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Job request: 19601

Organisation:
Bennett Institute
Workspace:
isaric-translation
ID:
uq2pg5pgw6tlb5f4
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Millie Green 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

Pipeline

Show project.yaml 
################################################################################
#
# Description: This script defines the project pipeline - it specifys the
#              execution orders for all the code in this repo using a series of
#              actions.
#
# Author(s): M Green
# Date last updated: 07/08/2023
#
################################################################################

version: '3.0'

expectations:
  population_size: 1000

actions:

  # Extract isaric data ----
  extract_first_isaric_admission:
    run: >
      ehrql:v0 generate-dataset analysis/dataset_definition_isaric.py
      --output 'output/admissions/isaric_admission1.csv.gz'
    outputs:
      highly_sensitive:
        csv: output/admissions/isaric_admission1.csv.gz

  # Extract sus data ----
  extract_sus_methodA_admission1_cohortextractor:
    run: >
      cohortextractor:latest generate_cohort
      --study-definition study_definition_sus
      --output-file output/admissions/sus_methodA_admission1_cohortextractor.csv.gz
      --param admission_number=1
      --param admission_method=A
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodA_admission1_cohortextractor.csv.gz

  extract_first_sus_admission_methodA_ehrQL:
    run: >
      ehrql:v0
        generate-dataset analysis/dataset_definition_sus.py
        --output output/admissions/sus_methodA_admission1_ehrQL.csv.gz
        --
        --admission_method A
    outputs:
      highly_sensitive:
        cohort: output/admissions/sus_methodA_admission1_ehrQL.csv.gz

  extract_first_sus_admission_methodB_ehrQL:
    run: >
      ehrql:v0
        generate-dataset analysis/dataset_definition_sus.py
        --output output/admissions/sus_methodB_admission1_ehrQL.csv.gz
        --
        --admission_method B
    outputs:
      highly_sensitive:
        cohort: output/admissions/sus_methodB_admission1_ehrQL.csv.gz

  extract_first_sus_admission_methodC_ehrQL:
    run: >
      ehrql:v0
        generate-dataset analysis/dataset_definition_sus.py
        --output output/admissions/sus_methodC_admission1_ehrQL.csv.gz
        --
        --admission_method C
    outputs:
      highly_sensitive:
        cohort: output/admissions/sus_methodC_admission1_ehrQL.csv.gz

  # Data properties ----
  data_properties:
    run: >
      r:latest
        analysis/data_properties.R
        output/admissions/isaric_admission1.csv.gz
        output/admissions/sus_methodA_admission1_cohortextractor.csv.gz
        output/admissions/sus_methodA_admission1_ehrQL.csv.gz
        output/data_properties
    needs: [extract_first_isaric_admission, extract_sus_methodA_admission1_cohortextractor, extract_first_sus_admission_methodA_ehrQL]
    outputs:
      moderately_sensitive:
        txt1: output/data_properties/*.txt

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:56:27

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

Job request

Status
Failed
Backend
TPP
Workspace
isaric-translation
Requested by
Millie Green
Branch
translation
Force run dependencies
No
Git commit hash
f22c98b
Requested actions
  • extract_first_isaric_admission
  • extract_sus_methodA_admission1_cohortextractor
  • extract_first_sus_admission_methodA_ehrQL
  • extract_first_sus_admission_methodB_ehrQL
  • extract_first_sus_admission_methodC_ehrQL
  • data_properties

Code comparison

Compare the code used in this job request