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Job request: 17884

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
collateral-imd
ID:
oyxmujfvkhno36r7
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:
# General population cohort
  generate_study_population:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition
      --index-date-range "2018-03-01 to 2021-12-31 by month" 
      --output-dir=output/measures 
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv

  generate_study_population_static_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_static --index-date-range "2019-01-01" --output-dir=output/measures/tables --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/input_static_2019-01-01.csv

  generate_study_population_static_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_static --index-date-range "2020-01-01" --output-dir=output/measures/tables --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/input_static_2020-01-01.csv
  
  generate_study_population_static_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_static --index-date-range "2021-01-01" --output-dir=output/measures/tables --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/input_static_2021-01-01.csv

 # join_cohorts:
 #   run: >
 #       cohort-joiner:v0.0.56
 #         --lhs output/measures/input_*.csv
 #         --rhs output/input_static.csv
 #         --output-dir output/measures/joined
 #   needs: [generate_study_population, generate_study_population_static]
 #   outputs: 
 #     highly_sensitive:
 #       cohort: output/measures/joined/input_*.csv

  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_*_rate.csv
# Diabetes subpopulation
  generate_study_population_dm:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition_dm
      --index-date-range "2018-03-01 to 2021-12-31 by month" 
      --output-dir=output/measures 
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/measures/input_dm_*.csv

  #join_cohorts_dm:
  #  run: >
  #      cohort-joiner:v0.0.56
  #        --lhs output/measures/input_dm_*.csv
  #        --rhs output/input_static.csv
  #        --output-dir output/measures/joined
  #  needs: [generate_study_population_dm, generate_study_population_static]
  #  outputs: 
  #    highly_sensitive:
  #      cohort: output/measures/joined/input_dm_*.csv

  calculate_measures_dm:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_dm --output-dir=output/measures
    needs: [generate_study_population_dm]
    outputs:
      moderately_sensitive:
        measure: output/measures/measure_dm*_rate.csv

# Respiratory subpopulation
  generate_study_population_resp:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition_resp
      --index-date-range "2018-03-01 to 2021-12-31 by month" 
      --output-dir=output/measures 
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/measures/input_resp_*.csv

  #join_cohorts_resp:
  #  run: >
  #      cohort-joiner:v0.0.56
  #        --lhs output/measures/input_resp_*.csv
  #        --rhs output/input_static.csv
  #        --output-dir output/measures/joined
  #  needs: [generate_study_population_resp, generate_study_population_static]
  #  outputs: 
  #    highly_sensitive:
  #      cohort: output/measures/joined/input_resp_*.csv

  calculate_measures_resp:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_resp --output-dir=output/measures
    needs: [generate_study_population_resp]
    outputs:
      moderately_sensitive:
        measure: output/measures/measure_resp_*_rate.csv

  create_baseline_tables:
    run: stata-mp:latest analysis/101_baseline_tables.do
    needs: [generate_study_population_static_2019, generate_study_population_static_2020, generate_study_population_static_2021]
    outputs:
      moderately_sensitive:
        log: logs/table1_descriptives.log
        output: output/tables/baseline_table_*.csv

  graphs:
    run: stata-mp:latest analysis/102_graphs.do
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        log: logs/graphs.log
        output: output/graphs/line_*.svg
        data: output/graphs/line_*.csv

 #check:
  #  run: stata-mp:latest analysis/data_check.do
   # needs: [generate_study_population_dm, join_cohorts_dm]
    #outputs:
     # moderately_sensitive:
      #  log: logs/check.log

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 04:07:24

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

Job information

Status
Succeeded
Backend
TPP
Workspace
collateral-imd
Requested by
Ruth Costello
Branch
main
Force run dependencies
No
Git commit hash
1c2d24d
Requested actions
  • generate_study_population_static_2019
  • generate_study_population_static_2020
  • generate_study_population_static_2021
  • create_baseline_tables

Code comparison

Compare the code used in this Job Request