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Job request: 26902

Organisation:
University of Oxford
Workspace:
surgical-site-infection-v1
ID:
7kyvlfzt63k7chfk
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_dataset_mandatory_2024-04_12months
    Status:
    Succeeded
    Job identifier:
    gjvaaqx4gask5ako
  • Action:
    table0
    Status:
    Succeeded
    Job identifier:
    mnyqtwnb3vaspyi4
  • Action:
    table0_pcsc
    Status:
    Succeeded
    Job identifier:
    ibayvvnda22ppyvi
  • Action:
    table10
    Status:
    Succeeded
    Job identifier:
    pjqveyplolfdcnku
  • Action:
    table11
    Status:
    Succeeded
    Job identifier:
    eevfmgr7gfvirjvn
  • Action:
    table1a
    Status:
    Succeeded
    Job identifier:
    5ypmq5fmhutpq63b
  • Action:
    table1b_pcsc
    Status:
    Succeeded
    Job identifier:
    wgmf3ii3g2lrnukd
  • Action:
    table3
    Status:
    Succeeded
    Job identifier:
    n77fjsyjkofhgane
  • Action:
    table9a
    Status:
    Succeeded
    Job identifier:
    77tdr3vtlmfyjqi4

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 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 0 0%
Running 0 0%
Succeeded 9 100%
Failed 0 0%

9 / 9 (100%) complete

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:40:32

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

Job request

Status
Succeeded
Backend
TPP
Workspace
surgical-site-infection-v1
Requested by
Louis Fisher
Branch
main
Force run dependencies
No
Git commit hash
a65ce7b
Requested actions
  • generate_dataset_mandatory_2024-04_12months
  • table0
  • table1a
  • table3
  • table9a
  • table10
  • table11
  • table0_pcsc
  • table1b_pcsc

Code comparison

Compare the code used in this job request