Skip to content

Job request: 21754

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
shielding_evaluation
ID:
pkpopurl7hxa5vzo
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 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
  
  HD_data_questions:
    run: > 
      r:latest
        analysis/SEIUHRD_HDdata_questions.r
    needs: [clean_the_data]
    outputs:
      moderately_sensitive:
        txt01: output/HDsynthesis/JDat9_HDdata_questions_answered_Hospital_wCH.txt
        txt02: output/HDsynthesis/JDat9_HDdata_questions_answered_Deaths_wCH.txt
        txt03: output/HDsynthesis/JDat9_HDdata_questions_answered_Shielding_wCH.txt
        txt04: output/HDsynthesis/JDat9_HDdata_questions_answered_Hospital.txt
        txt05: output/HDsynthesis/JDat9_HDdata_questions_answered_Deaths.txt
        txt06: output/HDsynthesis/JDat9_HDdata_questions_answered_Shielding.txt

  # HD_data:
    # run: > 
      # r:latest
        # analysis/runmkd.R
    # needs: [clean_the_data]
    # outputs:
      # moderately_sensitive:
        # csv01b: output/HDsynthesis/JDat8_Carehomes_included_H.csv
        # svg01b: output/HDsynthesis/JDat8_Carehomes_included_H.svg
        # csv02b: output/HDsynthesis/JDat8_Carehomes_included_D.csv
        # svg02b: output/HDsynthesis/JDat8_Carehomes_included_D.svg
        # csv03b: output/HDsynthesis/JDat8_Carehomes_included_DH.csv
        # svg03b: output/HDsynthesis/JDat8_Carehomes_included_DH.svg
        # csv04b: output/HDsynthesis/JDat8_Carehomes_included_DO.csv
        # svg04b: output/HDsynthesis/JDat8_Carehomes_included_DO.svg
        # csv05b: output/HDsynthesis/JDat8_Hdata.csv
        # svg051: output/HDsynthesis/JDat8_Hdata_all.svg
        # svg052: output/HDsynthesis/JDat8_Hdata_by_age.svg
        # svg053: output/HDsynthesis/JDat8_Hdata_by_shi.svg
        # svg054: output/HDsynthesis/JDat8_Hdata_s0_by_age.svg
        # svg055: output/HDsynthesis/JDat8_Hdata_s1_by_age.svg
        # csv06b: output/HDsynthesis/JDat8_HRdata.csv
        # svg061: output/HDsynthesis/JDat8_HRdata_all.svg
        # svg062: output/HDsynthesis/JDat8_HRdata_by_age.svg
        # svg063: output/HDsynthesis/JDat8_HRdata_by_shi.svg
        # svg064: output/HDsynthesis/JDat8_HRdata_s0_by_age.svg
        # svg065: output/HDsynthesis/JDat8_HRdata_s1_by_age.svg
        # csv07b: output/HDsynthesis/JDat8_DHdata.csv
        # svg071: output/HDsynthesis/JDat8_DHdata_all.svg
        # svg072: output/HDsynthesis/JDat8_DHdata_by_age.svg
        # svg073: output/HDsynthesis/JDat8_DHdata_by_shi.svg
        # svg074: output/HDsynthesis/JDat8_DHdata_s0_by_age.svg
        # svg075: output/HDsynthesis/JDat8_DHdata_s1_by_age.svg
        # csv08b: output/HDsynthesis/JDat8_DOdata.csv
        # svg081: output/HDsynthesis/JDat8_DOdata_all.svg
        # svg082: output/HDsynthesis/JDat8_DOdata_by_age.svg
        # svg083: output/HDsynthesis/JDat8_DOdata_by_shi.svg
        # svg084: output/HDsynthesis/JDat8_DOdata_s0_by_age.svg
        # svg085: output/HDsynthesis/JDat8_DOdata_s1_by_age.svg       
        # csv091: output/HDsynthesis/JDat8_H,HR,DH,DOdata_H.csv
        # csv092: output/HDsynthesis/JDat8_H,HR,DH,DOdata_HR.csv
        # csv093: output/HDsynthesis/JDat8_H,HR,DH,DOdata_DH.csv
        # csv094: output/HDsynthesis/JDat8_H,HR,DH,DOdata_DO.csv
        # svg09b: output/HDsynthesis/JDat8_H,HR,DH,DOdata.svg
        # html01: output/HDsynthesis/HDdata.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:07:22

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
Johnny Filipe
Branch
main
Force run dependencies
No
Git commit hash
9ca3e09
Requested actions
  • HD_data_questions

Code comparison

Compare the code used in this Job Request