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Job request: 10955

Organisation:
Bennett Institute
Workspace:
bmi-short-data-report-segmented
ID:
motzqp5ftvaodpud
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Robin Park 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: 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, execute_validation_analyses_high_backend_computed_bmi, execute_validation_analyses_high_computed_bmi]
    outputs:
      moderately_sensitive: 
        tables: output/validation/formatted_tables/*.csv

  generate_report_bmi_segmented:
    run: python:latest jupyter nbconvert /workspace/notebooks/report_bmi_segmented.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [consolidate_analyses, execute_validation_analyses_computed_bmi, execute_validation_analyses_backend_computed_bmi, execute_validation_analyses_high_computed_bmi, execute_validation_analyses_high_backend_computed_bmi, execute_validation_analyses_recorded_bmi, execute_validation_analyses_derived_bmi]
    outputs:
      moderately_sensitive:
        notebook: output/report_bmi_segmented.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:32

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

Job request

Status
Succeeded
Backend
TPP
Workspace
bmi-short-data-report-segmented
Requested by
Robin Park
Branch
separate-study-definitions
Force run dependencies
No
Git commit hash
63e032c
Requested actions
  • generate_report_bmi_segmented

Code comparison

Compare the code used in this job request