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Job request: 3460

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
covid-vaccine-neuro-research
ID:
cdehsfgqpy5he3rl
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Anna Schultze 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: 5000

actions:

  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sccs_and_historical_cohort
    outputs:
      highly_sensitive:
        cohort: output/input_sccs_and_historical_cohort.csv

  00_apply_exclusion_criteria:
    run: stata-mp:latest analysis/00_apply_exclusion_criteria.do 
    needs: [generate_cohort] 
    outputs:
      moderately_sensitive: 
        log: output/logs/00_apply_exclusion_criteria.log
      highly_sensitive:
        cohort_controls: output/input_historical_controls.csv
        cohort_az_cases: output/input_az_cases.csv
        cohort_pfizer_cases: output/input_pfizer_cases.csv 
        cohort_moderna_cases: output/input_moderna_cases.csv 

  SCCS_first_dose_only_analyses_neuro:
    run: stata-mp:latest analysis/SCCS_first_dose_only_analyses_neuro.do
    needs: [00_apply_exclusion_criteria] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_first_dose_only_analyses.log
        results: output/tables/results_summary.csv
      highly_sensitive:
        sccs_pop_BP: output/temp_data/sccs_popn_BP.dta
        sccs_pop_TM: output/temp_data/sccs_popn_TM.dta
        sccs_pop_GBS: output/temp_data/sccs_popn_GBS.dta

  SCCS_baseline_tables:
    run: stata-mp:latest analysis/SCCS_baseline_tables.do
    needs: [SCCS_first_dose_only_analyses_neuro] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_baseline_tables.log
        tables: output/tables/table1* 

  SCCS_assumption_checking:
    run: stata-mp:latest analysis/SCCS_assumption_checking.do
    needs: [SCCS_first_dose_only_analyses_neuro] 
    outputs:
      moderately_sensitive: 
        log: output/logs/SCCS_assumption_checking.log
        plots_S1: output/plots/S1*
        plots_S2: output/plots/S2*

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:20:43

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

Job request

Status
Failed
Backend
TPP
Workspace
covid-vaccine-neuro-research
Requested by
Anna Schultze
Branch
main
Force run dependencies
Yes
Git commit hash
4d8589b
Requested actions
  • run_all

Code comparison

Compare the code used in this job request