Job request: 12085

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Bang Zheng requested one or more actions to be run against real patient data in the 106 - Effectiveness safety sotrovimab molnupiravir project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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.

Pipeline

Show Hide 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



  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



  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

  data_preparation:
    run: stata-mp:latest analysis/data_preparation_and_descriptives.do
    needs: [generate_study_population_ukrr]
    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

  data_preparation_BA2:
    run: stata-mp:latest analysis/data_preparation_and_descriptives_BA2.do
    needs: [generate_study_population_ukrr]
    outputs:
      moderately_sensitive:
        log: logs/data_preparation_BA2.log
      highly_sensitive:
        data: output/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/phtest.svg  
        figure2: output/phtest_psw.svg

State

State is inferred from the related Jobs.

Status: Failed

JobRequestError: Internal error

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: -

Config