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Job request: 879

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
learning-disabilities-full
ID:
pgjh3n5cibhdrnp5
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:
    create_analysis
    Status:
    Status: Failed
    Job identifier:
    fwhtoowdfam5srtr
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    describe_cohort
    Status:
    Status: Failed
    Job identifier:
    i3qsxivjmjhrogjz
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    cox_regression
    Status:
    Status: Failed
    Job identifier:
    fupfd6c5hdrd26ll
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    cox_regression_child
    Status:
    Status: Failed
    Job identifier:
    aqxvpmdoiuz2fug4
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    cumulative_incidence
    Status:
    Status: Failed
    Job identifier:
    t44ive7lrk2qnfgp
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    tabulate_cohort
    Status:
    Status: Failed
    Job identifier:
    lhi4hddxevbdgljo
    Error:
    dependency_failed: Not starting as dependency failed

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:
     highly_sensitive:
        log: logs/001_clean_input_data.log
        clean1: analysis/data_base_cohort1.dta
        clean2: analysis/data_base_cohort2.dta

  create_analysis:
    run: stata-mp:latest analysis/002_create_ld_analysis_dataset.do
    needs: [clean]
    outputs:
     highly_sensitive:
        log: logs/002_create_ld_analysis_dataset.log
        an_data1: analysis/data_ldanalysis_cohort1.dta
        an_data2: analysis/data_ldanalysis_cohort2.dta

  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/AL004_cox_regression.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression.log
        hrs_adult: output/output_hrs_main.out
        rates_adult: output/output_rates.out

  cox_regression_child:
    run: stata-mp:latest analysis/AL005_cox_regression_child.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL005_cox_regression_child.log
        hrs_child: output/output_hrs_main_child.out
        rates_child: output/output_rates_child.out



  cumulative_incidence:
    run: stata-mp:latest analysis/AL003_cumulative_incidence.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL003_cumulative_incidence.log
        graph1: output/cumincidence_coviddeath.svg
        graph2: output/cumincidence_composite.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:05

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

Job request

Status
Failed
Backend
TPP
Workspace
learning-disabilities-full
Requested by
Elizabeth (Fizz) Williamson
Branch
master
Force run dependencies
No
Git commit hash
d8d1f09
Requested actions
  • create_analysis
  • describe_cohort
  • tabulate_cohort
  • cox_regression
  • cox_regression_child
  • cumulative_incidence

Code comparison

Compare the code used in this job request