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Job request: 20584

Organisation:
Bennett Institute
Workspace:
pax-usernonuser
ID:
cw4vbkmnnk5zfhkp
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Linda Nab 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: 5000

actions:

  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 
  ## Data extraction 
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 

  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_flowchart:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flowchart --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_flowchart.csv.gz

  generate_study_population_pax_trt:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pax_trt --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_pax_trt.csv.gz

  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 
  ## Data cleaning and description
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 

  data_process:
    run: r:latest analysis/data_process.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data1: output/data/data_processed.rds
        data2: output/data/data_processed_grace6.rds
        data3: output/data/data_processed_grace7.rds
        data4: output/data/data_processed_grace8.rds
        data1_excl: output/data/data_processed_excl_contraindicated.rds
        data2_excl: output/data/data_processed_excl_contraindicated_grace6.rds
        data3_excl: output/data/data_processed_excl_contraindicated_grace7.rds
        data4_excl: output/data/data_processed_excl_contraindicated_grace8.rds
        rds1: output/data_properties/n_excluded.rds
        rds2: output/data_properties/n_excluded_contraindicated.rds

  data_process_flowchart:
    run: r:latest analysis/data_process_flowchart.R
    needs: [generate_study_population_flowchart]
    outputs:
      highly_sensitive:
        data: output/data/data_flowchart_processed.rds
  
  data_properties:
    run: r:latest analysis/data_properties/data_properties.R output/data/data_processed.rds output/data_properties
    needs: [data_process]
    outputs:
      moderately_sensitive:
        txt1: output/data_properties/data_processed_skim.txt
        txt2: output/data_properties/data_processed_coltypes.txt
        txt3: output/data_properties/data_processed_tabulate.txt

  create_flowchart:
    run: r:latest analysis/flowchart.R
    needs: [data_process_flowchart, data_process]
    outputs:
      moderately_sensitive:
        csv1: output/flowchart/flowchart.csv
        csv2: output/flowchart/flowchart_redacted.csv

  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 
  ## Descriptive analyses
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # #

  describe_distr_trt_init:
    run: r:latest analysis/descriptives/describe_distr_trt_init.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        csv1: output/descriptives/distr_pax_init.csv
        csv2: output/descriptives/distr_pax_init_red.csv

  describe_outcomes_in_trt_window:
    run: r:latest analysis/descriptives/describe_outcomes_in_trt_window.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        csv1: output/descriptives/outcomes_in_trt_window.csv
        csv2: output/descriptives/outcomes_in_trt_window_red.csv
        csv3: output/descriptives/outcomes_day0.csv
  
  describe_prop_trt:
    run: r:latest analysis/descriptives/describe_prop_trt.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        csv1: output/descriptives/prop_trt.csv
        csv2: output/descriptives/prop_trt_red.csv

  describe_trt_contra:
    run: r:latest analysis/descriptives/describe_trt_contra.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        csv1: output/descriptives/trt_contra.csv
        csv2: output/descriptives/trt_contra_red.csv
        csvs1: output/descriptives/n_codes_*.csv

  describe_trt_preds_all_ci_pax:
    run: r:latest analysis/descriptives/describe_trt_preds.R all_ci Paxlovid
    needs: [data_process]
    outputs:
      highly_sensitive:
        model1: output/descriptives/psModel_Paxlovid_all_ci.rds     
      moderately_sensitive:
        csv1: output/descriptives/psDens_untrimmed_Paxlovid_all_ci.csv
        csv2: output/descriptives/psDens_trimmed_Paxlovid_all_ci.csv
        csv3: output/descriptives/psCoefs_Paxlovid_all_ci.csv
        csv4: output/descriptives/trimming_descriptives_Paxlovid_all_ci.csv

  describe_trt_preds_all_ci_sot:
    run: r:latest analysis/descriptives/describe_trt_preds.R all_ci Sotrovimab
    needs: [data_process]
    outputs:
      highly_sensitive:
        data1: output/descriptives/psModel_Sotrovimab_all_ci.rds     
      moderately_sensitive:
        csv1: output/descriptives/psDens_untrimmed_Sotrovimab_all_ci.csv
        csv2: output/descriptives/psDens_trimmed_Sotrovimab_all_ci.csv
        csv3: output/descriptives/psCoefs_Sotrovimab_all_ci.csv
        csv4: output/descriptives/trimming_descriptives_Sotrovimab_all_ci.csv    
        
