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Job request: 22273

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
shielding_evaluation
ID:
xi7aiixkk72z3jjh
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.

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:
    run: > 
      r:latest
        modelling/runmkd_main.R
    needs: [clean_the_data]
    outputs:
      moderately_sensitive:
        #HDdata.R - only run if iplatform>0
        csv011: output/HDsynthesis/J5i_Hdata_by_age.csv
        csv012: output/HDsynthesis/J5i_Hdata_by_age_long.csv
        csv013: output/HDsynthesis/J5i_Hdata_by_age_merged_long.csv
        csv014: output/HDsynthesis/J5i_Hdata_by_shi.csv
        csv015: output/HDsynthesis/J5i_Hdata_s_by_age.csv
        csv016: output/HDsynthesis/J5i_Hdata_all_long.csv
        csv021: output/HDsynthesis/J5i_DHdata_by_age.csv
        csv022: output/HDsynthesis/J5i_DHdata_by_age_long.csv        
        csv023: output/HDsynthesis/J5i_DHdata_by_age_merged_long.csv
        csv024: output/HDsynthesis/J5i_DHdata_by_shi.csv
        csv025: output/HDsynthesis/J5i_DHdata_s_by_age.csv
        csv026: output/HDsynthesis/J5i_DHdata_all_long.csv
        csv031: output/HDsynthesis/J5i_DOdata_by_age.csv
        csv032: output/HDsynthesis/J5i_DOdata_by_age_long.csv
        csv033: output/HDsynthesis/J5i_DOdata_by_age_merged_long.csv
        csv034: output/HDsynthesis/J5i_DOdata_by_shi.csv
        csv035: output/HDsynthesis/J5i_DOdata_s_by_age.csv
        csv036: output/HDsynthesis/J5i_DOdata_all_long.csv
        #contacts
        txt010: output/modelling/J5i_Contact_matrix_year-start-27Jan20_stats.txt
        #R0
        csv040: output/modelling/J5i_Simul_R0_by_week.csv
        svg010: output/modelling/J5i_Simul_R0_by_week.csv.svg
        #simulation - only run if iplatform==0
        #svg011: output/modelling/J5i_Simul_Infected_and_R0.pdf_1-3.svg
        #svg012: output/modelling/J5i_Simul_Infected_and_R0.pdf_4-6.svg
        #txt020: output/modelling/J5i_Simul_run.txt
        #fit
        #txt000: output/modelling/screen.txt
        html01: output/modelling/J5i_Main_Fit_Report.html
        txt021: output/modelling/J5i_Fit_summary_1.txt
        txt022: output/modelling/J5i_Fit_summary_2.txt  
        svg021: output/modelling/J5i_Fit_summary_1.svg
        svg022: output/modelling/J5i_Fit_summary_2.svg
        svg031: output/modelling/J5i_Fit_MCMC_marginalPlot.svg
        #svg032: output/modelling/J5i_Fit_MCMC_plotout_lastPage.svg
        svg033: output/modelling/J5i_Fit_MCMC_correlationPlot.svg
        svg034: output/modelling/J5i_Fit_MCMC_Overall.svg
        svg035: output/modelling/J5i_Fit_MCMC_PosteriorSample.svg
        svg036: output/modelling/J5i_Fit_MCMC_AgeProfile_H.svg
        svg037: output/modelling/J5i_Fit_MCMC_AgeProfile_DH.svg
        svg038: output/modelling/J5i_Fit_MCMC_AgeProfile_DO.svg
        svg039: output/modelling/J5i_Fit_MCMC_variables.svg

  
  # HD_data_questions:
    # run: > 
      # r:latest
        # analysis/HDdata_questions.r
    # needs: [clean_the_data]
    # outputs:
      # moderately_sensitive:
        # txt01: output/HDsynthesis/JDat12_HDdata_questions_answered_Hospital_wCH.txt
        # txt02: output/HDsynthesis/JDat12_HDdata_questions_answered_Deaths_wCH.txt
        # txt03: output/HDsynthesis/JDat12_HDdata_questions_answered_Shielding_wCH.txt
        # txt04: output/HDsynthesis/JDat12_HDdata_questions_answered_Hospital.txt
        # txt05: output/HDsynthesis/JDat12_HDdata_questions_answered_Deaths.txt
        # txt06: output/HDsynthesis/JDat12_HDdata_questions_answered_Shielding.txt

