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Job request: 23698

Organisation:
Bennett Institute
Workspace:
pharmacy-first-data-development
ID:
mhitsdktls3gr4en
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:
    data_development_pf_codes
    Status:
    Status: Failed
    Job identifier:
    tz4eeaubdf4johih
    Error:
    nonzero_exit: Job exited with an error: Job ran out of memory (limit was 128.00GB)

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_pf_codes_data_development:
    run: >
      ehrql:v1 generate-dataset analysis/dataset_definition_pf_data_development.py
        --test-data-file analysis/test_dataset_definition_pf_data_development.py
        --output output/data_development/pf_codes_data_development.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/data_development/pf_codes_data_development.csv.gz

  generate_med_status_data_development:
    run: >
      ehrql:v1 generate-dataset analysis/dataset_definition_med_status_data_development.py
        --output output/data_development/med_status_data_development.arrow
    outputs:
      highly_sensitive:
        dataset: output/data_development/med_status_data_development.arrow

  generate_measures_pf_codes:
    run: > 
      ehrql:v1 generate-measures analysis/measures_definition_clinical_codes.py
      --output output/clinical_codes/code_counts_measures.csv
    outputs:
      moderately_sensitive:
        measure: output/clinical_codes/code_counts_measures.csv

  data_development_med_status:
     run: r:latest analysis/data_development_med_status_counts.R
     needs: [generate_med_status_data_development]
     outputs:
       moderately_sensitive:
         dataset: output/data_development/med_status_counts.csv

  data_development_pf_codes:
    run: r:latest analysis/data_development_pf_code_counts.R
    needs: [generate_pf_codes_data_development]
    outputs:
      moderately_sensitive:
        dataset: output/data_development/pf_codes_counts.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:35:00

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

Job request

Status
Failed
Backend
TPP
Workspace
pharmacy-first-data-development
Requested by
Milan Wiedemann
Branch
main
Force run dependencies
No
Git commit hash
6e9254e
Requested actions
  • data_development_pf_codes

Code comparison

Compare the code used in this job request