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Job request: 684

Organisation:
Bennett Institute
Workspace:
covid-vaccine-preliminary-study_effectiveness
ID:
vvwufsbzmbbgv4zy
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 within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

  • Action:
    tte_plots
    Status:
    Status: Succeeded
    Job identifier:
    gy2lvkusvdshi2ts

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_delivery_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_delivery
    outputs:
      highly_sensitive:
        cohort: output/input_delivery.csv

  generate_eligibility_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_eligibility
    outputs:
      highly_sensitive:
        cohort: output/input_eligibility.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


  process_data:
    run: r:latest analysis/effectiveness/process_data.R
    needs: [generate_delivery_cohort]
    outputs:
      highly_sensitive:
        cohort: output/data/data_processed.rds
      moderately_sensitive:
        summary1: output/data_summary/summary_delivery.txt
        summary2: output/data_summary/summary_processed.txt
        summary3: output/data_summary/type_delivery.txt
        summary4: output/data_summary/type_processed.txt


  summarise_data:
    run: r:latest analysis/effectiveness/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.rds

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

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

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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:16

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

Job request

Status
Succeeded
Backend
TPP
Workspace
covid-vaccine-preliminary-study_effectiveness
Requested by
Will Hulme
Branch
effectiveness
Force run dependencies
No
Git commit hash
f9bbe18
Requested actions
  • tte_plots

Code comparison

Compare the code used in this job request