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Job request: 10554

Organisation:
Bennett Institute
Workspace:
mab-av-non-user-main
ID:
l6qxw2lspy6wy3nc
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher John Tazare 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 100000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input.csv.gz

  generate_study_population_ba2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ba2 --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_ba2.csv.gz

  data_process:
    run: r:latest analysis/data_process.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data1: output/data/data_processed_day0.rds
        data2: output/data/data_processed_day5.rds

  data_process_ba2:
    run: r:latest analysis/data_process_ba2.R
    needs: [generate_study_population_ba2]
    outputs:
      highly_sensitive:
        data1: output/data/ba2_data_processed_day0.rds
        data2: output/data/ba2_data_processed_day5.rds      

  data_properties_process_day0:
    run: r:latest analysis/data_properties.R output/data/data_processed_day0.rds output/data_properties
    needs: [data_process]
    outputs:
      moderately_sensitive:
        txt1: output/data_properties/data_processed_day0_skim.txt
        txt2: output/data_properties/data_processed_day0_coltypes.txt
        txt3: output/data_properties/data_processed_day0_tabulate.txt

  data_properties_process_day5:
    run: r:latest analysis/data_properties.R output/data/data_processed_day5.rds output/data_properties
    needs: [data_process]
    outputs:
      moderately_sensitive:
        txt1: output/data_properties/data_processed_day5_skim.txt
        txt2: output/data_properties/data_processed_day5_coltypes.txt
        txt3: output/data_properties/data_processed_day5_tabulate.txt

  data_properties_process_day0_ba2:
    run: r:latest analysis/data_properties.R output/data/ba2_data_processed_day0.rds output/data_properties
    needs: [data_process_ba2]
    outputs:
      moderately_sensitive:
        txt1: output/data_properties/ba2_data_processed_day0_skim.txt
        txt2: output/data_properties/ba2_data_processed_day0_coltypes.txt
        txt3: output/data_properties/ba2_data_processed_day0_tabulate.txt

  data_properties_process_day5_ba2:
    run: r:latest analysis/data_properties.R output/data/ba2_data_processed_day5.rds output/data_properties
    needs: [data_process_ba2]
    outputs:
      moderately_sensitive:
        txt1: output/data_properties/ba2_data_processed_day5_skim.txt
        txt2: output/data_properties/ba2_data_processed_day5_coltypes.txt
        txt3: output/data_properties/ba2_data_processed_day5_tabulate.txt

  crosstab_trt_outcomes:
    run: r:latest analysis/crosstab_trt_outcomes.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        csvsday5: output/data_properties/day5_*.csv 
        csvsday0: output/data_properties/day0_*.csv
        csvflowchart: output/data_properties/flowchart.csv
        csvflowchartrdctd: output/tables/flowchart_redacted.csv

  crosstab_trt_outcomes_ba2:
    run: r:latest analysis/crosstab_trt_outcomes_ba2.R
    needs: [data_process_ba2]
    outputs:
      moderately_sensitive:
        csvsday5: output/data_properties/ba2_day5_*.csv 
        csvsday0: output/data_properties/ba2_day0_*.csv
        csvflowchart: output/data_properties/flowchart_ba2.csv
        csvflowchartrdctd: output/tables/flowchart_redacted_ba2.csv

  table_1_day5:
    run: r:latest analysis/table_1.R day5
    needs: [data_process]
    outputs:
      highly_sensitive:
        data: output/tables/table1_redacted_day5.rds
      moderately_sensitive:
        table: output/tables/table1_redacted_day5.html

  table_1_day5_ba2:
    run: r:latest analysis/table_1_ba2.R day5
    needs: [data_process_ba2]
    outputs:
      highly_sensitive:
        data: output/tables/table1_redacted_day5_ba2.rds
      moderately_sensitive:
        table: output/tables/table1_redacted_day5_ba2.html

  cox_day5_full:
    run: r:latest analysis/cox_models.R day5 full
    needs: [data_process]
    outputs:
      highly_sensitive:
        data: output/tables/cox_models_day5_full.rds
      moderately_sensitive:
        figure1: output/figs/*_full_overlap_plot_day5_before_restriction.png
        figure2: output/figs/*_full_overlap_plot_day5_after_restriction.png
        figure3: output/figs/*_full_cumInc_day5.png
        table1: output/tables/cox_models_day5_full.csv
        table2: output/tables/log_cox_models_day5_full.csv
        model1: output/data_models/*_full_psModelFit.rds

