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Job request: 22710

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
udca-covid
ID:
26sgu5c3xefnnjek
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Ruth Costello 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: 1000

actions:

  generate_study_population_flowchart:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flowchart
    outputs:
      highly_sensitive:
        cohort: output/input_flowchart.csv

  generate_flowchart_stp:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_stp
    needs: [generate_study_population_flowchart]
    outputs:
      highly_sensitive:
        cohort: output/input_stp.csv

  flowchart_data:
    run: stata-mp:latest analysis/100_flowchart.do
    needs: [generate_study_population_flowchart, generate_study_population_pbc, generate_flowchart_stp]
    outputs:
      moderately_sensitive:
        log: logs/flowchart.log
        table: output/flowchart/values.txt

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  generate_study_population_pbc:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pbc
    outputs:
      highly_sensitive:
        cohort: output/input_pbc.csv

  generate_study_population_vacc:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vacc
    outputs:
      highly_sensitive:
        cohort: output/input_vacc.csv

  feasibility:
    run: stata-mp:latest analysis/feasibility.do
    needs: [generate_study_population, generate_study_population_pbc]
    outputs:
      moderately_sensitive:
        log: logs/feasibility.log
        table: output/tables/udca*.csv
        #table_oba: output/tables/oba*.csv
      
  extract_udca: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_additional
    needs: [generate_study_population_pbc]
    outputs:
      highly_sensitive:
        cohort: output/input_additional.csv

  extract_udca_vacc: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_addvacc
    needs: [generate_study_population_vacc]
    outputs:
      highly_sensitive:
        cohort: output/input_addvacc.csv


  prep_drug_data: 
    run: stata-mp:latest analysis/101_drug_prep.do
    needs: [extract_udca, generate_study_population_pbc, extract_udca_vacc, generate_study_population_vacc]
    outputs:
      moderately_sensitive:
        log: logs/drug_prep.log
      highly_sensitive:
        drug_data: output/time_varying_udca*.dta

  drug_descriptives:
    run: stata-mp:latest analysis/102_udca_descriptives.do
    needs: [prep_drug_data, generate_study_population_pbc]
    outputs:
      moderately_sensitive:
        summary: output/tables/udca_descriptives*.txt

  time_varying_prep:
    run: stata-mp:latest analysis/103_time_varying_prep.do
    needs: [generate_study_population_pbc, prep_drug_data, extract_udca_vacc, generate_study_population_vacc]
    outputs:
      highly_sensitive:
        datasets: output/tv*.dta
        analysis: output/an_*.dta
        

  baseline_tables:
    run: stata-mp:latest analysis/104_baseline_tables.do
    needs: [generate_study_population_pbc, generate_study_population_vacc, time_varying_prep]
    outputs:
      moderately_sensitive:
        chars: output/tables/baseline*.csv
        meds: output/tables/additional*.csv
      
  high_cost_drugs:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_hc_drugs
    needs: [generate_study_population_pbc]
    outputs:
      highly_sensitive:
        cohort: output/input_hc_drugs.csv

  hcd_descriptives:
    run: stata-mp:latest analysis/104_a_hcd_descriptives.do
    needs: [high_cost_drugs, generate_study_population_pbc]
    outputs:
      highly_sensitive:
        bl_data: output/baseline_oca_n.dta
      moderately_sensitive:
        table: output/tables/baseline_oca*.csv
        
  analysis_plots:
    run: stata-mp:latest analysis/105_analysis_plots.do
    needs: [time_varying_prep]
    outputs:
      moderately_sensitive:
        log: logs/analysis.log
        chars: output/graphs/adjcurv*.svg
        table: output/tables/cum_incidence.txt

  analysis_models:
    run: stata-mp:latest analysis/106_analysis_models.do
    needs: [time_varying_prep, hcd_descriptives]
    outputs:
      moderately_sensitive:
        tables: output/tables/cox*.txt
        graphs: output/graphs/schoenplot*.svg
        km_plots: output/graphs/km*.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:49:32

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

Job information

Status
Succeeded
Backend
TPP
Workspace
udca-covid
Requested by
Ruth Costello
Branch
main
Force run dependencies
No
Git commit hash
6f9c1ca
Requested actions
  • drug_descriptives
  • time_varying_prep
  • baseline_tables
  • analysis_models

Code comparison

Compare the code used in this Job Request