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Job request: 24239

Organisation:
University of Bristol
Workspace:
metformin-covid-main
ID:
lf4m56hbvxhlhtew
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

  • Action:
    study_dates
    Status:
    Status: Succeeded
    Job identifier:
    hhvy2xumssa6rtal
  • Action:
    generate_dataset
    Status:
    Status: Succeeded
    Job identifier:
    ncoddcu7sbv5h6zf
  • Action:
    generate_dataset_dm_algo
    Status:
    Status: Succeeded
    Job identifier:
    vieq75zqlojqg3xa
  • Action:
    data_process_dm_algo
    Status:
    Status: Succeeded
    Job identifier:
    qutfgjnuk5w6da3n
  • Action:
    data_process
    Status:
    Status: Succeeded
    Job identifier:
    wrxrv3lu5ownu3na
  • Action:
    km_estimates_agi_mono
    Status:
    Status: Failed
    Job identifier:
    nle2rlnnemo2tqz5
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    km_estimates_dpp4_mono
    Status:
    Status: Failed
    Job identifier:
    5w74e5vuz636pfh2
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    km_estimates_glp1_mono
    Status:
    Status: Failed
    Job identifier:
    patpvvufwyufj2wu
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    km_estimates_insulin_mono
    Status:
    Status: Failed
    Job identifier:
    t33lxxclpgl6txpm
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    km_estimates_megli_mono
    Status:
    Status: Succeeded
    Job identifier:
    blxyeeqhtbo3dmtb
  • Action:
    km_estimates_metfin
    Status:
    Status: Failed
    Job identifier:
    ltl6dxqb5btquvo3
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    km_estimates_metfin_mono
    Status:
    Status: Failed
    Job identifier:
    sa7djxlq24aishyw
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    km_estimates_sglt2_mono
    Status:
    Status: Failed
    Job identifier:
    p3ju6tvuv5cowgjp
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    km_estimates_sulfo_mono
    Status:
    Status: Failed
    Job identifier:
    k73m46ryxjm5kr7r
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    km_estimates_tzd_mono
    Status:
    Status: Failed
    Job identifier:
    i7atuibod6glatmw
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    plot_km_estimates
    Status:
    Status: Failed
    Job identifier:
    s7lelcyx3bt5s54n
    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:
        rds: output/data/data_processed_dm_algo.rds

  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
  
  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

  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_covid19_severe
      --max_fup=1095
      --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_covid19_severe
      --max_fup=1095
      --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_covid19_severe
      --max_fup=1095
      --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_covid19_severe
      --max_fup=1095
      --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_covid19_severe
      --max_fup=1095
      --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_covid19_severe
      --max_fup=1095
      --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_covid19_severe
      --max_fup=1095
      --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_covid19_severe
      --max_fup=1095
      --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_covid19_severe
      --max_fup=1095
      --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_covid19_severe
      --max_fup=1095
      --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_covid19_severe
#      --plot=TRUE
#    needs:
#    - data_process
#    outputs:
#      highly_sensitive:
#        output: output/km_estimates_metfin.feather

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 25:38:28

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

Job information

Status
Failed
Backend
TPP
Workspace
metformin-covid-main
Requested by
Alain Amstutz
Branch
main
Force run dependencies
Yes
Git commit hash
cffc436
Requested actions
  • 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