Skip to content

Job request: 22619

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
shielding_evaluation
ID:
z6zgpwyiogrhuhsw
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:
    fit_HDdata
    Status:
    Status: Succeeded
    Job identifier:
    6pqpgdpyaul4tcdz

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
  
  fit_HDdata:
  #fit_HDdata_woIC:
    run: > 
      r:latest
        modelling/runmkd_main.R
    needs: [clean_the_data]
    outputs:
      moderately_sensitive:
        #HDdata.R - only run if iplatform>0
        #csv011: output/HDsynthesis/J5nHbDfitP3_Hdata_by_age.csv
        csv012: output/HDsynthesis/J5nHbDfitP3_Hdata_by_age_long.csv
        #csv013: output/HDsynthesis/J5nHbDfitP3_Hdata_by_age_merged_long.csv
        #csv013: output/HDsynthesis/J5nHbDfitP3_Hdata_by_shi.csv
        #csv014: output/HDsynthesis/J5nHbDfitP3_Hdata_s_by_age.csv
        csv015: output/HDsynthesis/J5nHbDfitP3_Hdata_s_by_age_long.csv
        #csv016: output/HDsynthesis/J5nHbDfitP3_Hdata_all_long.csv       
        #csv021: output/HDsynthesis/J5nHbDfitP3_DHdata_by_age.csv
        csv022: output/HDsynthesis/J5nHbDfitP3_DHdata_by_age_long.csv        
        #csv023: output/HDsynthesis/J5nHbDfitP3_DHdata_by_age_merged_long.csv
        #csv023: output/HDsynthesis/J5nHbDfitP3_DHdata_by_shi.csv
        #csv024: output/HDsynthesis/J5nHbDfitP3_DHdata_s_by_age.csv
        csv025: output/HDsynthesis/J5nHbDfitP3_DHdata_s_by_age_long.csv
        #csv026: output/HDsynthesis/J5nHbDfitP3_DHdata_all_long.csv
        #csv031: output/HDsynthesis/J5nHbDfitP3_DOdata_by_age.csv
        csv032: output/HDsynthesis/J5nHbDfitP3_DOdata_by_age_long.csv
        #csv033: output/HDsynthesis/J5nHbDfitP3_DOdata_by_age_merged_long.csv
        #csv033: output/HDsynthesis/J5nHbDfitP3_DOdata_by_shi.csv
        #csv034: output/HDsynthesis/J5nHbDfitP3_DOdata_s_by_age.csv
        csv035: output/HDsynthesis/J5nHbDfitP3_DOdata_s_by_age_long.csv
        #csv036: output/HDsynthesis/J5nHbDfitP3_DOdata_all_long.csv
        #contacts
        txt010: output/modelling/J5nHbDfitP3_Contact_matrix_year-start-27Jan20_stats.txt
        #R0
        csv040: output/modelling/J5nHbDfitP3_Simul_R0_by_week.csv
        svg010: output/modelling/J5nHbDfitP3_Simul_R0_by_week.csv.svg
        #simulation - only run if iplatform==0
        #svg011: output/modelling/J5nHbDfitP3_Simul_Infected_and_R0.pdf_1-3.svg
        #svg012: output/modelling/J5nHbDfitP3_Simul_Infected_and_R0.pdf_4-6.svg
        #txt020: output/modelling/J5nHbDfitP3_Simul_run.txt
        #fit
        #txt000: output/modelling/screen.txt
        html01: output/modelling/J5nHbDfitP3_Main_Fit_Report.html
        txt021: output/modelling/J5nHbDfitP3_Fit_summary_1.txt
        txt022: output/modelling/J5nHbDfitP3_Fit_summary_2.txt  
        svg031: output/modelling/J5nHbDfitP3_Fit_MCMC_marginalPlot.svg
        #svg032: output/modelling/J5nHbDfitP3_Fit_MCMC_plotout_lastPage.svg
        svg033: output/modelling/J5nHbDfitP3_Fit_MCMC_correlationPlot.svg
        svg034: output/modelling/J5nHbDfitP3_Fit_MCMC_Overall.svg
        svg035: output/modelling/J5nHbDfitP3_Fit_MCMC_PosteriorSample.svg
        svg037: output/modelling/J5nHbDfitP3_Fit_MCMC_PosteriorSample_Prev_R0.svg
        svg036: output/modelling/J5nHbDfitP3_Fit_MCMC_AgeProfiles.svg
        svg038: output/modelling/J5nHbDfitP3_Fit_MCMC_plots_probs.svg


  
  HD_data_questions:
    run: > 
      r:latest
        analysis/HDdata_questions.r
    needs: [clean_the_data]
    outputs:
      moderately_sensitive:
        txt01: output/HDsynthesis/JDat13_HDdata_questions_answered_Hospital_wCH.txt
        txt02: output/HDsynthesis/JDat13_HDdata_questions_answered_Deaths_wCH.txt
        txt03: output/HDsynthesis/JDat13_HDdata_questions_answered_Shielding_wCH.txt
        txt04: output/HDsynthesis/JDat13_HDdata_questions_answered_Hospital.txt
        txt05: output/HDsynthesis/JDat13_HDdata_questions_answered_Deaths.txt
        txt06: output/HDsynthesis/JDat13_HDdata_questions_answered_Shielding.txt

