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Job request: 21024

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
udca-covid
ID:
k2fu6s6q2pxrhis4
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 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: 1000

actions:

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

  flowchart_data:
    run: stata-mp:latest analysis/100_flowchart.do
    needs: [generate_study_population_flowchart, generate_study_population_pbc]
    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

  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]
    outputs:
      moderately_sensitive:
        tables: output/tables/cox*.txt
        graphs: output/graphs/schoenplot*.svg
        km_plots: output/graphs/km*.svg
        
  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/hcd_descriptives.do
    needs: [high_cost_drugs]
    outputs:
      moderately_sensitive:
        log: logs/hcd_descriptives.log

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:02:36

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

Job request

Status
Succeeded
Backend
TPP
Workspace
udca-covid
Requested by
Ruth Costello
Branch
main
Force run dependencies
No
Git commit hash
1582bc7
Requested actions
  • high_cost_drugs
  • hcd_descriptives

Code comparison

Compare the code used in this job request