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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 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

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 information

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