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Job request: 1523

Organisation:
Bennett Institute
Workspace:
population-csvt-counts
ID:
bp6xbi664dbiho4x
View repo View project.yaml

This page shows the technical details of what happened when the 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 list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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.

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 2020-02-28 by month"
    outputs:
      highly_sensitive:
        measure_data: output/input_measu*.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]
    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:

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

Job information

Status
Failed 
ProjectValidationError: Output path output/input_measu*.csv is not unique
Backend
TPP
Workspace
population-csvt-counts
Requested by
Alex Walker
Branch
CSVT
Force run dependencies
No
Git commit hash
1931ef4
Requested actions
  • generate_cohort_2021
  • calculate_measures
  • draw_timeseries

Code comparison

Compare the code used in this Job Request