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Job request: 24241

Organisation:
University of Bristol
Workspace:
metformin-covid-main
ID:
iyhydtn7moiozneb
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 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

  • Action:
    study_dates
    Status:
    Status: Succeeded
    Job identifier:
    4ump5gu2hxqgcvsu
  • Action:
    generate_dataset_dm_algo
    Status:
    Status: Succeeded
    Job identifier:
    5b6xhuj75aczt2rj
  • Action:
    data_process_dm_algo
    Status:
    Status: Succeeded
    Job identifier:
    ziyj6cdetnlkna4t
  • Action:
    generate_dataset
    Status:
    Status: Succeeded
    Job identifier:
    tri5dqlic3ljgljh
  • Action:
    data_process
    Status:
    Status: Failed
    Job identifier:
    doaskwusdhbnrnox
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    km_estimates_tzd_mono
    Status:
    Status: Failed
    Job identifier:
    cpthkyo3nc7wu2dg
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    km_estimates_agi_mono
    Status:
    Status: Failed
    Job identifier:
    jgodosmvtohaa6fm
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    km_estimates_dpp4_mono
    Status:
    Status: Failed
    Job identifier:
    kzge7qy44izjhy4w
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    km_estimates_metfin_mono
    Status:
    Status: Failed
    Job identifier:
    6d63warciskpetww
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    km_estimates_sglt2_mono
    Status:
    Status: Failed
    Job identifier:
    dssnu52baf6twit5
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    km_estimates_sulfo_mono
    Status:
    Status: Failed
    Job identifier:
    gft6btoltipwishy
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    km_estimates_megli_mono
    Status:
    Status: Failed
    Job identifier:
    b3ddmurbarlqsxn4
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    km_estimates_metfin
    Status:
    Status: Failed
    Job identifier:
    u3ucyr5cwo3lbkfl
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    km_estimates_glp1_mono
    Status:
    Status: Failed
    Job identifier:
    2xjkxlbdtjmdiqt4
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    km_estimates_insulin_mono
    Status:
    Status: Failed
    Job identifier:
    ffabgageavk3njou
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    plot_km_estimates
    Status:
    Status: Failed
    Job identifier:
    hfc3nc532dquxupn
    Error:
    dependency_failed: Not starting as dependency failed

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_landmark.py --output output/dataset.arrow
  #  needs: 
  #  - study_dates
  #  outputs:
  #    highly_sensitive:
  #      dataset: output/dataset.arrow

  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
  #  - data_process_dm_algo
  #  outputs:
  #    highly_sensitive:
  #      rds: output/data/data_processed.rds
  #      feather: output/data/data_plots.feather
  #    moderately_sensitive:
  #      csv: output/data_properties/*.csv

  data_process:
    run: r:latest analysis/data_process.R
    needs:
    - generate_dataset
    outputs:
      highly_sensitive:
        rds: output/data/data_processed.rds
        feather: output/data/data_plots.feather
      moderately_sensitive:
        csv: output/data_properties/*.csv

  km_estimates_metfin:
    run: r:latest analysis/km.R 
      --df_input=output/data/data_plots.feather
      --dir_output=output/metfin
      --exposure=exp_bin_metfin_anytime
      --origin_date=elig_date_t2dm
      --event_date=exp_date_metfin_anytime
      --censor_date=out_date_severecovid
      --max_fup=730
      --plot=FALSE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        output: output/metfin/*.csv
  
  km_estimates_metfin_mono:
    run: r:latest analysis/km.R 
      --df_input=output/data/data_plots.feather
      --dir_output=output/metfin_mono
      --exposure=exp_bin_metfin_mono_anytime
      --origin_date=elig_date_t2dm
      --event_date=exp_date_metfin_mono_anytime
      --censor_date=out_date_severecovid
      --max_fup=730
      --plot=FALSE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        output: output/metfin_mono/*.csv

  km_estimates_dpp4_mono:
    run: r:latest analysis/km.R 
      --df_input=output/data/data_plots.feather
      --dir_output=output/dpp4_mono
      --exposure=exp_bin_dpp4_mono_anytime
      --origin_date=elig_date_t2dm
      --event_date=exp_date_dpp4_mono_anytime
      --censor_date=out_date_severecovid
      --max_fup=730
      --plot=FALSE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        output: output/dpp4_mono/*.csv

  km_estimates_tzd_mono:
    run: r:latest analysis/km.R 
      --df_input=output/data/data_plots.feather
      --dir_output=output/tzd_mono
      --exposure=exp_bin_tzd_mono_anytime
      --origin_date=elig_date_t2dm
      --event_date=exp_date_tzd_mono_anytime
      --censor_date=out_date_severecovid
      --max_fup=730
      --plot=FALSE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        output: output/tzd_mono/*.csv

