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Job request: 6370

Organisation:
The UK Renal Registry
Workspace:
renal_sdr
ID:
znxl4ppnufuack5p
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 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

  • Action:
    get_counts
    Status:
    Status: Succeeded
    Job identifier:
    3barlnxlrrsbc6q4

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 1000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition 
      --index-date-range "2019-01-01 to 2022-02-01 by month" 
      --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input*.csv.gz

  generate_study_population_rrt:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition_rrt
      --index-date-range "2019-01-01 to 2022-02-01 by month" 
      --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_rrt*.csv.gz

  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition_ethnicity
      --output-dir=output
      --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv.gz

  join_cohorts:
    run: >
      cohort-joiner:v0.0.9
        --lhs output/input_20*.csv.gz
        --rhs output/input_ethnicity.csv.gz
        --output-dir output/joined
    needs: [generate_study_population, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_20*.csv.gz

  join_cohorts_rrt:
    run: >
      cohort-joiner:v0.0.9
        --lhs output/input_rrt_20*.csv.gz
        --rhs output/input_ethnicity.csv.gz
        --output-dir output/joined
    needs: [generate_study_population_rrt, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_rrt_20*.csv.gz

  generate_measures:
    run: cohortextractor:latest generate_measures 
      --study-definition study_definition
      --output-dir=output/joined
    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        measure_csv: output/joined/measure_*_rate.csv

  generate_measures_rrt:
    run: cohortextractor:latest generate_measures 
      --study-definition study_definition_rrt
      --output-dir=output/joined
    needs: [join_cohorts_rrt]
    outputs:
      moderately_sensitive:
        measure_csv: output/joined/measure*_rate.csv

  get_counts:
    run: python:latest python analysis/combine_operators.py
    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        counts: output/*_count.csv

  generate_plots:
    run: python:latest python analysis/plot_measures.py
    needs: [generate_measures, generate_measures_rrt]
    outputs:
      moderately_sensitive:
        counts: output/figures/plot_*.jpeg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:07:35

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

Job information

Status
Succeeded
Backend
TPP
Workspace
renal_sdr
Requested by
Louis Fisher
Branch
main
Force run dependencies
No
Git commit hash
f15bbc5
Requested actions
  • get_counts

Code comparison

Compare the code used in this Job Request