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Job request: 10315

Organisation:
Bennett Institute
Workspace:
long-covid-tpp-imd
ID:
6r6u2akiiznn3tsv
View repo View project.yaml

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

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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.

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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:19:36

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

Job information

Status
Succeeded
Backend
TPP
Workspace
long-covid-tpp-imd
Requested by
Will Hulme
Branch
imd
Force run dependencies
No
Git commit hash
73cbe96
Requested actions
  • generate_cohort
  • count_by_strata
  • generate_report_notebook

Code comparison

Compare the code used in this Job Request