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Job request: 9430

Organisation:
Bennett Institute
Workspace:
opensafely-interactive
ID:
dvjhi5n4auzp3dkn
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher OpenSAFELY Interactive requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  codelist_report_02q97cY91the9QwVmnGkr9:
    run: >
      cohortextractor:latest generate_codelist_report
        --codelist-path=codelist.csv
        --start-date=2019-09-01
        --end-date=2022-06-08
        --output-dir output/02q97cY91the9QwVmnGkr9
    outputs:
      moderately_sensitive:
        table: output/02q97cY91the9QwVmnGkr9/counts_per_*.csv
        list_sizes: output/02q97cY91the9QwVmnGkr9/list_sizes.csv
        patient_count_table: output/02q97cY91the9QwVmnGkr9/patient_count.csv

  measures_02q97cY91the9QwVmnGkr9:
    run: python:latest python analysis/generate_measures.py output/02q97cY91the9QwVmnGkr9
    needs: [codelist_report_02q97cY91the9QwVmnGkr9]
    outputs:
      moderately_sensitive:
        measure: output/02q97cY91the9QwVmnGkr9/measure_counts_per_week_per_practice.csv
        events_count_table: output/02q97cY91the9QwVmnGkr9/event_counts.csv
        practice_count_table: output/02q97cY91the9QwVmnGkr9/practice_count.csv

  top_5_table_02q97cY91the9QwVmnGkr9:
    run: python:latest python analysis/top_codes_table.py output/02q97cY91the9QwVmnGkr9
    needs: [codelist_report_02q97cY91the9QwVmnGkr9]
    outputs:
      moderately_sensitive:
        table: output/02q97cY91the9QwVmnGkr9/top_5_code_table.csv

  deciles_charts_02q97cY91the9QwVmnGkr9:
    run: >
      deciles-charts:v0.0.24
        --input-files output/02q97cY91the9QwVmnGkr9/measure_counts_per_week_per_practice.csv
        --output-dir output/02q97cY91the9QwVmnGkr9
    config:
      show_outer_percentiles: false
      tables:
        output: true
      charts:
        output: true
    needs: [measures_02q97cY91the9QwVmnGkr9]
    outputs:
      moderately_sensitive:
        deciles_charts: output/02q97cY91the9QwVmnGkr9/deciles_*.*

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job information

Status
Failed 
GithubValidationError: Could not find commit on branch 'main': 4b775c44ac5cdf6e5ef077d6e560787cb3bdc354
Backend
TPP
Workspace
opensafely-interactive
Requested by
OpenSAFELY Interactive
Branch
main
Force run dependencies
Yes
Git commit hash
4b775c4
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request