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Job request: 1238

Workspace:
long-covid-emis
ID:
mdwo5d5fjqqqiewi
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Peter Inglesby 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: 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
        code_table2: output/all_long_covid_codes.csv
        practice_summ: output/practice_summ.txt

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:06

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

Job information

Status
Failed 
Job exited with an error code
Backend
EMIS
Workspace
long-covid-emis
Requested by
Peter Inglesby
Branch
EMIS
Force run dependencies
No
Git commit hash
4a19c20
Requested actions
  • generate_cohort
  • count_by_strata