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Job request: 21427

Organisation:
NHS England
Workspace:
vte-diagnoses-and-deaths
ID:
3showihhbuwmbthj
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Joshua Mutio 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 
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: 00:14:07

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

Job request

Status
Succeeded
Backend
TPP
Workspace
vte-diagnoses-and-deaths
Requested by
Joshua Mutio
Branch
main
Force run dependencies
Yes
Git commit hash
9657ba0
Requested actions
  • initial_analysis

Code comparison

Compare the code used in this job request