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Job request: 21520

Organisation:
Bennett Institute
Workspace:
waiting-list
ID:
helomkujha5f43vh
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: 1000

actions:

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

  # Closed (completed) RTT pathways
  generate_dataset_clockstops:
    run: ehrql:v0 generate-dataset analysis/dataset_definition_clockstops.py 
      --output output/data/dataset_clockstops.csv.gz
    outputs:
      highly_sensitive:
        cohort: output/data/dataset_clockstops.csv.gz  

  # Open (incomplete) RTT pathways
  generate_dataset_openpathways:
    run: ehrql:v0 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 number of pathways over time ####

  measures_checks:
    run: ehrql:v0 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:v0 generate-measures analysis/measures_opioid.py 
      --output output/measures/measures_any_opioid.csv
      --dummy-data-file dummy/dummy_any_opioid.csv
      --
      --codelist "opioid_codes"
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_any_opioid.csv

  measures_hi_opioid:
    run: ehrql:v0 generate-measures analysis/measures_opioid.py 
      --output output/measures/measures_hi_opioid.csv
      --
      --codelist "hi_opioid_codes"
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_hi_opioid.csv
      
  measures_opioid_weeks:
    run: ehrql:v0 generate-measures analysis/measures_opioid_weeks.py 
      --output output/measures/measures_opioid_weeks.csv
      --dummy-data-file dummy/dummy_opioid_weeks.csv
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_opioid_weeks.csv

  opioids_by_week:
   run: r:latest analysis/clockstops/opioids_by_week.R
   needs: [measures_any_opioid, measures_hi_opioid]
   outputs:
      moderately_sensitive:
        data: output/clockstops/opioid*.csv
      #  plots: output/clockstops/plo*.png
  
  opioids_by_week_group:
   run: r:latest analysis/clockstops/opioids_by_week_group.R
   needs: [measures_opioid_weeks]
   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

  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

  ortho_stats_clockstops:
   run: r:latest analysis/clockstops/ortho_stats_clockstops.R
   needs: [final_cohort_clockstops]
   outputs:
      moderately_sensitive:
        data0: output/clockstops/exclude_ortho.csv
        data1: output/clockstops/rtt_dates_ortho.csv
        data2: output/clockstops/cat_var_dist_ortho.csv
        data3: output/clockstops/wait_time_pcent_ortho.csv
        data4: output/clockstops/wait_time_ortho.csv
        data5: output/clockstops/med_by_period_ortho.csv
        data6: output/clockstops/wait_by_group_ortho.csv
        plot1: output/clockstops/wait_time_ortho.png
        plot2: output/clockstops/rtt_dates_ortho.png

  ortho_opioid_clockstops:
    run: r:latest analysis/clockstops/ortho_opioid_clockstops.R
    needs: [final_cohort_clockstops]
    outputs:
      moderately_sensitive:
        data1: output/clockstops/cumulative_opi.csv
        plot1: output/clockstops/cumulative_opi.png


  ##### Analysis - open pathways #####

  checks_cohort_openpathways:
   run: r:latest analysis/openpathways/checks_cohort_openpathways.R
   needs: [generate_dataset_openpathways]
   outputs:
      moderately_sensitive:
        data: output/openpathways/chec*.csv

  final_cohort_openpathways:
   run: r:latest analysis/openpathways/final_cohort_openpathways.R
   needs: [generate_dataset_openpathways]
   outputs:
      highly_sensitive:
        cohort: output/data/cohor*.csv.gz

  full_stats_openpathways:
   run: r:latest analysis/openpathways/full_stats_openpathways.R
   needs: [final_cohort_openpathways]
   outputs:
      moderately_sensitive:
        data1: output/openpathways/rtt_dates_full.csv
        data2: output/openpathways/cat_var_dist_full.csv
        data3: output/openpathways/wait_time_pcent_full.csv
        data4: output/openpathways/wait_time_full.csv
        data5: output/openpathways/wait_by_group_full.csv
        plot1: output/openpathways/wait_time_full.png
        plot2: output/openpathways/rtt_dates_full.png

  ortho_stats_openpathways:
   run: r:latest analysis/openpathways/ortho_stats_openpathways.R
   needs: [final_cohort_openpathways]
   outputs:
      moderately_sensitive:
        data0: output/openpathways/exclude_ortho.csv
        data1: output/openpathways/rtt_dates_ortho.csv
        data2: output/openpathways/cat_var_dist_ortho.csv
        data3: output/openpathways/wait_time_pcent_ortho.csv
        data4: output/openpathways/wait_time_ortho.csv
        data5: output/openpathways/wait_by_group_ortho.csv
        plot1: output/openpathways/wait_time_ortho.png
        plot2: output/openpathways/rtt_dates_ortho.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:55

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

Job request

Status
Succeeded
Backend
TPP
Workspace
waiting-list
Requested by
Andrea Schaffer
Branch
main
Force run dependencies
No
Git commit hash
2a99920
Requested actions
  • full_stats_openpathways

Code comparison

Compare the code used in this job request