Skip to content

Job request: 1621

Organisation:
Bennett Institute
Workspace:
factors-associated-with-covid-19-vaccination-wip
ID:
kl3245sizdvburmh
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Peter Inglesby 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:
    n4qbqryhvjrfqvkb
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_study_population_flow_chart_data
    Status:
    Status: Failed
    Job identifier:
    em7wqor6mz2ccvfo
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    flow_chart
    Status:
    Status: Failed
    Job identifier:
    dovd524czxpfhqvw
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    data_process_all
    Status:
    Status: Failed
    Job identifier:
    db73g5lphwfj4nim
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    data_properties_all
    Status:
    Status: Failed
    Job identifier:
    2ftbbth3ce4zcpoz
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    practice_id
    Status:
    Status: Failed
    Job identifier:
    ccjv7kex77zjfsht
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
######################################

# This script defines the project pipeline - it specifys the execution orders for all the code in this
# repo using a series of actions.

######################################

version: '3.0'

expectations:
  population_size: 1000000

actions:

  # Extract data for study population flow chart
  generate_study_population_flow_chart_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart
    outputs:
      highly_sensitive:
        cohort: output/input_flow_chart.csv

  # Calculate numbers for study population flow chart
  flow_chart:
    run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Study_definition_flow_chart.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [generate_study_population_flow_chart_data]
    outputs:
      moderately_sensitive:
        html: output/Study_definition_flow_chart.html
        
  # Extract study data
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv
        
  # Process data
  data_process_all:
    run: r:latest analysis/R/Scripts/00_process_data.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data1: output/data/data_all.rds
        
  # Summarise data
  data_properties_all:
    run: r:latest analysis/R/Scripts/01_data_properties.R output/data/data_all.rds output/data_properties
    needs: [data_process_all]
    outputs:
      moderately_sensitive:
        datasummary: output/data_properties/data_all*.txt
        
  # Practice ID summaries
  practice_id:
    run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Data_summaries_practices.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        html: output/Data_summaries_practices.html
        
  # Models
  cox_models:
    run: r:latest analysis/R/Scripts/02_Models.R
    needs: [generate_study_population, data_process_all]
    outputs:
      highly_sensitive :
        models: output/models/mod*.rds
        
  # Models summaries
  cox_models_summaries:
    run: r:latest -e 'rmarkdown::render("analysis/R/Markdown/Model_comparisons.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [generate_study_population, data_process_all, cox_models]
    outputs:
      moderately_sensitive:
        html: output/Model_comparisons.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:14

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

Job request

Status
Failed
Backend
EMIS
Workspace
factors-associated-with-covid-19-vaccination-wip
Requested by
Peter Inglesby
Branch
wip
Force run dependencies
Yes
Git commit hash
60158d3
Requested actions
  • generate_study_population_flow_chart_data
  • flow_chart
  • generate_study_population
  • data_process_all
  • data_properties_all
  • practice_id

Code comparison

Compare the code used in this job request