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Job request: 9763

Organisation:
NHSE/I
Workspace:
nhs_at_home_main
ID:
im3qdng5akjwia5r
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Jennifer Hall 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

  • Action:
    run_all
    Status:
    Status: Succeeded
    Job identifier:
    ofzh656p6wd2odcd

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

    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"
    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"
    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"
    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
  # generate_oximetry_timeseries:
  #   run: python:latest python analysis/analysis_oximetry_timeseries.py
  #   needs: [join_cohorts_oximetry]
  #   outputs:
  #     moderately_sensitive:
  #       oximetry_table_counts: output/oximetry_table_counts.csv
  #       oximetry_plot_timeseries: output/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_table_counts_*.csv
  #       oximetry_plot_timeseries_region: output/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_table_code_*.csv
  #       oximetry_plot_breakdowns: output/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_table_code_counts_*.csv
  #       oximetry_table_code_combinations: output/oximetry_table_code_combinations.csv
  # generate_oximetry_no_codes_analysis:
  #   run: python:latest python analysis/analysis_oximetry_no_codes.py
  #   needs: [join_cohorts_oximetry]
  #   outputs:
  #     moderately_sensitive:
  #       oximetry_table_no_codes_used: output/oximetry_table_no_codes_used.csv
  # generate_bp_timeseries:
  #   run: python:latest python analysis/analysis_bp_timeseries.py
  #   needs: [join_cohorts_bp]
  #   outputs:
  #     moderately_sensitive:
  #       bp_table_counts: output/bp_table_counts.csv
  #       bp_plot_timeseries: output/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_table_counts_*.csv
  #       bp_plot_timeseries_region: output/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_table_code_*.csv
  #       bp_plot_breakdowns: output/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_table_code_counts_*.csv
  #       bp_table_code_combinations: output/bp_table_code_combinations.csv
  # generate_bp_no_codes_analysis:
  #   run: python:latest python analysis/analysis_bp_no_codes.py
  #   needs: [join_cohorts_bp]
  #   outputs:
  #     moderately_sensitive:
  #       bp_table_no_codes_used: output/bp_table_no_codes_used.csv
  # generate_proactive_timeseries:
  #   run: python:latest python analysis/analysis_proactive_timeseries.py
  #   needs: [join_cohorts_proactive]
  #   outputs:
  #     moderately_sensitive:
  #       proactive_table_counts: output/proactive_table_counts.csv
  #       proactive_plot_timeseries: output/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_table_counts_*.csv
  #       proactive_plot_timeseries_region: output/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_table_code_*.csv
  #       proactive_plot_breakdowns: output/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_table_code_counts_*.csv
  # generate_proactive_no_codes_analysis:
  #   run: python:latest python analysis/analysis_proactive_no_codes.py
  #   needs: [join_cohorts_proactive]
  #   outputs:
  #     moderately_sensitive:
  #       proactive_table_no_codes_used: output/proactive_table_no_codes_used.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job request

Status
Succeeded
Backend
TPP
Workspace
nhs_at_home_main
Requested by
Jennifer Hall
Branch
main
Force run dependencies
No
Git commit hash
894ce25
Requested actions
  • run_all

Code comparison

Compare the code used in this job request