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Job request: 6601

Organisation:
ISARIC
Workspace:
hdruk-os-covid-paeds
ID:
7n3fjbqclmwbyzk3
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_study_population
    Status:
    Status: Failed
    Job identifier:
    ixnt3s5a5hksxfpg
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_high_admissions
    Status:
    Status: Failed
    Job identifier:
    bws6ktzzvprxb35j
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_high_outpatient
    Status:
    Status: Failed
    Job identifier:
    tqr3qjqqf7jxfmd3
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    descriptives
    Status:
    Status: Failed
    Job identifier:
    hpojtkrzs3ixcgdi
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    process_data
    Status:
    Status: Failed
    Job identifier:
    4kb67zmhbtc6jc6w
    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: 00:11:20

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
Yes
Git commit hash
6f6c4af
Requested actions
  • generate_high_admissions
  • generate_high_outpatient
  • process_data
  • descriptives

Code comparison

Compare the code used in this job request