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Job request: 3115

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
post-covid-competing-risks
ID:
uqny65g62zg2qivs
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: 20000

actions:
  generate_covid_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid
    outputs:
      highly_sensitive:
        cohort: output/input_covid.csv

  generate_covid_community_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_community
    outputs:
      highly_sensitive:
        cohort: output/input_covid_community.csv

  generate_covid_general_population_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_general_population
    outputs:
      highly_sensitive:
        cohort: output/input_general_population.csv

  generate_pneumonia_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pneumonia
    outputs:
      highly_sensitive:
        cohort: output/input_pneumonia.csv

  matching:
    run: python:latest python analysis/match_running.py
    needs: [generate_covid_cohort, generate_covid_general_population_cohort]
    outputs:
      moderately_sensitive: 
        matching_report: output/matching_report_general_population.txt  
      highly_sensitive: 
        combined: output/matched_combined_general_population.csv

  covid_rates_cohort:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid"
    needs: [generate_covid_cohort]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohort_rates_covid.dta
      moderately_sensitive:
        out_dist: output/tabfig/outcomes_in_hosp_covid.csv
        figs: output/tabfig/length_of_stay_covid.svg

  covid_community_rates_cohort:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid_community"
    needs: [generate_covid_community_cohort]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohort_rates_covid_community.dta

  pneumonia_rates_cohort:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "pneumonia"
    needs: [generate_pneumonia_cohort]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohort_rates_pneumonia.dta
      moderately_sensitive:
        out_dist: output/tabfig/outcomes_in_hosp_pneumonia.csv
        figs: output/tabfig/length_of_stay_pneumonia.svg

  gen_pop_rates_cohort:
    run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "matched_combined_general_population"
    needs: [matching]
    outputs:
      highly_sensitive:
        analysis_dataset: output/cohort_rates_gen_population.dta

  covid_rates:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "covid"
    needs: [covid_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_covid.csv

  covid_comm_rates:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "covid_community"
    needs: [covid_community_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_covid_community.csv

  pneumonia_rates:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "pneumonia"
    needs: [pneumonia_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_pneumonia.csv

  gen_pop_rates:
    run: stata-mp:latest analysis/201_cr_simple_rates.do "gen_population"
    needs: [gen_pop_rates_cohort]
    outputs:
      moderately_sensitive:
        rates: output/tabfig/rates_summary_gen_population.csv

  baseline_characteristics:
    run: stata-mp:latest analysis/400_baseline_characteristics.do
    needs: [covid_rates_cohort, covid_community_rates_cohort, pneumonia_rates_cohort, gen_pop_rates_cohort]
    outputs:
      moderately_sensitive:
        tables: output/tabfig/an_descriptiveTable_*.txt

  append_cohorts:
    run: stata-mp:latest analysis/300_cr_data_management_matching.do
    needs: [covid_rates_cohort, pneumonia_rates_cohort, gen_pop_rates_cohort]
    outputs:
      moderately_sensitive:
        log: output/append_cohorts.txt
      highly_sensitive: 
        dataset: output/combined_covid_pneumonia.dta
        dataset2: output/combined_covid_gen_population.dta

  cox_models:
    run: stata-mp:latest analysis/302_cox_models.do
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cox_models.txt
        dataset: output/tabfig/cox_model_summary.csv

  cox_models_time_strat:
    run: stata-mp:latest analysis/303_cox_models_time_stratified.do
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/cox_models_time_strat.txt
        dataset: output/tabfig/cox_model_summary_time_strat.csv

  fine_gray:
    run: stata-mp:latest analysis/302_competing_events.do
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/competing_events.txt
        dataset: output/tabfig/fine_gray_summary.csv
        figs: output/tabfig/cumInc_*.svg

  fine_gray_time_strat:
    run: stata-mp:latest analysis/303_competing_events_time_stratified.do
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/competing_events_time_strat_age_sex.txt
        dataset: output/tabfig/fine_gray_summary_time_strat_age_sex.csv

  logistic_models:
    run: stata-mp:latest analysis/500_logistic_models.do
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/logistic_models.txt
        dataset: output/tabfig/logistic_summary.csv
  
  follow_up:
    run: stata-mp:latest analysis/501_median_follow_up.do
    needs: [append_cohorts]
    outputs:
      moderately_sensitive:
        log: output/follow_up_median.txt
        dataset: output/tabfig/follow_up_summary.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 83:00:43

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

Job request

Status
Succeeded
Backend
TPP
Workspace
post-covid-competing-risks
Requested by
John Tazare
Branch
reviewer-updates
Force run dependencies
Yes
Git commit hash
dce0306
Requested actions
  • run_all

Code comparison

Compare the code used in this job request