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Job request: 11985

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
ra_outcomes
ID:
outekxgngqigngdh
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 within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

  • Action:
    bsr
    Status:
    Status: Succeeded
    Job identifier:
    ciz2viegwxof4dan

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: 00:04:31

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

Job request

Status
Succeeded
Backend
TPP
Workspace
ra_outcomes
Requested by
Ruth Costello
Branch
main
Force run dependencies
No
Git commit hash
9aae342
Requested actions
  • bsr

Code comparison

Compare the code used in this job request