  HD_data:
    run: > 
      r:latest
        analysis/runmkd.R
    needs: [clean_the_data]
    outputs:
      moderately_sensitive:
        csv01b: output/HDsynthesis/JDat13_Carehomes_included_H.csv
        svg01b: output/HDsynthesis/JDat13_Carehomes_included_H.svg
        csv02b: output/HDsynthesis/JDat13_Carehomes_included_D.csv
        svg02b: output/HDsynthesis/JDat13_Carehomes_included_D.svg
        csv03b: output/HDsynthesis/JDat13_Carehomes_included_DH.csv
        svg03b: output/HDsynthesis/JDat13_Carehomes_included_DH.svg
        csv04b: output/HDsynthesis/JDat13_Carehomes_included_DO.csv
        svg04b: output/HDsynthesis/JDat13_Carehomes_included_DO.svg
        csv051: output/HDsynthesis/JDat13_Hdata_all.csv
        svg051: output/HDsynthesis/JDat13_Hdata_all.svg
        csv052: output/HDsynthesis/JDat13_Hdata_by_age.csv
        csv055: output/HDsynthesis/JDat13_Hdata_by_age_long.csv
        svg052: output/HDsynthesis/JDat13_Hdata_by_age.svg
        csv05m: output/HDsynthesis/JDat13_Hdata_by_age_merged.csv
        csv05l: output/HDsynthesis/JDat13_Hdata_by_age_merged_long.csv
        svg05m: output/HDsynthesis/JDat13_Hdata_by_age_merged.svg
        csv053: output/HDsynthesis/JDat13_Hdata_by_shi.csv
        svg053: output/HDsynthesis/JDat13_Hdata_by_shi.svg
        csv054: output/HDsynthesis/JDat13_Hdata_s_by_age.csv
        svg054: output/HDsynthesis/JDat13_Hdata_s0_by_age.svg
        svg055: output/HDsynthesis/JDat13_Hdata_s1_by_age.svg
        csv061: output/HDsynthesis/JDat13_HRdata_all.csv
        svg061: output/HDsynthesis/JDat13_HRdata_all.svg
        csv062: output/HDsynthesis/JDat13_HRdata_by_age.csv
        svg062: output/HDsynthesis/JDat13_HRdata_by_age.svg
        csv063: output/HDsynthesis/JDat13_HRdata_by_shi.csv
        svg063: output/HDsynthesis/JDat13_HRdata_by_shi.svg
        csv064: output/HDsynthesis/JDat13_HRdata_s_by_age.csv
        svg064: output/HDsynthesis/JDat13_HRdata_s0_by_age.svg
        svg065: output/HDsynthesis/JDat13_HRdata_s1_by_age.svg
        csv071: output/HDsynthesis/JDat13_DHdata_all.csv
        svg071: output/HDsynthesis/JDat13_DHdata_all.svg
        csv072: output/HDsynthesis/JDat13_DHdata_by_age.csv
        csv075: output/HDsynthesis/JDat13_DHdata_by_age_long.csv        
        svg072: output/HDsynthesis/JDat13_DHdata_by_age.svg
        csv07m: output/HDsynthesis/JDat13_DHdata_by_age_merged.csv
        csv07l: output/HDsynthesis/JDat13_DHdata_by_age_merged_long.csv
        svg07m: output/HDsynthesis/JDat13_DHdata_by_age_merged.svg
        csv073: output/HDsynthesis/JDat13_DHdata_by_shi.csv
        svg073: output/HDsynthesis/JDat13_DHdata_by_shi.svg
        csv074: output/HDsynthesis/JDat13_DHdata_s_by_age.csv
        svg074: output/HDsynthesis/JDat13_DHdata_s0_by_age.svg
        svg075: output/HDsynthesis/JDat13_DHdata_s1_by_age.svg
        csv081: output/HDsynthesis/JDat13_DOdata_all.csv
        svg081: output/HDsynthesis/JDat13_DOdata_all.svg
        csv082: output/HDsynthesis/JDat13_DOdata_by_age.csv
        csv085: output/HDsynthesis/JDat13_DOdata_by_age_long.csv
        svg082: output/HDsynthesis/JDat13_DOdata_by_age.svg
        csv08m: output/HDsynthesis/JDat13_DOdata_by_age_merged.csv
        csv08l: output/HDsynthesis/JDat13_DOdata_by_age_merged_long.csv
        svg08m: output/HDsynthesis/JDat13_DOdata_by_age_merged.svg
        csv083: output/HDsynthesis/JDat13_DOdata_by_shi.csv
        svg083: output/HDsynthesis/JDat13_DOdata_by_shi.svg
        csv084: output/HDsynthesis/JDat13_DOdata_s_by_age.csv
        svg084: output/HDsynthesis/JDat13_DOdata_s0_by_age.svg
        svg085: output/HDsynthesis/JDat13_DOdata_s1_by_age.svg       
        csv091: output/HDsynthesis/JDat13_H,HR,DH,DOdata_H.csv
        csv092: output/HDsynthesis/JDat13_H,HR,DH,DOdata_HR.csv
        csv093: output/HDsynthesis/JDat13_H,HR,DH,DOdata_DH.csv
        csv094: output/HDsynthesis/JDat13_H,HR,DH,DOdata_DO.csv
        svg09b: output/HDsynthesis/JDat13_H,HR,DH,DOdata.svg
        html01: output/HDsynthesis/JDat13_Report_HDdata.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:06:40

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
b27e935
Requested actions
  • fit_HDdata

Code comparison

Compare the code used in this job request