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Job request: 15716

Organisation:
Bennett Institute
Workspace:
opensafely-internal-interactive
ID:
llrbsih3jpri5hgs
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher George Hickman 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
    Status:
    Status: Failed
    Job identifier:
    sanw24p4ob3upltr
    Error:
    nonzero_exit: Job exited with an error: Something went wrong with the database, please contact tech support
  • Action:
    create_notebook
    Status:
    Status: Succeeded
    Job identifier:
    swtkglapkmkyyps7
  • Action:
    generate_study_population_ethnicity
    Status:
    Status: Failed
    Job identifier:
    rys2ppst6qazsgjr
    Error:
    internal_error: Internal error: this usually means a platform issue rather than a problem for users to fix. The tech team are automatically notified of these errors and will be investigating.
  • Action:
    generate_measures
    Status:
    Status: Failed
    Job identifier:
    6ctwvvmu3dauampl
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    event_counts
    Status:
    Status: Failed
    Job identifier:
    ixiciav4tlavzjhi
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    join_cohorts
    Status:
    Status: Failed
    Job identifier:
    rscmieqjxmsx2y6f
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    top_5_table
    Status:
    Status: Failed
    Job identifier:
    jzlegf7fjbvyipbk
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_notebook
    Status:
    Status: Failed
    Job identifier:
    xfdprtunnlpwtah2
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    deciles_chart
    Status:
    Status: Failed
    Job identifier:
    ip2lbvn7p5ylorjl
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    plot_measure
    Status:
    Status: Failed
    Job identifier:
    bsk7fddykba2ugji
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_ethnicity 
      --param end_date="2023-02-15"
      --output-dir output/01GSZAAE74D9JCAT24AEHQ9P7K --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GSZAAE74D9JCAT24AEHQ9P7K/input_ethnicity.csv.gz


  generate_study_population:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --param codelist_1_path="codelists/codelist_1.csv"
      --param codelist_1_system="snomed"
      --param codelist_1_type="medication"
      --param codelist_2_path="codelists/codelist_2.csv"
      --param codelist_2_system="snomed"
      --param codelist_2_type="event"
      --param codelist_1_frequency="monthly"
      --param time_value="5"
      --param time_scale="years"
      --param time_event="before"
      --param codelist_2_comparison_date="event_1_date"
      --param operator="AND"
      --param population="all"
      --param breakdowns="age,sex"
      --index-date-range="2019-09-01 to 2023-02-15 by month"
      --output-dir=output/01GSZAAE74D9JCAT24AEHQ9P7K
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/01GSZAAE74D9JCAT24AEHQ9P7K/input_*.csv.gz

  join_cohorts:
    run: >
      cohort-joiner:v0.0.38
        --lhs output/01GSZAAE74D9JCAT24AEHQ9P7K/input_20*.csv.gz
        --rhs output/01GSZAAE74D9JCAT24AEHQ9P7K/input_ethnicity.csv.gz
        --output-dir output/01GSZAAE74D9JCAT24AEHQ9P7K/joined
    needs: [generate_study_population, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/01GSZAAE74D9JCAT24AEHQ9P7K/joined/input_20*.csv.gz

  generate_measures:
    run: >
      python:latest python analysis/measures.py
        --breakdowns="age,sex"
        --input_dir="output/01GSZAAE74D9JCAT24AEHQ9P7K/joined"
        --measure="med_review"

    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        measure: output/01GSZAAE74D9JCAT24AEHQ9P7K/joined/measure*rate.csv
        decile_measure: output/01GSZAAE74D9JCAT24AEHQ9P7K/joined/measure*rate_deciles.csv

  top_5_table:
    run: >
      python:latest python analysis/top_5.py
      --codelist-1-path="codelists/codelist_1.csv"
      --codelist-2-path="codelists/codelist_2.csv"
      --output-dir="output/01GSZAAE74D9JCAT24AEHQ9P7K"
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        tables: output/01GSZAAE74D9JCAT24AEHQ9P7K/joined/top_5*.csv

  deciles_chart:
    run: >
      deciles-charts:v0.0.33
        --input-files output/01GSZAAE74D9JCAT24AEHQ9P7K/joined/measure_practice_rate_deciles.csv
        --output-dir output/01GSZAAE74D9JCAT24AEHQ9P7K/joined
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        deciles_charts: output/01GSZAAE74D9JCAT24AEHQ9P7K/joined/deciles_*.*

  plot_measure:
    run: >
      python:latest python analysis/plot_measures.py
        --breakdowns="age,sex"
        --output-dir output/01GSZAAE74D9JCAT24AEHQ9P7K
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        measure: output/01GSZAAE74D9JCAT24AEHQ9P7K/plot_measure*.png

  event_counts:
    run: >
      python:latest python analysis/event_counts.py --input_dir="output/01GSZAAE74D9JCAT24AEHQ9P7K/joined" --output_dir="output/01GSZAAE74D9JCAT24AEHQ9P7K"
    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        measure: output/01GSZAAE74D9JCAT24AEHQ9P7K/event_counts.json

  create_notebook:
    run: >
      python:latest python analysis/create_notebook.py
      --output-dir "output/01GSZAAE74D9JCAT24AEHQ9P7K"
      --codelist-1-description="None"
      --codelist-2-description="None"
      --codelist-1-link="https://codelists.opensafely.org/codelist/opensafely/asthma-inhaler-salbutamol-medication/2020-04-15"
      --codelist-2-link="https://codelists.opensafely.org/codelist/pincer/ast/v1.8"
      --report-title="Medication Review Report"
      --measure-description="Medication Review"
      --population="all"
      --breakdowns="age,sex"
    outputs:
      moderately_sensitive:
        notebook: output/01GSZAAE74D9JCAT24AEHQ9P7K/report.ipynb

  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/output/01GSZAAE74D9JCAT24AEHQ9P7K/report.ipynb --execute --to html --output-dir=/workspace/output/01GSZAAE74D9JCAT24AEHQ9P7K --ExecutePreprocessor.timeout=86400 --no-input
    needs: [create_notebook, event_counts, deciles_chart, top_5_table, plot_measure]
    outputs:
      moderately_sensitive:
        notebook: output/01GSZAAE74D9JCAT24AEHQ9P7K/report.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:50:56

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

Job request

Status
Failed
Backend
TPP
Workspace
opensafely-internal-interactive
Requested by
George Hickman
Branch
main
Force run dependencies
Yes
Git commit hash
9309344
Requested actions
  • run_all

Code comparison

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