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Job request: 909

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
learning-disabilities-full
ID:
vqfhzr2o5qgo2s3b
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:
    cox_regression1
    Status:
    Status: Failed
    Job identifier:
    zeeomediabi7wmmq
    Error:
    No outputs found matching patterns: - logs/AL004_1_cox_regression.log
  • Action:
    cox_regression2
    Status:
    Status: Failed
    Job identifier:
    5lxa5hpl6dhfwerh
    Error:
    No outputs found matching patterns: - logs/AL004_2_cox_regression.log

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




  cox_regression1:
    run: stata-mp:latest analysis/AL004_1_cox_regression.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_1_cox_regression.log
        hrs_adult: output/output_hrs_main_2_coviddeath_ldr_group.out
        rates_adult: output/output_rates_2_coviddeath_ldr_group.out

  cox_regression2:
    run: stata-mp:latest analysis/AL004_2_cox_regression.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_2_cox_regression.log
        hrs_adult: output/output_hrs_main_2_covidadmission_ldr_group.out
        rates_adult: output/output_rates_2_covidadmission_ldr_group.out

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:03:29

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
c9179d6
Requested actions
  • cox_regression1
  • cox_regression2

Code comparison

Compare the code used in this job request