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Job request: 24294

Organisation:
Bennett Institute
Workspace:
pharmacy-first-report
ID:
x2j6nkqpnpoc7bwk
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Milan Wiedemann 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:
    create_tables
    Status:
    Status: Failed
    Job identifier:
    2wvmjlqbfcb4mm5u
    Error:
    nonzero_exit: Job exited with an error

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:

  generate_dataset_definition_tables:
    run: >
      ehrql:v1
       generate-dataset analysis/dataset_definition_tables.py
       --test-data-file analysis/test_dataset_definition_tables.py
       --dummy-data-file dummy_data/pf_tables_dataset.csv
       --output output/population/pf_tables_dataset.csv.gz
    outputs:
      highly_sensitive:
        cohort: output/population/pf_tables_dataset.csv.gz

  create_tables:
    run: r:v2 analysis/create_tables.R
    needs: [generate_dataset_definition_tables]
    outputs:
      moderately_sensitive:
        dataset: output/population/pf_tables.csv

  generate_pf_breakdown_measures:
    run: >
      ehrql:v1 generate-measures analysis/measures_definition_pf_breakdown.py
      --output output/measures/pf_breakdown_measures.csv
    outputs:
      moderately_sensitive:
        measure: output/measures/pf_breakdown_measures.csv

  generate_pf_condition_provider_measures:
    run: >
      ehrql:v1 generate-measures analysis/measures_definition_pf_condition_provider.py
      --output output/measures/pf_condition_provider_measures.csv
    outputs:
      moderately_sensitive:
        measure: output/measures/pf_condition_provider_measures.csv

  generate_pf_medications_measures:
    run: >
      ehrql:v1 generate-measures analysis/measures_definition_pf_medications.py
      --dummy-tables dummy_tables
      --output output/measures/pf_medications_measures.csv
    outputs:
      moderately_sensitive:
        measure: output/measures/pf_medications_measures.csv

  generate_pf_statistics_measures:
    run: >
      ehrql:v1 generate-measures analysis/measures_definition_pf_descriptive_stats.py
      --dummy-tables dummy_tables
      --output output/measures/pf_descriptive_stats_measures.csv
    outputs:
      moderately_sensitive:
        measure: output/measures/pf_descriptive_stats_measures.csv

  generate_pf_med_counts_measures:
    run: >
      ehrql:v1 generate-measures analysis/measures_definition_pf_consultation_med_counts.py
      --dummy-tables dummy_tables
      --output output/measures/consultation_med_counts_measures.csv
    outputs:
      moderately_sensitive:
        measure: output/measures/consultation_med_counts_measures.csv

  tidy_med_measures:
    run: r:latest analysis/tidy_measures_med_counts.R
    needs: [generate_pf_medications_measures, generate_pf_med_counts_measures]
    outputs:
      moderately_sensitive:
        measure_pf_meds: output/measures/pf_medications_measures_tidy.csv 
        measure_consult_meds: output/measures/consultation_med_counts_measures_tidy.csv
  
  # generate_pf_opensafely_report:
  #   run: >
  #     r:v2 -e 'rmarkdown::render(
  #       "reports/pharmacy_first_report.Rmd",
  #       knit_root_dir = "/workspace",
  #       output_dir = "/workspace/output/report"
  #     )'
  #   needs:
  #     - generate_pf_breakdown_measures
  #     - generate_pf_medications_measures
  #     - generate_pf_statistics_measures
  #     - generate_pf_med_counts_measures
  #     - tidy_med_measures
  #   outputs:
  #     moderately_sensitive:
  #       html: output/report/pharmacy_first_report.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:04:44

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

Job request

Status
Failed
Backend
TPP
Workspace
pharmacy-first-report
Requested by
Milan Wiedemann
Branch
main
Force run dependencies
No
Git commit hash
b4f8016
Requested actions
  • create_tables

Code comparison

Compare the code used in this job request