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Job request: 2413

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
sgtf-cfr-research
ID:
5qrggu5nifdpvchc
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:
    crNEW
    Status:
    Status: Succeeded
    Job identifier:
    jsonn2vfalboifmg
  • Action:
    anODDS_MOD
    Status:
    Status: Succeeded
    Job identifier:
    ltpesgsppgnwppeg
  • Action:
    anODDS_HOSP
    Status:
    Status: Succeeded
    Job identifier:
    jvvdmki67qbuxf7t

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 50000

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_analysis_dataset.do
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        log: logs/cr_analysis_dataset.log
      highly_sensitive:
        data: output/cr_analysis_dataset.dta

  crNEW:
    run: stata-mp:latest analysis/cr_analysis_new.do
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        log: logs/cr_analysis_new.log
      highly_sensitive:
        data: output/cr_analysis_new.dta

  crIMP:
    run: stata-mp:latest analysis/cr_imputed_dataset.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: logs/cr_imputed.log
      highly_sensitive:
        data: output/cr_imputed_dataset.dta

  anSUMM:
    run: stata-mp:latest analysis/an_summary.do
    needs: [crNEW]
    outputs:
      moderately_sensitive:
        log: logs/an_summary.log
        #figure1: output/sgtf_perc_region.svg
        #figure2: output/sgtf_perc_region.pdf

  anRISK_TAB1:
    run: stata-mp:latest analysis/an_risk28_table1.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: logs/an_risk28_table1.log
        table1text: output/table1_risk28.txt
        table1xlsx: output/table1_risk28.xlsx

  anCOX_TAB1:
    run: stata-mp:latest analysis/an_cox_table1.do
    needs: [crNEW]
    outputs:
      moderately_sensitive:
        log: logs/an_cox_table1.log
        table1text: output/table1_cox.txt
        table1xlsx: output/table1_cox.xlsx
        figure1: output/time_death_hist.svg
        figure2: output/time_date_death_hist.svg
        figure3: output/time_date_death_hist1.svg
        figure4: output/hosp_hist.svg
        figure5: output/hosp_kden.svg
        figure6: output/icu_hist.svg

  anHOSP_TAB1:
    run: stata-mp:latest analysis/an_hosp_table1.do
    needs: [crNEW]
    outputs:
      moderately_sensitive:
        log: logs/an_hosp_table1.log
        table1text: output/table1_hosp.txt
        table1xlsx: output/table1_hosp.xlsx
        figure1: output/time_death_hosp.svg

  anDEATH_TAB1:
    run: stata-mp:latest analysis/an_deaths_table1.do
    needs: [crNEW]
    outputs:
      moderately_sensitive:
        log: logs/an_deaths_table1.log
        table1text: output/table1_deaths1.txt
        table1xlsx: output/table1_deaths1.xlsx
        table2text: output/table1_deaths0.txt
        table2xlsx: output/table1_deaths0.xlsx      

  anCOX_STAB1:
    run: stata-mp:latest analysis/an_cox_stable1.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: logs/an_cox_stable1.log
        table1text: output/stable1_cox.txt
        table1xlsx: output/stable1_cox.xlsx
        table2text: output/stable1_cox_short.txt
        table2xlsx: output/stable1_cox_short.xlsx

#  anRISK_MOD:
#    run: stata-mp:latest analysis/an_risk_models.do
#    needs: [crMAIN]
#    outputs:
#      moderately_sensitive:
#        log: logs/an_risk_models.log

  anODDS_MOD:
    run: stata-mp:latest analysis/an_logit_models.do
    needs: [crNEW]
    outputs:
      moderately_sensitive:
        log: logs/an_logit_models.log
        table1text: output/table3_abs_risk.txt
        table1xlsx: output/table3_abs_risk.xlsx

  anODDS_HOSP:
    run: stata-mp:latest analysis/an_logit_hosp.do
    needs: [crNEW]
    outputs:
      moderately_sensitive:
        log: logs/an_logit_hosp.log
        table1text: output/table3_hosp_risk.txt
        table1xlsx: output/table3_hosp_risk.xlsx

  anODDS_MOD40:
    run: stata-mp:latest analysis/an_logit_models_40.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: logs/an_logit_models_40.log
        table1text: output/table3_abs_risk40.txt
        table1xlsx: output/table3_abs_risk40.xlsx

  anCOX_MOD:
    run: stata-mp:latest analysis/an_cox_models.do
    needs: [crNEW]
    outputs:
      moderately_sensitive:
        log: logs/an_cox_models.log
        figure1: output/cox_shoen.svg
        figure2: output/cox_km.svg
        figure3: output/cox_cumhaz.svg  
        figure4: output/cox_haz.svg
        table1text: output/table2_hr.txt
        table1xlsx: output/table2_hr.xlsx

  anCOX_HOSP:
    run: stata-mp:latest analysis/an_cox_hosp.do
    needs: [crNEW]
    outputs:
      moderately_sensitive:
        log: logs/an_cox_hosp.log
        figure1: output/cox_shoen_hosp.svg
        #figure2: output/cox_km.svg
        #figure3: output/cox_cumhaz.svg  
        figure2: output/cox_haz_hosp.svg
        table1text: output/table2_hr_hosp.txt
        table1xlsx: output/table2_hr_hosp.xlsx

  anCOX_DHOSP:
    run: stata-mp:latest analysis/an_cox_deathhosp.do
    needs: [crNEW]
    outputs:
      moderately_sensitive:
        log: logs/an_cox_deathhosp.log
        figure1: output/cox_shoen_deathhosp.svg
        #figure2: output/cox_km.svg
        #figure3: output/cox_cumhaz.svg  
        figure2: output/cox_haz_deathhosp.svg
        table1text: output/table2_hr_deathhosp.txt
        table1xlsx: output/table2_hr_deathhosp.xlsx

  anCOX_DICU:
    run: stata-mp:latest analysis/an_cox_deathicu.do
    needs: [crNEW]
    outputs:
      moderately_sensitive:
        log: logs/an_cox_deathicu.log
        figure1: output/cox_shoen_deathicu.svg
        #figure2: output/cox_km.svg
        #figure3: output/cox_cumhaz.svg  
        figure2: output/cox_haz_deathicu.svg
        table1text: output/table2_hr_deathicu.txt
        table1xlsx: output/table2_hr_deathicu.xlsx

  anCOX_SENS:
    run: stata-mp:latest analysis/an_cox_models_sgtf_sens.do
    needs: [crMAIN]
    outputs:
      moderately_sensitive:
        log: logs/an_cox_models_sgtf_sens.log

  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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:14:04

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

Job request

Status
Succeeded
Backend
TPP
Workspace
sgtf-cfr-research
Requested by
Daniel Grint
Branch
master
Force run dependencies
No
Git commit hash
4fcc30d
Requested actions
  • crNEW
  • anODDS_MOD
  • anODDS_HOSP

Code comparison

Compare the code used in this job request