Job request: 1204

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 Long COVID-19 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
xdahwqnjjr3sqqq5 succeeded generate_cohort
7oshsmzmlwftxkju succeeded count_by_strata

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 500

actions:

  generate_measure_cohort_1:
    # week 45 2020 to 20 2020 inclusive
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measure --index-date-range "2020-11-02 to 2021-01-03 by week"
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv

  generate_measure_cohort_2:
    # week 51 2020 to 03 2021 inclusive
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measure --index-date-range "2021-01-04 to 2021-03-07 by week"
    outputs:
      highly_sensitive:
        cohort: output/input*.csv

  calculate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_measure
    needs: [generate_measure_cohort_1, generate_measure_cohort_2]
    outputs:
      highly_sensitive:
        measure: output/measure_*_rate.csv

  standardise_and_plot:
    run: python:latest python analysis/time_series_plots.py
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        tables: output/*_rate.csv
        graph: output/time_series_plot.svg

  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
        code_table: output/first_long_covid_code.csv
        practice_summ: output/practice_summ.txt
        practice_histogram: output/practice_coding_histogram.svg

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 01:40:25

Config

  • Backend:
    TPP
  • Workspace:
    long-covid-descriptive
  • Branch:
    main
  • Creator:
    alexwalkercebm
  • Force run dependencies:
    False
  • Git Commit Hash:
    586fc50
  • Requested actions:
    • generate_cohort
    • count_by_strata