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Job request: 8359

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
covid-collateral
ID:
esjc3kumft42xnnu
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:
  # Generating static variables 
  generate_study_population_static:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_static --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/input_static.csv
  # Generates study population for CV - 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
  # Join static and time-varying variables
  join_cohorts_cvd:
    run: >
      cohort-joiner:v0.0.30
        --lhs output/measures/input_*.csv
        --rhs output/input_static.csv
        --output-dir output/measures/cvd
    needs: [generate_study_population, generate_study_population_static]
    outputs: 
      highly_sensitive:
        cohort: output/measures/cvd/input_*.csv
  # Generates study population for mental health outcomes - start date = 2018-03-01
  generate_study_population_mh:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_mh --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_mh_*.csv
  # Join static and time-varying variables
  join_cohorts_mh:
    run: >
      cohort-joiner:v0.0.30
        --lhs output/measures/input_mh_*.csv
        --rhs output/input_static.csv
        --output-dir output/measures/mh
    needs: [generate_study_population_mh, generate_study_population_static]
    outputs: 
      highly_sensitive:
        cohort: output/measures/mh/input_mh_*.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 
    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:
      moderately_sensitive:
        output: output/tables/baseline_table_*.csv

  # Generates summary measures for CV 
  calculate_measures:
    run: cohortextractor:latest  generate_measures --study-definition study_definition --output-dir=output/measures/cvd
    needs: [join_cohorts_cvd]
    outputs:
      moderately_sensitive:
        measure: output/measures/cvd/measure_*_rate.csv
  # Generates summary measures for mental health outcomes
  calculate_measures_mh:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_mh --output-dir=output/measures/mh
    needs: [join_cohorts_mh]
    outputs:
      moderately_sensitive:
        measure: output/measures/mh/measure_*_rate.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_*_rate.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_*_rate.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_*_rate.csv
  
  # Generates graphs for CVD & mental health outcomes
  graphs_mh_cvd:
    run: stata-mp:latest analysis/graphs_mh_cvd.do 
    needs: [calculate_measures, calculate_measures_mh]
    outputs: 
      moderately_sensitive:
        log: logs/graphs_mh_cvd.log
        output: output/graphs/line_*.svg
     
  # 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/graphs/line_dm_*.svg
      highly_sensitive:
        output: output/collapsed/collapse_measure_dm_*
  # 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/graphs/line_resp_*.svg

  # 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_mh]
    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_resp*.csv

  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_dm*.csv

  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_cvd_*.csv

  time_series_mh:
    run: stata-mp:latest analysis/time_series_mh.do
    needs: [calculate_measures_mh]
    outputs:
      moderately_sensitive:
        log: logs/tsreg_mh.log
        output: output/time_series/tsreg_mh*.csv

  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_mortality*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 57:04:16

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

Job information

Status
Succeeded
Backend
TPP
Workspace
covid-collateral
Requested by
Ruth Costello
Branch
main
Force run dependencies
No
Git commit hash
09061ed
Requested actions
  • generate_study_population_static
  • generate_study_population
  • join_cohorts_cvd
  • generate_study_population_mh
  • join_cohorts_mh

Code comparison

Compare the code used in this Job Request