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Job request: 3405

Organisation:
Bennett Institute
Workspace:
pulse_oximetry_sro
ID:
oexytuzyb7232fup
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 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

  • Action:
    generate_cohort
    Status:
    Status: Succeeded
    Job identifier:
    ublethxn7mhj6mpj
  • Action:
    msoa_read
    Status:
    Status: Succeeded
    Job identifier:
    7nqbrcnw6wllxbtt
  • Action:
    count_by_strata
    Status:
    Status: Succeeded
    Job identifier:
    4wqf4hpyxwiz672c
  • Action:
    generate_plots
    Status:
    Status: Succeeded
    Job identifier:
    etkuztlmf3tdupch

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

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

  msoa_read:
    run: python:latest python analysis/msoa.py
    needs: [generate_cohort]
    outputs:
      highly_sensitive:
        cohort: output/input_cohort2.feather

  count_by_strata:
    run: python:latest python analysis/all_time_counts.py
    needs: [msoa_read]
    outputs:
      moderately_sensitive:
        table: output/counts_table_tpp.csv
        table_historic: output/counts_table_hist_tpp.csv
        practice_distribution: output/practice_distribution_tpp.csv
        practice_distribution_historical: output/practice_distribution_historical_tpp.csv
        per_week: output/code_use_per_week_pulse_oximetry_tpp.csv
        historic_per_week: output/code_use_per_week_historic_pulse_oximetry_tpp.csv
        code_table: output/all_pulse_oximetry_codes_tpp.csv
        historic_code_table: output/all_historic_pulse_oximetry_codes_tpp.csv
        practice_summ: output/practice_summ_tpp.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_tpp.svg
        historical_plot_per week: output/historical_code_use_per_week_tpp.svg
        total_plot_per week: output/total_code_use_per_week_tpp.svg
        plot_distribution: output/practice_distribution_tpp.svg
        plot_historical_distribution: output/practice_historical_distribution_tpp.svg
        plot_total_distribution: output/total_practice_distribution_tpp.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: 36:56:19

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

Job information

Status
Succeeded
Backend
TPP
Workspace
pulse_oximetry_sro
Requested by
Colm Andrews
Branch
master
Force run dependencies
Yes
Git commit hash
bd1aab4
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request