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Job request: 23402

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
covid_collateral_hf
ID:
2weuixjeox2casmp
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Emily Herrett requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 100000

actions:
  #Study definition 
  generate_study_population_prevalent_2018:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prevalent_2018
    outputs:
      highly_sensitive:
        cohort: output/input_prevalent_2018.csv

  generate_study_population_prevalent_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prevalent_2019
    outputs:
      highly_sensitive:
        cohort: output/input_prevalent_2019.csv

  generate_study_population_prevalent_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prevalent_2020
    outputs:
      highly_sensitive:
        cohort: output/input_prevalent_2020.csv

  generate_study_population_prevalent_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prevalent_2021
    outputs:
      highly_sensitive:
        cohort: output/input_prevalent_2021.csv

  generate_study_population_prevalent_2022:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prevalent_2022
    outputs:
      highly_sensitive:
        cohort: output/input_prevalent_2022.csv

  generate_study_population_prevalent_2023:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prevalent_2023
    outputs:
      highly_sensitive:
        cohort: output/input_prevalent_2023.csv

  generate_study_population_incident:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_incident
    outputs:
      highly_sensitive:
        cohort: output/input_incident.csv      

# Generate datasets for analysis   000 and 001  
  generate_analysis_dataset_prevalent:
    run: stata-mp:latest analysis/000_cr_define_covariates_prevalent.do
    needs: [generate_study_population_prevalent_2018, generate_study_population_prevalent_2019, generate_study_population_prevalent_2020, generate_study_population_prevalent_2021, generate_study_population_prevalent_2022, generate_study_population_prevalent_2023]
    outputs:
      highly_sensitive:
        cohort: output/prevalent_cohort*.dta   

  generate_analysis_dataset_incident:
    run: stata-mp:latest analysis/001_cr_define_covariates_incident.do
    needs: [generate_study_population_incident]
    outputs:
      highly_sensitive:
        cohort: output/incident_cohort*.dta     

# Generate drug prevalence estimates for prevalent cohorts 202
  generate_drugprevalence_prevalent:
    run: stata-mp:latest analysis/202_cr_prevalent_cohort_prevalence.do
    needs: [generate_analysis_dataset_prevalent]
    outputs:
      moderately_sensitive:
        output: output/tabfig/prevalent_prevalences_summary*.csv 
        # graph: output/tabfig/prevalent_prevalences*.svg

# Generate rates for prevalent cohorts: 201 
  generate_rates_prevalent:
    run: stata-mp:latest analysis/201_cr_prevalent_cohort_simple_rates.do
    needs: [generate_analysis_dataset_prevalent]
    outputs:
      moderately_sensitive:
        output: output/tabfig/prevalent_rates_summary*.csv 

# Generate table 1: 204 
  generate_table1_prevalent:
    run: stata-mp:latest analysis/204_prevalent_cohort_table.do
    needs: [generate_analysis_dataset_prevalent]
    outputs:
      moderately_sensitive:
        output: output/tabfig/prevalent_table1*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:04:58

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

Job information

Status
Succeeded
Backend
TPP
Workspace
covid_collateral_hf
Requested by
Emily Herrett
Branch
main
Force run dependencies
No
Git commit hash
83cfef4
Requested actions
  • generate_table1_prevalent

Code comparison

Compare the code used in this Job Request