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Job request: 11967

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
ra_outcomes
ID:
3nd2rdj3ywaemulm
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

  • Action:
    bsr
    Status:
    Status: Succeeded
    Job identifier:
    eo2sbshhg2puejgs

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:
  # Study definition for objective 3
  # 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 outpatient objectives 1 & 2
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  generate_study_population_op:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_op_meas --index-date-range "2019-04-01 to 2022-04-30 by month" --output-dir=output/measures --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/measures/input_op_meas*.csv
  
  calculate_measures_op:
    run: cohortextractor:latest  generate_measures --study-definition study_definition_op_meas --output-dir=output/measures
    needs: [generate_study_population_op]
    outputs:
      moderately_sensitive:
        measure: output/measures/measure_op_*_rate.csv

  generate_study_population_other:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_other --index-date-range "2018-03-01 to 2022-04-30 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, calculate_measures_other]
    outputs:
      moderately_sensitive:
        log: logs/graphs.log
        graphs: output/graphs/line*.svg

  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

  time_series_checks:
    run: stata-mp:latest analysis/time_series_checks.do
    needs: [calculate_measures_other, 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_other, calculate_measures_op]
    outputs: 
      moderately_sensitive: 
        log: logs/time_series.log
        graphs: output/time_series/itsa*.svg
        tables: output/time_series/tsreg*.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/op 
    outputs:
      highly_sensitive:
        cohort: output/measures/op/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/op 
    outputs:
      highly_sensitive:
        cohort: output/measures/op/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/op 
    outputs:
      highly_sensitive:
        cohort: output/measures/op/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/tables/bsr_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:04:37

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
7326968
Requested actions
  • bsr

Code comparison

Compare the code used in this Job Request