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Job request: 12545

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
bias
ID:
lopmfmxved5uuluh
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Emily Herrett 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 100000

actions:

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

  # Generate objective 1a dataset
  create_dataset_1a:
    run: stata-mp:latest analysis/cr_dataset_1a.do
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        output: output/cr_dataset_1a.csv

  # Generate objective 1b dataset
  create_dataset_1b:
    run: stata-mp:latest analysis/cr_dataset_1b.do
    needs: [generate_study_population, create_dataset_1a]
    outputs:
      highly_sensitive:
        output: output/cr_dataset_1b.csv

  # Generate objective 1a table
  create_table_1a:
    run: stata-mp:latest analysis/tabulate_1a.do
    needs: [generate_study_population, create_dataset_1a]
    outputs:
      moderately_sensitive:
        output: output/tables/an_table_PublicationDescriptivesTable_1a_redacted.tsv      

  # Generate objective 1b table
  create_table_1b:
    run: stata-mp:latest analysis/tabulate_1b.do
    needs: [generate_study_population, create_dataset_1a, create_dataset_1b]
    outputs:
      moderately_sensitive:
        output: output/tables/an_table_PublicationDescriptivesTable_1b_os_redacted.tsv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:24:15

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

Job request

Status
Succeeded
Backend
TPP
Workspace
bias
Requested by
Emily Herrett
Branch
main
Force run dependencies
No
Git commit hash
f0fddf3
Requested actions
  • create_dataset_1b
  • create_table_1b

Code comparison

Compare the code used in this job request