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Job request: 5077

Organisation:
The UK Renal Registry
Workspace:
ckd-coverage-ve
ID:
nptkny3j7l5qnoeq
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Millie Green 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:
    bitwoysn32jq34me
    Error:
    Internal error
  • Action:
    vaccine_coverage
    Status:
    Status: Failed
    Job identifier:
    5dftafydxcdltne3
    Error:
    Internal error
  • Action:
    data_process
    Status:
    Status: Failed
    Job identifier:
    ntjqniepkqhn6423
    Error:
    Internal error
  • Action:
    data_properties
    Status:
    Status: Failed
    Job identifier:
    p6n5cxfap4znwiln
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    table_1
    Status:
    Status: Failed
    Job identifier:
    7bizhm5o72iya36n
    Error:
    Internal error

Pipeline

Show project.yaml 
######################################
# Script defines project pipeline via series of actions
######################################

version: '3.0'

expectations:
  population_size: 100000

actions:

  # Extract data ----
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data
    outputs:
      highly_sensitive:
        cohort: output/data/input.csv
  
# Process data ----
  data_process:
    run: r:latest analysis/data_process.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data: output/data/data_processed.rds
        csv: output/data/data_processed.csv
        
 # Data properties ----      
  data_properties:
    run: r:latest analysis/data_properties.R output/data/data_processed.rds output/data_properties
    needs: [data_process]
    outputs:
      moderately_sensitive:
        cohort: output/data_properties/data_processed*.txt
        
  # Table 1 ----
  table_1:
    run: r:latest analysis/table_1.R
    needs: [data_process]
    outputs:
      moderately_sensitive:
        table: output/tables/table1_redacted.html

  # Coverage summaries ----
  vaccine_coverage:
    run: r:latest -e 'rmarkdown::render("analysis/vaccine_coverage.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
    needs: [generate_study_population, data_process]
    outputs:
      moderately_sensitive:
        html: output/markdown/vaccine_coverage.html
        csv: output/data/coverage_over_time_redacted.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:36:59

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

Job request

Status
Failed
Backend
TPP
Workspace
ckd-coverage-ve
Requested by
Millie Green
Branch
main
Force run dependencies
No
Git commit hash
25069f4
Requested actions
  • generate_study_population
  • data_process
  • data_properties
  • table_1
  • vaccine_coverage

Code comparison

Compare the code used in this job request