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Job request: 1609

Organisation:
Bennett Institute
Workspace:
factors-associated-with-covid-19-vaccination-wip
ID:
pu4sdkaaee36o4kz
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 in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

  • Action:
    generate_study_population
    Status:
    Status: Failed
    Job identifier:
    tz7cjceyhpisahlq
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_study_population_flow_chart_data
    Status:
    Status: Failed
    Job identifier:
    v4nuljpnc5fau2lc
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    data_process_all
    Status:
    Status: Failed
    Job identifier:
    yy3cmpuwoop6l2a5
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    data_properties_all
    Status:
    Status: Failed
    Job identifier:
    ztauzsgtpx7yjobv
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    flow_chart
    Status:
    Status: Failed
    Job identifier:
    4wqgsacpbgj2wxx2
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    practice_id
    Status:
    Status: Failed
    Job identifier:
    wuolpddmvkjgm25a
    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: 00:00:15

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

Job information

Status
Failed
Backend
EMIS
Workspace
factors-associated-with-covid-19-vaccination-wip
Requested by
Peter Inglesby
Branch
wip
Force run dependencies
No
Git commit hash
4a028c5
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

  • No previous Job Request available for comparison