Job request: 1582

Organisation:: Bennett Institute
Workspace:: ncs-hospital-disruption-2
ID:: p6uft6fx6uxve5bq

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 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

Action:

generate_cohort_5

Status:

Status: Succeeded

Job identifier:

qgxrsbcywbe5unat
Action:

generate_cohort_2

Status:

Status: Succeeded

Job identifier:

qnloie3tr3y2wuog
Action:

generate_cohort_1

Status:

Status: Succeeded

Job identifier:

bi7xkoscz3kznfri
Action:

generate_cohort_4

Status:

Status: Succeeded

Job identifier:

xigr33ctgneskfnb
Action:

generate_cohort_3

Status:

Status: Succeeded

Job identifier:

aumyzqmricipo7dt
Action:

generate_cohort_imd_ethnicity

Status:

Status: Succeeded

Job identifier:

of2utvzlsbkb4ucr
Action:

join_ethnicity_imd

Status:

Status: Succeeded

Job identifier:

4sqelgaj5zbb6zal
Action:

calculate_measures

Status:

Status: Succeeded

Job identifier:

lyro2owh36deflxh
Action:

calculate_measures_demographics

Status:

Status: Succeeded

Job identifier:

opc7gvzep7xpqlg5
Action:

standardise_and_plot

Status:

Status: Succeeded

Job identifier:

zd6me4beeirlvz3z
Action:

standardise_and_plot_demographics

Status:

Status: Succeeded

Job identifier:

ehflgwkfpedgkycu

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/*_rate.csv
        graph: output/time_series_plot.svg

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

Timeline

Created: 3 years, 7 months ago 09 Apr 2021 15:32:43 UTC
Started: 3 years, 7 months ago 09 Apr 2021 15:33:19 UTC
Finished: 3 years, 7 months ago 10 Apr 2021 07:11:51 UTC
Runtime: 29:11:16

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

Job information

Status: Succeeded
Backend: TPP
Workspace: ncs-hospital-disruption-2
Requested by: Louis Fisher
Branch: icd-10-fix
Force run dependencies: Yes
Git commit hash: 5135658
Requested actions: run_all

Code comparison

Compare the code used in this Job Request