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Job request: 27180

Organisation:
University of Oxford
Workspace:
split-procedures
ID:
qz3owb4o4lb6kfo3
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher 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:
    generate_procedure_events
    Status:
    Running
    Job identifier:
    3gxmaddioicpki47
  • Action:
    parse_procedure_events
    Status:
    Pending
    Job identifier:
    gcrzph7g5jfbe5a5
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    count_mandatory_surgery_types
    Status:
    Pending
    Job identifier:
    uswkegwfdydn4qgz
    Status message:
    waiting_on_dependencies: Waiting on dependencies

Pipeline

Show project.yaml 
version: '5.0'
actions:

  # ####################################################################

  # DO NOT EDIT project.yaml DIRECTLY

  # This file is created by create_project_actions.py

  # Edit and run create_project_actions.py to update the project.yaml

  # ####################################################################

  # Generate input_2024-04_12months
  generate_dataset_2024-04_12months:
    run: ehrql:v1 generate-dataset analysis/dataset_definition/dataset_definition.py --output output/dataset_definition/input_2024-04_12months.csv.gz -- --index_date "2024-04" --span_months 12
    outputs:
      highly_sensitive:
        dataset: output/dataset_definition/input_2024-04_12months.csv.gz

  # Generate input_2015-04_120months
  generate_dataset_2015-04_120months:
    run: ehrql:v1 generate-dataset analysis/dataset_definition/dataset_definition.py --test-data-file analysis/dataset_definition/test_dataset_definition.py --output output/dataset_definition/input_2015-04_120months.csv.gz -- --index_date "2015-04" --span_months 120
    outputs:
      highly_sensitive:
        dataset: output/dataset_definition/input_2015-04_120months.csv.gz

  # Generate input_mandatory_2024-04_12months
  generate_dataset_mandatory_2024-04_12months:
    run: ehrql:v1 generate-dataset analysis/dataset_definition/dataset_definition.py --test-data-file analysis/dataset_definition/test_dataset_definition_mandatory.py --output output/dataset_definition/input_mandatory_2024-04_12months.csv.gz -- --index_date "2024-04" --span_months 12 --procedure_metadata "codelists/procedure_codes_metadata_mandatory.json"
    outputs:
      highly_sensitive:
        dataset: output/dataset_definition/input_mandatory_2024-04_12months.csv.gz

  generate_procedure_events:
    run: ehrql:v1 generate-dataset analysis/dataset_definition/procedure_events_dataset.py --dummy-tables dummy_tables --output output/dataset_definition/procedure_events.csv.gz -- --index_date "2024-04" --span_months 12 --procedure_metadata "codelists/procedure_codes_metadata_mandatory.json"
    outputs:
      highly_sensitive:
        procedure_events: output/dataset_definition/procedure_events.csv.gz

  parse_procedure_events:
    run: python:v2 python analysis/dataset_definition/parse_procedure_events.py
    needs:
    - generate_procedure_events
    outputs:
      highly_sensitive:
        procedure_event_rows: output/dataset_definition/procedure_events_rows.csv.gz

  count_mandatory_surgery_types:
    run: python:v2 python analysis/tables/count_mandatory_surgery_types.py
    needs:
    - parse_procedure_events
    outputs:
      moderately_sensitive:
        type_counts: output/tables/mandatory_surgery_type_counts.csv
        multi_type_counts: output/tables/mandatory_surgery_multi_type_counts.csv
        type_counts_round5: output/tables/mandatory_surgery_type_counts_round5.csv
        multi_type_counts_round5: output/tables/mandatory_surgery_multi_type_counts_round5.csv

  # Generate table0
  table0:
    run: python:v2 python analysis/tables/table0.py --index_date 2024-04 --span 12
    needs:
    - generate_dataset_mandatory_2024-04_12months
    outputs:
      moderately_sensitive:
        table0: output/tables/table0_mandatory_2024-04_12months.csv
        table0_round5: output/tables/table0_mandatory_2024-04_12months_round5.csv

  # Generate table1a
  table1a:
    run: python:v2 python analysis/tables/table1a.py --index_date 2024-04 --span 12
    needs:
    - generate_dataset_mandatory_2024-04_12months
    outputs:
      moderately_sensitive:
        table1a: output/tables/table1a_mandatory_2024-04_12months.csv

  # Generate table3
  table3:
    run: python:v2 python analysis/tables/table3.py --index_date 2024-04 --span 12
    needs:
    - generate_dataset_mandatory_2024-04_12months
    outputs:
      moderately_sensitive:
        table3: output/tables/table3_mandatory_2024-04_12months.csv
        table3_round5: output/tables/table3_mandatory_2024-04_12months_round5.csv

  # Generate table9a
  table9a:
    run: python:v2 python analysis/tables/table9a.py --index_date 2024-04 --span 12
    needs:
    - generate_dataset_mandatory_2024-04_12months
    outputs:
      moderately_sensitive:
        table9a: output/tables/table9a_mandatory_2024-04_12months.csv
        table9a_round5: output/tables/table9a_mandatory_2024-04_12months_round5.csv

  # Generate table10
  table10:
    run: python:v2 python analysis/tables/table10.py --index_date 2024-04 --span 12
    needs:
    - generate_dataset_mandatory_2024-04_12months
    outputs:
      moderately_sensitive:
        table10: output/tables/table10_mandatory_2024-04_12months.csv

  # Generate table11
  table11:
    run: python:v2 python analysis/tables/table11.py --index_date 2024-04 --span 12
    needs:
    - generate_dataset_mandatory_2024-04_12months
    outputs:
      moderately_sensitive:
        table11: output/tables/table11_mandatory_2024-04_12months.csv
        table11_round5: output/tables/table11_mandatory_2024-04_12months_round5.csv

  # Generate table0_pcsc
  table0_pcsc:
    run: python:v2 python analysis/tables/table0_pcsc.py --index_date 2024-04 --span 12
    needs:
    - generate_dataset_mandatory_2024-04_12months
    outputs:
      moderately_sensitive:
        table0_pcsc: output/tables/table0_pcsc_mandatory_2024-04_12months.csv
        table0_pcsc_round5: output/tables/table0_pcsc_mandatory_2024-04_12months_round5.csv

  # Generate table1b_pcsc
  table1b_pcsc:
    run: python:v2 python analysis/tables/table1b_pcsc.py --index_date 2024-04 --span 12
    needs:
    - generate_dataset_mandatory_2024-04_12months
    outputs:
      moderately_sensitive:
        table1b_pcsc: output/tables/table1b_pcsc_mandatory_2024-04_12months.csv
        table1b_pcsc_round5: output/tables/table1b_pcsc_mandatory_2024-04_12months_round5.csv

Job statistics

Status Count Percentage
Pending 2 66.7%
Running 1 33.3%
Succeeded 0 0%
Failed 0 0%

0 / 3 (0%) complete

Timeline

  • Created:

  • Started:

  • Runtime:

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

Job request

Status
Running
Backend
TPP
Workspace
split-procedures
Requested by
Louis Fisher
Branch
splitting-procedure-codes
Force run dependencies
No
Git commit hash
5df0a40
Requested actions
  • generate_procedure_events
  • parse_procedure_events
  • count_mandatory_surgery_types

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