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Job request: 24071

Organisation:
University of Bristol
Workspace:
metformin-covid-main
ID:
4wgp4vsvfisehkfu
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

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: kaplan-meier-function:v0.0.2 
      --df_input=output/data/data_plots.feather
      --dir_output=output/km_estimates_metfin.feather
      --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: 08:23:22

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
6231018
Requested actions
  • study_dates
  • generate_dataset_dm_algo
  • data_process_dm_algo
  • generate_dataset
  • data_process
  • km_estimates_metfin

Code comparison

Compare the code used in this job request