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Job request: 23584

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
sotrovimab_molnupiravir
ID:
jatvutfpcky6maxa
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Bang Zheng 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: 500000

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

  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

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

  generate_study_population_update_codelist:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_update_codelist
    outputs:
      highly_sensitive:
        cohort: output/update_codelist/input_update_codelist.csv

  data_preparation_update_codelist:
    run: stata-mp:latest analysis/data_preparation_and_descriptives_update_codelist.do
    needs: [generate_study_population_update_codelist]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation_update_codelist.log
      highly_sensitive:
        data: output/update_codelist/main_update_codelist.dta

  cox_regression_update_codelist:
    run: stata-mp:latest analysis/cox_update_codelist.do
    needs: [data_preparation_update_codelist]
    outputs:
      moderately_sensitive:
        log: logs/cox_update_codelist.log
        figure1: output/update_codelist/phtest.svg  
        figure2: output/update_codelist/phtest_psw.svg


  generate_study_population_BA2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_BA2
    outputs:
      highly_sensitive:
        cohort: output/BA2/input_BA2.csv

  data_preparation_BA2:
    run: stata-mp:latest analysis/data_preparation_and_descriptives_BA2.do
    needs: [generate_study_population_BA2]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation_BA2.log
      highly_sensitive:
        data: output/BA2/main_BA2.dta

  cox_regression_BA2:
    run: stata-mp:latest analysis/cox_BA2.do
    needs: [data_preparation_BA2]
    outputs:
      moderately_sensitive:
        log: logs/cox_BA2.log
        figure1: output/BA2/phtest.svg  
        figure2: output/BA2/phtest_psw.svg


  generate_study_population_ukrr:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ukrr
    outputs:
      highly_sensitive:
        cohort: output/ukrr/input_ukrr.csv
        
  data_preparation_ukrr:
    run: stata-mp:latest analysis/data_preparation_and_descriptives_ukrr.do
    needs: [generate_study_population_ukrr]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation_ukrr.log
      highly_sensitive:
        data: output/ukrr/main_ukrr.dta

  cox_regression_ukrr:
    run: stata-mp:latest analysis/cox_ukrr.do
    needs: [data_preparation_ukrr]
    outputs:
      moderately_sensitive:
        log: logs/cox_ukrr.log
        figure1: output/ukrr/phtest.svg  
        figure2: output/ukrr/phtest_psw.svg
        figure3: output/ukrr/psgraph.svg

  multiple_imputation_ukrr:
    run: stata-mp:latest analysis/multiple_imputation_ukrr.do
    needs: [data_preparation_ukrr]
    outputs:
      moderately_sensitive:
        log: logs/MI_ukrr.log

  generate_study_population_ukrr_untreated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ukrr_untreated
    outputs:
      highly_sensitive:
        cohort: output/ukrr/input_ukrr_untreated.csv

  data_preparation_ukrr_untreated:
    run: stata-mp:latest analysis/data_preparation_and_descriptives_ukrr_untreated.do
    needs: [generate_study_population_ukrr_untreated, data_preparation_ukrr]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation_ukrr_untreated.log
      highly_sensitive:
        data1: output/ukrr/ukrr_untreated.dta
        data2: output/ukrr/main_ukrr_untreated.dta

  cox_regression_ukrr_untreated:
    run: stata-mp:latest analysis/cox_ukrr_untreated.do
    needs: [data_preparation_ukrr_untreated]
    outputs:
      moderately_sensitive:
        log: logs/cox_ukrr_untreated.log


  data_preparation_ukrr_raw_rate:
    run: stata-mp:latest analysis/data_preparation_and_descriptives_ukrr_raw_rate.do
    needs: [generate_study_population_ukrr]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation_ukrr_raw_rate.log

  generate_study_population_ukrr_update:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ukrr_update
    outputs:
      highly_sensitive:
        cohort: output/ukrr/input_ukrr_update.csv
        
  data_preparation_ukrr_update:
    run: stata-mp:latest analysis/data_preparation_and_descriptives_ukrr_update.do
    needs: [generate_study_population_ukrr_update]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation_ukrr_update.log
      highly_sensitive:
        data: output/ukrr/main_ukrr_update.dta

