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Job request: 10450

Organisation:
NHSE/I
Workspace:
nhs_at_home_main
ID:
hr3isga5q3zbprzi
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Alexandra Benson 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.

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 1000

actions:
  generate_study_definition_static:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_static
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/input_static.csv

  # Oximetry
  generate_study_population_oximetry:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_oximetry
      --index-date-range "2019-04-01 to 2022-05-30 by week"
      --with-end-date-fix
    outputs:
      highly_sensitive:
        oximetry_cohort: output/oximetry/0.1_generate_study_population/input_oximetry*.csv

  join_cohorts_oximetry:
    run: cohort-joiner:v0.0.30
      --lhs output/oximetry/0.1_generate_study_population/input_oximetry*.csv
      --rhs output/input_static.csv 
      --output-dir output/oximetry/0.2_join_cohorts/
    needs:
      [generate_study_population_oximetry, generate_study_definition_static]
    outputs:
      highly_sensitive:
        cohort: output/oximetry/0.2_join_cohorts/input_oximetry*.csv

  # BP
  generate_study_population_bp:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_bp
      --index-date-range "2019-04-01 to 2022-05-30 by week"
      --with-end-date-fix
    outputs:
      highly_sensitive:
        bp_cohort: output/bp/0.1_generate_study_population/input_bp*.csv

  join_cohorts_bp:
    run: cohort-joiner:v0.0.30
      --lhs output/bp/0.1_generate_study_population/input_bp*.csv
      --rhs output/input_static.csv 
      --output-dir output/bp/0.2_join_cohorts/
    needs: [generate_study_population_bp, generate_study_definition_static]
    outputs:
      highly_sensitive:
        cohort: output/bp/0.2_join_cohorts/input_bp*.csv

  # Proactive
  generate_study_population_proactive:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_proactive
      --index-date-range "2019-04-01 to 2022-05-30 by week"
      --with-end-date-fix
    outputs:
      highly_sensitive:
        proactive_cohort: output/proactive/0.1_generate_study_population/input_proactive*.csv

  join_cohorts_proactive:
    run: cohort-joiner:v0.0.30
      --lhs output/proactive/0.1_generate_study_population/input_proactive*.csv
      --rhs output/input_static.csv 
      --output-dir output/proactive/0.2_join_cohorts/
    needs:
      [generate_study_population_proactive, generate_study_definition_static]
    outputs:
      highly_sensitive:
        cohort: output/proactive/0.2_join_cohorts/input_proactive*.csv

  # Analysis

  # Oximetry
  generate_oximetry_timeseries:
    run: python:latest python analysis/analysis_oximetry_timeseries.py
    needs: [join_cohorts_oximetry]
    outputs:
      moderately_sensitive:
        oximetry_table_counts: output/oximetry/0.3_analysis_outputs/oximetry_table_counts.csv
        oximetry_plot_timeseries: output/oximetry/0.3_analysis_outputs/oximetry_plot_timeseries.png

  generate_oximetry_regional_timeseries:
    run: python:latest python analysis/analysis_oximetry_region.py
    needs: [join_cohorts_oximetry]
    outputs:
      moderately_sensitive:
        oximetry_table_counts_region: output/oximetry/0.3_analysis_outputs/oximetry_table_counts_*.csv
        oximetry_plot_timeseries_region: output/oximetry/0.3_analysis_outputs/oximetry_plot_timeseries_region_*.png

  generate_oximetry_breakdowns:
    run: python:latest python analysis/analysis_oximetry_breakdowns.py
    needs: [join_cohorts_oximetry]
    outputs:
      moderately_sensitive:
        oximetry_table_breakdowns: output/oximetry/0.3_analysis_outputs/oximetry_table_code_*.csv
        oximetry_plot_breakdowns: output/oximetry/0.3_analysis_outputs/oximetry_plot_code_*.png

  generate_oximetry_codes_analysis:
    run: python:latest python analysis/analysis_oximetry_codes.py
    needs: [join_cohorts_oximetry]
    outputs:
      moderately_sensitive:
        oximetry_table_code_counts: output/oximetry/0.3_analysis_outputs/oximetry_table_code_counts_*.csv
        oximetry_table_code_combinations: output/oximetry/0.3_analysis_outputs/oximetry_table_code_combinations.csv
        oximetry_table_code_populations: output/oximetry/0.3_analysis_outputs/oximetry_patient_id_total_*.csv

