Skip to content

Job request: 3218

Organisation:
Bennett Institute
Workspace:
cohortextractor-v2-testing-long-covid
ID:
32quqg3umwlrsra5
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Dave Evans 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 2000

actions:

  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_cohort
    outputs:
      highly_sensitive:
        cohort: output/input_cohort.csv

  count_by_strata:
    run: python:latest python analysis/all_time_counts.py
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        table: output/counts_table.csv
        practice_distribution: output/practice_distribution.csv
        per_week: output/code_use_per_week_long_covid.csv
        per_week_pvf: output/code_use_per_week_post_viral_fatigue.csv
        code_table: output/all_long_covid_codes.csv
        practice_summ: output/practice_summ.txt

  # # to be run locally
  generate_report_notebook:
      run: jupyter:latest jupyter nbconvert /workspace/analysis/long_covid_coding_report.ipynb --execute --to html --output-dir=/workspace/released_outputs --ExecutePreprocessor.timeout=86400 --no-input
      outputs:
        moderately_sensitive:
          notebook: released_outputs/long_covid_coding_report.html

  # Uses V1 with ethnicity codes instead of categories, run locally to generate a
  # dummy data file for V2
  generate_cohort_v1_for_v2_comparison:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_cohort_v1_with_ethnicity_codes
    outputs:
      highly_sensitive:
        cohort: output/v2/input_cohort_v1_with_ethnicity_codes.csv

  # Cohort Extractor V2
  generate_cohort_v2:
    run: cohortextractor-v2:latest --cohort-definition analysis/study_definition_cohort_v2.py --output output/v2/input_cohort.csv --dummy-data-file analysis/dummy_data.csv
    outputs:
      highly_sensitive:
        cohort: output/v2/input_cohort.csv

  count_by_strata_v2:
    run: python:latest python analysis/all_time_counts_v2.py
    needs: [generate_cohort_v2]
    outputs:
      moderately_sensitive:
        table: output/v2/counts_table.csv
        practice_distribution: output/v2/practice_distribution.csv
        per_week: output/v2/code_use_per_week_long_covid.csv
        per_week_pvf: output/v2/code_use_per_week_post_viral_fatigue.csv
        code_table: output/v2/all_long_covid_codes.csv
        practice_summ: output/v2/practice_summ.txt

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:07:30

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

Job request

Status
Succeeded
Backend
TPP
Workspace
cohortextractor-v2-testing-long-covid
Requested by
Dave Evans
Branch
simplified-for-ce2
Force run dependencies
No
Git commit hash
c9260c7
Requested actions
  • generate_cohort_v2

Code comparison

Compare the code used in this job request