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Job request: 6607

Organisation:
ISARIC
Workspace:
hdruk-os-covid-paeds
ID:
crx6vyeh5n4qohli
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_high_admissions
    Status:
    Status: Failed
    Job identifier:
    gw3uqgh3ls45khmf
    Error:
    Internal error
  • Action:
    generate_high_gp
    Status:
    Status: Succeeded
    Job identifier:
    fmme7y2vcq4mutqz
  • Action:
    generate_high_outpatient
    Status:
    Status: Succeeded
    Job identifier:
    3dknfom3az5kim5q
  • Action:
    descriptives
    Status:
    Status: Failed
    Job identifier:
    egbl3ldzifur3dfb
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    process_data
    Status:
    Status: Failed
    Job identifier:
    lufmvmjk6b2ty4tj
    Error:
    dependency_failed: Not starting as dependency failed

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_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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 09:32:44

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
bc7195a
Requested actions
  • generate_high_admissions
  • generate_high_outpatient
  • generate_high_gp
  • process_data
  • descriptives

Code comparison

Compare the code used in this job request