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Job request: 8894

Organisation:
ISARIC
Workspace:
hdruk-os-covid-paeds
ID:
wbda556wsqx2ffbd
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

  • Action:
    process_patient_ids
    Status:
    Status: Succeeded
    Job identifier:
    weegnn3mhqstwnqf
  • Action:
    process_testing_data
    Status:
    Status: Failed
    Job identifier:
    brinny6drokizjpf
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    process_gp_data
    Status:
    Status: Failed
    Job identifier:
    fysxk6l3hnvhe4nj
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    process_outpatient_data
    Status:
    Status: Failed
    Job identifier:
    6hokyyvekwnulsdv
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    summary_datasets
    Status:
    Status: Failed
    Job identifier:
    nza4hgdaskgk5lb4
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    process_admissions_data
    Status:
    Status: Failed
    Job identifier:
    k62brf6332zb4rza
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    process_patient_data
    Status:
    Status: Failed
    Job identifier:
    6eja2ofdrct4rc6x
    Error:
    cancelled_by_user: Cancelled by user

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/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
    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 2022-05-02 by week"
        --output-format csv.gz
        --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 2022-05-02 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
        plots_admissions: output/descriptives/data_admissions/*.jpeg

  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
        plots_outpatient: output/descriptives/data_outpatient/*.jpeg

  process_gp_data:
    run: r:latest analysis/02_process_gp_data.R
    needs: [generate_gp, process_patient_ids]
    outputs:
      highly_sensitive:
        data_gp: output/data/data_gp.rds
      moderately_sensitive:
        diagnostics_gp: output/diagnostics/diagnostics_gp.csv
        plots_gp: output/descriptives/data_gp/*.jpeg

  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

  summary_datasets:
    run: r:latest -e 'rmarkdown::render("analysis/04_summary_datasets.Rmd", output_dir = "output/descriptives")'
    needs: [generate_covid_tests_negative, generate_covid_tests_positive, process_patient_ids]
    outputs:
      moderately_sensitive:
        summary_datasets_html: output/descriptives/04_summary_datasets.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:09:08

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

Job information

Status
Failed
Backend
TPP
Workspace
hdruk-os-covid-paeds
Requested by
James Farrell
Branch
main
Force run dependencies
No
Git commit hash
ef0094d
Requested actions
  • process_patient_ids
  • process_admissions_data
  • process_outpatient_data
  • process_gp_data
  • process_testing_data
  • process_patient_data
  • summary_datasets

Code comparison

Compare the code used in this Job Request