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Job request: 24265

Organisation:: University of Bristol
Workspace:: metformin-covid-main
ID:: frg234rggtw65ymy

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:

data_process

Status:

Status: Succeeded

Job identifier:

ggtr6igurgj4qdqg
Action:

km_estimates_agi_mono

Status:

Status: Succeeded

Job identifier:

xf26ktybylin5fkb
Action:

km_estimates_dpp4_mono

Status:

Status: Succeeded

Job identifier:

ngc7526dya4cbc5u
Action:

km_estimates_glp1_mono

Status:

Status: Succeeded

Job identifier:

xrc7yvkrlqqiy6u2
Action:

km_estimates_insulin_mono

Status:

Status: Succeeded

Job identifier:

gwkdfjrt54a54pew
Action:

km_estimates_megli_mono

Status:

Status: Succeeded

Job identifier:

67t7lkvw2s4y5fr2
Action:

km_estimates_metfin

Status:

Status: Succeeded

Job identifier:

xtswq2flru7ynepx
Action:

km_estimates_metfin_mono

Status:

Status: Succeeded

Job identifier:

pxs65m4hxotyhnf7
Action:

km_estimates_sglt2_mono

Status:

Status: Succeeded

Job identifier:

2jtg7brta5dp3eyr
Action:

km_estimates_sulfo_mono

Status:

Status: Succeeded

Job identifier:

zsqafp3y2e2rgfbj
Action:

km_estimates_tzd_mono

Status:

Status: Succeeded

Job identifier:

2f3q3uz4l2binv5z
Action:

table1

Status:

Status: Succeeded

Job identifier:

pbfbblddgyqw7drb
Action:

plot_km_estimates

Status:

Status: Succeeded

Job identifier:

ioftinphgk42kymr

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:
    run: r:latest analysis/km.R 
      --df_input=output/data/data_plots.feather
      --dir_output=output/metfin
      --origin_date=elig_date_t2dm
      --event_date=exp_date_metfin_anytime
      --censor_date=out_date_severecovid
      --max_fup=365
      --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
      --origin_date=elig_date_t2dm
      --event_date=exp_date_metfin_mono_anytime
      --censor_date=out_date_severecovid
      --max_fup=365
      --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=365
      --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=365
      --plot=FALSE
    needs:
    - data_process
    outputs:
      moderately_sensitive:
        output: output/tzd_mono/*.csv

  #km_estimates_tzd_mono_RA:
  #  run: kaplan-meier-function:v0.0.6 
  #    --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
  #    --plot=F
  #  needs:
  #  - data_process
  #  outputs:
  #    moderately_sensitive:
  #      output: output/tzd_mono/km_estimates_tzd_mono_RA.csv

  km_estimates_sglt2_mono:
    run: r:latest analysis/km.R 
      --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=out_date_severecovid
      --max_fup=365
      --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
      --origin_date=elig_date_t2dm
      --event_date=exp_date_sulfo_mono_anytime
      --censor_date=out_date_severecovid
      --max_fup=365
      --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
      --origin_date=elig_date_t2dm
      --event_date=exp_date_glp1_mono_anytime
      --censor_date=out_date_severecovid
      --max_fup=365
      --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
      --origin_date=elig_date_t2dm
      --event_date=exp_date_megli_mono_anytime
      --censor_date=out_date_severecovid
      --max_fup=365
      --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
      --origin_date=elig_date_t2dm
      --event_date=exp_date_agi_mono_anytime
      --censor_date=out_date_severecovid
      --max_fup=365
      --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
      --origin_date=elig_date_t2dm
      --event_date=exp_date_insulin_mono_anytime
      --censor_date=out_date_severecovid
      --max_fup=365
      --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_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:v0.0.6 
  #    --df_input=output/data/data_processed.arrow
  #    --dir_output=output/treat
  #    --exposure=exp_bin_treat
  #    --origin_date=elig_date_t2dm
  #    --event_date=out_date_severecovid
  #    --censor_date=qa_date_of_death
  #    --max_fup=365
  #    --plot=TRUE
  #  needs:
  #  - data_process
  #  outputs:
  #    moderately_sensitive:
  #      km_estimates: output/treat/*.csv
  #      plot: output/treat/*.png

Timeline

Created: 8 months, 1 week ago 20 Feb 2025 09:01:21 UTC
Started: 8 months, 1 week ago 20 Feb 2025 09:01:40 UTC
Finished: 8 months, 1 week ago 20 Feb 2025 09:14:37 UTC
Runtime: 00:15:49

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

Job request

Status: Succeeded
Backend: TPP
Workspace: metformin-covid-main
Requested by: Alain Amstutz
Branch: main
Force run dependencies: No
Git commit hash: f428ba8
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

table1

Code comparison

Compare the code used in this job request