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Job request: 26466

Organisation:
Bennett Institute
Workspace:
pifu-data-exploration
ID:
bhsqza6nktame2bd
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:
    tables
    Status:
    Succeeded
    Job identifier:
    o2xhbmgcw6mloilc

Pipeline

Show project.yaml 
version: '5.0'

actions:
  # generate_dataset_explore:
  #   run: ehrql:v1 generate-dataset analysis/dataset_definition_explore.py --output output/dataset_explore.csv.gz
  #   outputs:
  #     highly_sensitive:
  #       dataset: output/dataset_explore.csv.gz

  # table_explore:
  #   run: r:v2 analysis/process/data_exploration.R
  #   needs: [generate_dataset_explore]
  #   outputs:
  #     moderately_sensitive:
  #       table1: output/processed/table_explore.csv
  #       #table2: output/processed/table_pfu_explore.csv
  #       table3: output/processed/counts_explore.csv

  generate_dataset_everyone:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_everyone.py --output output/dataset_everyone.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/dataset_everyone.csv.gz

  generate_dataset_rheum:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_specialty.py --output output/dataset_rheumatology.csv.gz
      --
      --trt_func_code 410
    outputs:
      highly_sensitive:
        dataset: output/dataset_rheumatology.csv.gz
  
  generate_dataset_derm:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_specialty.py --output output/dataset_dermatology.csv.gz
      --
      --trt_func_code 330
    outputs:
      highly_sensitive:
        dataset: output/dataset_dermatology.csv.gz

  generate_dataset_gastro:
    run: ehrql:v1 generate-dataset analysis/dataset_definition_specialty.py --output output/dataset_gastroenterology.csv.gz
      --
      --trt_func_code 301
    outputs:
      highly_sensitive:
        dataset: output/dataset_gastroenterology.csv.gz

  measures_everyone:
    run: ehrql:v1 generate-measures analysis/measures_everyone.py --output output/measures/measures_everyone.csv
    outputs:
      moderately_sensitive:
        dataset: output/measures/measures_everyone.csv
    
  measures_rheum:
    run: ehrql:v1 generate-measures analysis/measures_specialty.py --output output/measures/measures_rheum.csv
      --
      --trt_func_code 410
    outputs:
      moderately_sensitive:
        dataset: output/measures/measures_rheum.csv
  
  measures_gastro:
    run: ehrql:v1 generate-measures analysis/measures_specialty.py --output output/measures/measures_gastro.csv
      --
      --trt_func_code 301
    outputs:
      moderately_sensitive:
        dataset: output/measures/measures_gastro.csv
  
  measures_derm:
    run: ehrql:v1 generate-measures analysis/measures_specialty.py --output output/measures/measures_derm.csv
      --
      --trt_func_code 330
    outputs:
      moderately_sensitive:
        dataset: output/measures/measures_derm.csv

  measures_time_rheum:
    run: ehrql:v1 generate-measures analysis/measures_time_specialty.py --output output/measures/measures_time_rheum.csv
      --
      --trt_func_code 410
    outputs:
      moderately_sensitive:
        dataset: output/measures/measures_time_rheum.csv

  measures_time_gastro:
    run: ehrql:v1 generate-measures analysis/measures_time_specialty.py --output output/measures/measures_time_gastro.csv
      --
      --trt_func_code 301
    outputs:
      moderately_sensitive:
        dataset: output/measures/measures_time_gastro.csv

  measures_time_derm:
    run: ehrql:v1 generate-measures analysis/measures_time_specialty.py --output output/measures/measures_time_derm.csv
      --
      --trt_func_code 330
    outputs:
      moderately_sensitive:
        dataset: output/measures/measures_time_derm.csv

  tables:
    run: r:v2 analysis/process/tables.R
    needs: [generate_dataset_everyone, generate_dataset_rheum, generate_dataset_gastro, generate_dataset_derm]
    outputs:
      moderately_sensitive:
        table: output/processed/table*.csv

  # time_series:
  #   run: r:v2 analysis/process/measures_process.R
  #   needs: [measures_everyone, measures_rheum, measures_gastro, measures_derm]
  #   outputs:
  #     moderately_sensitive:
  #       timeseries1: output/processed/time_series_overall.csv
  #       timeseries2: output/processed/time_series_specialty.csv

  # opa_time:
  #   run: r:v2 analysis/process/measures_time_process.R
  #   needs: [measures_time_rheum, measures_time_gastro, measure_time_derm]
  #   outputs:
  #     moderately_sensitive:
  #       table: output/processed/outpatient_time.csv

Job statistics

Status Count Percentage
Pending 0 0%
Running 0 0%
Succeeded 1 100%
Failed 0 0%

1 / 1 (100%) complete

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:19:24

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

Job request

Status
Succeeded
Backend
TPP
Workspace
pifu-data-exploration
Requested by
Andrea Schaffer
Branch
main
Force run dependencies
No
Git commit hash
f0fac7b
Requested actions
  • tables

Code comparison

Compare the code used in this job request