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Job request: 24321

Organisation:
University of Bristol
Workspace:
metformin-covid-main
ID:
fbvpnw7euy3ddrzf
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Alain Amstutz 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'

# Ignore this`expectation` block. It is required but not used, and will be removed in future versions.
expectations:
  population_size: 1000

actions:
  study_dates:
    run: r:latest analysis/metadates.R
    outputs:
      highly_sensitive:
        study_dates_json: output/study_dates.json

  generate_dataset_dm_algo:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_dm_algo.py --output output/dataset_dm_algo.arrow
    needs: 
    - study_dates
    outputs:
      highly_sensitive:
        dataset: output/dataset_dm_algo.arrow
  
  data_process_dm_algo:
    run: r:latest analysis/data_process_dm_algo.R
    needs:
    - generate_dataset_dm_algo
    outputs:
      highly_sensitive:
        dataset: output/data/data_processed_dm_algo.csv.gz

  generate_dataset:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_t2dm.py --output output/dataset.arrow
    needs: 
    - study_dates
    - generate_dataset_dm_algo
    - data_process_dm_algo
    outputs:
      highly_sensitive:
        dataset: output/dataset.arrow

  data_process:
    run: r:latest analysis/data_process.R
    needs:
    - generate_dataset
    outputs:
      highly_sensitive:
        dataset: output/data/data_processed.arrow
        dataset_plots: output/data/data_plots.feather
      moderately_sensitive:
        csv: output/data_description/*.csv

  km_estimates_metfin_RA:
    run: kaplan-meier-function:v0.0.8
      --df_input=output/data/data_plots.feather
      --dir_output=output/metfin
      --origin_date=elig_date_t2dm
      --event_date=exp_date_metfin_anytime
      --censor_date=qa_date_of_death
      --max_fup=548
      --plot=TRUE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        km_estimates: output/metfin/*.csv
        plot: output/metfin/*.png
  
  km_estimates_metfin_mono_RA:
    run: kaplan-meier-function:v0.0.8
      --df_input=output/data/data_plots.feather
      --dir_output=output/metfin_mono
      --origin_date=elig_date_t2dm
      --event_date=exp_date_metfin_mono_anytime
      --censor_date=qa_date_of_death
      --max_fup=548
      --plot=TRUE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        km_estimates: output/metfin_mono/*.csv
        plot: output/metfin_mono/*.png

  km_estimates_dpp4_mono_RA:
    run: kaplan-meier-function:v0.0.8
      --df_input=output/data/data_plots.feather
      --dir_output=output/dpp4_mono
      --origin_date=elig_date_t2dm
      --event_date=exp_date_dpp4_mono_anytime
      --censor_date=qa_date_of_death
      --max_fup=548
      --plot=TRUE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        km_estimates: output/dpp4_mono/*.csv
        plot: output/dpp4_mono/*.png

  #km_estimates_tzd_mono:
  #  run: r:latest analysis/km.R 
  #    --df_input=output/data/data_plots.feather
  #    --dir_output=output/tzd_mono
  #    --origin_date=elig_date_t2dm
  #    --event_date=exp_date_tzd_mono_anytime
  #    --censor_date=out_date_severecovid
  #    --max_fup=548
  #    --plot=FALSE
  #  needs:
  #  - data_process
  #  outputs:
  #    moderately_sensitive:
  #      output: output/tzd_mono/*.csv

  km_estimates_tzd_mono_RA:
    run: kaplan-meier-function:v0.0.8
      --df_input=output/data/data_plots.feather
      --dir_output=output/tzd_mono
      --origin_date=elig_date_t2dm
      --event_date=exp_date_tzd_mono_anytime
      --censor_date=qa_date_of_death
      --max_fup=548
      --plot=TRUE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        km_estimates: output/tzd_mono/*.csv
        plot: output/tzd_mono/*.png

  km_estimates_sglt2_mono_RA:
    run: kaplan-meier-function:v0.0.8
      --df_input=output/data/data_plots.feather
      --dir_output=output/sglt2_mono
      --origin_date=elig_date_t2dm
      --event_date=exp_date_sglt2_mono_anytime
      --censor_date=qa_date_of_death
      --max_fup=548
      --plot=TRUE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        km_estimates: output/sglt2_mono/*.csv
        plot: output/sglt2_mono/*.png

