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Job request: 19915

Organisation:
University of Manchester
Workspace:
adverse-event-prediction-model
ID:
2at2sfcw2aet2gdz
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 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:
    cox_uti_model
    Status:
    Status: Succeeded
    Job identifier:
    cyl7eqnbsrb5s4ag

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 30000

actions:
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ###
### study cohort ###

  generate_study_population_period_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1
    outputs:
      highly_sensitive:
        cohort: output/input_period_1.csv

  period_1_process:
    run: r:latest analysis/period_1_process.R
    needs: [generate_study_population_period_1]
    outputs:
      highly_sensitive: 
        csv1: output/period_1a.csv
        csv2: output/period_1_*.csv

  generate_study_population_period_1b:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1b
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1b.csv

  period_1b_quickcheck:
    run: r:latest analysis/period_1b_quickcheck.R
    needs: [generate_study_population_period_1b]
    outputs:
      moderately_sensitive: 
        csv1: output/period_1b_quickcheck.csv

  generate_study_population_period_1c:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1c
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1c.csv

  generate_study_population_period_1d:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1d
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1d.csv

  generate_study_population_period_1e:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1e
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1e.csv

  generate_study_population_period_1f:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1f
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1f.csv

  generate_study_population_period_1g:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1g
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1g.csv

  generate_study_population_period_1h:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1h
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1h.csv

  generate_study_population_period_1i:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1i
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1i.csv

  generate_study_population_period_1j:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1j
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1j.csv

  generate_study_population_period_1k:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1k
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1k.csv

  generate_study_population_period_1l:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1l
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1l.csv

  generate_study_population_period_1m:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1m
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1m.csv

  generate_study_population_period_1n:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1n
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1n.csv

  generate_study_population_period_1o:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1o
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1o.csv

  generate_study_population_period_1p:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1p
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1p.csv

  generate_study_population_period_1q:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1q
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1q.csv

  generate_study_population_period_1r:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1r
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1r.csv

  generate_study_population_period_1s:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1s
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1s.csv

  generate_study_population_period_1t:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1t
    needs: [period_1_process]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1t.csv

  period_1a_id:
    run: r:latest analysis/period_1a_id.R
    needs: [generate_study_population_period_1]
    outputs:
      highly_sensitive: 
        csv1: output/period_1a_id.csv

  generate_study_population_period_1a:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_period_1a
    needs: [period_1a_id]
    outputs:
      highly_sensitive:
        cohort: output/input_period_1a.csv

  process_cox_dataset:
    run: r:latest analysis/process_cox_dataset.R
    needs: [generate_study_population_period_1a,generate_study_population_period_1b,generate_study_population_period_1c,generate_study_population_period_1d,
    generate_study_population_period_1e,generate_study_population_period_1f,generate_study_population_period_1g,generate_study_population_period_1h,
    generate_study_population_period_1i,generate_study_population_period_1j,generate_study_population_period_1k,generate_study_population_period_1l,
    generate_study_population_period_1m,generate_study_population_period_1n,generate_study_population_period_1o,generate_study_population_period_1p,
    generate_study_population_period_1q,generate_study_population_period_1r,generate_study_population_period_1s,generate_study_population_period_1t]
    outputs:
      highly_sensitive: 
        rds: output/processed_data.rds

  process_kaplan_meier_plot:
    run: r:latest analysis/prediction/kaplan_meier_plot.R
    needs: [process_cox_dataset]
    outputs:
      moderately_sensitive: 
        plot1: output/KM_overall_with_CI.jpeg
        csv1: output/surv_df.csv

  process_kaplan_meier_plot_by_infection:
    run: r:latest analysis/prediction/kaplan_meier_plot_by_infection.R
    needs: [process_cox_dataset]
    outputs:
      moderately_sensitive: 
        plot1: output/KM_by_*_with_CI.jpeg

  cox_overall:
    run: r:latest analysis/prediction/cox_overall.R
    needs: [process_cox_dataset]
    outputs:
      moderately_sensitive: 
        plot1: output/spline_age.jpeg

  process_data_for_model:
    run: r:latest analysis/prediction/process_data_for_model.R
    needs: [process_cox_dataset]
    outputs:
      highly_sensitive: 
        rds: output/data_for_cox_model.rds
      moderately_sensitive: 
        csv: output/missing_data_count.csv

  cox_uti_model:
    run: r:latest analysis/prediction/cox_uti_model.R
    needs: [process_data_for_model]
    outputs:
      moderately_sensitive: 
        csv1: output/uti_model_evaluation.csv
        plot1: output/KM_Curves.jpeg
        plot2: output/High_Low_Risk_Patients.jpeg
        plot3: output/survival_plot_baseline_survival_curves.jpeg
        plot4: output/survival_plot_baseline_survival_curves2.jpeg

  cox_urti_model:
    run: r:latest analysis/prediction/cox_urti_model.R
    needs: [process_data_for_model]
    outputs:
      moderately_sensitive: 
        csv1: output/forward_selected_variables_urti.csv
        csv2: output/backward_selected_variables_urti.csv

  cox_lrti_model:
    run: r:latest analysis/prediction/cox_lrti_model.R
    needs: [process_data_for_model]
    outputs:
      moderately_sensitive: 
        csv1: output/forward_selected_variables_lrti.csv
        csv2: output/backward_selected_variables_lrti.csv

  cox_otexterna_model:
    run: r:latest analysis/prediction/cox_otexterna_model.R
    needs: [process_data_for_model]
    outputs:
      moderately_sensitive: 
        csv1: output/forward_selected_variables_otexterna.csv
        csv2: output/backward_selected_variables_otexterna.csv

  cox_otmedia_model:
    run: r:latest analysis/prediction/cox_otmedia_model.R
    needs: [process_data_for_model]
    outputs:
      moderately_sensitive: 
        csv1: output/forward_selected_variables_otmedia.csv
        csv2: output/backward_selected_variables_otmedia.csv

  cox_sinusitis_model:
    run: r:latest analysis/prediction/cox_sinusitis_model.R
    needs: [process_data_for_model]
    outputs:
      moderately_sensitive: 
        csv1: output/forward_selected_variables_sinusitis.csv
        csv2: output/backward_selected_variables_sinusitis.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:17:21

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

Job information

Status
Succeeded
Backend
TPP
Workspace
adverse-event-prediction-model
Requested by
Billy Zhong
Branch
ae_prediction
Force run dependencies
No
Git commit hash
3f79356
Requested actions
  • cox_uti_model

Code comparison

Compare the code used in this Job Request