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Job request: 14985

Organisation:
University of Liverpool
Workspace:
flucats
ID:
h5m7k6dxxdelv7es
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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  # this looks for whether each flucats var is ever recorded for each patient as of 2021-01-01
  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
  
  # this looks for whether each flucats var is recorded within a week of template code for each patient as of 2021-01-01
  generate_study_population_long_window:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_long_window --output-format=csv.gz --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/input_long_window.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

  generate_study_population_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-02-01 to 2021-03-01 by month" --output-format=csv.gz --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/inpu*.csv.gz
  
  #Gives until 2021-07-01. Only have ONS deaths until 2021-07-01
  generate_study_population_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-04-01 to 2021-06-01 by month" --output-format=csv.gz --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/inp*.csv.gz
  
  generate_study_population_v2_test:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_v2 --index-date-range "2021-04-01" --output-format=csv.gz --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/in*.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_4,
      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
    needs: [join_cohorts_monthly]
    outputs:
      moderately_sensitive:
        dataset_report: output/input_2021-06-01.html
  
  combined_input_files:
    run: python:latest python analysis/combine_input_files.py
    needs: [join_cohorts_monthly]
    outputs:
      highly_sensitive:
        attrition: output/joined/input_all_py.csv.gz

  column_counts:
    run: python:latest python analysis/test_column_counts.py
    needs: [generate_study_population_v2_test]
    outputs:
      moderately_sensitive:
        counts: output/column_counts/*.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

  compare_short_long_window:
    run: python:latest python analysis/compare_short_long_window.py
    needs: [generate_study_population_2, generate_study_population_long_window]
    outputs:
      moderately_sensitive:
        counts: output/compare_short_long_window.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: 01:02:25

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

Job request

Status
Failed
Backend
EMIS
Workspace
flucats
Requested by
Louis Fisher
Branch
main
Force run dependencies
No
Git commit hash
b195029
Requested actions
  • generate_study_population_v2_test

Code comparison

Compare the code used in this job request