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Job request: 26008

Organisation:
Bennett Institute
Workspace:
pharmacy-first-data-development
ID:
2hr4wjss5jxssfja
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Viveck Kingsley 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_measures_pf_codes
    Status:
    Succeeded
    Job identifier:
    jk5hbyivizgdr4vt
  • Action:
    generate_med_status_data_development
    Status:
    Succeeded
    Job identifier:
    wsl5zjkt4dgh65j4
  • Action:
    generate_pf_codes_data_development
    Status:
    Succeeded
    Job identifier:
    zh4yvusl2bysdq5l
  • Action:
    generate_med_status_counts_measures
    Status:
    Succeeded
    Job identifier:
    afeobnzdp5ujdfij
  • Action:
    data_development_med_status_post
    Status:
    Succeeded
    Job identifier:
    qhgpnxsc27unltss
  • Action:
    data_development_med_status_pre
    Status:
    Succeeded
    Job identifier:
    54v4wun2v43weixg
  • Action:
    data_development_med_status_combine
    Status:
    Succeeded
    Job identifier:
    m4y4ean4exp5zpzk
  • Action:
    data_development_pf_code_distinct
    Status:
    Failed
    Job identifier:
    6b4aa2yansog33tr
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    data_development_pf_code_events
    Status:
    Failed
    Job identifier:
    xqkzyltzhw5bmffi
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    data_development_pf_codes_pathways
    Status:
    Failed
    Job identifier:
    trld2tpe5yclxdjw
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    data_development_pf_codes_combine
    Status:
    Failed
    Job identifier:
    23vitonv6hns55qb
    Error:
    dependency_failed: Not starting as dependency failed

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.arrow
    outputs:
      highly_sensitive:
        dataset: output/data_development/pf_codes_data_development.arrow

  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_pre:
     run: r:latest analysis/data_development_med_status_pre_counts.R
     needs: [generate_med_status_data_development]
     outputs:
       moderately_sensitive:
         dataset: output/data_development/med_status_pre_counts.csv
  
  data_development_med_status_post:
     run: r:latest analysis/data_development_med_status_post_counts.R
     needs: [generate_med_status_data_development]
     outputs:
       moderately_sensitive:
         dataset: output/data_development/med_status_post_counts.csv

  data_development_med_status_combine:
     run: r:latest analysis/data_development_med_status_combine.R
     needs: [data_development_med_status_pre, data_development_med_status_post]
     outputs:
       moderately_sensitive:
         dataset: output/data_development/med_status_counts.csv

  data_development_pf_code_distinct:
    run: r:latest analysis/data_development_pf_code_count_distinct.R
    needs: [generate_pf_codes_data_development]
    outputs:
      moderately_sensitive:
        dataset: output/data_development/pf_codes_count_distinct.csv

  data_development_pf_code_events:
    run: r:latest analysis/data_development_pf_code_count_events.R
    needs: [generate_pf_codes_data_development]
    outputs:
      moderately_sensitive:
        dataset: output/data_development/pf_codes_count_events.csv

  data_development_pf_codes_pathways:
    run: r:latest analysis/data_development_pf_code_count_pathways.R
    needs: [generate_pf_codes_data_development]
    outputs:
      moderately_sensitive:
        dataset: output/data_development/pf_codes_count_pathways.csv

  data_development_pf_codes_combine:
    run: r:latest analysis/data_development_pf_code_count_combine.R
    needs: [data_development_pf_code_distinct, data_development_pf_code_events, data_development_pf_codes_pathways]
    outputs:
      moderately_sensitive:
        dataset: output/data_development/pf_codes_count_summary.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

  generate_med_status_counts_measures:
    run: >
      ehrql:v1 generate-measures analysis/measures_med_status_counts.py
      --output output/measures/measures_med_status_counts.csv
    outputs:
      moderately_sensitive:
        measure: output/measures/measures_med_status_counts.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 21:52:04

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
Viveck Kingsley
Branch
main
Force run dependencies
Yes
Git commit hash
66a7eb8
Requested actions
  • generate_pf_codes_data_development
  • generate_med_status_data_development
  • generate_measures_pf_codes
  • data_development_med_status_pre
  • data_development_med_status_post
  • data_development_med_status_combine
  • data_development_pf_code_distinct
  • data_development_pf_code_events
  • data_development_pf_codes_pathways
  • data_development_pf_codes_combine
  • generate_med_status_counts_measures

Code comparison

Compare the code used in this job request