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Job request: 5152

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
sgtf-omi
ID:
fvcryqazztlgaanu
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Daniel Grint 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

  • Action:
    generate_cohort
    Status:
    Status: Succeeded
    Job identifier:
    ui6asb2pksgxl2l7
  • Action:
    crMAIN
    Status:
    Status: Succeeded
    Job identifier:
    dmmsbvbwh4hnwx7f
  • Action:
    anTAB1
    Status:
    Status: Succeeded
    Job identifier:
    by44gsu7pk7hhhor
  • Action:
    anCOX
    Status:
    Status: Succeeded
    Job identifier:
    envh2wdsmnxaecjo
  • Action:
    crIMP
    Status:
    Status: Succeeded
    Job identifier:
    iqbnluwioouap2mv
  • Action:
    anRISK
    Status:
    Status: Succeeded
    Job identifier:
    kpd73vb6cty4unt3
  • Action:
    anSUMM
    Status:
    Status: Succeeded
    Job identifier:
    eson7s3yku2bclff
  • Action:
    anCOX_IMP
    Status:
    Status: Succeeded
    Job identifier:
    k63ig7jz4kgig5g5

Pipeline

Show 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
        
  anRISK:
    run: stata-mp:latest analysis/an_risk.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: logs/an_risk.log
        table1text: output/table3.txt
        table1xlsx: output/table3.xlsx

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:00:08

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

Job request

Status
Succeeded
Backend
TPP
Workspace
sgtf-omi
Requested by
Daniel Grint
Branch
main
Force run dependencies
No
Git commit hash
047fa27
Requested actions
  • generate_cohort
  • crMAIN
  • anSUMM
  • anTAB1
  • anCOX
  • crIMP
  • anCOX_IMP
  • anRISK

Code comparison

Compare the code used in this job request