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Job request: 23973

Organisation:
Bennett Institute
Workspace:
wp-work-package-1
ID:
fokknn5woday7wfj
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Jaidip Gill 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_patient_measures
    Status:
    Status: Failed
    Job identifier:
    y4hecg3bjpc3tgrj
    Error:
    nonzero_exit: Job exited with an error: Something went wrong with the database, please contact tech support
  • Action:
    generate_practice_measures
    Status:
    Status: Failed
    Job identifier:
    uuo6en6r4w4sucic
    Error:
    nonzero_exit: Job exited with an error: Something went wrong with the database, please contact tech support

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 1000

actions:
  generate_patient_measures:
    run: ehrql:v1 generate-measures --output output/patient_measures/patient_measures.csv.gz analysis/wp_patient_measures_def.py -- --drop_reason --drop_prescriptions --drop_indicat_prescript
    outputs:
       highly_sensitive:
         dataset: output/patient_measures/patient_measures.csv.gz
  #generate_practice_measures_keep_follow_up:
  #  run: ehrql:v1 generate-measures --output output/practice_measures/practice_measures_keep_follow_up.csv.gz analysis/wp_practice_measures_def.py -- --drop_reason --drop_prescriptions --drop_indicat_prescript
  #  outputs:
  #    highly_sensitive:
  #      dataset: output/practice_measures/practice_measures_keep_follow_up.csv.gz
  #generate_practice_measures_keep_reason:
  #  run: ehrql:v1 generate-measures --output output/practice_measures/practice_measures_keep_reason.csv.gz analysis/wp_practice_measures_def.py -- --drop_follow_up --drop_prescriptions --drop_indicat_prescript
  #  outputs:
  #    highly_sensitive:
  #      dataset: output/practice_measures/practice_measures_keep_reason.csv.gz
  #generate_practice_measures_keep_prescriptions:
  #  run: ehrql:v1 generate-measures --output output/practice_measures/practice_measures_keep_prescriptions.csv.gz analysis/wp_practice_measures_def.py -- --drop_follow_up --drop_reason --drop_indicat_prescript
  #  outputs:
  #    highly_sensitive:
  #      dataset: output/practice_measures/practice_measures_keep_prescriptions.csv.gz
  #generate_practice_measures_keep_indicat_prescript:
  #  run: ehrql:v1 generate-measures --output output/practice_measures/practice_measures_keep_indicat_prescript.csv.gz analysis/wp_practice_measures_def.py -- --drop_follow_up --drop_reason --drop_prescriptions
  #  outputs:
  #    highly_sensitive:
  #      dataset: output/practice_measures/practice_measures_keep_indicat_prescript.csv.gz
  generate_practice_measures:
    run: ehrql:v1 generate-measures --output output/practice_measures/practice_measures.csv.gz analysis/wp_practice_measures_def.py -- --drop_reason --drop_prescriptions --drop_indicat_prescript
    outputs:
      highly_sensitive:
        dataset: output/practice_measures/practice_measures.csv.gz
  # generate_app_measures:
  #   run: ehrql:v1 generate-measures --output output/appointments/app_measures.csv analysis/appointments/app_measures.py
  #   outputs:
  #     moderately_sensitive:
  #       dataset: output/appointments/app_measures.csv
  # generate_app_viz:
  #   run: r:latest analysis/appointments/app_viz.r
  #   needs: [generate_app_measures]
  #   outputs:
  #     moderately_sensitive:
  #       app_figures: output/appointments/*.png
  # generate_app_summary:
  #   run: python:latest analysis/appointments/app_summary.py
  #   needs: [generate_app_measures]
  #   outputs:
  #     moderately_sensitive:
  #       app_table: output/appointments/app_summary.csv
  # generate_pre_processing:
  #   run: python:latest analysis/pre_processing.py 
  #       --output output/practice_measures/processed_practice_measures.csv.gz
  #       --output output/patient_measures/processed_patient_measures.csv.gz
  #       --output output/patient_measures/frequency_table.csv
  #   needs: [generate_patient_measures, generate_practice_measures]
  #   outputs:
  #     highly_sensitive:
  #       practice_measure: output/practice_measures/processed_practice_measures.csv.gz
  #       patient_measure: output/patient_measures/processed_patient_measures.csv.gz
  #     moderately_sensitive:
  #       frequency_table: output/patient_measures/frequency_table.csv
  # generate_measures_viz:
  #   run: r:latest analysis/viz_measures.r
  #   needs: [generate_pre_processing]
  #   outputs:
  #     moderately_sensitive:
  #       app_figures: output/*/*.png
  #       total_measures: output/total_measures/*.csv
  # generate_test_data:
  #   run: ehrql:v1 generate-dataset analysis/dataset.py --output output/patient_measures/test.csv --test-data-file analysis/test_dataset.py
  #   outputs:
  #     highly_sensitive:
  #       dataset: output/patient_measures/test.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:38:47

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

Job request

Status
Failed
Backend
TPP
Workspace
wp-work-package-1
Requested by
Jaidip Gill
Branch
main
Force run dependencies
No
Git commit hash
1c6e345
Requested actions
  • generate_patient_measures
  • generate_practice_measures

Code comparison

Compare the code used in this job request