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Job request: 14503

Organisation:
Bennett Institute
Workspace:
strepa_scarlet
ID:
muylcqc5ntifqfmp
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Christine Cunningham 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_report_ethnicity:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition_ethnicity_report --output-dir output/report --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/report/input_ethnicity_report.csv.gz

  ### Curation check ###
  curation_monthly:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_report
      --index-date-range "2019-01-01 to 2019-01-01 by month"
      --param frequency=monthly
      --output-dir=output/curation
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/curation/input_report_2019-01-01.csv.gz

  dataset_report_monthly:
      run: python:latest python analysis/dataset_report.py
           --input-files output/curation/input_report_2019-01-01.csv.gz
           --output-dir output/curation/
           --granularity "year"
      needs: [curation_monthly]
      outputs:
        moderately_sensitive:
          # Only output the single summary file
          cohort_report: output/curation/input_report_2019-01-01.html

  curation_weekly:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_report
      --index-date-range "2022-07-01 to 2022-07-01 by week"
      --param frequency=weekly
      --output-dir=output/curation
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/curation/input_report_2022-07-01.csv.gz

  dataset_report_weekly:
      run: python:latest python analysis/dataset_report.py
           --input-files output/curation/input_report_2022-07-01.csv.gz
           --output-dir output/curation/
           --granularity "day"
      needs: [curation_weekly]
      outputs:
        moderately_sensitive:
          # Only output the single summary file
          cohort_report: output/curation/input_report_2022-07-01.html
  ### End curation check

  generate_study_population_report_monthly:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_report
      --index-date-range "2019-01-01 to 2022-06-01 by month"
      --param frequency=monthly
      --output-dir=output/report
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/report/input_*-01.csv.gz

  generate_study_population_report_weekly:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_report
      --index-date-range "2022-07-01 to 2023-01-08 by week"
      --param frequency=weekly
      --output-dir=output/report
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/report/input_*.csv.gz

  join_cohorts_report:
    run: >
      cohort-joiner:v0.0.38
        --lhs output/report/input_report_20*.csv.gz
        --rhs output/report/input_ethnicity_report.csv.gz
        --output-dir output/report/joined
    needs: [generate_study_population_report_monthly, generate_study_population_report_weekly, generate_study_population_report_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/report/joined/input_report_20*.csv.gz

  generate_measures_report:
    run: cohortextractor:latest generate_measures --study-definition study_definition_report --output-dir=output/report/joined
    needs: [join_cohorts_report]
    outputs:
      moderately_sensitive:
        measure_csv: output/report/joined/measure_event_*_rate.csv

  join_measures:
      run: python:latest python analysis/join_and_round.py
           --input-files output/report/joined/measure_*_rate.csv
           --output-dir output/report/joined
           --output-name "measure_all.csv"
           --skip-round
      needs: [generate_measures_report]
      outputs:
        moderately_sensitive:
          # Only output the single summary file
          measure_csv: output/report/joined/measure_all.csv

  top_5_table_report:
    run: >
      python:latest python analysis/report/top_5_report.py
      --input-file output/report/joined/measure_all.csv
      --output-dir output/report/joined
    needs: [join_measures]
    outputs:
      moderately_sensitive:
        tables: output/report/joined/top_5*.csv

  plot_measure_report:
    run: >
      python:latest python analysis/report/plot_measures_report.py
      --measure-path output/report/joined/measure_all.csv
      --output-dir output/report/joined
    needs: [join_measures]
    outputs:
      moderately_sensitive:
        measure: output/report/joined/*measures*.jpeg

  event_counts_report:
    run: >
      python:latest python analysis/report/event_counts.py --input-dir="output/report/joined" --output-dir="output/report" --measures="amoxicillin,azithromycin,clarithromycin,erythromycin,phenoxymethypenicillin"
    needs: [join_cohorts_report]
    outputs:
      moderately_sensitive:
        measure: output/report/event_counts_*.json

  # create_notebook:
  #   run: python:latest python analysis/report/create_notebook.py
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/report/report.ipynb

  # generate_notebook:
  #   run: jupyter:latest jupyter nbconvert /workspace/output/report/report.ipynb --execute --to html --output-dir=/workspace/output/report --ExecutePreprocessor.timeout=86400 --no-input
  #   needs: [create_notebook, event_counts_report, deciles_chart_report, top_5_table_report, plot_measure_report]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/report/report.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 23:30:18

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

Job information

Status
Succeeded
Backend
TPP
Workspace
strepa_scarlet
Requested by
Christine Cunningham
Branch
main
Force run dependencies
No
Git commit hash
c141d6a
Requested actions
  • curation_monthly
  • dataset_report_monthly
  • curation_weekly
  • dataset_report_weekly

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