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Job request: 8527

Organisation:
UKHSA
Workspace:
lt-repeat-antimicrobial-prescribing
ID:
tlnc22spj7ep2zpb
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Alex Orlek requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 100

actions:

  # generate cohorts
  generate_study_population_precovid:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-01-01 to 2020-01-01 by month"
    outputs:
      highly_sensitive:
        cohort: output/input_2020-01-01.csv

  generate_study_population_covid:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-01-01 to 2021-01-01 by month"
    outputs:
      highly_sensitive:
        cohort: output/input_2021-01-01.csv

  # analyse cohorts
  describe_precovid:
    run: r:latest analysis/cohort_report.R 2020-01-01
    needs: [generate_study_population_precovid]
    outputs:
      moderately_sensitive:
        lt_repeat_prop_table: output/n_lt_repeat_2020-01-01.csv
        age_dist_figure: output/demographic_pyramid_2020-01-01.pdf

  describe_covid:
    run: r:latest analysis/cohort_report.R 2021-01-01
    needs: [generate_study_population_covid]
    outputs:
      moderately_sensitive:
        lt_repeat_prop_table: output/n_lt_repeat_2021-01-01.csv
        age_dist_figure: output/demographic_pyramid_2021-01-01.pdf

  # generate measures
  generate_measure_populations:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2020-01-01 to 2022-01-01 by month" --output-dir=output/measures
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_measures --output-dir=output/measures
    needs: [generate_measure_populations]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 10:26:30

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

Job information

Status
Succeeded
Backend
TPP
Workspace
lt-repeat-antimicrobial-prescribing
Requested by
Alex Orlek
Branch
main
Force run dependencies
Yes
Git commit hash
1471fd8
Requested actions
  • run_all

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