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Job request: 26891

Organisation:
University of Oxford
Workspace:
surgical-site-infection-v1
ID:
xzopc5go24vgppbo
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Harry T Mason 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:
    table0
    Status:
    Succeeded
    Job identifier:
    xu27yapd2ckyfg6v
  • Action:
    table1a
    Status:
    Succeeded
    Job identifier:
    os467hmw2kanslda
  • Action:
    table3
    Status:
    Succeeded
    Job identifier:
    pm36pf5alw4tbnnh
  • Action:
    table9a
    Status:
    Succeeded
    Job identifier:
    av7lazxr25vz52gi
  • Action:
    table10
    Status:
    Succeeded
    Job identifier:
    ost6tsrsr5nh7lqq
  • Action:
    table11
    Status:
    Succeeded
    Job identifier:
    tzpdmcaq6x3e4ssd
  • Action:
    table0_pcsc
    Status:
    Succeeded
    Job identifier:
    7cfdj5fdtio7w4ae
  • Action:
    table1b_pcsc
    Status:
    Succeeded
    Job identifier:
    jvydnd7bpg642aif

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 8 100%
Failed 0 0%

8 / 8 (100%) complete

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:07:27

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
Harry T Mason
Branch
main
Force run dependencies
No
Git commit hash
ac45ffe
Requested actions
  • table0
  • table1a
  • table3
  • table9a
  • table10
  • table11
  • table0_pcsc
  • table1b_pcsc

Code comparison

Compare the code used in this job request