  # HD_data:
    # run: > 
      # r:latest
        # analysis/runmkd.R
    # needs: [clean_the_data]
    # outputs:
      # moderately_sensitive:
        # csv01b: output/HDsynthesis/JDat12_Carehomes_included_H.csv
        # svg01b: output/HDsynthesis/JDat12_Carehomes_included_H.svg
        # csv02b: output/HDsynthesis/JDat12_Carehomes_included_D.csv
        # svg02b: output/HDsynthesis/JDat12_Carehomes_included_D.svg
        # csv03b: output/HDsynthesis/JDat12_Carehomes_included_DH.csv
        # svg03b: output/HDsynthesis/JDat12_Carehomes_included_DH.svg
        # csv04b: output/HDsynthesis/JDat12_Carehomes_included_DO.csv
        # svg04b: output/HDsynthesis/JDat12_Carehomes_included_DO.svg
        # csv051: output/HDsynthesis/JDat12_Hdata_all.csv
        # svg051: output/HDsynthesis/JDat12_Hdata_all.svg
        # csv052: output/HDsynthesis/JDat12_Hdata_by_age.csv
        # csv055: output/HDsynthesis/JDat12_Hdata_by_age_long.csv
        # svg052: output/HDsynthesis/JDat12_Hdata_by_age.svg
        # csv05m: output/HDsynthesis/JDat12_Hdata_by_age_merged.csv
        # csv05l: output/HDsynthesis/JDat12_Hdata_by_age_merged_long.csv
        # svg05m: output/HDsynthesis/JDat12_Hdata_by_age_merged.svg
        # csv053: output/HDsynthesis/JDat12_Hdata_by_shi.csv
        # svg053: output/HDsynthesis/JDat12_Hdata_by_shi.svg
        # csv054: output/HDsynthesis/JDat12_Hdata_s_by_age.csv
        # svg054: output/HDsynthesis/JDat12_Hdata_s0_by_age.svg
        # svg055: output/HDsynthesis/JDat12_Hdata_s1_by_age.svg
        # csv061: output/HDsynthesis/JDat12_HRdata_all.csv
        # svg061: output/HDsynthesis/JDat12_HRdata_all.svg
        # csv062: output/HDsynthesis/JDat12_HRdata_by_age.csv
        # svg062: output/HDsynthesis/JDat12_HRdata_by_age.svg
        # csv063: output/HDsynthesis/JDat12_HRdata_by_shi.csv
        # svg063: output/HDsynthesis/JDat12_HRdata_by_shi.svg
        # csv064: output/HDsynthesis/JDat12_HRdata_s_by_age.csv
        # svg064: output/HDsynthesis/JDat12_HRdata_s0_by_age.svg
        # svg065: output/HDsynthesis/JDat12_HRdata_s1_by_age.svg
        # csv071: output/HDsynthesis/JDat12_DHdata_all.csv
        # svg071: output/HDsynthesis/JDat12_DHdata_all.svg
        # csv072: output/HDsynthesis/JDat12_DHdata_by_age.csv
        # csv075: output/HDsynthesis/JDat12_DHdata_by_age_long.csv        
        # svg072: output/HDsynthesis/JDat12_DHdata_by_age.svg
        # csv07m: output/HDsynthesis/JDat12_DHdata_by_age_merged.csv
        # csv07l: output/HDsynthesis/JDat12_DHdata_by_age_merged_long.csv
        # svg07m: output/HDsynthesis/JDat12_DHdata_by_age_merged.svg
        # csv073: output/HDsynthesis/JDat12_DHdata_by_shi.csv
        # svg073: output/HDsynthesis/JDat12_DHdata_by_shi.svg
        # csv074: output/HDsynthesis/JDat12_DHdata_s_by_age.csv
        # svg074: output/HDsynthesis/JDat12_DHdata_s0_by_age.svg
        # svg075: output/HDsynthesis/JDat12_DHdata_s1_by_age.svg
        # csv081: output/HDsynthesis/JDat12_DOdata_all.csv
        # svg081: output/HDsynthesis/JDat12_DOdata_all.svg
        # csv082: output/HDsynthesis/JDat12_DOdata_by_age.csv
        # csv085: output/HDsynthesis/JDat12_DOdata_by_age_long.csv
        # svg082: output/HDsynthesis/JDat12_DOdata_by_age.svg
        # csv08m: output/HDsynthesis/JDat12_DOdata_by_age_merged.csv
        # csv08l: output/HDsynthesis/JDat12_DOdata_by_age_merged_long.csv
        # svg08m: output/HDsynthesis/JDat12_DOdata_by_age_merged.svg
        # csv083: output/HDsynthesis/JDat12_DOdata_by_shi.csv
        # svg083: output/HDsynthesis/JDat12_DOdata_by_shi.svg
        # csv084: output/HDsynthesis/JDat12_DOdata_s_by_age.csv
        # svg084: output/HDsynthesis/JDat12_DOdata_s0_by_age.svg
        # svg085: output/HDsynthesis/JDat12_DOdata_s1_by_age.svg       
        # csv091: output/HDsynthesis/JDat12_H,HR,DH,DOdata_H.csv
        # csv092: output/HDsynthesis/JDat12_H,HR,DH,DOdata_HR.csv
        # csv093: output/HDsynthesis/JDat12_H,HR,DH,DOdata_DH.csv
        # csv094: output/HDsynthesis/JDat12_H,HR,DH,DOdata_DO.csv
        # svg09b: output/HDsynthesis/JDat12_H,HR,DH,DOdata.svg
        # html01: output/HDsynthesis/JDat12_Report_HDdata.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job request

Status
Failed 
GitRepoNotReachableError: Could not read from https://github.com/opensafely/shielding-evaluation
Backend
TPP
Workspace
shielding_evaluation
Requested by
Johnny Filipe
Branch
main
Force run dependencies
No
Git commit hash
98da718
Requested actions
  • fit_HDdata

Code comparison

Compare the code used in this job request