Job request: 1237

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
2ms57iusc2bg4emd succeeded generate_covid_cohort
7xweekmfld57anti succeeded generate_covid_community_cohort
b4ihwngqhr3v7ve4 succeeded generate_covid_general_population_cohort
q47za6jn3htlfa2n succeeded generate_pneumonia_cohort
hdrj3pc2arsv4fbg succeeded matching
hnetyehructah7qa succeeded covid_rates_cohort
hgh6cne2z3sqbhlx succeeded covid_community_rates_cohort
m2v243rdgnlsqerk succeeded pneumonia_rates_cohort
bdfuviul726tcgnn succeeded gen_pop_rates_cohort
3ru3lh7eetw2a7r4 succeeded covid_rates
6ak5sdslspb65yeu succeeded covid_comm_rates
ojxlgjrjo3zy2wp3 succeeded pneumonia_rates
hnofx7fxvshbzmt6 succeeded gen_pop_rates
7cl7vxhqhfjhbw2d succeeded baseline_characteristics
gbt6akbxhc2jyjgm succeeded append_cohorts
zymmcgtcxvxbvxdr 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: 11:39:02

Config

  • Backend:
    TPP
  • Workspace:
    post-covid-research
  • Branch:
    master
  • Creator:
    alexwalkercebm
  • Force run dependencies:
    True
  • Git Commit Hash:
    81ad279
  • Requested actions:
    • run_all