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Job request: 13905

Organisation:
University of Liverpool
Workspace:
flucats
ID:
6uklsxkjav2gk3x2
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 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.

Jobs

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_study_population_test:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_test --output-format=csv.gz --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/input_test.csv.gz
   
  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 2021-06-01 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/input_2021-01-01.csv.gz
        --output-dir output
    needs: [generate_study_population_2]
    outputs:
      moderately_sensitive:
        dataset_report: output/input_2021-01-01.html
  
  combined_input_files:
    run: python:latest python analysis/combine_input_files.py
    needs: [generate_study_population_1, generate_study_population_2]
    outputs:
      highly_sensitive:
        attrition: output/input_all_py.csv.gz

  column_counts:
    run: python:latest python analysis/test_column_counts.py
    needs: [generate_study_population_test, combined_input_files, generate_study_population_2]
    outputs:
      moderately_sensitive:
        counts: output/column_counts/combine*.csv

  generate_first_outputs:
    run: r:latest analysis/flucats_descriptive_basic.R


    needs: [combined_input_files]
    outputs:
      moderately_sensitive:
        attrition: output/attrition.csv
        histogram_age: output/age_hist.png
        date_plot: output/weekly_template.png
        flucat_tables: output/flucat*.csv
        sex_table: output/sex_table.csv
        region_table: output/region_table.csv

  # check_codes:
  #   run: r:latest analysis/check_codes.R
  #   needs: [generate_study_population_2]
  #   outputs:
  #     moderately_sensitive:
  #       text: output/text.txt

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:13

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

Job information

Status
Succeeded
Backend
EMIS
Workspace
flucats
Requested by
Louis Fisher
Branch
main
Force run dependencies
No
Git commit hash
e19a408
Requested actions
  • generate_first_outputs

Code comparison

Compare the code used in this Job Request