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Job request: 14519

Organisation:
University of Manchester
Workspace:
sepsis_hosp_admission
ID:
pxgibvtyg4ybqmfr
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Billy Zhong 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: 30000

actions:

### study cohort ###
  generate_study_population_case:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case
    outputs:
      highly_sensitive:
        cohort: output/input_case.csv

  generate_study_population_control_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_1
    outputs:
      highly_sensitive:
        cohort: output/input_control_1.csv

  generate_study_population_control_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_2
    outputs:
      highly_sensitive:
        cohort: output/input_control_2.csv

  case_check:  
    run: r:latest analysis/case_check.R
    needs: [generate_study_population_case]
    outputs:
      highly_sensitive:
        cohort: output/case_ch.csv
      moderately_sensitive:
        table1: output/case_check.csv
        table2: output/case_frequency_check.csv

  sepsis_trend:  
    run: r:latest analysis/sepsis_trend.R
    needs: [case_check]
    outputs:
      moderately_sensitive:
        plot1: output/figure_2.1.jpeg
        plot2: output/figure_2.2.jpeg
        plot3: output/figure_2.3.jpeg

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2022-12-31 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv.gz

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_*.csv

  sepsis_trend_rate:  
    run: r:latest analysis/sepsis_trend_rate.R
    needs: [case_check,generate_measures]
    outputs:
      moderately_sensitive:
        plot1: output/figure_rate.jpeg

  sepsis_trend_rate_com:  
    run: r:latest analysis/sepsis_trend_rate_com.R
    needs: [case_check,generate_measures]
    outputs:
      moderately_sensitive:
        plot1: output/figure_rate_com.jpeg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:42:22

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

Job request

Status
Succeeded
Backend
TPP
Workspace
sepsis_hosp_admission
Requested by
Billy Zhong
Branch
sepsis
Force run dependencies
No
Git commit hash
abf6b74
Requested actions
  • generate_study_population_control_1
  • generate_study_population_control_2

Code comparison

Compare the code used in this job request