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Job request: 16687

Organisation:
Bennett Institute
Workspace:
vax-fourth-dose-rd-baseline
ID:
e4xivrofu56k2jgk
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Andrea Schaffer 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.

Pipeline

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

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

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


version: '3.0'

expectations:
  population_size: 10000000

actions:

# Generate study population and extract baseline characteristics at Sep 3, 2022
  generate_study_pop_baseline:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_baseline
      --output-dir=feather 
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_baseline.feather
      
# Data cleaning, defining exclusions, saving final study pop
  data_process_baseline:
    run: r:latest analysis/processing/data_process_baseline.R
    needs: [generate_study_pop_baseline]
    outputs:
      highly_sensitive:
        cohort: output/cohort/cohort_*.csv
      moderately_sensitive:
        descriptive: output/descriptive/total_*.csv

 # Extract outcomes based on final study pop
  generate_study_pop_outcomes:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_outcomes
      --index-date-range "2022-09-03 to 2023-01-31 by week" 
      --output-dir=feather 
      --output-format=feather
    needs: [data_process_baseline]
    outputs:
      highly_sensitive:
        cohort: output/index/input_outcomes_*.feather

# Data cleaning of outcome data
  data_process_outcomes:
    run: r:latest analysis/processing/data_process_outcomes.R
    needs: [generate_study_pop_outcomes]
    outputs:
      highly_sensitive:
        outcomes: output/cohort/outcomes*.csv

# Plots of COVID booster uptake by age
  booster_uptake:
   run: r:latest analysis/descriptive/cumulative_vax_byage.R
   needs: [data_process_baseline]
   outputs:
      moderately_sensitive:
        rates_csv: output/cumulative_rates/final_*.csv 
        plot: output/cumulative_rates/plot_*.png

# Outcome plots #
  covid_outcomes:
   run: r:latest analysis/descriptive/plot_outcomes_byage.R
   needs: [data_process_outcomes]
   outputs:
      moderately_sensitive:
        measure_csv: output/covid_outcomes/primary_*.csv
        plot: output/covid_outcomes/plot_outcomes_*.png

        
# Check max #
  check_max:
   run: r:latest analysis/processing/check_max.R
   needs: [generate_study_pop_outcomes]
   outputs:
      moderately_sensitive:
        log: metadata/check_max.log
   

# Discontinuity of demographics
  # demographics:
  #  run: r:latest analysis/descriptive/demographics_byage.R
  #  needs: [generate_study_pop_baseline, data_process_baseline]
  #  outputs:
  #     moderately_sensitive:
  #       measures_csv: output/descriptive/demographics_*.csv


# Flu vaccine uptake #
  # flu_vax:
  #  run: r:latest analysis/descriptive/flu_vax_byage.R
  #  needs: [generate_study_pop]
  #  outputs:
  #     moderately_sensitive:
  #       measure_csv: output/cumulative_rates/flu_*.csv
  #       plot: output/cumulative_rates/plot_flu_vax_byage.png

# ITT analysis #
  itt_analysis:
   run: r:latest analysis/statistical_analysis/itt_analysis.R
   needs: [data_process_outcomes]
   outputs:
      moderately_sensitive:
        measure_csv: output/covid_outcomes/outcome_*.csv

# Outcome plots #
  # covid_outcomes:
  #  run: r:latest analysis/descriptive/covid_outcomes_byage.R
  #  needs: [generate_study_pop]
  #  outputs:
  #     moderately_sensitive:
  #       measure_csv: output/covid_outcomes/covid_*.csv
  #       plot: output/covid_outcomes/plot_outcomes_*.png
  




# IV analysis #

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job information

Status
Failed 
ProjectValidationError: Invalid project: 
1 validation error for Pipeline
actions -> check_max -> outputs -> __root__
  Output path metadata/check_max.log is not permitted: should not include the metadata directory (type=value_error)
Backend
TPP
Workspace
vax-fourth-dose-rd-baseline
Requested by
Andrea Schaffer
Branch
Protocol-updates
Force run dependencies
No
Git commit hash
8cf0157
Requested actions
  • check_max

Code comparison

Compare the code used in this Job Request