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Job request: 4351

Organisation:
Bennett Institute
Workspace:
sro-smr
ID:
pckouzoxwil6434a
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher 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_study_population_smr
    Status:
    Status: Failed
    Job identifier:
    h5pcwm5glkexb2f6
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_notebook
    Status:
    Status: Failed
    Job identifier:
    3txca5ravf7flwpb
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_plots_smr
    Status:
    Status: Failed
    Job identifier:
    um3tsjav7uanl2f3
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_measures_smr
    Status:
    Status: Failed
    Job identifier:
    v3kf7darvs4mm2bi
    Error:
    cancelled_by_user: Cancelled by user

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  generate_study_population_smr:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-09-01 to 2021-01-01 by month" --output-dir=output/measures
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv

  
  
  generate_measures_smr:
      run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/measures
      needs: [generate_study_population_smr]
      outputs:
        moderately_sensitive:
          measure_csv: output/measures/measure_*.csv

  
  
  generate_plots_smr:
    run: python:latest python analysis/generate_plots_smr.py
    needs: [generate_measures_smr]
    outputs:
      moderately_sensitive:
        figure1: output/figures/population_rates.jpeg
        figure2: output/figures/sex_rates.jpeg
        figure3: output/figures/region_rates.jpeg
        figure4: output/figures/age_rates.jpeg
        figure5: output/figures/care_home_status_rates.jpeg
        figure6: output/figures/falls_rates.jpeg
        figure7: output/figures/hospital_admission_rates.jpeg
        figure8: output/figures/smr_decile_chart.jpeg
        

  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/SMR_Notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_measures_smr]
    outputs:
      moderately_sensitive:
        notebook: output/SMR_Notebook.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:16:21

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

Job request

Status
Failed
Backend
TPP
Workspace
sro-smr
Requested by
Louis Fisher
Branch
master
Force run dependencies
No
Git commit hash
b6abf2a
Requested actions
  • generate_plots_smr
  • generate_notebook

Code comparison

Compare the code used in this job request