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Job request: 775

Organisation:
Bennett Institute
Workspace:
covid-vaccineeffectiveness-research_main
ID:
i3fkfwoa3klerfzt
View repo View project.yaml

This page shows the technical details of what happened when the 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 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:
    summarise_data
    Status:
    Status: Succeeded
    Job identifier:
    eqstnpdz2wdifu7t

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: 00:01:29

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

Job information

Status
Succeeded
Backend
TPP
Workspace
covid-vaccineeffectiveness-research_main
Requested by
Will Hulme
Branch
main
Force run dependencies
No
Git commit hash
4ab794a
Requested actions
  • summarise_data

Code comparison

Compare the code used in this Job Request