Job request: 3447

View Repo View project.yaml

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

Jobs

ID Status Action
ir76jhr3rmdjmls7 succeeded design
wkx3lkc7ek6rc2ug succeeded extract
5bxdejgvpu5mjar7 succeeded process
ok7sckjaz5vnmgil succeeded descr_table1
jgrhtadw747nbn6k succeeded descr_vaxdate
bo6ay2l6sour4pzl succeeded descr_diagnoses
7gtx6whi7u5ltvee succeeded rmd_report

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 10000

actions:


  design:
    run: r:latest analysis/design.R
    outputs:
      moderately_sensitive:
        dates: analysis/lib/dates.json
        groups: analysis/lib/diagnosis_groups.json
        lookup: analysis/lib/diagnosis_groups_lookup.rds
        labels: analysis/lib/variable_labels.rds


  extract:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
      --output-format feather
    # dummy_data_file: -- not yet in use because of https://github.com/opensafely-core/cohort-extractor/issues/611#issuecomment-893544024
    needs: [design]
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  process:
    run: r:latest analysis/process.R
    needs: [design, extract]
    outputs:
      highly_sensitive:
        cohort: output/data/data_cohort.rds

  descr_table1:
    run: r:latest analysis/table1.R
    needs: [design, process]
    outputs:
      highly_sensitive:
        rds: output/table1/*.rds
      moderately_sensitive:
        html: output/table1/*.html
        csv: output/table1/*.csv

  descr_vaxdate:
    run: r:latest analysis/vax_date.R
    needs: [design, process]
    outputs:
      highly_sensitive:
        rds: output/vaxdate/*.rds
      moderately_sensitive:
        png: output/vaxdate/*.png

  descr_diagnoses:
    run: r:latest analysis/diagnoses.R
    needs: [design, process]
    outputs:
      highly_sensitive:
        rds: output/diagnoses/*.rds
      moderately_sensitive:
        png: output/diagnoses/*.png


  rmd_report:
    run: r:latest -e 'rmarkdown::render("analysis/report.Rmd",  knit_root_dir
      = "/workspace",  output_dir = "/workspace/output/report"   )'
    needs: [design, descr_table1, descr_vaxdate, descr_diagnoses]
    outputs:
      moderately_sensitive:
        html: output/report/report.html
        md: output/report/report.md
        figures: output/report/figures/*.png

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 11:22:32

Config