ID:
5ylpdwtmpswv2gor
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Brian MacKenna (PHC) requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_study_population_ethnicity_01GYAEK0G72W0DFY4ZFJ0DPA6Y:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_ethnicity
      --param end_date="2023-03-31"
      --output-dir output/01GYAEK0G72W0DFY4ZFJ0DPA6Y --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GYAEK0G72W0DFY4ZFJ0DPA6Y/input_ethnicity.csv.gz


  generate_study_population_01GYAEK0G72W0DFY4ZFJ0DPA6Y:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --param codelist_1_path="interactive_codelists/codelist_1.csv"
      --param codelist_1_type="medication"
      --param codelist_2_path="interactive_codelists/codelist_2.csv"
      --param codelist_2_type="medication"
      --param codelist_1_frequency="monthly"
      --param time_value="1"
      --param time_ever="False"
      --param time_scale="weeks"
      --param time_event="before"
      --param codelist_2_comparison_date="end_date"
      --param operator="AND"
      --param population="adults"
      --param breakdowns="sex,age,ethnicity,imd,region"
      --index-date-range="2019-09-01 to 2023-03-31 by month"
      --output-dir=output/01GYAEK0G72W0DFY4ZFJ0DPA6Y
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GYAEK0G72W0DFY4ZFJ0DPA6Y/input_*.csv.gz

  join_cohorts_01GYAEK0G72W0DFY4ZFJ0DPA6Y:
    run: >
      cohort-joiner:v0.0.38
        --lhs output/01GYAEK0G72W0DFY4ZFJ0DPA6Y/input_20*.csv.gz
        --rhs output/01GYAEK0G72W0DFY4ZFJ0DPA6Y/input_ethnicity.csv.gz
        --output-dir output/01GYAEK0G72W0DFY4ZFJ0DPA6Y/joined
    needs: [generate_study_population_01GYAEK0G72W0DFY4ZFJ0DPA6Y, generate_study_population_ethnicity_01GYAEK0G72W0DFY4ZFJ0DPA6Y]
    outputs:
      highly_sensitive:
        cohort: output/01GYAEK0G72W0DFY4ZFJ0DPA6Y/joined/input_20*.csv.gz

  generate_measures_01GYAEK0G72W0DFY4ZFJ0DPA6Y:
    run: >
      python:latest -m analysis.measures
        --breakdowns="sex,age,ethnicity,imd,region"
        --input_dir="output/01GYAEK0G72W0DFY4ZFJ0DPA6Y/joined"

    needs: [join_cohorts_01GYAEK0G72W0DFY4ZFJ0DPA6Y]
    outputs:
      moderately_sensitive:
        measure: output/01GYAEK0G72W0DFY4ZFJ0DPA6Y/joined/measure_all.csv
        decile_measure: output/01GYAEK0G72W0DFY4ZFJ0DPA6Y/joined/measure_practice_rate_deciles.csv

  top_5_table_01GYAEK0G72W0DFY4ZFJ0DPA6Y:
    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/01GYAEK0G72W0DFY4ZFJ0DPA6Y"
    needs: [generate_measures_01GYAEK0G72W0DFY4ZFJ0DPA6Y]
    outputs:
      moderately_sensitive:
        tables: output/01GYAEK0G72W0DFY4ZFJ0DPA6Y/joined/top_5*.csv

  plot_measure_01GYAEK0G72W0DFY4ZFJ0DPA6Y:
    run: >
      python:latest python analysis/plot_measures.py
        --breakdowns="sex,age,ethnicity,imd,region"
        --output-dir output/01GYAEK0G72W0DFY4ZFJ0DPA6Y
    needs: [generate_measures_01GYAEK0G72W0DFY4ZFJ0DPA6Y]
    outputs:
      moderately_sensitive:
        measure: output/01GYAEK0G72W0DFY4ZFJ0DPA6Y/plot_measure*.png
        deciles: output/01GYAEK0G72W0DFY4ZFJ0DPA6Y/deciles_chart.png

  event_counts_01GYAEK0G72W0DFY4ZFJ0DPA6Y:
    run: >
      python:latest python analysis/event_counts.py --input_dir="output/01GYAEK0G72W0DFY4ZFJ0DPA6Y/joined" --output_dir="output/01GYAEK0G72W0DFY4ZFJ0DPA6Y"
    needs: [join_cohorts_01GYAEK0G72W0DFY4ZFJ0DPA6Y]
    outputs:
      moderately_sensitive:
        measure: output/01GYAEK0G72W0DFY4ZFJ0DPA6Y/event_counts.json

  generate_report_01GYAEK0G72W0DFY4ZFJ0DPA6Y:
    run: >
      python:latest python analysis/render_report.py
      --output-dir="output/01GYAEK0G72W0DFY4ZFJ0DPA6Y"
      --population="adults"
      --breakdowns="sex,age,ethnicity,imd,region"
      --codelist-1-name="Doxycycline (tetracyclines)"
      --codelist-2-name="Oral prednisolone codes"
      --codelist-1-link="user/alexorlek/doxycycline-tetracyclines/4458c45a"
      --codelist-2-link="primis-covid19-vacc-uptake/astrxm2/v1.5.3"
      --time-value="1"
      --time-scale="weeks"
      --time-event="before"
      --start-date="2019-09-01"
      --end-date="2023-03-31"
    needs: [event_counts_01GYAEK0G72W0DFY4ZFJ0DPA6Y, top_5_table_01GYAEK0G72W0DFY4ZFJ0DPA6Y, plot_measure_01GYAEK0G72W0DFY4ZFJ0DPA6Y]
    outputs:
      moderately_sensitive:
        notebook: output/01GYAEK0G72W0DFY4ZFJ0DPA6Y/report.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 19:16:57

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

Job information

Status
Succeeded
Backend
TPP
Workspace
the-impact-of-covid-19-on-prescribing-of-antimicrobials-interactive
Requested by
Brian MacKenna (PHC)
Branch
main
Force run dependencies
Yes
Git commit hash
e939537
Requested actions
  • run_all

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