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Job request: 737

Organisation:
Bennett Institute
Workspace:
covid-vaccineeffectiveness-research_main
ID:
7fcjyveiz7nwlvrs
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:
    extract_data
    Status:
    Status: Succeeded
    Job identifier:
    yatmgulcuksr4xyu
  • Action:
    get_packages
    Status:
    Status: Succeeded
    Job identifier:
    ksr547xi5y26oynm
  • Action:
    process_data
    Status:
    Status: Succeeded
    Job identifier:
    ev4n5mhymegbzv5z
  • Action:
    summarise_data
    Status:
    Status: Succeeded
    Job identifier:
    jiwt5jkk5pymiaz3
  • Action:
    vaccine_tables
    Status:
    Status: Succeeded
    Job identifier:
    nhuwkqntk4ebtuhk
  • Action:
    tte_tables
    Status:
    Status: Succeeded
    Job identifier:
    xzo5uqvv2yzlqnat
  • Action:
    tte_plots
    Status:
    Status: Succeeded
    Job identifier:
    b4wtrpdnrze72nme

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

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: 03:27:16

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
Yes
Git commit hash
5949dd8
Requested actions
  • run_all

Code comparison

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