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Job request: 26863

Organisation:
University of Oxford
Workspace:
pad-inequalities
ID:
anur3gb6wgubk3cf
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Billy Zhong 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:
    generate_trends_2017
    Status:
    Succeeded
    Job identifier:
    zyprizqd2slq4j63
  • Action:
    generate_covid_2020
    Status:
    Failed
    Job identifier:
    7hrqsck5hikhfiba
    Status message:
    nonzero_exit: Job exited with an error: You do not have the required permissions for the ehrQL you are trying to run
  • Action:
    generate_incident
    Status:
    Failed
    Job identifier:
    ahggjgazbtu3j5xm
    Status message:
    nonzero_exit: Job exited with an error: You do not have the required permissions for the ehrQL you are trying to run
  • Action:
    generate_procedure
    Status:
    Failed
    Job identifier:
    4wpjb6bezn4vcizl
    Status message:
    nonzero_exit: Job exited with an error: You do not have the required permissions for the ehrQL you are trying to run
  • Action:
    prepare
    Status:
    Failed
    Job identifier:
    nedhgxke2s6dqtga
    Status message:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '5.0'
actions:
  generate_incident:
    run: ehrql:v1 generate-dataset analysis/dataset_definition.py --output output/raw/incident.csv.gz
      -- --cohort incident
    needs: []
    outputs:
      highly_sensitive:
        dataset: output/raw/incident.csv.gz
  generate_procedure:
    run: ehrql:v1 generate-dataset analysis/dataset_definition.py --output output/raw/procedure.csv.gz
      -- --cohort procedure
    needs: []
    outputs:
      highly_sensitive:
        dataset: output/raw/procedure.csv.gz
  generate_trends_2017:
    run: ehrql:v1 generate-measures analysis/measures_definition.py --output output/raw/trends_2017.csv
      -- --year 2017 --mode trends
    needs: []
    outputs:
      highly_sensitive:
        measures: output/raw/trends_2017.csv
  generate_trends_2018:
    run: ehrql:v1 generate-measures analysis/measures_definition.py --output output/raw/trends_2018.csv
      -- --year 2018 --mode trends
    needs: []
    outputs:
      highly_sensitive:
        measures: output/raw/trends_2018.csv
  generate_trends_2019:
    run: ehrql:v1 generate-measures analysis/measures_definition.py --output output/raw/trends_2019.csv
      -- --year 2019 --mode trends
    needs: []
    outputs:
      highly_sensitive:
        measures: output/raw/trends_2019.csv
  generate_trends_2020:
    run: ehrql:v1 generate-measures analysis/measures_definition.py --output output/raw/trends_2020.csv
      -- --year 2020 --mode trends
    needs: []
    outputs:
      highly_sensitive:
        measures: output/raw/trends_2020.csv
  generate_trends_2021:
    run: ehrql:v1 generate-measures analysis/measures_definition.py --output output/raw/trends_2021.csv
      -- --year 2021 --mode trends
    needs: []
    outputs:
      highly_sensitive:
        measures: output/raw/trends_2021.csv
  generate_trends_2022:
    run: ehrql:v1 generate-measures analysis/measures_definition.py --output output/raw/trends_2022.csv
      -- --year 2022 --mode trends
    needs: []
    outputs:
      highly_sensitive:
        measures: output/raw/trends_2022.csv
  generate_trends_2023:
    run: ehrql:v1 generate-measures analysis/measures_definition.py --output output/raw/trends_2023.csv
      -- --year 2023 --mode trends
    needs: []
    outputs:
      highly_sensitive:
        measures: output/raw/trends_2023.csv
  generate_trends_2024:
    run: ehrql:v1 generate-measures analysis/measures_definition.py --output output/raw/trends_2024.csv
      -- --year 2024 --mode trends
    needs: []
    outputs:
      highly_sensitive:
        measures: output/raw/trends_2024.csv
  generate_trends_2025:
    run: ehrql:v1 generate-measures analysis/measures_definition.py --output output/raw/trends_2025.csv
      -- --year 2025 --mode trends
    needs: []
    outputs:
      highly_sensitive:
        measures: output/raw/trends_2025.csv
  generate_covid_2020:
    run: ehrql:v1 generate-measures analysis/measures_definition.py --output output/raw/covid_2020.csv
      -- --year 2020 --mode covid
    needs: []
    outputs:
      highly_sensitive:
        measures: output/raw/covid_2020.csv
