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Job request: 2607

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
hh-classification-research
ID:
37npqed6tm6vcaji
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Kevin Wing 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: 100000

actions:
  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  W2_generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_W2
    outputs:
      highly_sensitive:
        cohort: output/input_W2.csv

  01_hhClassif_cr_analysis_dataset:
    run: stata-mp:latest analysis/01_hhClassif_cr_analysis_dataset.do MAIN
    needs: [generate_cohort]
    outputs:
      highly_sensitive:
        allHHSizes: output/allHH_beforeDropping_largerThan10_MAIN.dta
        allHHSizes1_20: output/allHH_sizedBetween1And20_MAIN.dta
        allvars: output/hhClassif_analysis_datasetMAIN.dta
        allvarsEthMiss: output/hhClassif_analysis_dataset_with_missing_ethnicityMAIN.dta
        allVarsAgeSpline: output/hhClassif_analysis_dataset_ageband_*MAIN.dta 
        allVarsAgeStratStset: output/hhClassif_analysis_dataset_STSET_*_ageband_*MAIN.dta 
      moderately_sensitive:
        log: logs/01_hhClassif_cr_analysis_dataset.log

  01_hhClassif_cr_analysis_dataset_W2:
    run: stata-mp:latest analysis/01_hhClassif_cr_analysis_dataset.do W2
    needs: [W2_generate_cohort]
    outputs:
      highly_sensitive:
        allHHSizes: output/allHH_beforeDropping_largerThan10_W2.dta
        allHHSizes1_20: output/allHH_sizedBetween1And20_W2.dta
        allvars: output/hhClassif_analysis_datasetW2.dta
        allvarsEthMiss: output/hhClassif_analysis_dataset_with_missing_ethnicityW2.dta
        allVarsAgeSpline: output/hhClassif_analysis_dataset_ageband_*W2.dta 
        allVarsAgeStratStset: output/hhClassif_analysis_dataset_STSET_*_ageband_*W2.dta 
      moderately_sensitive:
        log: logs/01_hhClassif_cr_analysis_dataset_W2.log

  02_hhClassif_an_data_checks:
    run: stata-mp:latest analysis/02_hhClassif_an_data_checks.do MAIN
    needs: [01_hhClassif_cr_analysis_dataset]
    outputs:
      moderately_sensitive:
        log: logs/02_hhClassif_an_data_checks.log

  02_hhClassif_an_data_checks_W2:
    run: stata-mp:latest analysis/02_hhClassif_an_data_checks.do W2
    needs: [01_hhClassif_cr_analysis_dataset_W2]
    outputs:
      moderately_sensitive:
        log: logs/02_hhClassif_an_data_checks_W2.log

  03a_hhClassif_an_hist_hhSizebyEthnicity:
    run: stata-mp:latest analysis/03a_hhClassif_an_hist_hhSizebyEthnicity.do MAIN
    needs: [01_hhClassif_cr_analysis_dataset]
    outputs:
      moderately_sensitive:
        log: logs/03a_hhClassif_an_hist_hhSizebyEthnicity_MAIN.log
        gph1: output/overallHHSizeDist_MAIN.gph 
        gph2: output/whiteHHSizeDist_MAIN.gph 
        gph3: output/southAsianHHSizeDist_MAIN.gph
        gph4: output/blackHHSizeDist_MAIN.gph
        gph5: output/HHdistHists_MAIN.pdf

  03b_hhClassif_an_hist_ov65hhSizebyEthnicity:
    run: stata-mp:latest analysis/03b_hhClassif_an_hist_ov65hhSizebyEthnicity.do MAIN
    needs: [01_hhClassif_cr_analysis_dataset]
    outputs:
      moderately_sensitive:
        log: logs/03b_hhClassif_an_hist_ov65hhSizebyEthnicity_MAIN.log
        gph1: output/ov65OverallHHSizeDist_MAIN.gph 
        gph2: output/ov65WhiteHHSizeDist_MAIN.gph 
        gph3: output/ov65SouthAsianHHSizeDist_MAIN.gph
        gph4: output/ov65BlackHHSizeDist_MAIN.gph
        gph5: output/ov65HHdistHists_MAIN.pdf

  03c_hhClassif_an_hist_ov65hhSizebyEthnicity_woAllSameAge:
    run: stata-mp:latest analysis/03c_hhClassif_an_hist_ov65hhSizebyEthnicity_woAllSameAge.do MAIN
    needs: [01_hhClassif_cr_analysis_dataset]
    outputs:
      highly_sensitive:
        over65OnlyHH: output/housesWithOnly65yrOldsInThem_MAIN.dta
      moderately_sensitive:
        log: logs/03c_hhClassif_an_hist_ov65hhSizebyEthnicity_woAllSameAge_MAIN.log
        gph1: output/ov65OverallHHSizeDist_woAllSameAge_MAIN.gph 
        gph2: output/ov65WhiteHHSizeDist_woAllSameAge_MAIN.gph 
        gph3: output/ov65SouthAsianHHSizeDist_woAllSameAge_MAIN.gph
        gph4: output/ov65BlackHHSizeDist_woAllSameAge_MAIN.gph
        gph5: output/ov65HHdistHists_woAllSameAge_MAIN.pdf

