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Job request: 24677

Organisation:
Bennett Institute
Workspace:
death-report
ID:
riucrpua7xmb34vw
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Martina Pesce 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:
    dataset_death_date_diff
    Status:
    Status: Succeeded
    Job identifier:
    pwknqlczk54tmsve
  • Action:
    measures_overall
    Status:
    Status: Failed
    Job identifier:
    pttrehss6ccg2233
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    summary_stat
    Status:
    Status: Failed
    Job identifier:
    5bvzsvdra3ba32sc
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    table_DoD
    Status:
    Status: Failed
    Job identifier:
    s7uppdyz2wiud35i
    Error:
    nonzero_exit: Job exited with an error
  • Action:
    table_measure_rate
    Status:
    Status: Failed
    Job identifier:
    p2soosu7q6h3yas7
    Error:
    cancelled_by_user: Cancelled by user

Pipeline

Show project.yaml 
version: '4.0'

actions:
#Dataset for diff time
  dataset_death_date_diff:
    run: ehrql:v1 generate-dataset analysis/dataset_definition.py --output output/dataset_death_date_diff.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/dataset_death_date_diff.csv.gz
  
  summary_stat:
    run: r:v2 analysis/summary_stats.R
      --output output/DoD/summary_stats_DoD.csv 
    needs: [dataset_death_date_diff]
    outputs:
      moderately_sensitive:
        continuous: output/DoD/summary_stats_DoD.csv
        categorical: output/DoD/table_freq_DoD.csv

  table_DoD:
    run: r:v2 analysis/Table_DoD.R
      --output output/report/*.csv 
    needs: [dataset_death_date_diff]
    outputs:
      moderately_sensitive:
        categorical1: output/report/collate_death_source_table.csv
        categorical2: output/report/collate_DoD_diff_table.csv




# Measures
  measures_overall:
    run: ehrql:v1 generate-measures analysis/measure_def.py 
      --output output/measures/measures_overall.csv
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measures_overall.csv
  
  table_measure_rate:
    run: r:v2 analysis/Table_measure_rate.R
      --output output/report/*.csv 
    needs: [measures_overall]
    outputs:
      moderately_sensitive:
        categorical: output/report/collate_measures_rate_table.csv

  measures_by_practice:
    run: ehrql:v1 generate-measures analysis/measure_practice.py 
      --output output/measures/measures_by_practice.csv
    outputs:
      highly_sensitive:
        measure_csv: output/measures/measures_by_practice.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 08:51:24

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

Job request

Status
Failed
Backend
TPP
Workspace
death-report
Requested by
Martina Pesce
Branch
main
Force run dependencies
Yes
Git commit hash
6b22db1
Requested actions
  • dataset_death_date_diff
  • summary_stat
  • table_DoD
  • measures_overall
  • table_measure_rate

Code comparison

Compare the code used in this job request