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Job request: 8769

Organisation:
Bennett Institute
Workspace:
primary-care-covid-codes-research
ID:
gb4umm53wosfjm5i
View repo View project.yaml

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

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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: 10000

actions:

  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  generate_report:
    run: cohort-report:v3.0.0 output/input.feather
    needs: [generate_cohort]
    config:
      output_path: output/cohort_reports_outputs
    outputs:
      moderately_sensitive:
        reports: output/cohort_reports_outputs/descriptives_input.html
        reports_charts: output/cohort_reports_outputs/*.png

  counts:
    run: python:latest python analysis/counts.py
    needs: [generate_cohort]
    outputs:
      moderately_sensitive: 
        tabdata: output/tabledata.csv
        cohort_2: output/codecounts_week.csv
        df2: output/events_pp.csv
        
  freq_plots:
    run: python:latest python analysis/freq_plot.py
    needs: [counts]
    outputs:
      moderately_sensitive:  
        plots: output/plots.svg
#        figs: output/figs.svg

  km_plots:
    run: python:latest python analysis/km_plot.py
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:  
        figs: output/figs.svg

  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly --index-date-range "2020-03-01 to 2021-03-01 by month" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/monthly/input_monthly_*.feather

  generate_study_population_2:
      run: cohortextractor:latest generate_cohort --study-definition study_definition_monthly --index-date-range "2021-04-01 to 2022-05-01 by month" --output-format feather
      outputs:
        highly_sensitive:
          cohort: output/monthly/input_monthly*.feather

  generate_measures:
    run: >
      cohortextractor:latest generate_measures
        --study-definition study_definition_monthly
        --output-dir output/monthly
    needs: [generate_study_population_1,generate_study_population_2]
    outputs:
      moderately_sensitive:
        measure: output/monthly/measure_*.csv     

  notebook_md:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/primary-care-covid-codes.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_cohort,km_plots,counts,generate_measures]
    outputs:
      moderately_sensitive:
        md: output/primary-care-covid-codes.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 05:12:34

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

Job information

Status
Succeeded
Backend
TPP
Workspace
primary-care-covid-codes-research
Requested by
Colm Andrews
Branch
master
Force run dependencies
No
Git commit hash
8882e18
Requested actions
  • generate_study_population_1
  • generate_study_population_2
  • generate_measures
  • notebook_md

Code comparison

Compare the code used in this Job Request