  03d_hhClassif_an_hist_ov65hhSizebyEthnicity_RuralUrban:
    run: stata-mp:latest analysis/03d_hhClassif_an_hist_ov65hhSizebyEthnicity_RuralUrban.do MAIN
    needs: [01_hhClassif_cr_analysis_dataset]
    outputs:
      moderately_sensitive:
        log: logs/03d_hhClassif_an_hist_ov65hhSizebyEthnicity_RuralUrban_MAIN.log
        gph1: output/ov65OverallHHSizeDist_*_MAIN.gph 
        gph2: output/ov65WhiteHHSizeDist_*_MAIN.gph 
        gph3: output/ov65SouthAsianHHSizeDist_*_MAIN.gph
        gph4: output/ov65BlackHHSizeDist_*_MAIN.gph
        gph5: output/ov65HHdistHists_*_MAIN.pdf

  03e_hhClassif_an_descriptive_table_1:
    run: stata-mp:latest analysis/03e_hhClassif_an_descriptive_table_1.do MAIN
    needs: [01_hhClassif_cr_analysis_dataset]
    outputs:
      moderately_sensitive:
        log: logs/03e_hhClassif_an_descriptive_table_1_MAIN.log
        tableTxt: output/table1_hhClassifMAIN.txt
        tableExcel: output/table1_hhClassifMAIN.xlsx

  03d_hhClassif_an_descriptive_table_1_W2:
    run: stata-mp:latest analysis/03d_hhClassif_an_descriptive_table_1.do W2
    needs: [01_hhClassif_cr_analysis_dataset_W2]
    outputs:
      moderately_sensitive:
        log: logs/03e_hhClassif_an_descriptive_table_1_W2.log
        tableTxt: output/table1_hhClassifW2.txt
        tableExcel: output/table1_hhClassifW2.xlsx

  04_hhClassif_an_univariable_analysis:
    needs: [01_hhClassif_cr_analysis_dataset]
    run: stata-mp:latest analysis/04_hhClassif_an_univariable_analysis.do MAIN
    outputs:
      moderately_sensitive:
        log: logs/04_hhClassif_an_univariable_analysis_MAIN.log
        data: output/hhClassif_univariableAnalysis_*_ageband_*MAIN.ster

  04_hhClassif_an_univariable_analysis_W2:
    needs: [01_hhClassif_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/04_hhClassif_an_univariable_analysis.do W2
    outputs:
      moderately_sensitive:
        log: logs/04_hhClassif_an_univariable_analysis_W2.log
        data: output/hhClassif_univariableAnalysis_*_ageband_*W2.ster

  05_hhClassif_an_multivariable_analysis:
    needs: [01_hhClassif_cr_analysis_dataset]
    run: stata-mp:latest analysis/05_hhClassif_an_multivariable_analysis.do MAIN
    outputs:
      moderately_sensitive:
        log: logs/05_hhClassif_an_multivariable_analysis_MAIN.log
        data: output/hhClassif_multivariableAllEthnicities_*_ageband_*MAIN.ster

  05_hhClassif_an_multivariable_analysis_W2:
    needs: [01_hhClassif_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/05_hhClassif_an_multivariable_analysis.do W2
    outputs:
      moderately_sensitive:
        log: logs/05_hhClassif_an_multivariable_analysis_W2.log
        data: output/hhClassif_multivariableAllEthnicities_*_ageband_*W2.ster

  #06_hhClassif_an_multivariable_analysis_eth5Interaction:
  #  needs: [01_hhClassif_cr_analysis_dataset]
  #  run: stata-mp:latest analysis/06_hhClassif_an_multivariable_analysis_eth5Interaction.do MAIN
  #  outputs:
  #    moderately_sensitive:
  #      log: logs/06_hhClassif_an_eth5Interaction_analysis_MAIN.log
  #      data: output/hhClassif_multvariableAnalysisEth5Interaction_*_ageband_*MAIN.ster

  #06_hhClassif_an_multivariable_analysis_eth5Interaction_W2:
  #  needs: [01_hhClassif_cr_analysis_dataset_W2]
  #  run: stata-mp:latest analysis/06_hhClassif_an_multivariable_analysis_eth5Interaction.do W2
  #  outputs:
  #    moderately_sensitive:
  #      log: logs/06_hhClassif_an_eth5Interaction_analysis_W2.log
  #      data: output/hhClassif_multvariableAnalysisEth5Interaction_*_ageband_*W2.ster

  07_hhClassif_an_multivariable_analysis_perEth5Group:
    needs: [01_hhClassif_cr_analysis_dataset]
    run: stata-mp:latest analysis/07_hhClassif_an_multivariable_analysis_perEth5Group.do MAIN
    outputs:
      moderately_sensitive:
        log: logs/07_hhClassif_an_multivariable_analysis_perEth5Group_MAIN.log
        data: output/hhClassif_multvariableAnalysisPerEth5_*_ageband_*_ethnicity_*MAIN.ster

  07_hhClassif_an_multivariable_analysis_perEth5Group_W2:
    needs: [01_hhClassif_cr_analysis_dataset_W2]
    run: stata-mp:latest analysis/07_hhClassif_an_multivariable_analysis_perEth5Group.do W2
    outputs:
      moderately_sensitive:
        log: logs/07_hhClassif_an_multivariable_analysis_perEth5Group_W2.log
        data: output/hhClassif_multvariableAnalysisPerEth5_*_ageband_*_ethnicity_*W2.ster

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:02:43

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

Job information

Status
Succeeded
Backend
TPP
Workspace
hh-classification-research
Requested by
Kevin Wing
Branch
master
Force run dependencies
No
Git commit hash
46ddf51
Requested actions
  • 03d_hhClassif_an_hist_ov65hhSizebyEthnicity_RuralUrban

Code comparison

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