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Job request: 2081

Organisation:
Bennett Institute
Workspace:
immunosuppressant-meds-research
ID:
a2xldmpp6ydxtg6q
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Nick Kennedy 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 50000

actions:

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

  create_cohorts:
    run: stata-mp:latest analysis/000_define_covariates.do
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        log1: logs/start_create_analysis_dataset.smcl 
        data1: output/data/file_imid.dta
        data2: output/data/file_joint.dta
        data3: output/data/file_skin.dta
        data4: output/data/file_bowel.dta
        data5: output/data/file_imiddrugcategory.dta
        data6: output/data/file_standtnf.dta
        data7: output/data/file_standtnf3m.dta
        data8: output/data/file_tnfmono.dta
        data9: output/data/file_standil6.dta
        data10: output/data/file_standil17.dta
        data11: output/data/file_standil23.dta
        data12: output/data/file_standjaki.dta
        data13: output/data/file_standritux.dta
        data14: output/data/file_standinflix.dta

  run_baseline_tables:
    run: stata-mp:latest analysis/100_baseline_characteristics.do
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/descriptive_tables.smcl 
      
  run_cox_models_imid:
    run: stata-mp:latest analysis/202_cox_models.do "imid"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_imid.smcl 
        data1: output/data/cox_model_summary_imid.dta
        data2: output/data/cox_model_summary_haemonc_imid.dta
        
  run_cox_models_joint:
    run: stata-mp:latest analysis/202_cox_models.do "joint"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_joint.smcl 
        data1: output/data/cox_model_summary_joint.dta
        data2: output/data/cox_model_summary_haemonc_joint.dta

  run_cox_models_skin:
    run: stata-mp:latest analysis/202_cox_models.do "skin"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_skin.smcl 
        data1: output/data/cox_model_summary_skin.dta
        data2: output/data/cox_model_summary_haemonc_skin.dta
 
  run_cox_models_bowel:
    run: stata-mp:latest analysis/202_cox_models.do "bowel"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_bowel.smcl 
        data1: output/data/cox_model_summary_bowel.dta
        data2: output/data/cox_model_summary_haemonc_bowel.dta
 
  run_cox_models_imiddrugcategory:
    run: stata-mp:latest analysis/202_cox_models.do "imiddrugcategory"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_imiddrugcategory.smcl 
        data1: output/data/cox_model_summary_imiddrugcategory.dta
        data2: output/data/cox_model_summary_haemonc_imiddrugcategory.dta
  
  run_cox_models_standtnf:
    run: stata-mp:latest analysis/202_cox_models.do "standtnf"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_standtnf.smcl 
        data1: output/data/cox_model_summary_standtnf.dta
        data2: output/data/cox_model_summary_haemonc_standtnf.dta

  run_cox_models_standtnf3m:
    run: stata-mp:latest analysis/202_cox_models.do "standtnf3m"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_standtnf3m.smcl 
        data1: output/data/cox_model_summary_standtnf3m.dta
        data2: output/data/cox_model_summary_haemonc_standtnf3m.dta
       
  run_cox_models_tnfmono:
    run: stata-mp:latest analysis/202_cox_models.do "tnfmono"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_tnfmono.smcl 
        data1: output/data/cox_model_summary_tnfmono.dta
        data2: output/data/cox_model_summary_haemonc_tnfmono.dta
  
  run_cox_models_standil6:
    run: stata-mp:latest analysis/202_cox_models.do "standil6"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_standil6.smcl 
        data1: output/data/cox_model_summary_standil6.dta
        data2: output/data/cox_model_summary_haemonc_standil6.dta
  
  run_cox_models_standil17:
    run: stata-mp:latest analysis/202_cox_models.do "standil17"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_standil17.smcl 
        data1: output/data/cox_model_summary_standil17.dta
        data2: output/data/cox_model_summary_haemonc_standil17.dta
 
  run_cox_models_standil23:
    run: stata-mp:latest analysis/202_cox_models.do "standil23"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_standil23.smcl 
        data1: output/data/cox_model_summary_standil23.dta
        data2: output/data/cox_model_summary_haemonc_standil23.dta
 
  run_cox_models_standjaki:
    run: stata-mp:latest analysis/202_cox_models.do "standjaki"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_standjaki.smcl 
        data1: output/data/cox_model_summary_standjaki.dta
        data2: output/data/cox_model_summary_haemonc_standjaki.dta
  
  run_cox_models_standritux:
    run: stata-mp:latest analysis/202_cox_models.do "standritux"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_standritux.smcl 
        data1: output/data/cox_model_summary_standritux.dta
        data2: output/data/cox_model_summary_haemonc_standritux.dta
        