  cox_regression_ukrr_update:
    run: stata-mp:latest analysis/cox_ukrr_update.do
    needs: [data_preparation_ukrr_update]
    outputs:
      moderately_sensitive:
        log: logs/cox_ukrr_update.log
        figure1: output/ukrr/phtest_update.svg  
        figure2: output/ukrr/phtest_psw_update.svg
        figure3: output/ukrr/psgraph_update.svg

  generate_study_population_anaphylaxis:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_anaphylaxis
    outputs:
      highly_sensitive:
        cohort: output/input_anaphylaxis.csv

  anaphylaxis:
    run: stata-mp:latest analysis/anaphylaxis.do
    needs: [generate_study_population_anaphylaxis]
    outputs:
      moderately_sensitive:
        log: logs/anaphylaxis.log

  generate_study_population_anaphylaxis_untreated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_anaphylaxis_untreated
    outputs:
      highly_sensitive:
        cohort: output/input_anaphylaxis_untreated.csv

  anaphylaxis_untreated:
    run: stata-mp:latest analysis/anaphylaxis_untreated.do
    needs: [generate_study_population_anaphylaxis_untreated]
    outputs:
      moderately_sensitive:
        log: logs/anaphylaxis_untreated.log

  generate_study_population_anaphylaxis_update:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_anaphylaxis_update
    outputs:
      highly_sensitive:
        cohort: output/input_anaphylaxis_update.csv

  anaphylaxis_update:
    run: stata-mp:latest analysis/anaphylaxis_update.do
    needs: [generate_study_population_anaphylaxis_update]
    outputs:
      moderately_sensitive:
        log: logs/anaphylaxis_update.log

  anaphylaxis_update_R:
    run: r:latest  analysis/anaphylaxis_update.R
    needs: [generate_study_population_anaphylaxis_update]
    outputs:
      moderately_sensitive:
        log: logs/anaphylaxis_update.txt


  generate_study_population_anaphylaxis_untreated_update:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_anaphylaxis_untreated_update
    outputs:
      highly_sensitive:
        cohort: output/input_anaphylaxis_untreated_update.csv

  anaphylaxis_untreated_update:
    run: stata-mp:latest analysis/anaphylaxis_untreated_update.do
    needs: [generate_study_population_anaphylaxis_untreated_update]
    outputs:
      moderately_sensitive:
        log: logs/anaphylaxis_untreated_update.log

  anaphylaxis_untreated_update_R:
    run: r:latest analysis/anaphylaxis_untreated_update.r
    needs: [generate_study_population_anaphylaxis_untreated_update]
    outputs:
      moderately_sensitive:
        log: logs/anaphylaxis_untreated_update.txt

  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
      highly_sensitive:
        data: output/main_feasibility.dta

  generate_study_population_feasibility2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_feasibility2
    outputs:
      highly_sensitive:
        cohort: output/input_feasibility2.csv

  data_preparation_feasibility2:
    run: stata-mp:latest analysis/data_preparation_and_descriptives_feasibility2.do
    needs: [generate_study_population_feasibility2]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation_feasibility2.log
      highly_sensitive:
        data: output/main_feasibility2.dta

  cox_regression_feasibility2:
    run: stata-mp:latest analysis/cox_feasibility2.do
    needs: [data_preparation_feasibility2]
    outputs:
      moderately_sensitive:
        log: logs/cox_feasibility2.log
        figure1: output/phtest_feasibility2.svg  
        figure2: output/phtest_psw_feasibility2.svg
        figure3: output/psgraph_feasibility2.svg

  # Study population for NICE figures 26th February 2024
  generate_study_population_nice:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_nice
    outputs:
      highly_sensitive:
        cohort: output/input_nice.csv

  nice_data:
    run: stata-mp:latest analysis/data_preparation_and_descriptives_nice.do
    needs: [generate_study_population_nice]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation_nice.log
        table: output/nice/mortality_nice.txt

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:02:01

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

Job information

Status
Succeeded
Backend
TPP
Workspace
sotrovimab_molnupiravir
Requested by
Bang Zheng
Branch
main
Force run dependencies
No
Git commit hash
5dd58f2
Requested actions
  • data_preparation_feasibility

Code comparison

Compare the code used in this Job Request