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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 authorised researcher Elizabeth (Fizz) Williamson 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:
    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 information

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