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Job request: 861

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
learning-disabilities
ID:
gu6uc2cph4oe3lql
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Elizabeth (Fizz) Williamson 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:
    generate_cohort1
    Status:
    Status: Succeeded
    Job identifier:
    zl6ibqbnj7psrmol
  • Action:
    generate_cohort2
    Status:
    Status: Succeeded
    Job identifier:
    vtmwkpp72op7siep
  • Action:
    clean
    Status:
    Status: Succeeded
    Job identifier:
    2z3msuxjmbwibpa6
  • Action:
    create_analysis
    Status:
    Status: Succeeded
    Job identifier:
    tj4qhlgd7qpmqsyh
  • Action:
    describe_cohort
    Status:
    Status: Succeeded
    Job identifier:
    mbcolbelt4qlgq6b
  • Action:
    tabulate_cohort
    Status:
    Status: Succeeded
    Job identifier:
    hpvjmujut3hr77di
  • Action:
    cox_regression
    Status:
    Status: Succeeded
    Job identifier:
    dopnfevqxrrafifl
  • Action:
    cox_regression_child
    Status:
    Status: Succeeded
    Job identifier:
    p3yyzi6rwtmwd6wk

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_cohort1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-03-01"
    outputs:
      highly_sensitive:
        cohort: output/input_2020-03-01.csv

  generate_cohort2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-09-01"
    outputs:
      highly_sensitive:
        cohort: output/input_2020-09-01.csv

  clean:
    run: stata-mp:latest analysis/001_clean_input_data.do
    needs: [generate_cohort1, generate_cohort2]
    outputs:
      moderately_sensitive:
        log: logs/001_clean_input_data.log

  create_analysis:
    run: stata-mp:latest analysis/002_create_ld_analysis_dataset.do
    needs: [clean]
    outputs:
      moderately_sensitive:
        log: logs/002_create_ld_analysis_dataset.log

  describe_cohort:
    run: stata-mp:latest analysis/AL001_describe_cohort.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL001_describe_cohort.log

  tabulate_cohort:
    run: stata-mp:latest analysis/AL002_tabulate_cohort_descriptives.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL002_tabulate_cohort_descriptives.log
        model: output/basetable1.txt
 
  cox_regression:
    run: stata-mp:latest analysis/AL003_cox_regression.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL003_cox_regression.log
        hrs_adult: output/output_hrs_main.out
        rates_adult: output/output_rates.out

  cox_regression_child:
    run: stata-mp:latest analysis/AL004_cox_regression_child.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_child.log
        hrs_child: output/output_hrs_main_child.out
        rates_child: output/output_rates_child.out

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:25:52

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

Job request

Status
Succeeded
Backend
TPP
Workspace
learning-disabilities
Requested by
Elizabeth (Fizz) Williamson
Branch
master
Force run dependencies
No
Git commit hash
7c5fd8d
Requested actions
  • run_all

Code comparison

Compare the code used in this job request

  • No previous job request available for comparison