Skip to content

Job request: 1525

Organisation:
Bennett Institute
Workspace:
population-csvt-counts
ID:
xrycmeoxcakla6lm

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 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: 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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:59:38

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

Job information

Status
Succeeded
Backend
TPP
Requested by
Alex Walker
Branch
CSVT
Force run dependencies
No
Git commit hash
acb37fa
Requested actions
  • generate_cohort_2020
  • generate_cohort_2021
  • calculate_measures
  • draw_timeseries

Code comparison

Compare the code used in this Job Request