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Job request: 12052

Organisation:
University of Liverpool
Workspace:
flucats_test
ID:
a5huss2clqv2rwlr
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher requested one or more actions to be run against real patient data within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

  • Action:
    test_analysis
    Status:
    Status: Succeeded
    Job identifier:
    cnp7daqzcswptl3p

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: 00:00:16

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

Job request

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_analysis

Code comparison

Compare the code used in this job request