Skip to content

Job request: 11412

Organisation:
Bennett Institute
Workspace:
date_window_test
ID:
zywiy2o6docy6g56
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 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:

  generate_study_population_before_fix_mon:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --output-dir=output/before_fix
      --index-date-range "2020-02-03"
    outputs:
      highly_sensitive:
        cohort: output/before_fix/input_2020-02-03.csv

  generate_study_population_after_fix_mon:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --output-dir=output/after_fix
      --index-date-range "2020-02-03"
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/after_fix/input_2020-02-03.csv

  generate_study_population_before_fix_tues:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --output-dir=output/before_fix
      --index-date-range "2020-02-04"
    outputs:
      highly_sensitive:
        cohort: output/before_fix/input_2020-02-04.csv

  generate_study_population_after_fix_tues:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --output-dir=output/after_fix
      --index-date-range "2020-02-04"
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/after_fix/input_2020-02-04.csv

  generate_study_population_before_fix_weds:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --output-dir=output/before_fix
      --index-date-range "2020-02-05"
    outputs:
      highly_sensitive:
        cohort: output/before_fix/input_2020-02-05.csv

  generate_study_population_after_fix_weds:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --output-dir=output/after_fix
      --index-date-range "2020-02-05"
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/after_fix/input_2020-02-05.csv

  generate_study_population_before_fix_thurs:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --output-dir=output/before_fix
      --index-date-range "2020-02-06"
    outputs:
      highly_sensitive:
        cohort: output/before_fix/input_2020-02-06.csv

  generate_study_population_after_fix_thurs:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --output-dir=output/after_fix
      --index-date-range "2020-02-06"
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/after_fix/input_2020-02-06.csv

  generate_study_population_before_fix_fri:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --output-dir=output/before_fix
      --index-date-range "2020-02-07"
    outputs:
      highly_sensitive:
        cohort: output/before_fix/input_2020-02-07.csv

  generate_study_population_after_fix_fri:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --output-dir=output/after_fix
      --index-date-range "2020-02-07"
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/after_fix/input_2020-02-07.csv

  generate_study_population_before_fix_sat:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --output-dir=output/before_fix
      --index-date-range "2020-02-08"
    outputs:
      highly_sensitive:
        cohort: output/before_fix/input_2020-02-08.csv

  generate_study_population_after_fix_sat:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --output-dir=output/after_fix
      --index-date-range "2020-02-08"
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/after_fix/input_2020-02-08.csv

  generate_study_population_before_fix_sun:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --output-dir=output/before_fix
      --index-date-range "2020-02-09"
    outputs:
      highly_sensitive:
        cohort: output/before_fix/input_2020-02-09.csv

  generate_study_population_after_fix_sun:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --output-dir=output/after_fix
      --index-date-range "2020-02-09"
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/after_fix/input_2020-02-09.csv

  counts_script:
    run: python:latest python analysis/counts.py
    needs: [generate_study_population_before_fix_mon, generate_study_population_after_fix_mon, generate_study_population_before_fix_tues, generate_study_population_after_fix_tues, generate_study_population_before_fix_weds, generate_study_population_after_fix_weds, generate_study_population_before_fix_thurs, generate_study_population_after_fix_thurs, generate_study_population_before_fix_fri, generate_study_population_after_fix_fri, generate_study_population_before_fix_sat, generate_study_population_after_fix_sat, generate_study_population_before_fix_sun, generate_study_population_after_fix_sun]
    outputs:
      moderately_sensitive:
        counts_3: output/counts_2020-02-03.csv
        counts_4: output/counts_2020-02-04.csv
        counts_5: output/counts_2020-02-05.csv
        counts_6: output/counts_2020-02-06.csv
        counts_7: output/counts_2020-02-07.csv
        counts_8: output/counts_2020-02-08.csv
        counts_9: output/counts_2020-02-09.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 24:31:57

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

Job request

Status
Succeeded
Backend
TPP
Workspace
date_window_test
Requested by
Alex Walker
Branch
main
Force run dependencies
Yes
Git commit hash
8d18531
Requested actions
  • run_all

Code comparison

Compare the code used in this job request