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Job request: 19744

Organisation:
Bennett Institute
Workspace:
opioids-covid-research
ID:
cz36gpdm7pa4ppg7

This page shows the technical details of what happened when 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 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
######################################
# 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:

  generate_dataset_table:
    run: ehrql:v0 generate-dataset analysis/define_dataset_table.py 
      --output output/data/dataset_table.csv.gz
    outputs:
      highly_sensitive:
        cohort: output/data/dataset_table.csv.gz  

  # Measures - overall
  measures_overall:
    run: ehrql:v0 generate-measures analysis/measures_overall.py 
      --output output/measures/measures_overall.csv
      --
      --start-date "2018-01-01"
      --intervals 3
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_overall.csv

  # Measures - by demographic categories
  measures_demo:
    run: ehrql:v0 generate-measures analysis/measures_demo.py 
      --output output/measures/measures_demo.csv
      --
      --start-date "2018-01-01"
      --intervals 54
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_demo.csv

  # Measures - by opioid type
  measures_type:
    run: ehrql:v0 generate-measures analysis/measures_type.py 
      --output output/measures/measures_type.csv
      --
      --start-date "2018-01-01"
      --intervals 54
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_type.csv 

  # Measures - in people in care home
  measures_carehome:
    run: ehrql:v0 generate-measures analysis/measures_carehome.py 
      --output output/measures/measures_carehome.csv
      --
      --start-date "2018-01-01"
      --intervals 54
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_carehome.csv
        
  ## Process data - time series
  process_data_ts:
   run: r:latest analysis/process/process_data_ts.R
   needs: [measures_overall, measures_demo, measures_type, measures_carehome]
   outputs:
      moderately_sensitive:
        timeseries_csv: output/timeseries/ts_*.csv

  ## Time series - rounding
  rounding_ts:
   run: r:latest analysis/process/rounding_ts.R
   needs: [process_data_ts]
   outputs:
      moderately_sensitive:
        timeseries_csv: output/timeseries/ts*.csv

  ## Process data - table
  process_data_table:
   run: r:latest analysis/process/process_data_table.R
   needs: [generate_dataset_table]
   outputs:
      highly_sensitive:
        table_csv: output/processed/final_tables.csv

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

  
  # OLD COHORTEXTRACTOR CODE

  # ## 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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:00:39

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

Job information

Status
Succeeded
Backend
TPP
Requested by
Andrea Schaffer
Branch
main
Force run dependencies
No
Git commit hash
6bf09a7
Requested actions
  • measures_overall

Code comparison

Compare the code used in this Job Request