Job Request: 2970 k53zgjn3d2z7zn24

This page shows the technical details of what happened when authorised researcher HelenCEBM requested one or more actions to be run against real patient data in the COVID-19 Vaccine Preliminary 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.

State

State is inferred from the related Jobs
Status: succeeded

Config

Backend: tpp
Workspace: covid-vaccine-preliminary-study-master (master)
Creator: HelenCEBM
Force run dependencies?: False
Git Commit Hash: 77815fc
Requested Actions:
  • generate_notebook
  • generate_simple_report
  • generate_report_second_doses

Timings

Created: 1 week ago
Started: 1 week ago
Finished: 1 week ago
Runtime: 01:33:45

Pipeline

version: '3.0'

expectations:
population_size: 50000
# dummy population size must be at least 50000 to ensure the STP analysis can run successfully

actions:

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


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
figures: interim-outputs/figures/*
tables: interim-outputs/tables/*
csvs: machine_readable_outputs/*/* # two possible subfolders
text: interim-outputs/text/*


generate_simple_report:
run: jupyter:latest env IMAGE_FORMAT=png jupyter nbconvert /workspace/notebooks/opensafely_vaccine_report_overall.ipynb --execute --to html --template basic --output=/workspace/output/opensafely_vaccine_report_overall_simple.html --ExecutePreprocessor.timeout=86400 --no-input

needs: [generate_delivery_cohort, generate_notebook]
outputs:
moderately_sensitive:
notebook: output/opensafely_vaccine_report_overall_simple.html
csvs: machine_readable_outputs/table_csvs/*


generate_report_second_doses:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/second_doses.ipynb --execute --to html --template basic --output-dir=/workspace/output/second_doses --ExecutePreprocessor.timeout=86400 --no-input

needs: [generate_notebook]
outputs:
moderately_sensitive:
notebook: output/second_doses/second_doses.html
tables: output/second_doses/*.csv

Jobs

ID Status Action
fwx3frjaxxtryveu succeeded generate_notebook View
p5i7miiepsfgoesp succeeded generate_simple_report View
oekl5igzfeorbe2o succeeded generate_report_second_doses View