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Job request: 6253

Organisation:
University of Surrey
Workspace:
pancreatic_cancer
ID:
5xlwgg243g7prbzc
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher AgzLeman 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: 1000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format=csv
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  generate_denominator_1:    
    run: cohortextractor:latest generate_cohort --study-definition study_definition_denominator --index-date-range "2015-01-01 to 2019-01-01 by month" --skip-existing --output-dir=output --output-format=feather
    outputs:      
      highly_sensitive:
        cohort: output/measures/input*.feather
  
  generate_denominator_2:    
    run: cohortextractor:latest generate_cohort --study-definition study_definition_denominator --index-date-range "2019-02-01 to 2022-02-01 by month" --skip-existing --output-dir=output --output-format=feather
    outputs:      
      highly_sensitive:
        cohort: output/measures/inpu*.feather

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_denominator --skip-existing --output-dir=output/measures
    needs: 
      [
        generate_denominator_1,
        generate_denominator_2,
      ]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_registered*_rate.csv

  describe_data:
    run: r:latest analysis/analysis_counts_average.R
    needs: 
      [
        generate_study_population,
        generate_measures,
      ]
    outputs:
      moderately_sensitive:
        Fig1: output/paca_time_table.png
        Fig2: output/paca_time_table_year.png
        Fig3: output/paca_time_rates.png
        Fig4: output/paca_time_rates_year.png
        Tab1: output/monthly_count.csv
        Tab2: output/monthly_median.csv
        Tab3: output/monthly_average.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 17:13:59

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

Job information

Status
Succeeded
Backend
TPP
Workspace
pancreatic_cancer
Requested by
AgzLeman
Branch
main
Force run dependencies
Yes
Git commit hash
55e0a72
Requested actions
  • run_all