Skip to content

Job request: 8170

Organisation:
ISARIC
Workspace:
hdruk-os-covid-paeds
ID:
v42zl5jf7fxki4pj
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

  • Action:
    generate_admissions
    Status:
    Status: Failed
    Job identifier:
    sqq2c4x75hiqyeeu
    Error:
    nonzero_exit: Job exited with error code 5: Something went wrong with the database, please contact tech support

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 "2019-12-30 to 2020-12-28 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:

  • Started:

  • Finished:

  • Runtime: 04:18:19

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

Job request

Status
Failed
Backend
TPP
Workspace
hdruk-os-covid-paeds
Requested by
James Farrell
Branch
main
Force run dependencies
No
Git commit hash
68e8ebb
Requested actions
  • generate_admissions

Code comparison

Compare the code used in this job request