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Job request: 843

Organisation:
Bennett Institute
Workspace:
covid-vaccineeffectiveness-research_doses
ID:
dr4m73vhyib5fm7i
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_doses_data
    Status:
    Status: Succeeded
    Job identifier:
    wdkljfs3lcgbfdcs
  • Action:
    data_models
    Status:
    Status: Succeeded
    Job identifier:
    zrbwpi47axgqrb6q

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

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

  extract_doses_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_doses
    outputs:
      highly_sensitive:
        cohort: output/input_doses.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


  data_models:
    run: r:latest analysis/R/data_doses_process.R
    needs: [extract_doses_data]
    outputs:
      moderately_sensitive:
        log: output/cox.txt

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

  data_process:
    run: r:latest analysis/R/data_process.R
    needs: [extract_data]
    outputs:
      highly_sensitive:
        cohort: output/data/data_vaccinated.rds

  data_properties:
    run: r:latest analysis/R/data_properties.R output/data/data_vaccinated.rds output/data_properties
    needs: [data_process]
    outputs:
      moderately_sensitive:
        summary: output/data_properties/data_vaccinated_colsummary.txt
        types: output/data_properties/data_vaccinated_coltypes.txt

  data_summarise:
    run: r:latest analysis/R/data_summarise.R
    needs: [data_process]
    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/summary_stats.json

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

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

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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 08:31:35

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

Job information

Status
Succeeded
Backend
TPP
Workspace
covid-vaccineeffectiveness-research_doses
Requested by
Will Hulme
Branch
doses
Force run dependencies
No
Git commit hash
5538e94
Requested actions
  • extract_doses_data
  • data_models

Code comparison

Compare the code used in this Job Request