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Job request: 4903

Organisation:
Bennett Institute
Workspace:
primary-care-covid-codes-research
ID:
srch4oqsm72v5cf4
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

  • Action:
    generate_cohort
    Status:
    Status: Succeeded
    Job identifier:
    5kx26bdt46ul4hb6
  • Action:
    km_plots
    Status:
    Status: Succeeded
    Job identifier:
    4e7zgco7pcqnkb7z
  • Action:
    counts
    Status:
    Status: Succeeded
    Job identifier:
    sztseh4h533bkd2s
  • Action:
    freq_plots
    Status:
    Status: Succeeded
    Job identifier:
    5gntndaerpuynqls
  • Action:
    notebook_md
    Status:
    Status: Succeeded
    Job identifier:
    p7f6ee6lyt7g3bjv

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

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

  counts:
    run: python:latest python analysis/counts.py
    needs: [generate_cohort]
    outputs:
      moderately_sensitive: 
        tabdata: output/tabledata.csv
        cohort_2: output/codecounts_week.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

  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]
    outputs:
      moderately_sensitive:
        md: output/primary-care-covid-codes.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:24:10

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
Yes
Git commit hash
f0bacc0
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request