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Job request: 6567

Organisation:
Bennett Institute
Workspace:
counts
ID:
sdzck7pnm5bxqd4y
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Colm Andrews 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:
    initial_counts
    Status:
    Status: Succeeded
    Job identifier:
    3l26ynobmrvwo4o3
  • Action:
    rmd_report
    Status:
    Status: Succeeded
    Job identifier:
    flwrc33p3xaf4hso

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:
  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition  --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input.csv.gz

  initial_counts:
    run: r:latest analysis/highlevelcount.r
    needs: [generate_cohort]
    outputs:      
      moderately_sensitive:
        table: output/ctv3_primis.csv
        table2: output/ctv3_primis_perc.csv
        rds: output/ethnicity_compare.rds
  
  rmd_report:
    run: r:latest -e 'rmarkdown::render("analysis/output.Rmd",  knit_root_dir = "/workspace",  output_dir = "/workspace/notebook", output_format = c("html_document","rmarkdown::github_document")   )'
    needs:
    - initial_counts

    outputs:
      moderately_sensitive:
        html: notebook/output.html
        md: notebook/output.md

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:20:28

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

Job request

Status
Succeeded
Backend
TPP
Workspace
counts
Requested by
Colm Andrews
Branch
count
Force run dependencies
No
Git commit hash
72a38ac
Requested actions
  • initial_counts
  • rmd_report

Code comparison

Compare the code used in this job request