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Job request: 22213

Organisation:
Bennett Institute
Workspace:
waiting-list
ID:
lg7fehz4fdntsd2i
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 
version: '3.0'

expectations:
  population_size: 100000

actions:

  ##### Dataset definitions #####

  # Closed (completed) RTT pathways
  generate_dataset_clockstops:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_clockstops.py 
      --output output/data/dataset_clockstops.csv.gz
      #--dummy-data-file dummy/dummy_ortho_clockstops.arrow
    outputs:
      highly_sensitive:
        cohort: output/data/dataset_clockstops.csv.gz

  # Open (incomplete) RTT pathways
  # generate_dataset_openpathways:
  #   run: ehrql:v1 generate-dataset analysis/dataset_definition_openpathways.py 
  #     --output output/data/dataset_openpathways.csv.gz
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/data/dataset_openpathways.csv.gz  

  #### Check missing end date ####

  # generate_dataset_clockstops_missing:
  #   run: ehrql:v1 generate-dataset analysis/dataset_definition_clockstops_missing.py 
  #     --output output/data/dataset_clockstops_missing.csv.gz
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/data/dataset_clockstops_missing.csv.gz  

  # checks_missing_clockstops:
  #  run: r:latest analysis/clockstops/checks_missing_clockstops.R
  #  needs: [generate_dataset_clockstops_missing]
  #  outputs:
  #     moderately_sensitive:
  #       data: output/clockstops/check_missing_dates.csv 
  
  
  #### Check number of pathways over time ####

  measures_checks:
    run: ehrql:v1 generate-measures analysis/measures_checks.py 
      --output output/measures/measures_checks.csv
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_checks.csv

  checks_overall_clockstops:
   run: r:latest analysis/clockstops/checks_overall_clockstops.R
   needs: [measures_checks]
   outputs:
      moderately_sensitive:
        data: output/clockstops/chec*.csv


  ##### Opioid measures - closed pathways #####

  measures_any_opioid:
    run: ehrql:v1 generate-measures analysis/measures_opioid.py 
      --output output/measures/measures_any_opioid.csv
      --
      --codelist "opioid_codes"
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_any_opioid.csv

  measures_long_opioid:
    run: ehrql:v1 generate-measures analysis/measures_opioid.py 
      --output output/measures/measures_long_opioid.csv
      --
      --codelist "long_opioid_codes"
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_long_opioid.csv

  measures_short_opioid:
    run: ehrql:v1 generate-measures analysis/measures_opioid.py 
      --output output/measures/measures_short_opioid.csv
      --
      --codelist "short_opioid_codes"
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_short_opioid.csv
  
  measures_weak_opioid:
    run: ehrql:v1 generate-measures analysis/measures_opioid.py 
      --output output/measures/measures_weak_opioid.csv
      --
      --codelist "weak_opioid_codes"
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_weak_opioid.csv

  measures_strong_opioid:
    run: ehrql:v1 generate-measures analysis/measures_opioid.py 
      --output output/measures/measures_strong_opioid.csv
      --
      --codelist "strong_opioid_codes"
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_strong_opioid.csv

  # measures_opioid_stratified:
  #   run: ehrql:v1 generate-measures analysis/measures_opioid_stratified.py 
  #     --output output/measures/measures_opioid_stratified.csv
  #     --
  #     --codelist "opioid_codes"
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: output/measures/measures_opioid_stratified.csv

  # Combine measures
  opioids_by_week:
    run: r:latest analysis/clockstops/opioids_by_week.R
    needs: [measures_any_opioid, measures_weak_opioid, measures_strong_opioid, measures_long_opioid, measures_short_opioid]
    outputs:
      moderately_sensitive:
        data: output/clockstops/opioid*.csv
  
