Job request: 1525

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Alex Walker requested one or more actions to be run against real patient data in the CSVT Population Counts 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

ID Status Action
h57yeaj34bwvfawc succeeded generate_cohort_2020
53nqwg4tdzxsjy2u succeeded generate_cohort_2021
ndf4t654jmtkxxwd succeeded calculate_measures
zp6db3kfilbuaon7 succeeded draw_timeseries

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_cohort_2017:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2017-01-01 to 2017-12-31 by month"
    outputs:
      highly_sensitive:
        measure_data: output/input_measures*.csv

  generate_cohort_2018:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2018-01-01 to 2018-12-31 by month"
    outputs:
      highly_sensitive:
        measure_data: output/input_measure*.csv

  generate_cohort_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2019-01-01 to 2019-12-31 by month"
    outputs:
      highly_sensitive:
        measure_data: output/input_measur*.csv

  generate_cohort_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2020-01-01 to 2020-12-31 by month"
    outputs:
      highly_sensitive:
        measure_data: output/input_measu*.csv

  generate_cohort_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2021-01-01 to 2021-02-28 by month"
    outputs:
      highly_sensitive:
        measure_data: output/input_meas*.csv

  calculate_measures:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_measures
    needs: [generate_cohort_2017, generate_cohort_2018, generate_cohort_2019, generate_cohort_2020, generate_cohort_2021]
    outputs:
      moderately_sensitive:
        measure: output/measure_*_rate.csv

  draw_timeseries:
    run: python:latest python analysis/time_series_plots.py
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        graph: output/event_count_time_series.svg
        tables: output/table_*.csv

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 00:59:38

Config

  • Backend:
    TPP
  • Workspace:
    population-csvt-counts
  • Branch:
    CSVT
  • Creator:
    alexwalkercebm
  • Force run dependencies:
    False
  • Git Commit Hash:
    acb37fa
  • Requested actions:
    • generate_cohort_2020
    • generate_cohort_2021
    • calculate_measures
    • draw_timeseries