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Job request: 20716

Organisation:
Bennett Institute
Workspace:
bmi-short-data-report-segmented
ID:
74f7a3ik222lfan2
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Colm Andrews 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

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: 00:01:04

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

Job information

Status
Failed
Backend
TPP
Workspace
bmi-short-data-report-segmented
Requested by
Colm Andrews
Branch
separate-study-definitions
Force run dependencies
No
Git commit hash
306e294
Requested actions
  • generate_report_bmi_segmented

Code comparison

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