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Job request: 7748

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
covid-collateral
ID:
33oy5mctpiknohnl
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Ruth Costello 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: 1000

actions:
  # Generates study population for CV, mental health outcomes - start date = 2018-03-01
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-03-01 to 2022-01-31 by month" --output-dir=output/measures --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv
  # Generates study population for diabetes outcomes
  generate_study_population_dm:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_dm --index-date-range "2018-03-01 to 2022-01-31 by month" --output-dir=output/measures/dm --output-format=csv --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/measures/dm/input_dm_*.csv

  # Generates study population for respiratory outcomes
  generate_study_population_resp:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_resp --index-date-range "2018-03-01 to 2022-01-31 by month" --output-dir=output/measures/resp --output-format=csv --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/measures/resp/input_resp_*.csv

  # Generates study population for mortality
  generate_study_population_mortality:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_mortality --index-date-range "2019-02-01 to 2022-01-31 by month" --output-dir=output/measures/mortality --output-format=csv --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/measures/mortality/input_mortality_*.csv
  
  # Generates study populations for baseline tables at 3 timepoints
  generate_study_population_tables_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_tables --index-date-range "2019-01-01" --output-dir=output/measures/tables --output-format=csv --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/measures/tables/input_tables_2019-01-01.csv
  generate_study_population_tables_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_tables --index-date-range "2020-01-01" --output-dir=output/measures/tables --output-format=csv --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/measures/tables/input_tables_2020-01-01.csv
  generate_study_population_tables_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_tables --index-date-range "2021-01-01" --output-dir=output/measures/tables --output-format=csv --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/measures/tables/input_tables_2021-01-01.csv
  
  # Generates baseline tables
  create_baseline_tables:
    run: stata-mp:latest analysis/baseline_tables.do
    needs: [generate_study_population_tables_2019, generate_study_population_tables_2020, generate_study_population_tables_2021]
    outputs:
      highly_sensitive:
        output: output/measures/tables/baseline_table_*.xlsx

  # Generates summary measures for CV and mental health outcomes
  calculate_measures:
    run: cohortextractor:latest  generate_measures --study-definition study_definition --output-dir=output/measures
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        measure: output/measures/measure_*.csv
  # Generates summary measures for diabetes outcomes  
  calculate_measures_dm:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_dm --output-dir=output/measures/dm
    needs: [generate_study_population_dm]
    outputs:
      moderately_sensitive:
        measure: output/measures/dm/measure_dm_*.csv

  # Generates summary measures for respiratory outcomes  
  calculate_measures_resp:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_resp --output-dir=output/measures/resp
    needs: [generate_study_population_resp]
    outputs:
      moderately_sensitive:
        measure: output/measures/resp/measure_*.csv

  # Generates summary measures for mortality outcomes  
  calculate_measures_mortality:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_mortality --output-dir=output/measures/mortality
    needs: [generate_study_population_mortality]
    outputs:
      moderately_sensitive:
        measure: output/measures/mortality/measure_*.csv
  
  # Generates graphs for CVD & mental health outcomes
  graphs_mh_cvd:
    run: stata-mp:latest analysis/graphs_mh_cvd.do 
    needs: [calculate_measures]
    outputs: 
      moderately_sensitive:
        log: logs/graphs_mh_cvd.log
        output: output/line_*.eps
      highly_sensitive:
        output: output/measures/collapse_measure_*
  # Generates graphs for diabetes outcomes
  graphs_dm:
    run: stata-mp:latest analysis/graphs_dm.do 
    needs: [calculate_measures_dm]
    outputs: 
      moderately_sensitive:
        log: logs/graphs_dm.log
        output: output/line_dm_*.eps
      highly_sensitive:
        output: output/measures/dm/collapse_measure_*
  # Generate graphs for respiratory outcomes
  graphs_resp:
    run: stata-mp:latest analysis/graphs_resp.do 
    needs: [calculate_measures_resp]
    outputs: 
      moderately_sensitive:
        log: logs/graphs_resp.log
        output: output/line_resp_*.eps
      highly_sensitive:
        output: output/measures/resp/collapse_measure_*

  # Generate graphs for mortality
  graphs_mortality:
    run: stata-mp:latest analysis/graphs_mortality.do 
    needs: [calculate_measures_mortality]
    outputs: 
      moderately_sensitive:
        log: logs/graphs_mortality.log
        output: output/graphs/line_mortality_*.svg
      highly_sensitive:
        output: output/collapsed/collapse_measure_*
        
  # Running analysis scripts
  model_checks_dm:
    run: stata-mp:latest analysis/model_check_dm.do
    needs: [calculate_measures_dm]
    outputs:
      moderately_sensitive: 
        log: logs/model_checks_dm.log
        output: output/time_series/dm_*.svg

  model_checks_resp:
    run: stata-mp:latest analysis/model_check_resp.do
    needs: [calculate_measures_resp]
    outputs:
      moderately_sensitive: 
        log: logs/model_checks_resp.log
        output: output/time_series/resp_*.svg

  model_checks_cvd:
    run: stata-mp:latest analysis/model_check_cvd.do
    needs: [calculate_measures]
    outputs:
      moderately_sensitive: 
        log: logs/model_checks_cvd.log
        output: output/time_series/cvd_*.svg

  model_checks_mh:
    run: stata-mp:latest analysis/model_check_mh.do
    needs: [calculate_measures]
    outputs:
      moderately_sensitive: 
        log: logs/model_checks_mh.log
        output: output/time_series/mh_*.svg

  model_checks_mortality:
    run: stata-mp:latest analysis/model_check_mortality.do
    needs: [calculate_measures_mortality]
    outputs:
      moderately_sensitive: 
        log: logs/model_checks_mortality.log
        output: output/time_series/mortality_*.svg
  
  time_series_resp:
    run: stata-mp:latest analysis/time_series_resp.do
    needs: [calculate_measures_resp]
    outputs:
      moderately_sensitive:
        log: logs/tsreg_resp.log
        output: output/time_series/tsreg_tables_resp.xlsx

  time_series_dm:
    run: stata-mp:latest analysis/time_series_dm.do
    needs: [calculate_measures_dm]
    outputs:
      moderately_sensitive:
        log: logs/tsreg_dm.log
        output: output/time_series/tsreg_tables_dm.xlsx

  time_series_cvd:
    run: stata-mp:latest analysis/time_series_cvd.do
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        log: logs/tsreg_cvd.log
        output: output/time_series/tsreg_tables_cvd.xlsx

  time_series_mh:
    run: stata-mp:latest analysis/time_series_mh.do
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        log: logs/tsreg_mh.log
        output: output/time_series/tsreg_tables_mh.xlsx

  time_series_mortality:
    run: stata-mp:latest analysis/time_series_mortality.do
    needs: [calculate_measures_mortality]
    outputs:
      moderately_sensitive:
        log: logs/tsreg_mortality.log
        output: output/time_series/tsreg_tables_mortality.xlsx

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 30:39:06

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

Job information

Status
Failed
Backend
TPP
Workspace
covid-collateral
Requested by
Ruth Costello
Branch
main
Force run dependencies
No
Git commit hash
6263a10
Requested actions
  • generate_study_population_mortality
  • generate_study_population_tables_2019
  • generate_study_population_tables_2020
  • generate_study_population_tables_2021
  • calculate_measures_mortality
  • graphs_mortality
  • model_checks_mortality
  • time_series_mortality

Code comparison

Compare the code used in this Job Request