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Job request: 21284

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
shielding_evaluation
ID:
rpamcecnyig53ywe
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Johnny Filipe requested one or more actions to be run against real patient data within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

  • Action:
    SEIUHRD_fit
    Status:
    Status: Succeeded
    Job identifier:
    ome5wjzcqzmk4xhk

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
  

  SEIUHRD_fit:
    run: > 
      r:latest
        modelling/SEIRmodel_main.r
    needs: [clean_the_data]
    outputs:
      moderately_sensitive:
        txt10: output/modelling/J4h_Simul_run.txt
        csv10: output/modelling/J4h_Simul_R0_by_week.csv
        txt11: output/modelling/J4h_Contact_matrix_year-start-24Feb20_stats.txt
        pdf10: output/modelling/J4h_Data_Incidence.pdf
        pdf11: output/modelling/J4h_Fit_MCMC_BT.pdf
        pdf12: output/modelling/J4h_Fit_Variables_estimated.pdf
        pdf13: output/modelling/J4h_Fit_Variables_data1.pdf
        pdf14: output/modelling/J4h_Fit_Variables_data2.pdf
        txt12: output/modelling/J4h_Fit_Bayesian_report.txt
        pdf15: output/figures/J4h_covid_hosp_over_time2again.pdf
        pdf16: output/figures/J4h_covid_deaths_over_time2again.pdf

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:53:15

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

Job request

Status
Succeeded
Backend
TPP
Workspace
shielding_evaluation
Requested by
Johnny Filipe
Branch
main
Force run dependencies
No
Git commit hash
cb05f28
Requested actions
  • SEIUHRD_fit

Code comparison

Compare the code used in this job request