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Job request: 24201

Organisation:
Bennett Institute
Workspace:
tpp-database-schema
ID:
3cnypjtdyfsnjizn
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Jon Massey 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

  • Action:
    run_all
    Status:
    Status: Succeeded
    Job identifier:
    4pbyc3c7yexifl2v

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 1000

actions:
  query:
    run: >
      sqlrunner:latest
        --output output/rows.csv
        --log-file output/log.json
        analysis/query.sql
    outputs:
      moderately_sensitive:
        rows: output/rows.csv
        log: output/log.json

  data_dictionary_query:
    run: >
      sqlrunner:latest
        --output output/data_dictionary.csv
        --log-file output/data_dictionary_log.json
        analysis/data_dictionary_query.sql
    outputs:
      moderately_sensitive:
        rows: output/data_dictionary.csv
        log: output/data_dictionary_log.json

  decision_support_value_reference_query:
    run: >
      sqlrunner:latest
        --output output/decision_support_value_reference.csv
        --log-file output/decision_support_value_reference_log.json
        analysis/decision_support_value_reference_query.sql
    outputs:
      moderately_sensitive:
        rows: output/decision_support_value_reference.csv
        log: output/decision_support_value_reference_log.json

  make-html-reports:
    # --execute
    #   execute notebooks before converting them to HTML reports
    # --no-input
    #   exclude input cells and output prompts from HTML reports
    # --to=html
    #   convert notebooks to HTML reports (not e.g. to PDF reports)
    # --template basic
    #   use the basic (unstyled) template for HTML reports
    # --output-dir=output
    #   write HTML reports to the `output` directory
    run: >
      python:latest jupyter nbconvert
        --execute
        --no-input
        --to=html
        --template basic
        --output-dir=output
        analysis/*.ipynb
    needs:
      - query
    outputs:
      moderately_sensitive:
        reports: output/*.html

  categorical_columns:
    run: >
      sqlrunner:latest
        --output output/results_categorical_columns.csv
        --dummy-data-file analysis/dummy_results.csv
        analysis/query_tpp_categorical_columns.sql
    outputs:
      moderately_sensitive:
        results: output/results_categorical_columns.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job information

Status
Succeeded
Backend
TPP
Workspace
tpp-database-schema
Requested by
Jon Massey
Branch
main
Force run dependencies
No
Git commit hash
a9f1165
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request