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Job request: 24317

Organisation:
Bennett Institute
Workspace:
main
ID:
lz2z4djgoqocksad
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Alex Walker requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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: "4.0"

actions:
  generate_measures_alt:
    run: >
      ehrql:v1 generate-measures
        analysis/measure_definition.py
        --output output/measures_alt.csv
        --
        --codelist codelists/opensafely-alanine-aminotransferase-alt-tests.csv
    outputs:
      moderately_sensitive:
        measures: output/measures_alt.csv

  generate_measures_chol:
    run: >
      ehrql:v1 generate-measures
        analysis/measure_definition.py
        --output output/measures_chol.csv
        --
        --codelist codelists/opensafely-cholesterol-tests.csv
    outputs:
      moderately_sensitive:
        measures: output/measures_chol.csv

  generate_measures_hba1c:
    run: >
      ehrql:v1 generate-measures
        analysis/measure_definition.py
        --output output/measures_hba1c.csv
        --
        --codelist codelists/opensafely-glycated-haemoglobin-hba1c-tests.csv
    outputs:
      moderately_sensitive:
        measures: output/measures_hba1c.csv

  generate_measures_rbc:
    run: >
      ehrql:v1 generate-measures
        analysis/measure_definition.py
        --output output/measures_rbc.csv
        --
        --codelist codelists/opensafely-red-blood-cell-rbc-tests.csv
    outputs:
      moderately_sensitive:
        measures: output/measures_rbc.csv

  generate_measures_sodium:
    run: >
      ehrql:v1 generate-measures
        analysis/measure_definition.py
        --output output/measures_sodium.csv
        --
        --codelist codelists/opensafely-sodium-tests-numerical-value.csv
    outputs:
      moderately_sensitive:
        measures: output/measures_sodium.csv

  # Runs test to ensure correctness of measures queries
  generate_test_dataset:
    run: >
      ehrql:v1 generate-dataset
        analysis/dataset_definition.py
        --output output/test_dataset.csv
        --test-data-file analysis/test_dataset_definition.py
        --
        --codelist codelists/opensafely-alanine-aminotransferase-alt-tests.csv
    outputs:
      highly_sensitive:
        dataset: output/test_dataset.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 08:28:18

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

Job information

Status
Failed
Backend
TPP
Workspace
main
Requested by
Alex Walker
Branch
main
Force run dependencies
No
Git commit hash
a4e8c40
Requested actions
  • generate_measures_alt
  • generate_measures_chol
  • generate_measures_hba1c
  • generate_measures_rbc
  • generate_measures_sodium

Code comparison

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