Job request: 9694

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Robin Park requested one or more actions to be run against real patient data in the BMI Short Data Report project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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

ID Status Action
uusurqwuhqliawvg succeeded consolidate_analyses
3h3rewhkbdw3l6tn failed execute_validation_analyses_all_definitions

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input.feather

  generate_study_population_derived_bmi:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_derived_bmi --output-dir=output/data --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_derived_bmi.feather

  generate_study_population_recorded_bmi:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_recorded_bmi --output-dir=output/data --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_recorded_bmi.feather

  generate_study_population_snomed_hw:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_snomed_hw --output-dir=output/data --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_snomed_hw.feather

  generate_study_population_ctv3_hw:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ctv3_hw --output-dir=output/data --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_ctv3_hw.feather

  preprocess_derived_bmi_input:
    run: python:latest python analysis/preprocess_bmi_inputs.py "derived_bmi" --output-format feather
    needs: [generate_study_population_derived_bmi]
    outputs:
      highly_sensitive:
        cohort_with_duration: output/data/input_processed_derived_bmi.feather

  preprocess_recorded_bmi_input:
    run: python:latest python analysis/preprocess_bmi_inputs.py "recorded_bmi" --output-format feather
    needs: [generate_study_population_recorded_bmi]
    outputs:
      highly_sensitive:
        cohort_with_duration: output/data/input_processed_recorded_bmi.feather

  preprocess_computed_bmi_input:
    run: python:latest python analysis/preprocess_hw_inputs.py "height" "weight" "snomed" "computed_bmi" --output-format feather
    needs: [generate_study_population_snomed_hw]
    outputs:
      highly_sensitive:
        cohort_with_duration: output/data/input_processed_computed_bmi.feather

  preprocess_backend_computed_bmi_input:
    run: python:latest python analysis/preprocess_hw_inputs.py "height_backend" "weight_backend" "ctv3" "backend_computed_bmi" --output-format feather
    needs: [generate_study_population_ctv3_hw]
    outputs:
      highly_sensitive:
        cohort_with_duration: output/data/input_processed_backend_computed_bmi.feather

  join_cohorts:
    run: >
      cohort-joiner:v0.0.35
        --lhs output/data/input_processed*.feather
        --rhs output/data/input.feather
        --output-dir output/joined
    needs: [generate_study_population, preprocess_derived_bmi_input, preprocess_recorded_bmi_input, preprocess_computed_bmi_input, preprocess_backend_computed_bmi_input]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_processed*.feather

  preprocess_age_dates:
    run: python:latest python analysis/preprocess_age_dates.py --output-format feather
    needs: [join_cohorts]
    outputs:
      highly_sensitive:
        cohort1: output/joined/input_processed_backend_computed_bmi.feather
        cohort2: output/joined/input_processed_computed_bmi.feather
        cohort3: output/joined/input_processed_derived_bmi.feather
        cohort4: output/joined/input_processed_recorded_bmi.feather

  execute_validation_analyses_derived_bmi:
    run: python:latest python analysis/validation_script_single_definition.py "derived_bmi"
    needs: [preprocess_age_dates]
    outputs:
      moderately_sensitive: 
        tables: output/validation/tables/derived_bmi/*.csv

  execute_validation_analyses_recorded_bmi:
    run: python:latest python analysis/validation_script_single_definition.py "recorded_bmi"
    needs: [preprocess_age_dates]
    outputs:
      moderately_sensitive: 
        tables: output/validation/tables/recorded_bmi/*.csv

  execute_validation_analyses_computed_bmi:
    run: python:latest python analysis/validation_script_single_definition.py "computed_bmi"
    needs: [preprocess_age_dates]
    outputs:
      moderately_sensitive: 
        tables: output/validation/tables/computed_bmi/*.csv

  execute_validation_analyses_backend_computed_bmi:
    run: python:latest python analysis/validation_script_single_definition.py "backend_computed_bmi"
    needs: [preprocess_age_dates]
    outputs:
      moderately_sensitive: 
        tables: output/validation/tables/backend_computed_bmi/*.csv

  execute_validation_analyses_high_computed_bmi:
    run: python:latest python analysis/validation_script_high_bmi.py "computed_bmi"
    needs: [preprocess_age_dates]
    outputs:
      moderately_sensitive: 
        tables: output/validation/tables/high_computed_bmi/*.csv
        
  execute_validation_analyses_high_backend_computed_bmi:
    run: python:latest python analysis/validation_script_high_bmi.py "backend_computed_bmi"
    needs: [preprocess_age_dates]
    outputs:
      moderately_sensitive: 
        tables: output/validation/tables/high_backend_computed_bmi/*.csv

  execute_validation_analyses_all_definitions:
    run: python:latest python analysis/validation_script_all_definitions.py
    needs: [preprocess_age_dates]
    outputs:
      moderately_sensitive: 
        tables: output/validation/tables/comparison/*.csv

  consolidate_analyses:
    run: python:latest python analysis/consolidate_analyses.py
    needs: [execute_validation_analyses_derived_bmi, execute_validation_analyses_recorded_bmi, execute_validation_analyses_backend_computed_bmi, execute_validation_analyses_computed_bmi]
    outputs:
      moderately_sensitive: 
        tables: output/validation/formatted_tables/*.csv

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 00:14:26

Config

  • Backend:
    TPP
  • Workspace:
    bmi-short-data-report-segmented
  • Branch:
    separate-study-definitions
  • Creator:
    robinyjpark
  • Force run dependencies:
    False
  • Git Commit Hash:
    a7ae091
  • Requested actions:
    • execute_validation_analyses_all_definitions
    • consolidate_analyses