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Job request: 6937

Organisation:
ISARIC
Workspace:
hdruk-os-covid-paeds
ID:
dt7j4wliqeubbwih
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:
    create_cohorts
    Status:
    Status: Succeeded
    Job identifier:
    ts7jjuxjprl3r5u3
  • Action:
    obj_1_analysis
    Status:
    Status: Failed
    Job identifier:
    dxwmmvldukzj3fjs
    Error:
    nonzero_exit: Job exited with error code 137: likely means it ran out of memory

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_high_admissions:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_high_admissions --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_high_admissions.csv.gz

  generate_high_outpatient:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_high_outpatient --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_high_outpatient.csv.gz

  generate_high_gp:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_high_gp --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_high_gp.csv.gz

  process_data:
    run: r:latest analysis/01_process_data.R
    needs: [generate_study_population, generate_high_admissions, generate_high_outpatient, generate_high_gp]
    outputs:
      highly_sensitive:
        data1: output/data/*.rds
      moderately_sensitive:
        diagnostics: output/diagnostics/*.csv

  descriptives:
    run: r:latest analysis/02_descriptives.R
    needs: [process_data]
    outputs:
      moderately_sensitive:
        plots: output/descriptive/plots/*.jpeg
        tables: output/descriptive/tables/*.csv

  create_cohorts:
    run: r:latest analysis/03_create_cohorts.R
    needs: [process_data]
    outputs:
      highly_sensitive:
        data1: output/data/cohorts/*.rds

  obj_1_analysis:
    run: r:latest analysis/04_analysis_obj_1.R
    needs: [process_data, create_cohorts]
    outputs:
      moderately_sensitive:
        plots: output/descriptive/obj_1/*.jpeg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 09:40:21

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
060ed6e
Requested actions
  • create_cohorts
  • obj_1_analysis

Code comparison

Compare the code used in this job request