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Job request: 374

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
post-covid-thrombosis
ID:
h7mir4aoxa4l4lg2
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher John Tazare 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

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 10000

actions:
  generate_cohorts:
    run: cohortextractor:latest generate_cohort
    outputs:
      highly_sensitive:
        covid_cohort: output/input_covid.csv
        pneumonia_cohort: output/input_pneumonia.csv
        ctrl_2019_cohort: output/input_control_2019.csv
        ctrl_2020_cohort: output/input_control_2020.csv

  000_covid:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid"
    needs: [generate_cohorts]
    outputs:
      moderately_sensitive:
        graph: output/length_of_stay_covid.svg
      highly_sensitive:
        analysis_dataset: output/cohort_rates_covid.dta

  000_pneumonia:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "pneumonia"
    needs: [generate_cohorts]
    outputs:
      moderately_sensitive:
        graph: output/length_of_stay_pneumonia.svg
      highly_sensitive:
        analysis_dataset: output/cohort_rates_pneumonia.dta

  201_covid:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "covid"
    needs: [000_covid]
    outputs:
      moderately_sensitive:
        graph: output/tabfig/rates_summary_covid.csv

  201_pneumonia:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "pneumonia"
    needs: [000_pneumonia]
    outputs:
      moderately_sensitive:
        graph: output/tabfig/rates_summary_pneumonia.csv

  matching_control_2019:
    run: python:latest python analysis/match_running.py "control_2019"
    needs: [generate_cohorts]
    outputs:
      moderately_sensitive:
        matching_report: output/matching_report_control_2019.txt
      highly_sensitive:
        combined: output/matched_combined_control_2019.csv

  matching_control_2020:
    run: python:latest python analysis/match_running.py "control_2020"
    needs: [generate_cohorts]
    outputs:
      moderately_sensitive:
        matching_report: output/matching_report_control_2020.txt
      highly_sensitive:
        combined: output/matched_combined_control_2020.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:02:43

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

Job request

Status
Succeeded
Backend
TPP
Workspace
post-covid-thrombosis
Requested by
John Tazare
Branch
master
Force run dependencies
Yes
Git commit hash
30c9b9c
Requested actions
  • run_all

Code comparison

Compare the code used in this job request