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Job request: 1983

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
vaccine-characteristics-research
ID:
jnvvnszotfiwnfje
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Anna Schultze requested one or more actions to be run against real patient data in the 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.

Jobs

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 100000

actions:

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

  00_data_management:
    run: stata-mp:latest analysis/00_data_management.do output/input.csv output/tempdata/temp_data
    needs: [generate_cohort] 
    outputs:
      highly_sensitive:
        data: output/tempdata/temp_data.dta
      moderately_sensitive:
        log: output/logs/00_data_management.log

  01_study_population:
    run: stata-mp:latest analysis/01_study_population.do output/tempdata/temp_data.dta output/tempdata/study_population output/tempdata/study_population.csv
    needs: [00_data_management] 
    outputs:
      highly_sensitive:
        data: output/tempdata/study_population.dta
        csv: output/tempdata/study_population.csv
      moderately_sensitive:
        log: output/logs/01_study_population.log

  02_baseline_characteristics:
    run: stata-mp:latest analysis/02_baseline_characteristics.do output/tempdata/study_population.dta output/tables/table1.txt
    needs: [01_study_population] 
    outputs:
      moderately_sensitive:
        log: output/logs/02_baseline_characteristics.log
        table: output/tables/table1.txt

  03_logistic_regression:
    run: stata-mp:latest analysis/03_logistic_regression.do output/tempdata/study_population.dta output/tables/table2.txt
    needs: [01_study_population] 
    outputs:
      moderately_sensitive:
        log: output/logs/03_logistic_regression.log
        table: output/tables/table2.txt


  04_plots_over_time:
    run: r:latest analysis/04_plots_over_time.R 
    needs: [01_study_population] 
    outputs:
      moderately_sensitive:
        table: output/plots/plot1.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:59:34

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

Job information

Status
Succeeded
Backend
TPP
Workspace
vaccine-characteristics-research
Requested by
Anna Schultze
Branch
master
Force run dependencies
Yes
Git commit hash
c6d9081
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request