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Job request: 14136

Organisation:
Bennett Institute
Workspace:
opioids-covid-research
ID:
hcor5tul6nshyloz
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 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

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
  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 2022-03-01 by month" 
      --output-dir=output 
      --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/i*.csv

  ## Add ethnicity
  join_cohorts_test:
    run: >
      cohort-joiner:v0.0.48
        --lhs output/i*.csv
        --rhs output/input_ethnicity.csv
        --output-dir output/data
    needs: [generate_study_population_test, generate_ethnicity_cohort]
    outputs:
      highly_sensitive:
        cohort: output/data/input*.csv 
        
  ## Generate measures
  generate_measures_test:
    run: >
      cohortextractor:latest generate_measures 
        --study-definition study_definition_test
        --output-dir output/data
    needs: [join_cohorts_test]
    outputs:
      moderately_sensitive:
        measure_csv: output/data/measure*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 05:07:14

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

Job request

Status
Succeeded
Backend
TPP
Workspace
opioids-covid-research
Requested by
Andrea Schaffer
Branch
main
Force run dependencies
No
Git commit hash
742c3e9
Requested actions
  • generate_study_population_test
  • join_cohorts_test
  • generate_measures_test

Code comparison

Compare the code used in this job request