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Job request: 3808

Organisation:
Bennett Institute
Workspace:
post-vax-ae-attendance_main
ID:
psm7bt7rvadrvy57
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 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

  • Action:
    process
    Status:
    Status: Succeeded
    Job identifier:
    rwddkycw4gmvukyh
  • Action:
    descr_vaxdate
    Status:
    Status: Succeeded
    Job identifier:
    oux2k2oot4ffimy2
  • Action:
    descr_table1
    Status:
    Status: Succeeded
    Job identifier:
    33ct3jttvl5hdhzc
  • Action:
    descr_diagnoses
    Status:
    Status: Succeeded
    Job identifier:
    xwy7f6srbzw76kz5
  • Action:
    rmd_report
    Status:
    Status: Succeeded
    Job identifier:
    vc33yza62afhgla2

Pipeline

Show 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_codes.json
        lookup: analysis/lib/diagnosis_codes_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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:14:55

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

Job information

Status
Succeeded
Backend
TPP
Workspace
post-vax-ae-attendance_main
Requested by
Will Hulme
Branch
main
Force run dependencies
No
Git commit hash
f2dd242
Requested actions
  • process
  • descr_table1
  • descr_vaxdate
  • descr_diagnoses
  • rmd_report

Code comparison

Compare the code used in this Job Request