Job request: 1983

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 Vaccine Characteristics 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

ID Status Action
hwqu2vngy7pbwwyx succeeded generate_cohort
kbub5cljcf5nsqtw succeeded 00_data_management
dqbm7sayrdellzda succeeded 01_study_population
4x4vlsnfr4yb7jfw succeeded 02_baseline_characteristics
j5keppq7jivurfaq succeeded 03_logistic_regression
u3hjkdxlurnld54u succeeded 04_plots_over_time

Pipeline

Show Hide 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

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 01:59:34

Config