Skip to content

Job request: 10806

Organisation:
ISARIC
Workspace:
hdruk-os-covid-paeds
ID:
kmbnhvsfneagt6bb
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 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: 5000

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/01_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 2022-05-02 by week"
        --output-format csv.gz
        --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 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    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_disorder:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_disorder
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    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_disorder_20*.csv.gz

  generate_gp_finding:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_finding
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    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_finding_20*.csv.gz

  generate_gp_procedure:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_procedure
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    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_procedure_20*.csv.gz

  generate_gp_regime_therapy:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_regime_therapy
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    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_regime_therapy_20*.csv.gz

  generate_gp_observable_entity:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_observable_entity
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    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_observable_entity_20*.csv.gz

  generate_gp_specimen:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_gp_specimen
        --index-date-range "2018-12-31 to 2022-05-02 by week"
        --output-format csv.gz
        --output-dir=output/data_weekly
        --with-end-date-fix
    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_specimen_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 2022-05-02 by week"
        --output-format csv.gz
        --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 2022-05-02 by week"
        --output-format csv.gz
        --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_patient_ids:
    run: r:latest analysis/02_process_patient_ids.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data_id: output/data/data_id.rds

  process_admissions_data:
    run: r:latest analysis/02_process_admissions_data.R
    needs: [generate_admissions, process_patient_ids]
    outputs:
      highly_sensitive:
        data_admissions: output/data/data_admissions.rds
      moderately_sensitive:
        diagnostics_admissions: output/diagnostics/diagnostics_admissions.csv

  process_outpatient_data:
    run: r:latest analysis/02_process_outpatient_data.R
    needs: [generate_outpatient, process_patient_ids]
    outputs:
      highly_sensitive:
        data_outpatient: output/data/data_outpatient.rds
      moderately_sensitive:
        diagnostics_outpatient: output/diagnostics/diagnostics_outpatient.csv

  process_gp_data:
    run: r:latest analysis/02_process_gp_data.R
    needs: [generate_gp_disorder, generate_gp_finding, generate_gp_procedure, generate_gp_regime_therapy,
            generate_gp_specimen, process_patient_ids]
    outputs:
      highly_sensitive:
        data_gp: output/data/data_gp.rds
      moderately_sensitive:
        diagnostics_gp: output/diagnostics/diagnostics_gp.csv

  process_testing_data:
    run: r:latest analysis/02_process_testing_data.R
    needs: [generate_covid_tests_negative, generate_covid_tests_positive, process_patient_ids]
    outputs:
      highly_sensitive:
        data_testing: output/data/data_testing.rds
      moderately_sensitive:
        diagnostics_testing: output/diagnostics/diagnostics_testing.csv
        plots_testing: output/descriptives/data_testing/*.jpeg

  process_patient_data:
    run: r:latest analysis/02_process_patient_data.R
    needs: [generate_study_population, process_admissions_data, process_testing_data]
    outputs:
      highly_sensitive:
        data_patient: output/data/data_patient.rds

  summarise_datasets:
    run: r:latest analysis/03_summary_datasets.R
    needs: [process_patient_data, process_testing_data, process_admissions_data, process_outpatient_data, process_gp_data]
    outputs:
      moderately_sensitive:
        summary_datasets_tables: output/descriptives/summary_datasets/*.csv
        summary_datasets_plots: output/descriptives/summary_datasets/*.jpeg

  calculate_epi_stats:
    run: r:latest analysis/04_epidemiology.R
    needs: [process_patient_data]
    outputs:
      moderately_sensitive:
        summary_datasets_tables: output/descriptives/epidemiology/*.csv
        summary_datasets_plots: output/descriptives/epidemiology/*.jpeg

  healthcare_use_2019_2022:
    run: r:latest analysis/05_healthcare_use_2019_2022.R
    needs: [process_patient_data, process_testing_data, process_admissions_data, process_outpatient_data, process_gp_data]
    outputs:
      moderately_sensitive:
        healthcare_use_2019_2022_tables: output/descriptives/healthcare_use_2019_2022/*.csv

  create_matched_cohort:
    run: r:latest analysis/06_matched_cohort.R
    needs: [process_patient_data, process_testing_data]
    outputs:
      highly_sensitive:
        data_matched: output/data/data_matched.rds
      moderately_sensitive:
        create_matched_cohort_tables: output/descriptives/matched_cohort/*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:24:10

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

Job request

Status
Succeeded
Backend
TPP
Workspace
hdruk-os-covid-paeds
Requested by
James Farrell
Branch
main
Force run dependencies
No
Git commit hash
6c70ddb
Requested actions
  • create_matched_cohort

Code comparison

Compare the code used in this job request