Job request: 5021

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher dgrint requested one or more actions to be run against real patient data in the SGTF-Omi 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

ID Status Action
rx37yaca4jzz7lci succeeded anCOX
6n2onb64ctih262j succeeded anCOX_IMP
myizeaea3seezpyj succeeded anSUMM
syd7aurbzqcfnfyp succeeded anTAB1
6p6dmy4xdb74j7qo succeeded crIMP
lpqbyge5no7uf2ri succeeded crMAIN
shm76a3zkqeyphul succeeded generate_cohort

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 10000

actions:

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

  crMAIN:
    run: stata-mp:latest analysis/cr_main.do
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        log: logs/cr_main.log
      highly_sensitive:
        data: output/main.dta
        
  anSUMM:
    run: stata-mp:latest analysis/an_summary.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: logs/an_summary.log
        figure1: output/sgtf_perc_region.svg
        figure2: output/sgtf_perc_region.pdf
        
  anTAB1:
    run: stata-mp:latest analysis/an_table1.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: logs/an_table1.log
        table1text: output/table1.txt
        table1xlsx: output/table1.xlsx
        figure1: output/time_ae_hist.svg
        figure2: output/date_ae_hist.svg
        figure3: output/date_ae_hist1.svg
        figure4: output/ae_hist.svg
        figure5: output/ae_kden.svg

  anCOX:
    run: stata-mp:latest analysis/an_cox.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: logs/an_cox.log
        figure1: output/cox_shoen.svg
        figure2: output/cox_km.svg
        figure3: output/cox_cumhaz.svg  
        figure4: output/cox_haz.svg
        table1text: output/table2.txt
        table1xlsx: output/table2.xlsx
        
  crIMP:
    run: stata-mp:latest analysis/cr_imputed.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: logs/cr_imputed.log
      highly_sensitive:
        data: output/main_imputed.dta
        
  anCOX_IMP:
    run: stata-mp:latest analysis/an_cox_imputed.do
    needs: [crIMP]
    outputs:
      moderately_sensitive:
        log: logs/an_cox_imputed.log
      highly_sensitive:
        data2: output/an_imputed_eth2.ster

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 02:21:50

Config

  • Backend:
    TPP
  • Workspace:
    sgtf-omi
  • Branch:
    main
  • Creator:
    dgrint
  • Force run dependencies:
    False
  • Git Commit Hash:
    8dd6b0b
  • Requested actions:
    • generate_cohort
    • crMAIN
    • anSUMM
    • anTAB1
    • anCOX
    • crIMP
    • anCOX_IMP