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Job request: 22288

Organisation:
Bennett Institute
Workspace:
waiting-list
ID:
6ajp5qdhdmo2azpb
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

  • Action:
    measures_any_opioid
    Status:
    Status: Failed
    Job identifier:
    toiqs3d4rcfzld7w
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    measures_long_opioid
    Status:
    Status: Failed
    Job identifier:
    hlmeex43fjomrdsb
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    measures_short_opioid
    Status:
    Status: Failed
    Job identifier:
    bigqnrugwvzdut6a
    Error:
    internal_error: Internal error: this usually means a platform issue rather than a problem for users to fix. The tech team are automatically notified of these errors and will be investigating.
  • Action:
    measures_strong_opioid
    Status:
    Status: Failed
    Job identifier:
    fe5wkte2b67impkd
    Error:
    internal_error: Internal error: this usually means a platform issue rather than a problem for users to fix. The tech team are automatically notified of these errors and will be investigating.
  • Action:
    measures_weak_opioid
    Status:
    Status: Failed
    Job identifier:
    7lcvdr2e4lbtnfuw
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    opioids_by_week
    Status:
    Status: Failed
    Job identifier:
    qll4w65bgd7khckh
    Error:
    dependency_failed: Not starting as dependency failed

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.arrow
      --dummy-data-file dummy/dummy_ortho_clockstops.arrow
    outputs:
      highly_sensitive:
        cohort: output/data/dataset_clockstops.arrow
  
  
  #### 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


  ##### 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

  # 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
      
       
  ##### 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

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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 10:27:53

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
6c525b9
Requested actions
  • measures_any_opioid
  • measures_long_opioid
  • measures_short_opioid
  • measures_weak_opioid
  • measures_strong_opioid
  • opioids_by_week

Code comparison

Compare the code used in this job request