  generate_covid_2021:
    run: ehrql:v1 generate-measures analysis/measures_definition.py --output output/raw/covid_2021.csv
      -- --year 2021 --mode covid
    needs: []
    outputs:
      highly_sensitive:
        measures: output/raw/covid_2021.csv
  generate_covid_2022:
    run: ehrql:v1 generate-measures analysis/measures_definition.py --output output/raw/covid_2022.csv
      -- --year 2022 --mode covid
    needs: []
    outputs:
      highly_sensitive:
        measures: output/raw/covid_2022.csv
  generate_covid_2023:
    run: ehrql:v1 generate-measures analysis/measures_definition.py --output output/raw/covid_2023.csv
      -- --year 2023 --mode covid
    needs: []
    outputs:
      highly_sensitive:
        measures: output/raw/covid_2023.csv
  generate_covid_2024:
    run: ehrql:v1 generate-measures analysis/measures_definition.py --output output/raw/covid_2024.csv
      -- --year 2024 --mode covid
    needs: []
    outputs:
      highly_sensitive:
        measures: output/raw/covid_2024.csv
  generate_covid_2025:
    run: ehrql:v1 generate-measures analysis/measures_definition.py --output output/raw/covid_2025.csv
      -- --year 2025 --mode covid
    needs: []
    outputs:
      highly_sensitive:
        measures: output/raw/covid_2025.csv
  prepare:
    run: r:v2 analysis/prepare.R
    needs:
    - generate_incident
    - generate_procedure
    outputs:
      highly_sensitive:
        cohorts: output/internal/*.rds
        flow: output/internal/flow.csv
        quality: output/internal/quality.csv
  describe:
    run: r:v2 analysis/descriptive.R
    needs:
    - prepare
    outputs:
      highly_sensitive:
        counts: output/internal/counts.csv
  analyse_outcomes:
    run: r:v2 analysis/outcomes.R
    needs:
    - prepare
    outputs:
      highly_sensitive:
        curves: output/internal/curves.csv
        estimates: output/internal/survival_estimates.csv
        diagnostics: output/internal/survival_diagnostics.csv
  check_trends:
    run: r:v2 analysis/check_measures.R trends
    needs:
    - generate_trends_2017
    - generate_trends_2018
    - generate_trends_2019
    - generate_trends_2020
    - generate_trends_2021
    - generate_trends_2022
    - generate_trends_2023
    - generate_trends_2024
    - generate_trends_2025
    outputs:
      highly_sensitive:
        checked: output/internal/trends_checked.rds
        quality: output/internal/trends_quality.csv
  analyse_trends:
    run: r:v2 analysis/trends.R
    needs:
    - check_trends
    outputs:
      highly_sensitive:
        rates: output/internal/rates.csv
        estimates: output/internal/its_estimates.csv
        diagnostics: output/internal/its_diagnostics.csv
  check_covid:
    run: r:v2 analysis/check_measures.R covid
    needs:
    - generate_covid_2020
    - generate_covid_2021
    - generate_covid_2022
    - generate_covid_2023
    - generate_covid_2024
    - generate_covid_2025
    outputs:
      highly_sensitive:
        checked: output/internal/covid_checked.rds
        quality: output/internal/covid_quality.csv
  analyse_covid:
    run: r:v2 analysis/covid.R
    needs:
    - check_covid
    outputs:
      highly_sensitive:
        rates: output/internal/covid_rates.csv
        estimates: output/internal/covid_estimates.csv
        diagnostics: output/internal/covid_diagnostics.csv
  prepare_release:
    run: r:v2 analysis/release.R
    needs:
    - describe
    - analyse_outcomes
    - analyse_trends
    - analyse_covid
    outputs:
      moderately_sensitive:
        population: output/release/01_population_pathways*.csv
        rates: output/release/02_rates*.csv
        curves: output/release/03_outcome_curves*.csv
        models: output/release/04_models_diagnostics*.csv
      highly_sensitive:
        manifest: output/internal/release_manifest.csv

Job statistics

Status Count Percentage
Pending 0 0%
Running 0 0%
Succeeded 1 20%
Failed 4 80%

5 / 5 (100%) complete

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:48:43

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

Job request

Status
Failed
Backend
TPP
Workspace
pad-inequalities
Requested by
Billy Zhong
Branch
main
Force run dependencies
No
Git commit hash
7921de7
Requested actions
  • generate_trends_2017
  • generate_covid_2020
  • prepare

Code comparison

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