  cox_day5_full_ba2:
    run: r:latest analysis/cox_models_ba2.R day5 full
    needs: [data_process_ba2]
    outputs:
      highly_sensitive:
        data: output/tables/cox_models_day5_full_ba2.rds
      moderately_sensitive:
        figure1: output/figs/*_full_overlap_plot_day5_before_restriction_ba2.png
        figure2: output/figs/*_full_overlap_plot_day5_after_restriction_ba2.png
        figure3: output/figs/*_full_cumInc_day5_ba2.png
        table1: output/tables/cox_models_day5_full_ba2.csv
        table2: output/tables/log_cox_models_day5_full_ba2.csv
        model1: output/data_models/*_full_psModelFit_ba2.rds

  cox_day5_age_sex:
    run: r:latest analysis/cox_models.R day5 agesex
    needs: [data_process]
    outputs:
      highly_sensitive:
        data: output/tables/cox_models_day5_agesex.rds
      moderately_sensitive:
        figure1: output/figs/*_agesex_overlap_plot_day5_before_restriction.png
        figure2: output/figs/*_agesex_overlap_plot_day5_after_restriction.png
        figure3: output/figs/*_agesex_cumInc_day5.png
        table1: output/tables/cox_models_day5_agesex.csv
        table2: output/tables/log_cox_models_day5_agesex.csv
        model1: output/data_models/*_agesex_psModelFit.rds

  cox_day5_age_sex_ba2:
    run: r:latest analysis/cox_models_ba2.R day5 agesex
    needs: [data_process_ba2]
    outputs:
      highly_sensitive:
        data: output/tables/cox_models_day5_agesex_ba2.rds
      moderately_sensitive:
        figure1: output/figs/*_agesex_overlap_plot_day5_before_restriction_ba2.png
        figure2: output/figs/*_agesex_overlap_plot_day5_after_restriction_ba2.png
        figure3: output/figs/*_agesex_cumInc_day5_ba2.png
        table1: output/tables/cox_models_day5_agesex_ba2.csv
        table2: output/tables/log_cox_models_day5_agesex_ba2.csv
        model1: output/data_models/*_agesex_psModelFit_ba2.rds
  
  cox_day5_crude:
    run: r:latest analysis/cox_models.R day5 crude
    needs: [data_process]
    outputs:
      highly_sensitive:
        data: output/tables/cox_models_day5_crude.rds
      moderately_sensitive:
        table1: output/tables/cox_models_day5_crude.csv
        table2: output/tables/log_cox_models_day5_crude.csv

  cox_day5_crude_ba2:
    run: r:latest analysis/cox_models_ba2.R day5 crude
    needs: [data_process_ba2]
    outputs:
      highly_sensitive:
        data: output/tables/cox_models_day5_crude_ba2.rds
      moderately_sensitive:
        table1: output/tables/cox_models_day5_crude_ba2.csv
        table2: output/tables/log_cox_models_day5_crude_ba2.csv
        
  trt_pat_day5:
    run: r:latest analysis/treatment_distributions.R day5
    needs: [data_process]
    outputs:
      moderately_sensitive:
        figure: output/figs/day5_treatment_pattern.png

  cox_day0:
    run: r:latest analysis/cox_models_day0.R
    needs: [data_process]
    outputs:
      highly_sensitive:
        data: output/tables/cox_models_day0.rds
      moderately_sensitive:
        table1: output/tables/cox_models_day0.csv
        table2: output/tables/estimates_day0.csv
        table3: output/tables/log_cox_models_day0.csv
        table4: output/tables/outcomes_day0.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 04:15:49

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

Job request

Status
Succeeded
Backend
TPP
Workspace
mab-av-non-user-main
Requested by
John Tazare
Branch
main
Force run dependencies
No
Git commit hash
a6e36be
Requested actions
  • generate_study_population_ba2
  • data_process_ba2
  • data_properties_process_day0_ba2
  • data_properties_process_day5_ba2
  • crosstab_trt_outcomes_ba2
  • table_1_day5_ba2
  • cox_day5_full_ba2
  • cox_day5_age_sex_ba2
  • cox_day5_crude_ba2

Code comparison

Compare the code used in this job request