  km_estimates_sglt2_mono:
    run: r:latest analysis/km.R 
      --df_input=output/data/data_plots.feather
      --dir_output=output/sglt2_mono
      --exposure=exp_bin_sglt2_mono_anytime
      --origin_date=elig_date_t2dm
      --event_date=exp_date_sglt2_mono_anytime
      --censor_date=out_date_severecovid
      --max_fup=730
      --plot=FALSE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        output: output/sglt2_mono/*.csv

  km_estimates_sulfo_mono:
    run: r:latest analysis/km.R 
      --df_input=output/data/data_plots.feather
      --dir_output=output/sulfo_mono
      --exposure=exp_bin_sulfo_mono_anytime
      --origin_date=elig_date_t2dm
      --event_date=exp_date_sulfo_mono_anytime
      --censor_date=out_date_severecovid
      --max_fup=730
      --plot=FALSE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        output: output/sulfo_mono/*.csv

  km_estimates_glp1_mono:
    run: r:latest analysis/km.R 
      --df_input=output/data/data_plots.feather
      --dir_output=output/glp1_mono
      --exposure=exp_bin_glp1_mono_anytime
      --origin_date=elig_date_t2dm
      --event_date=exp_date_glp1_mono_anytime
      --censor_date=out_date_severecovid
      --max_fup=730
      --plot=FALSE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        output: output/glp1_mono/*.csv

  km_estimates_megli_mono:
    run: r:latest analysis/km.R 
      --df_input=output/data/data_plots.feather
      --dir_output=output/megli_mono
      --exposure=exp_bin_megli_mono_anytime
      --origin_date=elig_date_t2dm
      --event_date=exp_date_megli_mono_anytime
      --censor_date=out_date_severecovid
      --max_fup=730
      --plot=FALSE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        output: output/megli_mono/*.csv

  km_estimates_agi_mono:
    run: r:latest analysis/km.R 
      --df_input=output/data/data_plots.feather
      --dir_output=output/agi_mono
      --exposure=exp_bin_agi_mono_anytime
      --origin_date=elig_date_t2dm
      --event_date=exp_date_agi_mono_anytime
      --censor_date=out_date_severecovid
      --max_fup=730
      --plot=FALSE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        output: output/agi_mono/*.csv

  km_estimates_insulin_mono:
    run: r:latest analysis/km.R 
      --df_input=output/data/data_plots.feather
      --dir_output=output/insulin_mono
      --exposure=exp_bin_insulin_mono_anytime
      --origin_date=elig_date_t2dm
      --event_date=exp_date_insulin_mono_anytime
      --censor_date=out_date_severecovid
      --max_fup=730
      --plot=FALSE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        output: output/insulin_mono/*.csv

  plot_km_estimates:
    run: r:latest analysis/km_plot.R 
    needs:
    - km_estimates_metfin
    - km_estimates_metfin_mono
    - km_estimates_dpp4_mono
    - km_estimates_tzd_mono
    - km_estimates_sglt2_mono
    - km_estimates_sulfo_mono
    - km_estimates_glp1_mono
    - km_estimates_megli_mono
    - km_estimates_agi_mono
    - km_estimates_insulin_mono
    outputs:
      moderately_sensitive:
        plot: output/data_properties/*.png

#  km_estimates_metfin:
#    run: kaplan-meier-function:v0.0.2 
#      --df_input=output/data/data_plots.feather
#      --dir_output=output/km_estimates_metfin.feather ### double-check!!!
#      --exposure=exp_bin_metfin_anytime
#      --origin_date=elig_date_t2dm
#      --event_date=exp_date_metfin_anytime
#      --censor_date=out_date_severecovid
#      --plot=TRUE
#    needs:
#    - data_process
#    outputs:
#      highly_sensitive:
#        output: output/km_estimates_metfin.feather

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 25:17:00

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

Job request

Status
Failed
Backend
TPP
Workspace
metformin-covid-main
Requested by
Alain Amstutz
Branch
main
Force run dependencies
Yes
Git commit hash
d5e1268
Requested actions
  • study_dates
  • generate_dataset_dm_algo
  • data_process_dm_algo
  • generate_dataset
  • data_process
  • km_estimates_metfin
  • km_estimates_metfin_mono
  • km_estimates_dpp4_mono
  • km_estimates_tzd_mono
  • km_estimates_sglt2_mono
  • km_estimates_sulfo_mono
  • km_estimates_glp1_mono
  • km_estimates_megli_mono
  • km_estimates_agi_mono
  • km_estimates_insulin_mono
  • plot_km_estimates

Code comparison

Compare the code used in this job request