Job request: 5516

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 Diabetes Test Levels 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
6npchxuhdf7jovhj succeeded calculate_measures
eqg6pb5524wi33no succeeded generate_charts
yqosxxgwmzx5fhrx succeeded generate_elev_predm_inputs
uk746rnukqdlnmas succeeded generate_study_population
qho55euqe7rizzhd succeeded generate_study_population_elev_predm
j2vpu2de5f7o2gs6 succeeded generate_study_population_ethnicity
m7virpo37xfvlp7g succeeded join_ethnicity_all_patients
7ucv4thk3treuv5m succeeded join_ethnicity_elev_predm
qhej6ckqsk2mffk2 succeeded redact_measures

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 10000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all_patients --index-date-range "2019-01-01 to 2021-06-01 by month" --output-dir=output/data 
    outputs:
      highly_sensitive:
        cohort: output/data/input_all_patients_*.csv

  generate_study_population_elev_predm:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_elev_predm --index-date-range "2019-01-01 to 2021-06-01 by month" --output-dir=output/data 
    outputs:
      highly_sensitive:
        cohort: output/data/input_elev_predm_*.csv

  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output/data 
    outputs:
      highly_sensitive:
        cohort: output/data/input_ethnicity.csv
        
  join_ethnicity_all_patients:
    run: python:latest python analysis/join_ethnicity.py "input_all_patients"
    needs: [generate_study_population, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/data/input_all_patients*.csv

  join_ethnicity_elev_predm:
    run: python:latest python analysis/join_ethnicity.py "input_elev_predm"
    needs: [generate_study_population_elev_predm, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/data/input_elev_predm*.csv

  calculate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_all_patients --output-dir=output/data
    needs: [join_ethnicity_all_patients]
    outputs:
      moderately_sensitive:
        measure_csv: output/data/measure_*.csv

  redact_measures:
    run: python:latest python analysis/redact_measures.py
    needs: [calculate_measures]
    outputs:
      moderately_sensitive:
        measure_csv: output/data/measure*.csv

  generate_data_description:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/data_description.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [join_ethnicity_all_patients]
    outputs:
      moderately_sensitive:
        notebook: output/data_description.html

  generate_elev_predm_inputs: 
    run: python:latest python analysis/elev_predm_input.py
    needs: [join_ethnicity_elev_predm]
    outputs:
      moderately_sensitive:
        cohorts1: output/data/calc_t2dm_elev*.csv
        cohorts2: output/data/calc_predm*.csv

  generate_charts:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/charts.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [redact_measures, generate_elev_predm_inputs]
    outputs:
      moderately_sensitive:
        notebook: output/charts.html

  generate_tables:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/tables.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [join_ethnicity_all_patients]
    outputs:
      moderately_sensitive:
        notebook: output/tables.html

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 29:42:23

Config

  • Backend:
    TPP
  • Workspace:
    hba1c-levels-report
  • Branch:
    master
  • Creator:
    robinyjpark
  • Force run dependencies:
    True
  • Git Commit Hash:
    4f07c45
  • Requested actions:
    • generate_study_population_elev_predm
    • join_ethnicity_elev_predm
    • generate_elev_predm_inputs
    • generate_charts