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Job request: 12424

Organisation:
Bennett Institute
Workspace:
sro-measures
ID:
sxyj7zw7xsgdcmgs
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher 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_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_population --index-date-range "2019-01-01 to 2022-05-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_population*.feather

  join_ethnicity_population:
    run: >
      cohort-joiner:v0.0.46
        --lhs output/input_population_20*.feather
        --rhs output/input_ethnicity.feather
        --output-dir output/joined
    needs: [generate_study_population_population, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_population_20*.feather

  get_moved_count:
    run: python:latest python analysis/population_count.py
    needs: [join_ethnicity_population]
    outputs:
      moderately_sensitive:
        text: output/move*.json


  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2019-12-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_*.feather

  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-01-01 to 2020-12-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input*.feather

  generate_study_population_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-01-01 to 2021-06-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/inpu*.feather

  generate_study_population_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-07-01 to 2021-12-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/in*.feather

  generate_study_population_5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2022-01-01 to 2022-05-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/i*.feather


  get_patient_count:
    run: python:latest python analysis/get_patients_counts.py
    needs: [generate_study_population_4, generate_study_population_5, join_ethnicity]
    outputs:
      moderately_sensitive:
        text: output/patient_count.json

  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.feather

  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py
    needs:
      [
        generate_study_population_1,
        generate_study_population_2,
        generate_study_population_3,
        generate_study_population_ethnicity,
      ]
    outputs:
      highly_sensitive:
        cohort: output/inp*.feather

  get_practice_count:
    run: python:latest python analysis/get_practice_count.py
    needs: [join_ethnicity, generate_study_population_4, generate_study_population_5]
    outputs:
      moderately_sensitive:
        text: output/practice_count.json

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
    needs: [join_ethnicity, generate_study_population_4, generate_study_population_5]
    outputs:
      moderately_sensitive:
        measure_csv: output/measure_*_rate.csv

  generate_measures_cleaned:
    run: python:latest python analysis/clean_measures.py
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        measure_csv: output/measure_cleaned_*.csv


  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/sentinel_measures.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs:
      [
        generate_measures,
        generate_measures_cleaned,
        get_practice_count,
        get_patient_count,
      ]
    outputs:
      moderately_sensitive:
        notebook: output/sentinel_measures.html
        subplots: output/sentinel_measures_subplots.png
        code_tables: output/code_table_*.csv
        events_count: output/event_count.json

  generate_notebook_updating:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/sentinel_measures_updating.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs:
      [
        generate_measures,
        generate_measures_cleaned,
        get_practice_count,
        get_patient_count,
      ]
    outputs:
      moderately_sensitive:
        notebook: output/sentinel_measures_updating.html
        code_tables: output/code_table*.csv
        practices: output/num_practices_included*.csv

  run_tests_population_count:
    run: python:latest python -m pytest tests/test_population_count.py --junit-xml=output/pytest.xml --verbose
    outputs:
      moderately_sensitive:
        log: output/pytest.xml

  # run_tests:
  #   run: python:latest python -m pytest --junit-xml=output/pytest.xml --verbose
  #   outputs:
  #     moderately_sensitive:
  #       log: output/pytest.xml

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:46:15

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

Job request

Status
Succeeded
Backend
TPP
Workspace
sro-measures
Requested by
Louis Fisher
Branch
master
Force run dependencies
No
Git commit hash
2647ef4
Requested actions
  • get_moved_count

Code comparison

Compare the code used in this job request