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Job request: 22620

Organisation:
PrescQIPP
Workspace:
the_effects_of_covid-19_on_doac_prescribing
ID:
samo3wqnitejfney
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Rachel Seeley 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: 10000

actions:
  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-01-01 to 2019-12-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input*.feather

  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-01-01 to 2022-06-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_*.feather
  
  generate_study_population_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2022-07-01 to 2024-03-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/inp*.feather


  generate_dose:
    run: python:latest python analysis/calculate_dose_scaled_back.py
    needs: [generate_study_population_1, generate_study_population_2, generate_study_population_3]
    outputs:
      highly_sensitive:
        cohort: output/inpu*.feather
  
  filter_population:
    run: python:latest python analysis/filter_population.py
    needs: [generate_dose]
    outputs:
      highly_sensitive:
        cohort: output/filtered/input*.feather
  
  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/filtered
    needs: [filter_population]
    outputs: 
      moderately_sensitive:
        measure_csv: output/filtered/measure_*_rate.csv

  generate_plots:
    run: python:v2 python analysis/report.py
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        plots: output/filtered/*.png
        tables: output/filtered/*.csv

  # to be run localy
  generate_notebook_local:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/report_local.ipynb --execute --to html --template basic --output-dir=/workspace/released_outputs --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        notebook: released_outputs/report_local.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 21:16:34

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

Job request

Status
Succeeded
Backend
TPP
Workspace
the_effects_of_covid-19_on_doac_prescribing
Requested by
Rachel Seeley
Branch
main
Force run dependencies
No
Git commit hash
7ae4c25
Requested actions
  • generate_study_population_3
  • generate_dose
  • filter_population
  • generate_measures
  • generate_plots
  • generate_notebook_local

Code comparison

Compare the code used in this job request