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Job request: 1903

Organisation:
Workspace:
group-video-consultation
ID:
kobnmmg36atydfwq
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Martina Fonseca 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_cohorts_long:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2019-01-01 to 2021-03-01 by month" --output-dir=output/measures
    outputs:
      highly_sensitive:
        cohort1: output/measures/input_measures_*.csv

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

  run_model_long:
      run: r:latest analysis/03-createnattrends_codes.R
      needs: [generate_cohorts_long]
      outputs:
        moderately_sensitive:
          log: logs/log-03-createnattrends.txt
          tb01: output/tables/sc03_tb01_nattrends.csv
          fig01: output/plots/sc03_fig01_nattrends.svg
          fig02: output/plots/sc03_fig02_nattrends.svg
          fig03: output/plots/sc03_fig03_pracnatcoverage.svg
          fig04: output/plots/sc03_fig04_pracbyregcoverage.svg
          fig04b: output/plots/sc03_fig04b_pracbyregcoverage.svg

  run_model_measures:
        run: r:latest analysis/02-createtemporal.R
        needs: [generate_cohorts_long,generate_measures]
        outputs:
          moderately_sensitive:
            log: logs/log-02-createtemporal.txt
            red_measures: output/tables/redacted_*.csv
            #figall: output/plots/plot_each_*_practice.svg
            figquant: output/plots/plot_quantiles_*_practice.svg
            figlogquant: output/plots/plot_logquantiles_*_practice.svg


  ### Weekly tallies
  generate_cohorts_weekly2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures_weekly --index-date-range "2019-04-01 to 2021-03-29 by week" --output-dir=output/measures-week
    outputs:
      highly_sensitive:
        cohort: output/measures-week/input_measures_weekly_*.csv

  generate_measures_weekly2021:
    run: cohortextractor:latest generate_measures --study-definition study_definition_measures_weekly --output-dir=output/measures-week
    needs: [generate_cohorts_weekly2021]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures-week/measure_*.csv

  run_model_weekly2021:
    run: r:latest analysis/04-weekly2021.R
    needs: [generate_cohorts_weekly2021,generate_measures_weekly2021]
    outputs:
      moderately_sensitive:
        log: logs/log-04-weekly2021.txt
        tab1: output/tables/sc04-weeklynattrend.csv
        figx: output/plots/sc04_*.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 22:52:55

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

Job request

Status
Succeeded
Backend
TPP
Workspace
group-video-consultation
Requested by
Martina Fonseca
Branch
snomed-version
Force run dependencies
Yes
Git commit hash
97ed0aa
Requested actions
  • run_model_measures
  • run_model_weekly2021

Code comparison

Compare the code used in this job request