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Job request: 24395

Organisation:
Bennett Institute
Workspace:
tpp-database-schema
ID:
pgs3xw4j4kjtdah6
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Becky Smith 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

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: 00:09:21

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

Job request

Status
Succeeded
Backend
TPP
Workspace
tpp-database-schema
Requested by
Becky Smith
Branch
main
Force run dependencies
Yes
Git commit hash
82d52de
Requested actions
  • query
  • data_dictionary_query
  • decision_support_value_reference_query
  • make-html-reports
  • categorical_columns

Code comparison

Compare the code used in this job request