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Job request: 2304

Organisation:
Bennett Institute
Workspace:
ncs-hospital-disruption
ID:
t427zjzanlplmxzp
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher 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: 10000

actions:


  generate_cohort_imd_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_imd_ethnicity
    outputs:
      highly_sensitive:
        cohort: output/input_imd_ethnicity.csv
  

  generate_cohort_1:
    # week 1 2019 to 21 2019 inclusive
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-12-31 to 2019-05-26 by week"
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv

  generate_cohort_2:
    # week 22 2019 to 42 2019 inclusive
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-05-27 to 2019-10-20 by week"
    outputs:
      highly_sensitive:
        cohort: output/input*.csv

  generate_cohort_3:
    # week  43 2019 to 11 2020 inclusive
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-10-21 to 2020-03-15 by week"
    outputs:
      highly_sensitive:
        cohort: output/inpu*.csv

  generate_cohort_4:
    # week 12 2020 to 32 2020 inclusive
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-03-16 to 2020-08-09 by week"
    outputs:
      highly_sensitive:
        cohort: output/inp*.csv

  generate_cohort_5:
    # week 33 2020 to week 53 2020 inclusive
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-08-10 to 2021-01-03 by week"
    outputs:
      highly_sensitive:
        cohort: output/in*.csv

  join_ethnicity_imd:
    run: python:latest python analysis/join_ethnicity_imd.py
    needs: [generate_cohort_1, generate_cohort_2, generate_cohort_3, generate_cohort_4, generate_cohort_5, generate_cohort_imd_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/i*.csv
   
  calculate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition
    needs: [join_ethnicity_imd]
    outputs:
      moderately_sensitive:
        measure: output/measure_*_rate.csv

  calculate_measures_demographics:
    run: python:latest python analysis/generate_measures_demographics.py
    needs: [join_ethnicity_imd]
    outputs:
      moderately_sensitive:
        csvs: output/measure_*_rate_*.csv
        

  standardise_and_plot:
    run: python:latest python analysis/time_series_plots.py
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        tables: output/*_table.csv
        graph: output/*_time_series_plot.svg

  standardise_and_plot_demographics:
    run: python:latest python analysis/time_series_plots_demographics.py
    needs: [calculate_measures, calculate_measures_demographics]
    outputs:
      moderately_sensitive:
        tables: output/*_breakdown.csv
        tables_combined: output/combined_disease_*.csv
#         graph: output/time_series_plot_*.svg
#         combined_graph: output/combined_diseases_time_series.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 53:27:58

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

Job request

Status
Succeeded
Backend
TPP
Workspace
ncs-hospital-disruption
Requested by
Louis Fisher
Branch
master
Force run dependencies
No
Git commit hash
9f019d0
Requested actions
  • generate_cohort_imd_ethnicity
  • generate_cohort_1
  • generate_cohort_2
  • generate_cohort_3
  • generate_cohort_4
  • generate_cohort_5
  • join_ethnicity_imd
  • calculate_measures
  • calculate_measures_demographics
  • standardise_and_plot

Code comparison

Compare the code used in this job request