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Job request: 18677

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
shielding_evaluation
ID:
f7ukpicvknqyyrl3
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Alasdair Henderson 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: 1000

actions:

  generate_dataset:
    run: >
      databuilder:v0 
        generate-dataset analysis/databuilder_definition.py --output output/dataset_all.csv.gz
    outputs:
      highly_sensitive:
        dataset_all: output/dataset_all.csv.gz
  
  clean_the_data: 
    run: > 
      r:latest
        analysis/010_import_data.R
    needs: [generate_dataset]
    outputs: 
      highly_sensitive:
        cleandata: output/data_edited.gz.parquet
      moderately_sensitive: 
        txt1: output/data_properties/clean_dataset_skim.txt
        txt2: output/data_properties/clean_dataset_tabulate.txt
      
  create_table1: 
    run: > 
      r:latest
        analysis/020_create_table1.R
    needs: [clean_the_data]
    outputs: 
      moderately_sensitive: 
        table1: output/tables/shielding_table1.html
        table1_r: output/tables/shielding_table1_redacted.html
        table1_data: output/table1_data.csv
        table2_shielding_v0: output/tables/shielding_table2.html
        table2_shielding_v1: output/tables/shielding_v1_table2.html
        table2_shielding_v2: output/tables/shielding_v2_table2.html
  
  plot_hospitalisations: 
    run: > 
      r:latest
        analysis/030_plot_hospitalisations.R
    needs: [clean_the_data]
    outputs: 
      moderately_sensitive: 
        shielding_comparison: output/data_properties/different_shielding.txt
        fig1_v1: output/figures/covid_hosp_over_time_v1.pdf
        fig2_v1: output/figures/covid_hosp_over_time_cumsum_v1.pdf
        fig1_v2: output/figures/covid_hosp_over_time_v2.pdf
        fig2_v2: output/figures/covid_hosp_over_time_cumsum_v2.pdf
  
  plot_hospitalisations2:
    run: > 
      r:latest
        analysis/040_plot_hospitalisations.R
    needs: [clean_the_data]
    outputs: 
      moderately_sensitive: 
        fig3: output/figures/covid_hosp_over_time2.pdf
        fig4: output/figures/covid_hosp_over_time_cumsum2.pdf
        
  plot_deaths2:
    run: > 
      r:latest
        analysis/050_plot_deaths.R
    needs: [clean_the_data]
    outputs: 
      moderately_sensitive: 
        fig5: output/figures/covid_deaths_over_time2.pdf
        fig6: output/figures/covid_deaths_over_time_cumsum2.pdf

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 11:18:03

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

Job information

Status
Succeeded
Backend
TPP
Workspace
shielding_evaluation
Requested by
Alasdair Henderson
Branch
main
Force run dependencies
No
Git commit hash
c379d6e
Requested actions
  • generate_dataset
  • clean_the_data

Code comparison

Compare the code used in this Job Request