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Job request: 5220

Organisation:
Bennett Institute
Workspace:
hba1c-levels-report
ID:
atlc2ym2gvscoxfp
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 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: 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_median:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_median --index-date-range "2019-01-01 to 2021-06-01 by month" --output-dir=output/data 
    outputs:
      highly_sensitive:
        cohort: output/data/input_median_*.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

  join_ethnicity_median:
    run: python:latest python analysis/join_ethnicity.py "input_median"
    needs: [generate_study_population_median, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/data/input_median*.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_change_inputs: 
    run: python:latest python analysis/mean_change_input.py
    needs: [join_ethnicity_median]
    outputs:
      moderately_sensitive:
        cohort: output/data/calc_chg_t2dm*.csv

  generate_median_inputs: 
    run: python:latest python analysis/median_input.py
    needs: [join_ethnicity_median]
    outputs:
      moderately_sensitive:
        cohort: output/data/calc_med_t2dm*.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_change_inputs, generate_median_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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 05:18:49

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

Job information

Status
Succeeded
Backend
TPP
Workspace
hba1c-levels-report
Requested by
Robin Park
Branch
master
Force run dependencies
No
Git commit hash
2214c79
Requested actions
  • generate_study_population_elev_predm
  • join_ethnicity_elev_predm

Code comparison

Compare the code used in this Job Request