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Job request: 765

Organisation:
Bennett Institute
Workspace:
covid-vaccineeffectiveness-research_main
ID:
guyq64b4if77tfvv
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Will Hulme requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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:
    process_data
    Status:
    Status: Succeeded
    Job identifier:
    j6oykqbtug2zzyva
  • Action:
    summarise_data
    Status:
    Status: Succeeded
    Job identifier:
    mzaf4elhiefotki5
  • Action:
    vaccine_tables
    Status:
    Status: Succeeded
    Job identifier:
    aofnkgcwkttttka6
  • Action:
    tte_tables
    Status:
    Status: Succeeded
    Job identifier:
    owu6ieaaa4wqlqcv
  • Action:
    tte_plots
    Status:
    Status: Failed
    Job identifier:
    fap3rxubyrhm7g3n

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 100000

actions:

  extract_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  # generate_notebook:
  #   run: jupyter:latest jupyter nbconvert /workspace/notebooks/population_characteristics.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
  #
  #   needs: [generate_delivery_cohort]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/population_characteristics.html


  get_packages:
    run: r:latest analysis/R/export_package_names.R
    outputs:    
      moderately_sensitive:
        cohort: output/available_packages.csv

  process_data:
    run: r:latest analysis/R/process_data.R
    needs: [extract_data]
    outputs:
      highly_sensitive:
        cohort1: output/data/data_processed.rds
        cohort2: output/data/data_vaccinated.rds
      moderately_sensitive:
        summary1: output/data_summary/summary_extract.txt
        summary2: output/data_summary/summary_processed.txt
        summary3: output/data_summary/summary_vaccinated.txt
        summary4: output/data_summary/type_extract.txt
        summary5: output/data_summary/type_processed.txt
        summary6: output/data_summary/type_vaccinated.txt


  summarise_data:
    run: r:latest analysis/R/summarise_data.R
    needs: [process_data]
    outputs:
      moderately_sensitive:
        summary1: output/variable_summary/categorical.txt
        summary2: output/variable_summary/numeric.txt
        summary3: output/variable_summary/date.txt
        summarytables: output/variable_summary/tables/categorical_*.csv
        summarystats: output/data_summary/summary_stats.json

  vaccine_tables:
    run: r:latest analysis/R/vaccine_type.R
    needs: [process_data]
    outputs:
      moderately_sensitive:
        tables: output/vaccine_type/tables/vaccine_type_*.csv

  tte_tables:
    run: r:latest analysis/R/tte_tables.R
    needs: [process_data]
    outputs:
      moderately_sensitive:
        tables: output/tte/tables/event_rates_*.csv

  tte_plots:
    run: r:latest analysis/R/tte_plots.R
    needs: [process_data]
    outputs:
      moderately_sensitive:
        plots: output/tte/figures/plot_*.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:49:55

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

Job information

Status
Failed
Backend
TPP
Workspace
covid-vaccineeffectiveness-research_main
Requested by
Will Hulme
Branch
main
Force run dependencies
No
Git commit hash
759f3a4
Requested actions
  • process_data
  • summarise_data
  • vaccine_tables
  • tte_tables
  • tte_plots

Code comparison

Compare the code used in this Job Request