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Job request: 27350

Organisation:
Bennett Institute
Workspace:
tpp-database-schema
ID:
eqhxxzdi2oilymvi
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Alice Wong 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

  • Action:
    query
    Status:
    Pending
    Job identifier:
    c66fopl3mnvgrhtb
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    data_dictionary_query
    Status:
    Pending
    Job identifier:
    eqwoqwzd4fo2md63
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    decision_support_value_reference_query
    Status:
    Pending
    Job identifier:
    y5kl2tixi2wdncr2
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    make-html-reports
    Status:
    Pending
    Job identifier:
    atoxz2jaytym5dd7
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    vaccination_reference_query
    Status:
    Pending
    Job identifier:
    k2reswbqduwo3l62
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    categorical_columns
    Status:
    Pending
    Job identifier:
    4afnspz3xayawnhv
    Status message:
    waiting_on_db_workers: Waiting on available database workers

Pipeline

Show project.yaml 
version: "5.0"

actions:
  query:
    run: >
      sqlrunner:v1
        --output output/files_for_release/rows.csv
        --log-file logs/log.json
        analysis/query.sql
    outputs:
      moderately_sensitive:
        rows: output/files_for_release/rows.csv
        log: logs/log.json

  data_dictionary_query:
    run: >
      sqlrunner:v1
        --output output/files_for_release/data_dictionary.csv
        --log-file logs/data_dictionary_log.json
        analysis/data_dictionary_query.sql
    outputs:
      moderately_sensitive:
        rows: output/files_for_release/data_dictionary.csv
        log: logs/data_dictionary_log.json

  decision_support_value_reference_query:
    run: >
      sqlrunner:v1
        --output output/files_for_release/decision_support_value_reference.csv
        --log-file logs/decision_support_value_reference_log.json
        analysis/decision_support_value_reference_query.sql
    outputs:
      moderately_sensitive:
        rows: output/files_for_release/decision_support_value_reference.csv
        log: logs/decision_support_value_reference_log.json

  vaccination_reference_query:
    run: >
      sqlrunner:v1
        --output output/files_for_release/vaccination_reference.csv
        --log-file logs/vaccination_reference_log.json
        analysis/vaccination_reference_query.sql
    outputs:
      moderately_sensitive:
        rows: output/files_for_release/vaccination_reference.csv
        log: logs/vaccination_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:v2 jupyter nbconvert
        --execute
        --no-input
        --to=html
        --template basic
        --output-dir=output/files_for_release
        analysis/*.ipynb
    needs:
      - query
      - vaccination_reference_query
    outputs:
      moderately_sensitive:
        reports: output/files_for_release/*.html

  categorical_columns:
    run: >
      sqlrunner:v1
        --output output/files_for_release/results_categorical_columns.csv
        --dummy-data-file analysis/dummy_results.csv
        analysis/query_tpp_categorical_columns.sql
    outputs:
      moderately_sensitive:
        results: output/files_for_release/results_categorical_columns.csv

Job statistics

Status Count Percentage
Pending 6 100%
Running 0 0%
Succeeded 0 0%
Failed 0 0%

0 / 6 (0%) complete

Timeline

  • Created:

  • Runtime:

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

Job request

Status
Pending
Backend
TPP
Workspace
tpp-database-schema
Requested by
Alice Wong
Branch
main
Force run dependencies
Yes
Git commit hash
4ad9426
Requested actions
  • run_all

Code comparison

Compare the code used in this job request