Job request: 1264

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Alex Walker requested one or more actions to be run against real patient data in the Post-COVID-19 Thrombosis project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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

ID Status Action
y26misnkpgpu4aj2 succeeded covid_rates_cohort
rh22th6uqr3xtir5 succeeded covid_community_rates_cohort
kzf2jvz6zyni7i3a succeeded pneumonia_rates_cohort
hkqpj53euhrpx44c succeeded gen_pop_rates_cohort
p6uv7d3xao4pjdrf succeeded covid_rates
du3dmexhcydk6zha succeeded covid_comm_rates
ktwzoqbzqykyxgb7 succeeded pneumonia_rates
wx2xjyrwbdxzwe5o succeeded gen_pop_rates
wjsxutcnlvxrgc3i succeeded baseline_characteristics
drq5mpdpdfskwfbe succeeded append_cohorts
wbt26l3egnntks2z succeeded cox_models

Pipeline

Show Hide 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

  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

  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

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 02:34:58

Config

  • Backend:
    TPP
  • Workspace:
    post-covid-research
  • Branch:
    master
  • Creator:
    alexwalkercebm
  • Force run dependencies:
    False
  • Git Commit Hash:
    722b503
  • Requested actions:
    • covid_rates_cohort
    • covid_community_rates_cohort
    • pneumonia_rates_cohort
    • gen_pop_rates_cohort
    • covid_rates
    • covid_comm_rates
    • pneumonia_rates
    • gen_pop_rates
    • baseline_characteristics
    • append_cohorts
    • cox_models