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Job request: 12191

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
sotrovimab_molnupiravir
ID:
it3w24g5o6x5lf5h
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_Paxlovid:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_Paxlovid
    outputs:
      highly_sensitive:
        cohort: output/Paxlovid/input_Paxlovid.csv

  data_preparation_Paxlovid:
    run: stata-mp:latest analysis/data_preparation_and_descriptives_Paxlovid.do
    needs: [generate_study_population_Paxlovid]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation_Paxlovid.log
      highly_sensitive:
        data: output/Paxlovid/main_Paxlovid.dta

  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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:02:09

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

Job information

Status
Failed
Backend
TPP
Workspace
sotrovimab_molnupiravir
Requested by
Bang Zheng
Branch
main
Force run dependencies
No
Git commit hash
6df7b14
Requested actions
  • cox_regression_ukrr

Code comparison

Compare the code used in this Job Request