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Job request: 8278

Organisation:
Bennett Institute
Workspace:
antidepressant-prescribing-lda
ID:
2eqzfjlgrc5zvc5g
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Christine Cunningham 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_ethnicity
    Status:
    Status: Succeeded
    Job identifier:
    bj6a676ohldtnvul
  • Action:
    generate_study_population
    Status:
    Status: Failed
    Job identifier:
    b3t7pafsey537xam
    Error:
    nonzero_exit: Job exited with error code 255
  • Action:
    generate_table1
    Status:
    Status: Failed
    Job identifier:
    qxrvea3ulmgrcqlq
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_measures
    Status:
    Status: Failed
    Job identifier:
    rhajekh3k6hnj6aa
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_deciles_charts
    Status:
    Status: Failed
    Job identifier:
    mrbxq4jrodezckvg
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_groups
    Status:
    Status: Failed
    Job identifier:
    x3py3wjthigjuzeh
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_report
    Status:
    Status: Failed
    Job identifier:
    atk2vppuqamcl3ia
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_percentage_groups
    Status:
    Status: Failed
    Job identifier:
    d4b33gdww6xl52vq
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    join_cohorts
    Status:
    Status: Failed
    Job identifier:
    pje7lml6ogkv47sl
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  ####################
  # Cohort Generation
  ####################

  # Since this runs on everyone, we can reuse for both studies 
  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv.gz

  # Generate depression register, dep003, depression and prescription variables by month
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2022-01-01 by month" --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv.gz

  ####################
  # Join ethnicity to all generated input files
  # Efficiency fix https://github.com/opensafely/research-template
  # BUT BEWARE STALE DATA
  ###################

  join_cohorts:
    run: >
      cohort-joiner:v0.0.18
        --lhs output/input_*.csv.gz
        --rhs output/input_ethnicity.csv.gz
        --output-dir output/joined
    needs: [generate_study_population_ethnicity, generate_study_population]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_*.csv.gz

  ####################
  # Measures 
  ####################

  # Output the summary values by date
  generate_measures:
      run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/joined
      needs: [join_cohorts]
      outputs:
        moderately_sensitive:
          # Only output the single summary file
          measure_csv: output/joined/measure_*_rate.csv

  #############################
  # Plotting
  #############################
  generate_deciles_charts:
    run: >
            deciles-charts:v0.0.15
            --input-files output/joined/measure_*_practice_rate.csv
            --output-dir output/joined
    config:
      show_outer_percentiles: false
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        cohort: output/joined/deciles_*_*.*

  generate_groups:
    run: >
            python:latest python analysis/group_charts.py
            --input-files output/joined/measure_*.csv
            --output-dir output/joined
            --date-lines "2019-03-31" "2020-03-31" "2021-03-31"
            --scale "rate"
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        cohort: output/joined/group_chart_*.png

  # TODO: overwriting plots for small subset the require percentage
  generate_percentage_groups:
    run: >
            python:latest python analysis/group_charts.py
            --input-files output/joined/measure_dep003*.csv
            --output-dir output/joined
            --date-lines "2019-03-31" "2020-03-31" "2021-03-31"
            --scale "percentage"
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        cohort: output/joined/group_chart_dep003*.png


  generate_table1:
    run: >
            python:latest python analysis/table1.py
            --input-dir output/joined
            --output-dir output/joined
            --measure-attribute "antidepressant_any"
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        cohort: output/joined/table1.csv

  #############################
  # Display
  #############################
  generate_report:
    run: >
            python:latest python analysis/report.py
            --input-dir output/joined
            --output-dir output/joined
            --resource-dir analysis/resources
    needs: [generate_deciles_charts, generate_groups, generate_percentage_groups]
    outputs:
      moderately_sensitive:
        cohort: output/joined/report.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:17:15

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

Job request

Status
Failed
Backend
TPP
Workspace
antidepressant-prescribing-lda
Requested by
Christine Cunningham
Branch
main
Force run dependencies
Yes
Git commit hash
e82a628
Requested actions
  • run_all

Code comparison

Compare the code used in this job request