  describe_trt_preds_all_ci_mol:
    run: r:latest analysis/descriptives/describe_trt_preds.R all_ci Molnupiravir
    needs: [data_process]
    outputs:
      highly_sensitive:
        data1: output/descriptives/psModel_Molnupiravir_all_ci.rds     
      moderately_sensitive:
        csv1: output/descriptives/psDens_untrimmed_Molnupiravir_all_ci.csv
        csv2: output/descriptives/psDens_trimmed_Molnupiravir_all_ci.csv
        csv3: output/descriptives/psCoefs_Molnupiravir_all_ci.csv
        csv4: output/descriptives/trimming_descriptives_Molnupiravir_all_ci.csv

  visualise_trt_preds_dens:
    run: r:latest analysis/descriptives/visualise_trt_preds_dens.R
    needs: [describe_trt_preds_all_ci_pax, describe_trt_preds_all_ci_sot, describe_trt_preds_all_ci_mol]
    outputs:   
      moderately_sensitive:
        png1: output/descriptives/psOverlap_untrimmed_*_all_ci.png
        png2: output/descriptives/psOverlap_trimmed_*_all_ci.png
 
  create_table1:
    run: r:latest analysis/descriptives/table1.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        csv1: output/tables/table1.csv
        csv2: output/tables/table1_red.csv
        csv3: output/tables/table1_red_unf.csv
        csv4: output/tables/table1_full.csv
        csv5: output/tables/table1_full_red.csv
        csv6: output/tables/table1_full_red_unf.csv
        csv7: output/tables/table1_trt_untrt.csv
        csv8: output/tables/table1_trt_untrt_red.csv
        csv9: output/tables/table1_trt_untrt_red_unf.csv
  
  create_table1_stratified_by_3months:
    run: r:latest analysis/descriptives/table1_subsets.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        csv1: output/tables/stratified_3months/table1.csv
        csv2: output/tables/stratified_3months/table1_red.csv
        csv3: output/tables/stratified_3months/table1_red_unf.csv
        csv4: output/tables/stratified_3months/table1_full.csv
        csv5: output/tables/stratified_3months/table1_full_red.csv
        csv6: output/tables/stratified_3months/table1_full_red_unf.csv
        csv7: output/tables/stratified_3months/table1_trt_untrt.csv
        csv8: output/tables/stratified_3months/table1_trt_untrt_red.csv
        csv9: output/tables/stratified_3months/table1_trt_untrt_red_unf.csv

  describe_trt_groups:
    run: r:latest analysis/descriptives/describe_trt_groups.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        csv1: output/descriptives/trt_groups.csv
        csv2: output/descriptives/trt_groups_red.csv

  describe_fup_outcomes:
    run: r:latest analysis/descriptives/describe_fup_outcomes.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        csv1: output/descriptives/overview_fup_outcomes.csv
        csv2: output/descriptives/overview_fup_outcomes_red.csv
  
  describe_postest_pop:
    run: r:latest analysis/descriptives/describe_postest_pop.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        csv1: output/descriptives/postest_pop.csv
        csv2: output/descriptives/postest_pop_red.csv
    
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # # 
  ## Sequential trials
  ## # # # # # # # # # # # # # # # # # # # 
  ## # # # # # # # # # # # # # # # # # # #
  data_select_and_simplify:
    run: r:latest analysis/seq_trials/select_and_simplify_data.R
    needs: [data_process]
    outputs:
      highly_sensitive:
        data1: output/data/data_processed_excl_contraindicated.feather

  data_prepare_seq_trials_month:
    run: r:latest analysis/seq_trials/prepare_data.R --period=month
    needs: [data_select_and_simplify]
    outputs:
      highly_sensitive:
        data1: output/data/data_seq_trials_monthly.feather

  describe_size_trials_month:
    run: r:latest analysis/seq_trials/descriptives/describe_size_trials.R --period=month
    needs: [data_process, data_prepare_seq_trials_month]
    outputs:
      moderately_sensitive:
        csv1: output/seq_trials/descriptives/data_flow_seq_trials_monthly.csv
        csv2: output/seq_trials/descriptives/data_flow_seq_trials_monthly_red.csv
        csv3: output/seq_trials/descriptives/sense_check_for_data_flow.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:08:39

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

Job request

Status
Succeeded
Backend
TPP
Workspace
pax-usernonuser
Requested by
Linda Nab
Branch
main
Force run dependencies
No
Git commit hash
7a7aa25
Requested actions
  • data_select_and_simplify
  • data_prepare_seq_trials_month

Code comparison

Compare the code used in this job request