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Job request: 7363

Organisation:
ISARIC
Workspace:
hdruk-os-covid-paeds
ID:
wz6dmlxhvhnpdf3x
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_contact_counts:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_contact_counts --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_contact_counts.csv.gz

  descriptives_count_data:
    run: r:latest analysis/00_count_data.R
    needs: [generate_contact_counts]
    outputs:
      moderately_sensitive:
        plots: output/descriptive/counts/*.jpeg
        tables: output/descriptive/counts/*.csv

  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_covid_tests_negative:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_tests_negative --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_covid_tests_negative.csv.gz

  generate_covid_tests_negative_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_tests_negative_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_covid_tests_negative_high.csv.gz

  generate_covid_tests_positive:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_tests_positive --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_covid_tests_positive.csv.gz

  generate_covid_tests_positive_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_tests_positive_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_covid_tests_positive_high.csv.gz

  generate_admissions_2018:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2018 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2018.csv.gz

  generate_admissions_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2019 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2019.csv.gz

  generate_admissions_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2020 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2020.csv.gz

  generate_admissions_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2021 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2021.csv.gz

  generate_admissions_2022:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2022 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2022.csv.gz

  generate_admissions_2018_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2018_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2018_high.csv.gz

  generate_admissions_2019_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2019_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2019_high.csv.gz

  generate_admissions_2020_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2020_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2020_high.csv.gz

  generate_admissions_2021_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2021_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2021_high.csv.gz

  generate_admissions_2022_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_admissions_2022_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_admissions_2022_high.csv.gz

  generate_gp_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_gp_2019 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_gp_2019.csv.gz

  generate_gp_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_gp_2020 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_gp_2020.csv.gz

  generate_gp_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_gp_2021 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_gp_2021.csv.gz

  generate_gp_2022:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_gp_2022 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_gp_2022.csv.gz

  generate_gp_2019_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_gp_2019_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_gp_2019_high.csv.gz

  generate_gp_2020_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_gp_2020_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_gp_2020_high.csv.gz

  generate_gp_2021_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_gp_2021_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_gp_2021_high.csv.gz

  generate_gp_2022_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_gp_2022_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_gp_2022_high.csv.gz

  generate_outpatient_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outpatient_2019 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_outpatient_2019.csv.gz

  generate_outpatient_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outpatient_2020 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_outpatient_2020.csv.gz

  generate_outpatient_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outpatient_2021 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_outpatient_2021.csv.gz

  generate_outpatient_2022:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outpatient_2022 --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_outpatient_2022.csv.gz

  generate_outpatient_2019_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outpatient_2019_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_outpatient_2019_high.csv.gz

  generate_outpatient_2020_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outpatient_2020_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_outpatient_2020_high.csv.gz

  generate_outpatient_2021_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outpatient_2021_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_outpatient_2021_high.csv.gz

  generate_outpatient_2022_high:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_outpatient_2022_high --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_outpatient_2022_high.csv.gz

  process_data:
    run: r:latest analysis/01_process_data.R
    needs: [generate_study_population,
            generate_covid_tests_negative, generate_covid_tests_negative_high, generate_covid_tests_positive, generate_covid_tests_positive_high,
            generate_admissions_2018, generate_admissions_2019, generate_admissions_2020, generate_admissions_2021, generate_admissions_2022,
            generate_admissions_2018_high, generate_admissions_2019_high, generate_admissions_2020_high, generate_admissions_2021_high, generate_admissions_2022_high,
            generate_gp_2019, generate_gp_2020, generate_gp_2021, generate_gp_2022,
            generate_gp_2019_high, generate_gp_2020_high, generate_gp_2021_high, generate_gp_2022_high,
            generate_outpatient_2019, generate_outpatient_2020, generate_outpatient_2021, generate_outpatient_2022,
            generate_outpatient_2019_high, generate_outpatient_2020_high, generate_outpatient_2021_high, generate_outpatient_2022_high]
    outputs:
      highly_sensitive:
        data1: output/data/*.rds
      moderately_sensitive:
        diagnostics: output/diagnostics/*.csv
    
  descriptives:
    run: r:latest analysis/02_summary.R
    needs: [process_data]
    outputs:
      moderately_sensitive:
        plots: output/descriptive/plots/*.jpeg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 07:19:11

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
015813f
Requested actions
  • generate_gp_2019_high

Code comparison

Compare the code used in this Job Request