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Job request: 2961

Organisation:
Bennett Institute
Workspace:
pulse_oximetry_sro
ID:
us3vuakhulbin3e2
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Colm Andrews 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

  • Action:
    generate_cohort
    Status:
    Status: Succeeded
    Job identifier:
    cogtw6q4skdcx3jg
  • Action:
    count_by_strata
    Status:
    Status: Succeeded
    Job identifier:
    b6rzyt2n3zltklfc
  • Action:
    hazard_ratio
    Status:
    Status: Failed
    Job identifier:
    4pslmjpr27l6iq7d
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_plots
    Status:
    Status: Succeeded
    Job identifier:
    wphfxfqq5jxdvsf3

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_cohort
    outputs:
      highly_sensitive:
        cohort: output/input_cohort.csv
      
  count_by_strata:
    run: python:latest python analysis/all_time_counts.py
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        table: output/counts_table.csv
        table_historic: output/counts_table_hist.csv
        practice_distribution: output/practice_distribution.csv
        practice_distribution_historical: output/practice_distribution_historical.csv
        per_week: output/code_use_per_week_pulse_oximetry.csv
        historic_per_week: output/code_use_per_week_historic_pulse_oximetry.csv
        code_table: output/all_pulse_oximetry_codes.csv
        historic_code_table: output/all_historic_pulse_oximetry_codes.csv
        practice_summ: output/practice_summ.txt

  generate_plots:
    run: python:latest python analysis/local_graphs.py
    needs: [count_by_strata]
    outputs:
      moderately_sensitive:
        plot_per week: output/code_use_per_week.svg
        historical_plot_per week: output/historical_code_use_per_week.svg
        total_plot_per week: output/total_code_use_per_week.svg
        plot_distribution: output/practice_distribution.svg
        plot_historical_distribution: output/practice_historical_distribution.svg
        plot_total_distribution: output/total_practice_distribution.svg
        

  hazard_ratio:
    run: r:latest analysis/hr.r
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        PHsum: output/Cox_summary.csv
        PHassumpt: output/Cox_assumption.csv
        PHresid: output/deviance_resid.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 05:03:44

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

Job request

Status
Failed
Backend
TPP
Workspace
pulse_oximetry_sro
Requested by
Colm Andrews
Branch
master
Force run dependencies
Yes
Git commit hash
ec6d943
Requested actions
  • run_all

Code comparison

Compare the code used in this job request