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Job request: 4510

Organisation:
Bennett Institute
Workspace:
sro-measures
ID:
6jhdpt3msgz7otwu
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

  • Action:
    generate_study_population_1
    Status:
    Succeeded
    Job identifier:
    adofh5szpiluo6zk
  • Action:
    generate_study_population_3
    Status:
    Succeeded
    Job identifier:
    6h4kw5ee4c455ill
  • Action:
    generate_study_population_2
    Status:
    Succeeded
    Job identifier:
    ksat6lm7mfxtqubx
  • Action:
    generate_study_population_ethnicity
    Status:
    Succeeded
    Job identifier:
    y5qkurcbkruphr4r
  • Action:
    join_ethnicity
    Status:
    Succeeded
    Job identifier:
    wdsrduyfnq6dj4wf
  • Action:
    get_patient_count
    Status:
    Succeeded
    Job identifier:
    cht3mkjgb2rnpqtp
  • Action:
    get_population_count
    Status:
    Succeeded
    Job identifier:
    4o5sxca3i2fveto6
  • Action:
    generate_measures
    Status:
    Succeeded
    Job identifier:
    fuqhr7h5h2bs4d5c
  • Action:
    get_practice_count
    Status:
    Succeeded
    Job identifier:
    atfhuwkecdfpn6l3
  • Action:
    generate_measures_cleaned
    Status:
    Succeeded
    Job identifier:
    4jjft4kw62ttunp3
  • Action:
    generate_notebook
    Status:
    Succeeded
    Job identifier:
    wx6yijyi6o45bw53

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000
   
    
actions:

  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2019-11-01 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 "2019-12-01 to 2020-10-01 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 "2020-11-01 to 2021-10-01 by month" --output-dir=output --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/inpu*.feather
        
  get_patient_count:
    run: python:latest python analysis/get_patients_counts.py
    needs: [generate_study_population_1, generate_study_population_2, generate_study_population_3]
    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]
    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]
    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_measures_demographics:
    run: python:latest python analysis/calculate_measures.py
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        measure: output/combined_measure_*.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, get_practice_count, get_patient_count]
    outputs:
      moderately_sensitive:
        notebook: output/sentinel_measures.html
        subplots: output/sentinel_measures_subplots.png
  

  generate_notebook_demographics:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/sentinel_measures_demographics.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_measures, generate_measures_demographics]
    outputs:
      moderately_sensitive:
        notebook: output/sentinel_measures_demographics.html

  get_population_count:
    run: python:latest python analysis/population_counts.py
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        text: output/*_count.csv

  demographic_changes:
    run: python:latest python analysis/demographic_change.py
    needs: [generate_measures_demographics]
    outputs:
      moderately_sensitive:
        csv: output/demographics_differences.csv
        csv_sorted: output/demographics_differences_sorted.csv
        

#   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: 37:36:57

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
b65d1e3
Requested actions
  • generate_study_population_1
  • generate_study_population_2
  • generate_study_population_3
  • get_patient_count
  • generate_study_population_ethnicity
  • join_ethnicity
  • get_practice_count
  • generate_measures
  • generate_measures_cleaned
  • generate_notebook
  • get_population_count

Code comparison

Compare the code used in this job request