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Job request: 21439

Organisation:
NHS England
Workspace:
vte-diagnoses-and-deaths
ID:
fy4cv4vlfcdkaky2
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Jon Massey 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: '3.0'

expectations:
  population_size: 1000

actions:

  generate_dataset:
    run: ehrql:v0 generate-dataset analysis/dataset_definition.py --output output/dataset.csv.gz
    outputs:
      highly_sensitive:
        cohort: output/dataset.csv.gz

  generate_pivoted_dataset:
    run: ehrql:v0 generate-dataset analysis/dataset_definition_pivoted.py --output output/dataset_pivoted.csv.gz
    outputs:
      highly_sensitive:
        cohort: output/dataset_pivoted.csv.gz

  initial_analysis:
    run: r:latest analysis/analysis.R
    needs: [generate_dataset]
    outputs:
      moderately_sensitive:
        histogram_primary: output/df_primary_midpoint_rounded.png
        histogram_secondary: output/df_secondary_midpoint_rounded.png
        histogram_secondary_mb: output/df_secondary_mb_midpoint_rounded.png
        histogram_primary_precursor: output/vte_primary_diagnosis_frequency_distribution.csv
        histogram_secondary_precursor: output/vte_secondary_admission_frequency_distribution.csv
        histogram_secondary_mb_precursor: output/vte_secondary_mb_admission_frequency_distribution.csv
        crosstab_secondary: output/crosstab_secondary_codelists_midpoint_rounded.csv
        crosstab_primary_secondary: output/crosstab_primary_secondary_midpoint_rounded.csv

  aggregate_pivots:
    run: python:latest analysis/aggregate_pivots.py
    needs: [generate_pivoted_dataset]
    outputs:
      moderately_sensitive:
        code_counts: output/vte_primary_events*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:08:14

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

Job information

Status
Succeeded
Backend
TPP
Workspace
vte-diagnoses-and-deaths
Requested by
Jon Massey
Branch
main
Force run dependencies
Yes
Git commit hash
b6d06fe
Requested actions
  • aggregate_pivots

Code comparison

Compare the code used in this Job Request