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Job request: 8121

Organisation:
ISARIC
Workspace:
hdruk-os-covid-paeds
ID:
vmgtj4ebri24frqb
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher James Farrell 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:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input.csv.gz

  generate_dummy_data:
    run: r:latest analysis/generate_dummy_data.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        dummy_data_admissions: output/dummy_data/dummy_data_admissions.csv.gz
        dummy_data_outpatient: output/dummy_data/dummy_data_outpatient.csv.gz
        dummy_data_gp: output/dummy_data/dummy_data_gp.csv.gz
        dummy_data_testing_negative: output/dummy_data/dummy_data_testing_negative.csv.gz
        dummy_data_testing_positive: output/dummy_data/dummy_data_testing_positive.csv.gz

  generate_admissions:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_admissions
        --index-date-range "2018-10-01 to 2019-12-30 by week"
        --output-format csv.gz
        --skip-existing 
        --output-dir=output/data_weekly
    dummy_data_file: output/dummy_data/dummy_data_admissions.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_admissions: output/data_weekly/input_admissions_20*.csv.gz

  generate_outpatient:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_outpatient
        --index-date-range "2019-03-11 to 2022-01-31 by week"
        --output-format csv.gz
        --skip-existing 
        --output-dir=output/data_weekly
    dummy_data_file: output/dummy_data/dummy_data_outpatient.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_outpatient: output/data_weekly/input_outpatient_20*.csv.gz

  generate_gp:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp
        --index-date-range "2018-12-31 to 2022-01-31 by week"
        --output-format csv.gz
        --skip-existing 
        --output-dir=output/data_weekly
    dummy_data_file: output/dummy_data/dummy_data_gp.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_gp_contacts: output/data_weekly/input_gp_20*.csv.gz

  generate_covid_tests_negative:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_covid_tests_negative
        --index-date-range "2019-12-30 to 2022-01-31 by week"
        --output-format csv.gz
        --skip-existing 
        --output-dir=output/data_weekly
    dummy_data_file: output/dummy_data/dummy_data_testing_negative.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_negative_tests: output/data_weekly/input_covid_tests_negative_20*.csv.gz

  generate_covid_tests_positive:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_covid_tests_positive
        --index-date-range "2019-12-30 to 2022-01-31 by week"
        --output-format csv.gz
        --skip-existing 
        --output-dir=output/data_weekly
    dummy_data_file: output/dummy_data/dummy_data_testing_positive.csv.gz
    needs: [generate_dummy_data]
    outputs:
      highly_sensitive:
        data_positive_tests: output/data_weekly/input_covid_tests_positive_20*.csv.gz

  process_data:
    run: r:latest analysis/04_summarise_admissions.R
    needs: [generate_study_population, generate_admissions, generate_outpatient,
            generate_gp, generate_covid_tests_negative, generate_covid_tests_positive]
    outputs:
      highly_sensitive:
        datasets: output/datasets/*.rds
      moderately_sensitive:
        plots: output/extract_descriptives/figures/*.jpeg
        tables: output/extract_descriptives/tables/*.csv

Timeline

  • Created:

  • Finished:

  • Runtime:

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

Job information

Status
Succeeded
Backend
TPP
Workspace
hdruk-os-covid-paeds
Requested by
James Farrell
Branch
main
Force run dependencies
No
Git commit hash
b215db0
Requested actions
  • generate_admissions

Code comparison

Compare the code used in this Job Request