Skip to content

Job request: 20935

Organisation:
Workspace:
waiting-list
ID:
7nk5wmvaquhnjeqi

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
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  

  ##### Analysis - closed pathways #####
  
  checks_clockstops:
   run: r:latest analysis/clockstops/checks_clockstops.R
   needs: [generate_dataset_clockstops]
   outputs:
      moderately_sensitive:
        data: output/clockstops/*.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.csv
        data2: output/clockstops/cat_var_dist.csv
        data3: output/clockstops/wait_time_pcent.csv
        data4: output/clockstops/wait_time.csv
        data5: output/clockstops/med_counts_by_period.csv
        plots: output/clockstops/plot_*.png

  ortho_stats_clockstops:
   run: r:latest analysis/clockstops/ortho_stats_clockstops.R
   needs: [final_cohort_clockstops]
   outputs:
      moderately_sensitive:
        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_counts_by_period_ortho.csv
        plots: output/clockstops/plot*.png  

  ##### Opioid measures - closed pathways #####
  
  measures_any_opioid:
    run: ehrql:v0 generate-measures analysis/measures_any_opioid.py 
      --output output/measures/measures_any_opioid.csv
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_any_opioid.csv
  
  measures_hi_opioid:
    run: ehrql:v0 generate-measures analysis/measures_hi_opioid.py 
      --output output/measures/measures_hi_opioid.csv
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_hi_opioid.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

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

  # checks_openpathways:
  #  run: r:latest analysis/openpathways/checks_openpathways.R
  #  needs: [generate_dataset_openpathways]
  #  outputs:
  #     moderately_sensitive:
  #       data: output/openpathways/*.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_open.csv
  #       data2: output/openpathways/cat_var_dist_open.csv
  #       data3: output/openpathways/wait_time_pcent_open.csv
  #       data4: output/openpathways/wait_time_open.csv
  #       data5: output/openpathways/med_counts_by_period_open.csv
  #       plots: output/openpathways/plot_*.png

  # ortho_stats_openpathways:
  #  run: r:latest analysis/openpathways/ortho_stats_openpathways.R
  #  needs: [final_cohort_openpathways]
  #  outputs:
  #     moderately_sensitive:
  #       data1: output/openpathways/rtt_dates_ortho_open.csv
  #       data2: output/openpathways/cat_var_dist_ortho_open.csv
  #       data3: output/openpathways/wait_time_pcent_ortho_open.csv
  #       data4: output/openpathways/wait_time_ortho_open.csv
  #       data5: output/openpathways/med_counts_by_period_ortho_open.csv
  #       plots: output/openpathways/plot*.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 70:32:41

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

Job information

Status
Succeeded
Backend
TPP
Workspace
waiting-list
Requested by
Andrea Schaffer
Branch
main
Force run dependencies
No
Git commit hash
08b3d5e
Requested actions
  • measures_any_opioid
  • measures_hi_opioid
  • opioids_by_week