  run_cox_models_standinflix:
    run: stata-mp:latest analysis/202_cox_models.do "standinflix"
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/cox_models_standinflix.smcl 
        data1: output/data/cox_model_summary_standinflix.dta
        data2: output/data/cox_model_summary_haemonc_standinflix.dta
  
  run_survival_curves:
    run: stata-mp:latest analysis/301_survival_curves.do
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/graphs.smcl 
        figure1: output/figures/survcurv_imiddrugcategory_icuordeath.svg
        figure2: output/figures/imiddrugcategory_graph.gph
        figure3: output/figures/survcurv_imiddrugcategory_died.svg
        figure4: output/figures/survcurv_bowel_icuordeath.svg
        figure5: output/figures/bowel_graph.gph
        figure6: output/figures/survcurv_bowel_died.svg
        figure7: output/figures/survcurv_skin_icuordeath.svg
        figure8: output/figures/skin_graph.gph
        figure9: output/figures/survcurv_skin_died.svg
        figure10: output/figures/survcurv_joint_icuordeath.svg
        figure11: output/figures/joint_graph.gph
        figure12: output/figures/survcurv_joint_died.svg
        figure13: output/figures/survcurv_imid_icuordeath.svg
        figure14: output/figures/imid_graph.gph
        figure15: output/figures/survcurv_imid_died.svg
        figure16: output/figures/survcurv_imiddrugcategory_hospital.svg
        figure17: output/figures/survcurv_bowel_hospital.svg
        figure18: output/figures/survcurv_skin_hospital.svg
        figure19: output/figures/survcurv_joint_hospital.svg
        figure20: output/figures/survcurv_imid_hospital.svg

  run_outcomes_check:
    run: r:latest analysis/outcomes_check_withandwithoutpositivetest.R
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        data1: output/data/outcomes_check.csv
  
  run_export_csv:
    run: stata-mp:latest analysis/400_export_csv.do
    needs: [run_cox_models_imid,run_cox_models_joint,run_cox_models_bowel,run_cox_models_imiddrugcategory,run_cox_models_standtnf,run_cox_models_standtnf3m,run_cox_models_tnfmono,run_cox_models_standil6,run_cox_models_standil17,run_cox_models_standil23,run_cox_models_standjaki,run_cox_models_standritux,run_cox_models_standinflix]
    outputs:
      moderately_sensitive:
        log: logs/export_csv.smcl
        csv_imid: output/data/csv_imid.csv
        csvhaemonc_imid: output/data/csvhaemonc_imid.csv
        csv_joint: output/data/csv_joint.csv
        csvhaemonc_joint: output/data/csvhaemonc_joint.csv
#        csv_skin: output/data/csv_skin.csv
#        csvhaemonc_skin: output/data/csvhaemonc_skin.csv
        csv_bowel: output/data/csv_bowel.csv
        csvhaemonc_bowel: output/data/csvhaemonc_bowel.csv
        csv_imiddrugcategory: output/data/csv_imiddrugcategory.csv
        csvhaemonc_imiddrugcategory: output/data/csvhaemonc_imiddrugcategory.csv
        csv_standtnf: output/data/csv_standtnf.csv
        csvhaemonc_standtnf: output/data/csvhaemonc_standtnf.csv
        csv_standtnf3m: output/data/csv_standtnf3m.csv
        csvhaemonc_standtnf3m: output/data/csvhaemonc_standtnf3m.csv
        csv_tnfmono: output/data/csv_tnfmono.csv
        csvhaemonc_tnfmono: output/data/csvhaemonc_tnfmono.csv
        csv_standil6: output/data/csv_standil6.csv
        csvhaemonc_standil6: output/data/csvhaemonc_standil6.csv
        csv_standil17: output/data/csv_standil17.csv
        csvhaemonc_standil17: output/data/csvhaemonc_standil17.csv
        csv_standil23: output/data/csv_standil23.csv
        csvhaemonc_standil23: output/data/csvhaemonc_standil23.csv
        csv_standjaki: output/data/csv_standjaki.csv
        csvhaemonc_standjaki: output/data/csvhaemonc_standjaki.csv
        csv_standritux: output/data/csv_standritux.csv
        csvhaemonc_standritux: output/data/csvhaemonc_standritux.csv
        csv_standinflix: output/data/csv_standinflix.csv
        csvhaemonc_standinflix: output/data/csvhaemonc_standinflix.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 57:38:06

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

Job information

Status
Succeeded
Backend
TPP
Workspace
immunosuppressant-meds-research
Requested by
Nick Kennedy
Branch
master
Force run dependencies
No
Git commit hash
f7f0fbc
Requested actions
  • run_cox_models_skin

Code comparison

Compare the code used in this Job Request