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Job request: 18869

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
safety-sotrovimab-paxlovid-molnupiravir
ID:
w5ywqcsjinpqco4t
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Katie Bechman 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_study_population
    Status:
    Status: Succeeded
    Job identifier:
    d4pkyjyztzjeh55y
  • Action:
    data_properties
    Status:
    Status: Succeeded
    Job identifier:
    dnmjbuw7vywencsi
  • Action:
    PS_model
    Status:
    Status: Failed
    Job identifier:
    7gdkua2katznhsxt
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    define_covariates
    Status:
    Status: Failed
    Job identifier:
    2ewlsjasx4rh6k5j
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    cox_model
    Status:
    Status: Failed
    Job identifier:
    rfe5kfqajzlfbx27
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    baseline_characteristic
    Status:
    Status: Failed
    Job identifier:
    jz5dchsnxud35xfj
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    preceed_rate
    Status:
    Status: Failed
    Job identifier:
    bhwgiwktja3x3pj4
    Error:
    cancelled_by_user: Cancelled by user

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
        
  data_properties:
    run: r:latest analysis/data_properties.R output/input.csv output
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        cohort: output/input*.txt

  define_covariates:
    run: stata-mp:latest analysis/000_define_covariates.do
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        log: logs/cleaning_dataset.log 
      highly_sensitive:
        data: output/data/main.dta

  baseline_characteristic:
    run: stata-mp:latest analysis/100_baseline_characteristics.do
    needs: [define_covariates]
    outputs:
      moderately_sensitive:
        log: logs/baseline_characterisitcs.log 


  cox_model:
    run: stata-mp:latest analysis/200_cox_model.do
    needs: [define_covariates]
    outputs:
      moderately_sensitive:
        log: logs/cox_model.log 
        data: output/tables/cox_model_summary.dta
        survrisk_ae_all: output/figures/survrisk_ae_all.svg
        survrisk_ae_spc_all: output/figures/survrisk_ae_spc_all.svg
        survrisk_ae_drug_all: output/figures/survrisk_ae_drug_all.svg
        survrisk_ae_imae_all: output/figures/survrisk_ae_imae_all.svg
        survrisk_allcause_emerg_aande: output/figures/survrisk_allcause_emerg_aande.svg
        survrisk_covid_hosp_date: output/figures/survrisk_covid_hosp_date.svg
        survrisk_all_hosp_date: output/figures/survrisk_all_hosp_date.svg
        survrisk_died_date_ons: output/figures/survrisk_died_date_ons.svg
        survhaz_ae_all: output/figures/survhaz_ae_all.svg
        survhaz_ae_spc_all: output/figures/survhaz_ae_spc_all.svg
        survhaz_ae_drug_all: output/figures/survhaz_ae_drug_all.svg
        survhaz_ae_imae_all: output/figures/survhaz_ae_imae_all.svg
        survhaz_allcause_emerg_aande: output/figures/survhaz_allcause_emerg_aande.svg
        survhaz_covid_hosp_date: output/figures/survhaz_covid_hosp_date.svg
        survhaz_all_hosp_date: output/figures/survhaz_all_hosp_date.svg
        survhaz_died_date_ons: output/figures/survhaz_died_date_ons.svg 
        survcur_ae_all: output/figures/survcur_ae_all.svg
        survcur_ae_spc_all: output/figures/survcur_ae_spc_all.svg
        survcur_ae_drug_all: output/figures/survcur_ae_drug_all.svg
        survcur_ae_imae_all: output/figures/survcur_ae_imae_all.svg
        survcur_allcause_emerg_aande: output/figures/survcur_allcause_emerg_aande.svg
        survcur_covid_hosp_date: output/figures/survcur_covid_hosp_date.svg
        survcur_all_hosp_date: output/figures/survcur_all_hosp_date.svg
        survcur_died_date_ons: output/figures/survcur_died_date_ons.svg

  PS_model:
    run: stata-mp:latest analysis/300_ps_model.do
    needs: [define_covariates]
    outputs:
      moderately_sensitive:
        log: logs/ps_model.log
        data: output/tables/cox_model_propensity.dta
        histogram_agesex: output/figures/histogram_agesex.svg
        histogram_adj: output/figures/histogram_adj.svg
        histogram_fuladj1: output/figures/histogram_fulladj1.svg
        histogram_fulladj2: output/figures/histogram_fulladj2.svg
        match_agesex: output/figures/match_agesex.svg
        match_adj: output/figures/match_adj.svg
        match_fulladj1: output/figures/match_fulladj1.svg
        match_fulladj2: output/figures/match_fulladj2.svg  
  
  preceed_rate:
    run: stata-mp:latest analysis/400_preceeding_rate.do
    needs: [define_covariates]
    outputs:
      moderately_sensitive:
        log: logs/preceed_rate.log 
        data: output/tables/comparator_rate_summary.dta

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 25:21:37

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

Job request

Status
Failed
Backend
TPP
Workspace
safety-sotrovimab-paxlovid-molnupiravir
Requested by
Katie Bechman
Branch
main
Force run dependencies
No
Git commit hash
d7e6959
Requested actions
  • generate_study_population
  • data_properties
  • define_covariates
  • baseline_characteristic
  • cox_model
  • PS_model
  • preceed_rate
  • run_all

Code comparison

Compare the code used in this job request