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Job request: 10807

Organisation:
UKHSA
Workspace:
lt-repeat-antimicrobial-prescribing
ID:
q7b27cc3syvdmqka
View repo View project.yaml

This page shows the technical details of what happened when the 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 list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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:
        n_prescribing_table: output/n_prescribing_2020-01-01.csv
        n_indications_repeat_amr_table: output/n_indications_repeat_amr_2020-01-01.csv
        n_indications_non_repeat_amr_table: output/n_indications_non_repeat_amr_2020-01-01.csv
        n_indications_co_occurrence_repeat_amr_table: output/n_indications_co_occurrence_repeat_amr_2020-01-01.csv
        n_indications_co_occurrence_non_repeat_amr_table: output/n_indications_co_occurrence_non_repeat_amr_2020-01-01.csv
        n_repeat_amr_table: output/n_repeat_amr_2020-01-01.csv
        n_non_repeat_amr_table: output/n_non_repeat_amr_2020-01-01.csv
        demographics_table: output/demographics_table_2020-01-01.csv

  describe_covid:
    run: r:latest analysis/cohort_report.R 2021-01-01
    needs: [generate_study_population_covid]
    outputs:
      moderately_sensitive:
        n_prescribing_table: output/n_prescribing_2021-01-01.csv
        n_indications_repeat_amr_table: output/n_indications_repeat_amr_2021-01-01.csv
        n_indications_non_repeat_amr_table: output/n_indications_non_repeat_amr_2021-01-01.csv
        n_indications_co_occurrence_repeat_amr_table: output/n_indications_co_occurrence_repeat_amr_2021-01-01.csv
        n_indications_co_occurrence_non_repeat_amr_table: output/n_indications_co_occurrence_non_repeat_amr_2021-01-01.csv
        n_repeat_amr_table: output/n_repeat_amr_2021-01-01.csv
        n_non_repeat_amr_table: output/n_non_repeat_amr_2021-01-01.csv
        demographics_table: output/demographics_table_2021-01-01.csv

  # 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

  describe_measures:
    run: r:latest analysis/measures_report.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        measures_figure: output/measures/measure_prescribing.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 06:13:20

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
eef8e9e
Requested actions
  • describe_precovid
  • describe_covid

Code comparison

Compare the code used in this Job Request