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Job request: 21591

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
ra_outcomes
ID:
2u54aob62dxsqbjk
View repo View project.yaml

This page shows the technical details of what happened when 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 indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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: 10000

actions:
  # Study definition for objective 3 - on hold
  # First for baseline tables
  # generate_study_population_monitor_2018:
  #  run: cohortextractor:latest generate_cohort --study-definition study_definition_monitor_bl --index-date-range "2018-03-01"
  #  outputs:
  #    highly_sensitive:
  #      cohort: output/input_monitor_bl_2018-03-01.csv
  
  #generate_study_population_monitor_2020:
  #  run: cohortextractor:latest generate_cohort --study-definition study_definition_monitor_bl --index-date-range "2020-03-23"
  #  outputs:
  #    highly_sensitive:
  #      cohort: output/input_monitor_bl_2020-03-23.csv
  
  # Generate baseline tables objective 3
  #baseline_monitor:
  #  run: stata-mp:latest analysis/check.do
  #  needs: [generate_study_population_monitor_2018, generate_study_population_monitor_2020]
  #  outputs:
  #    moderately_sensitive:
  #      log: logs/baseline.log
  
  # Study definition for flowchart
  generate_study_population_flowchart:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flowchart
    outputs:
      highly_sensitive:
        cohort: output/input_flowchart.csv
  flowchart:
    run: stata-mp:latest analysis/flowchart.do
    needs: [generate_study_population_flowchart]
    outputs:
      moderately_sensitive:
        log: logs/flowchart.log
        table: output/flowchart/values.txt
  #Study definition for outpatient objectives 1 & 2
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv
  
  
  #Static study population for measures
  
  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
  #Study population for time-series
  generate_study_population_op:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_op_meas --index-date-range "2019-04-01 to 2023-11-30 by month" --output-dir=output/measures --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/measures/input_op_meas*.csv

  join_cohorts:
    run: >
      cohort-joiner:v0.0.56
        --lhs output/measures/input_op_meas*.csv
        --rhs output/input_static.csv
        --output-dir output/measures/join/
    needs: [generate_study_population_op, generate_study_population_static]
    outputs: 
      highly_sensitive:
        cohort: output/measures/join/input_op*.csv
  
  calculate_measures_op:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_op_meas --output-dir=output/measures/join
    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        measure: output/measures/join/measure_op_*_rate.csv
        measure_drug: output/measures/join/measure_med_*_rate.csv
        measure_hosp: output/measures/join/measure_hosp_*_rate.csv

  #generate_study_population_other:
  #  run: cohortextractor:latest generate_cohort --study-definition study_definition_other --index-date-range "2019-03-01 to 2022-03-31 by month" --output-dir=output/measures --output-format=csv
  #  outputs:
  #    highly_sensitive:
  #      cohort: output/measures/input_other*.csv
  
  #calculate_measures_other:
  #  run: cohortextractor:latest  generate_measures --study-definition study_definition_other --output-dir=output/measures
  #  needs: [generate_study_population_other]
  #  outputs:
  #    moderately_sensitive:
  #      measure: output/measures/measure_hosp_*_rate.csv
  #      measure_drug: output/measures/measure_med_*_rate.csv

  # Generate baseline tables
  graphs:
    run: stata-mp:latest analysis/graphs.do
    needs: [calculate_measures_op]
    outputs:
      moderately_sensitive:
        log: logs/graphs.log
        graphs: output/graphs/line*.svg 
        table: output/graphs/elective_data.csv 

  outpatients:
    run: stata-mp:latest analysis/outpatients.do
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        log: logs/outpatients.log
        output: output/tables/op_*.csv
        tables: output/tables/characteristics*.csv
        temp: output/tables/logistic*.csv
        drug: output/tables/drug*.csv
       # plot: output/tables/coef*

  sankey:
    run: r:latest analysis/sankey.r
    needs: [generate_study_population]
    outputs: 
      moderately_sensitive:
        graphs: output/sankey_compact.csv

  #time_series_checks:
  #  run: stata-mp:latest analysis/time_series_checks.do
  #  needs: [generate_study_population_op, calculate_measures_op]
  #  outputs: 
  #    moderately_sensitive: 
  #      log: logs/time_series_checks.log
  #      graphs: output/time_series/checks*.svg

  time_series:
    run: stata-mp:latest analysis/time_series.do
    needs: [calculate_measures_op]
    outputs: 
      moderately_sensitive: 
        log: logs/time_series.log
        graphs: output/time_series/itsa*.svg
        data: output/tables/all_itsa_output.csv
        plots: output/time_series/plot_data*.csv
        data_check: output/measures/join/measure_op_appt_all_n_rate.csv
  
  #Study definition for outpatient objectives - population for BSR abstract
  generate_study_population_bsr_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_bsr --index-date-range "2019-04-01" --output-dir=output/measures
    outputs:
      highly_sensitive:
        #cohort: output/measures/op/input_bsr_2019-04-01.csv - file for BSR abstract 
        cohort: output/measures/input_bsr_2019-04-01.csv

  generate_study_population_bsr_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_bsr --index-date-range "2020-04-01" --output-dir=output/measures
    outputs:
      highly_sensitive:
        #cohort: output/measures/op/input_bsr_2020-04-01.csv - file for BSR abstract 
        cohort: output/measures/input_bsr_2020-04-01.csv

  generate_study_population_bsr_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_bsr --index-date-range "2021-04-01" --output-dir=output/measures
    outputs:
      highly_sensitive:
        #cohort: output/measures/op/input_bsr_2021-04-01.csv - file for BSR abstract 
        cohort: output/measures/input_bsr_2021-04-01.csv
  bsr: 
    run: stata-mp:latest analysis/bsr.do
    needs: [generate_study_population_bsr_2019, generate_study_population_bsr_2020, generate_study_population_bsr_2021]
    outputs:
      moderately_sensitive:
        log: logs/bsr.log
        output: output/op_long/bsr*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 24:03:46

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

Job information

Status
Succeeded
Backend
TPP
Workspace
ra_outcomes
Requested by
Ruth Costello
Branch
main
Force run dependencies
No
Git commit hash
0077fe3
Requested actions
  • generate_study_population
  • generate_study_population_static
  • generate_study_population_op
  • join_cohorts
  • calculate_measures_op

Code comparison

Compare the code used in this Job Request