  # measures_opioid_weeks_during:
  #   run: ehrql:v1 generate-measures analysis/measures_opioid_weeks_during.py 
  #     --output output/measures/measures_opioid_weeks_during.csv
  #     --dummy-data-file dummy/dummy_opioid_weeks_during.csv
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: output/measures/measures_opioid_weeks_during.csv

  # measures_opioid_weeks_post:
  #   run: ehrql:v1 generate-measures analysis/measures_opioid_weeks_post.py 
  #     --output output/measures/measures_opioid_weeks_post.csv
  #     --dummy-data-file dummy/dummy_opioid_weeks_post.csv
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: output/measures/measures_opioid_weeks_post.csv

  # opioids_by_week_group:
  #  run: r:latest analysis/clockstops/opioids_by_week_group.R
  #  needs: [measures_opioid_weeks_during, measures_opioid_weeks_post]
  #  outputs:
  #     moderately_sensitive:
  #       data: output/clockstops/opioid_by_week_group.csv
  #       plots: output/clockstops/opioid_by_week_group*.png
        
       
  ##### Analysis - closed pathways #####
  
  # checks_cohort_clockstops:
  #  run: r:latest analysis/clockstops/checks_cohort_clockstops.R
  #  needs: [generate_dataset_clockstops]
  #  outputs:
  #     moderately_sensitive:
  #       data: output/clockstops/check*.csv

  final_cohort_clockstops:
   run: r:latest analysis/clockstops/final_cohort_clockstops.R
   needs: [generate_dataset_clockstops]
   outputs:
      highly_sensitive:
        cohort: output/data/cohort*.csv.gz
      moderately_sensitive:
        exclusions1: output/clockstops/cohort_full_exclusions.csv
        exclusions2: output/clockstops/exclude_ortho.csv
        
  ortho_clockstops_wait_time:
   run: r:latest analysis/clockstops/ortho_clockstops_wait_time.R
   needs: [final_cohort_clockstops]
   outputs:
      moderately_sensitive:
        data1: output/clockstops/rtt_dates_ortho.csv
        data2: output/clockstops/wait_time_pcent_ortho.csv
        data3: output/clockstops/wait_time_ortho.csv
        data4: output/clockstops/wait_by_group_ortho.csv

  ortho_clockstops_freq_dist:
   run: r:latest analysis/clockstops/ortho_clockstops_freq_dist.R
   needs: [final_cohort_clockstops]
   outputs:
      moderately_sensitive:
        data1: output/clockstops/cat_var_dist_ortho.csv
        data2: output/clockstops/cat_var_dist_ortho_prior.csv

  ortho_clockstops_prescribing:
   run: r:latest analysis/clockstops/ortho_clockstops_prescribing.R
   needs: [final_cohort_clockstops]
   outputs:
      moderately_sensitive:
        data1: output/clockstops/med_by_period_ortho.csv
       # data2: output/clockstops/meds_dist_ortho.csv

  # full_stats_clockstops:
  #  run: r:latest analysis/clockstops/full_stats_clockstops.R
  #  needs: [final_cohort_clockstops]
  #  outputs:
  #     moderately_sensitive:
  #       data1: output/clockstops/rtt_dates_full.csv
  #       data2: output/clockstops/cat_var_dist_full.csv
  #       data3: output/clockstops/wait_time_pcent_full.csv
  #       data4: output/clockstops/wait_time_full.csv
  #       data5: output/clockstops/med_by_period_full.csv
  #       data6: output/clockstops/wait_by_group_full.csv
  #       plot1: output/clockstops/wait_time_full.png
  #       plot2: output/clockstops/rtt_dates_full.png

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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:40:29

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

Job request

Status
Failed
Backend
TPP
Workspace
waiting-list
Requested by
Andrea Schaffer
Branch
main
Force run dependencies
No
Git commit hash
5103081
Requested actions
  • ortho_clockstops_wait_time
  • ortho_clockstops_freq_dist
  • ortho_clockstops_prescribing

Code comparison

Compare the code used in this job request