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Job request: 12046

Organisation:
University of Liverpool
Workspace:
flucats_test
ID:
ddink2zups2yybhx
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Louis Fisher 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

  • Action:
    test_action
    Status:
    Status: Succeeded
    Job identifier:
    fafo6vw44fsejdvz

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  test_action:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-03-01 to 2021-03-01 by month" --output-format=csv.gz --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/input_2021-03-01.csv.gz

  test_analysis:
    run: python:latest python analysis/test_analysis.py
    needs: [test_action]
    outputs:
      moderately_sensitive:
        counts: output/test_output_2.csv

  

  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-03-01 to 2020-07-01 by month" --output-format=csv.gz --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv.gz

  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-08-01 to 2021-01-01 by month" --output-format=csv.gz --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/input*.csv.gz

  # Gives until 2021-07-01. Only have ONS deaths until 2021-07-01
  generate_study_population_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-02-01 to 2022-06-01 by month" --output-format=csv.gz --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/inpu*.csv.gz
  

  generate_study_population_end:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_end --output-format=csv.gz --with-end-date-fix 
    outputs:
      highly_sensitive:
        cohort: output/input_end.csv.gz

  join_cohorts_monthly:
    run: >
      cohort-joiner:v0.0.44
        --lhs output/input_20*.csv.gz
        --rhs output/input_end.csv.gz
        --output-dir output/joined
    needs: [
      generate_study_population_1,
      generate_study_population_2,
      generate_study_population_3,
      generate_study_population_end]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_20*.csv.gz


  generate_dataset_report:
    run: >
      dataset-report:v0.0.24
        --input-files output/joined/input_2021-06-01.csv.gz
        --output-dir output/joined
    needs: [join_cohorts_monthly]
    outputs:
      moderately_sensitive:
        dataset_report: output/joined/input_2021-06-01.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:49:37

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

Job information

Status
Succeeded
Backend
EMIS
Workspace
flucats_test
Requested by
Louis Fisher
Branch
study-def-performance
Force run dependencies
No
Git commit hash
b28be49
Requested actions
  • test_action

Code comparison

Compare the code used in this Job Request