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Job request: 14737

Organisation:
Bennett Institute
Workspace:
opioids-covid-research
ID:
qwmpwcbvwqltmina
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Andrea Schaffer 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 
######################################

# This script defines the project pipeline - it specifies the execution orders for all the code in this
# repo using a series of actions.

######################################

version: '3.0'

expectations:
  population_size: 10000

actions:

  # Extract data ----
  
  ## Cohort data
  generate_study_population_1:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2018-01-01 to 2018-12-01 by month" 
      --output-dir=output 
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv

  generate_study_population_2:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition
      --index-date-range "2019-01-01 to 2019-12-01 by month" 
      --output-dir=output 
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/input*.csv

  generate_study_population_3:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition
      --index-date-range "2020-01-01 to 2020-12-01 by month" 
      --output-dir=output 
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/inpu*.csv

  generate_study_population_4:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition
      --index-date-range "2021-01-01 to 2021-12-01 by month" 
      --output-dir=output 
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/inp*.csv
  
  generate_study_population_5:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition
      --index-date-range "2022-01-01 to 2022-03-01 by month" 
      --output-dir=output 
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/in*.csv

  ## Ethnicity      
  generate_ethnicity_cohort:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_ethnicity
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv


  # Data processing ----
  
  ## Add ethnicity
  join_cohorts:
    run: >
      cohort-joiner:v0.0.48
        --lhs output/input_*.csv
        --rhs output/input_ethnicity.csv
        --output-dir output/data
    needs: [generate_study_population_1,  generate_study_population_2, 
      generate_study_population_5, generate_study_population_3, 
      generate_study_population_4, generate_ethnicity_cohort]
    outputs:
      highly_sensitive:
        cohort: output/data/input_*.csv 


  ## Generate measures - full population
  generate_measures:
    run: >
      cohortextractor:latest generate_measures 
        --study-definition study_definition
        --output-dir output/data
    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        measure_csv: output/data/measure_*.csv


  ## Process data - time series
  process_data_ts:
   run: r:latest analysis/process/process_data_ts.R
   needs: [generate_measures, join_cohorts]
   outputs:
      moderately_sensitive:
        measure_csv: output/joined/final_*.csv

  ## Process data - table
  process_data_table:
   run: r:latest analysis/process/process_data_table.R
   needs: [generate_measures, join_cohorts]
   outputs:
      moderately_sensitive:
        measure_csv: output/joined/final*.csv


  # Results ---

  ## Time series
  timeseries:
    run: r:latest analysis/descriptive/time_series_stand.R
    needs: [process_data_ts]
    outputs:
      moderately_sensitive:
        table: output/time series/ts_*.csv  
  
  ## Time series graphs
  # graphs:
  #   run: r:latest analysis/descriptive/graphs.R
  #   needs: [timeseries]
  #   outputs:
  #     moderately_sensitive:
  #       plot: output/time series/graphs/graph*.png

  ## Table 
  table:
    run: r:latest analysis/descriptive/table_stand.R
    needs: [process_data_table]
    outputs:
      moderately_sensitive:
        table: output/tables/table_*.csv

  
 ##################### TESTING ########################

 
  generate_study_population_test:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition_test
      --index-date-range "2020-01-01 to 2022-12-01 by month" 
      --output-dir=output 
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/i*.csv
        
  ## Generate measures
  generate_measures_test:
    run: >
      cohortextractor:latest generate_measures 
        --study-definition study_definition_test
        --output-dir output/
    needs: [generate_study_population_test]
    outputs:
      moderately_sensitive:
        measure_csv: output/measure*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 06:31:22

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

Job information

Status
Succeeded
Backend
TPP
Workspace
opioids-covid-research
Requested by
Andrea Schaffer
Branch
main
Force run dependencies
No
Git commit hash
f4372bb
Requested actions
  • generate_study_population_test
  • generate_measures_test

Code comparison

Compare the code used in this Job Request