  # Blood pressure
  generate_bp_timeseries:
    run: python:latest python analysis/analysis_bp_timeseries.py
    needs: [join_cohorts_bp]
    outputs:
      moderately_sensitive:
        bp_table_counts: output/bp/0.3_analysis_outputs/bp_table_counts.csv
        bp_plot_timeseries: output/bp/0.3_analysis_outputs/bp_plot_timeseries.png

  generate_bp_regional_timeseries:
    run: python:latest python analysis/analysis_bp_region.py
    needs: [join_cohorts_bp]
    outputs:
      moderately_sensitive:
        bp_table_counts_region: output/bp/0.3_analysis_outputs/bp_table_counts_*.csv
        bp_plot_timeseries_region: output/bp/0.3_analysis_outputs/bp_plot_timeseries_region_*.png

  generate_bp_breakdowns:
    run: python:latest python analysis/analysis_bp_breakdowns.py
    needs: [join_cohorts_bp]
    outputs:
      moderately_sensitive:
        bp_table_breakdowns: output/bp/0.3_analysis_outputs/bp_table_code_*.csv
        bp_plot_breakdowns: output/bp/0.3_analysis_outputs/bp_plot_code_*.png

  generate_bp_codes_analysis:
    run: python:latest python analysis/analysis_bp_codes.py
    needs: [join_cohorts_bp]
    outputs:
      moderately_sensitive:
        bp_table_code_counts: output/bp/0.3_analysis_outputs/bp_table_code_counts_*.csv
        bp_table_code_combinations: output/bp/0.3_analysis_outputs/bp_table_code_combinations.csv
        bp_table_code_populations: output/bp/0.3_analysis_outputs/bp_patient_id_total_*.csv

  # Proactive Care
  generate_proactive_timeseries:
    run: python:latest python analysis/analysis_proactive_timeseries.py
    needs: [join_cohorts_proactive]
    outputs:
      moderately_sensitive:
        proactive_table_counts: output/proactive/0.3_analysis_outputs/proactive_table_counts.csv
        proactive_plot_timeseries: output/proactive/0.3_analysis_outputs/proactive_plot_timeseries.png

  generate_proactive_regional_timeseries:
    run: python:latest python analysis/analysis_proactive_region.py
    needs: [join_cohorts_proactive]
    outputs:
      moderately_sensitive:
        proactive_table_counts_region: output/proactive/0.3_analysis_outputs/proactive_table_counts_*.csv
        proactive_plot_timeseries_region: output/proactive/0.3_analysis_outputs/proactive_plot_timeseries_region_*.png

  generate_proactive_breakdowns:
    run: python:latest python analysis/analysis_proactive_breakdowns.py
    needs: [join_cohorts_proactive]
    outputs:
      moderately_sensitive:
        proactive_table_breakdowns: output/proactive/0.3_analysis_outputs/proactive_table_code_*.csv
        proactive_plot_breakdowns: output/proactive/0.3_analysis_outputs/proactive_plot_code_*.png

  generate_proactive_codes_analysis:
    run: python:latest python analysis/analysis_proactive_codes.py
    needs: [join_cohorts_proactive]
    outputs:
      moderately_sensitive:
        proactive_table_code_counts: output/proactive/0.3_analysis_outputs/proactive_table_code_counts_*.csv
        proactive_table_code_combinations: output/proactive/0.3_analysis_outputs/proactive_table_code_combinations.csv
        proactive_table_code_populations: output/proactive/0.3_analysis_outputs/proactive_patient_id_total_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job request

Status
Failed 
JobRequestError: generate_study_population_oximetry failed on a previous run and must be re-run
Backend
TPP
Workspace
nhs_at_home_main
Requested by
Alexandra Benson
Branch
main
Force run dependencies
No
Git commit hash
354bdd5
Requested actions
  • run_all

Code comparison

Compare the code used in this job request