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Job request: 21880

Organisation:
Bennett Institute
Workspace:
paxlovid_sotrovimab_molnupiravir_followup
ID:
4dzeqq6agaibavxl
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Qing Wen 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: 50000

actions:

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

  data_preparation:
    run: stata-mp:latest analysis/data_preparation_and_descriptives.do
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation.log
      highly_sensitive:
        data: output/main.dta
        data2: output/sensitivity.dta

  cox_regression:
    run: stata-mp:latest analysis/cox.do
    needs: [data_preparation]
    outputs:
      moderately_sensitive:
        log: logs/cox.log
        figure1: output/phtest.svg  
        figure2: output/phtest_psw.svg
        figure3: output/psgraph.svg 

  multiple_imputation:
    run: stata-mp:latest analysis/multiple_imputation.do
    needs: [data_preparation]
    outputs:
      moderately_sensitive:
        log: logs/MI.log


  data_preparation_molnupiravir:
    run: stata-mp:latest analysis/data_preparation_and_descriptives_molnupiravir.do
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation_mol.log
      highly_sensitive:
        data: output/main_mol.dta

  cox_regression_molnupiravir:
    run: stata-mp:latest analysis/cox_molnupiravir.do
    needs: [data_preparation_molnupiravir]
    outputs:
      moderately_sensitive:
        log: logs/cox_mol.log
        figure1: output/psgraph_mol.svg 

  plot:
    run: stata-mp:latest analysis/plot.do
    needs: [data_preparation, data_preparation_molnupiravir]
    outputs:
      moderately_sensitive:
        log: logs/plot.log
        figure1: output/kmcurve.svg 
        figure2: output/kmcurve_mol.svg 

  generate_study_population_update:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_update
    outputs:
      highly_sensitive:
        cohort: output/input_update.csv

  data_preparation_update:
    run: stata-mp:latest analysis/data_preparation_and_descriptives_update.do
    needs: [generate_study_population_update]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation_update.log
      highly_sensitive:
        data: output/main_update.dta
        data2: output/sensitivity_update.dta

  cox_regression_update:
    run: stata-mp:latest analysis/cox_update.do
    needs: [data_preparation_update]
    outputs:
      moderately_sensitive:
        log: logs/cox_update.log
        figure1: output/phtest_update.svg  
        figure2: output/phtest_psw_update.svg
        figure3: output/psgraph_update.svg 

  multiple_imputation_update:
    run: stata-mp:latest analysis/multiple_imputation_update.do
    needs: [data_preparation_update]
    outputs:
      moderately_sensitive:
        log: logs/MI_update.log

  data_preparation_molnupiravir_update:
    run: stata-mp:latest analysis/data_preparation_and_descriptives_molnupiravir_update.do
    needs: [generate_study_population_update]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation_mol_update.log
      highly_sensitive:
        data: output/main_mol_update.dta

  cox_regression_molnupiravir_update:
    run: stata-mp:latest analysis/cox_molnupiravir_update.do
    needs: [data_preparation_molnupiravir_update]
    outputs:
      moderately_sensitive:
        log: logs/cox_mol_update.log
        figure1: output/psgraph_mol_update.svg 


  generate_study_population_raw_rate:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_raw_rate
    outputs:
      highly_sensitive:
        cohort: output/input_raw_rate.csv

  data_preparation_raw_rate:
    run: stata-mp:latest analysis/data_preparation_and_descriptives_raw_rate.do
    needs: [generate_study_population_raw_rate]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation_raw_rate.log
        table1: output/table.csv

  generate_study_population_feasibility:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_feasibility
    outputs:
      highly_sensitive:
        cohort: output/input_feasibility.csv

  data_preparation_feasibility:
    run: stata-mp:latest analysis/data_preparation_and_descriptives_feasibility.do
    needs: [generate_study_population_feasibility]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation_feasibility.log

  generate_study_population_feasibility_update:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_feasibility_update
    outputs:
      highly_sensitive:
        cohort: output/input_feasibility_update.csv

  data_preparation_feasibility_update:
    run: stata-mp:latest analysis/data_preparation_and_descriptives_feasibility_update.do
    needs: [generate_study_population_feasibility_update]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation_feasibility_update.log

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:07:02

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

Job request

Status
Succeeded
Backend
TPP
Workspace
paxlovid_sotrovimab_molnupiravir_followup
Requested by
Qing Wen
Branch
main
Force run dependencies
No
Git commit hash
efde6a4
Requested actions
  • data_preparation

Code comparison

Compare the code used in this job request