  km_estimates_sulfo_mono_RA:
    run: kaplan-meier-function:v0.0.8
      --df_input=output/data/data_plots.feather
      --dir_output=output/sulfo_mono
      --origin_date=elig_date_t2dm
      --event_date=exp_date_sulfo_mono_anytime
      --censor_date=qa_date_of_death
      --max_fup=548
      --plot=TRUE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        km_estimates: output/sulfo_mono/*.csv
        plot: output/sulfo_mono/*.png

  km_estimates_glp1_mono_RA:
    run: kaplan-meier-function:v0.0.8
      --df_input=output/data/data_plots.feather
      --dir_output=output/glp1_mono
      --origin_date=elig_date_t2dm
      --event_date=exp_date_glp1_mono_anytime
      --censor_date=qa_date_of_death
      --max_fup=548
      --plot=TRUE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        km_estimates: output/glp1_mono/*.csv
        plot: output/glp1_mono/*.png

  km_estimates_megli_mono_RA:
    run: kaplan-meier-function:v0.0.8
      --df_input=output/data/data_plots.feather
      --dir_output=output/megli_mono
      --origin_date=elig_date_t2dm
      --event_date=exp_date_megli_mono_anytime
      --censor_date=qa_date_of_death
      --max_fup=548
      --plot=TRUE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        km_estimates: output/megli_mono/*.csv
        plot: output/megli_mono/*.png

  km_estimates_agi_mono_RA:
    run: kaplan-meier-function:v0.0.8
      --df_input=output/data/data_plots.feather
      --dir_output=output/agi_mono
      --origin_date=elig_date_t2dm
      --event_date=exp_date_agi_mono_anytime
      --censor_date=qa_date_of_death
      --max_fup=548
      --plot=TRUE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        km_estimates: output/agi_mono/*.csv
        plot: output/agi_mono/*.png

  km_estimates_insulin_mono_RA:
    run: kaplan-meier-function:v0.0.8
      --df_input=output/data/data_plots.feather
      --dir_output=output/insulin_mono
      --origin_date=elig_date_t2dm
      --event_date=exp_date_insulin_mono_anytime
      --censor_date=qa_date_of_death
      --max_fup=548
      --plot=TRUE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        km_estimates: output/insulin_mono/*.csv
        plot: output/insulin_mono/*.png

  plot_km_estimates:
    run: r:latest analysis/km_plot.R 
    needs:
    - km_estimates_metfin_RA
    - km_estimates_metfin_mono_RA
    - km_estimates_dpp4_mono_RA
    - km_estimates_tzd_mono_RA
    - km_estimates_sglt2_mono_RA
    - km_estimates_sulfo_mono_RA
    - km_estimates_glp1_mono_RA
    - km_estimates_megli_mono_RA
    - km_estimates_agi_mono_RA
    - km_estimates_insulin_mono_RA
    outputs:
      moderately_sensitive:
        plot: output/data_description/*.png

  table1:
    run: r:latest analysis/table1.R
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        table1: output/data_description/table1_midpoint6.csv

  km_treat:
    run: kaplan-meier-function:v0.0.8 
      --df_input=output/data/data_processed.arrow
      --dir_output=output/treat
      --exposure=exp_bin_treat
      --origin_date=elig_date_t2dm
      --event_date=out_date_severecovid2
      --censor_date=qa_date_of_death
      --max_fup=548
      --plot=TRUE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        km_treat_estimates: output/treat/*.csv
        png: output/treat/*.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 06:52:16

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

Job information

Status
Succeeded
Backend
TPP
Workspace
metformin-covid-main
Requested by
Alain Amstutz
Branch
main
Force run dependencies
No
Git commit hash
1a7d99d
Requested actions
  • data_process
  • km_estimates_metfin_RA
  • km_estimates_metfin_mono_RA
  • km_estimates_dpp4_mono_RA
  • km_estimates_tzd_mono_RA
  • km_estimates_sglt2_mono_RA
  • km_estimates_sulfo_mono_RA
  • km_estimates_glp1_mono_RA
  • km_estimates_megli_mono_RA
  • km_estimates_agi_mono_RA
  • km_estimates_insulin_mono_RA
  • plot_km_estimates

Code comparison

Compare the code used in this Job Request