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Job request: 19802

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
safety-sotrovimab-paxlovid-molnupiravir
ID:
pjkorwzh6afn4ya4
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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 50000

actions:

  generate_study_population_control:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control
    outputs:
      highly_sensitive:
        cohort: output/input_control.csv
        
  generate_study_population_treatment:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_treatment
    outputs:
      highly_sensitive:
        cohort: output/input_treatment.csv

  data_properties:
    run: r:latest analysis/data_properties.R output/input_control.csv output/input_treatment.csv output/data_properties
    needs: [generate_study_population_control, generate_study_population_treatment]
    outputs:
      moderately_sensitive:
        cohort: output/data_properties/input*.txt

  define_covariates_combine:
    run: stata-mp:latest analysis/003_define_covariates_combine.do
    needs: [generate_study_population_control, generate_study_population_treatment]
    outputs:
      moderately_sensitive:
        log: logs/cleaning_dataset_combine.log 
      highly_sensitive:
        data: output/data/main.dta

  baseline_characteristic:
    run: stata-mp:latest analysis/100_baseline_characteristics.do
    needs: [define_covariates_combine]
    outputs:
      moderately_sensitive:
        log: logs/baseline_characterisitcs.log 
        data: output/tables/baseline_allpts.csv      

  cox_model:
    run: stata-mp:latest analysis/200_cox_model.do
    needs: [define_covariates_combine]
    outputs:
      moderately_sensitive:
        log: logs/cox_model.log 
        data: output/tables/cox_model_summary_csv.csv 
        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_ae_all: output/figures/survrisk_ae_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
        survrisk_ae_diverticulitis: output/figures/survrisk_ae_diverticulitis.svg
        survrisk_ae_diarrhoea: output/figures/survrisk_ae_diarrhoea.svg
        survrisk_ae_taste: output/figures/survrisk_ae_taste.svg
        survrisk_ae_rash: output/figures/survrisk_ae_rash.svg
        survrisk_ae_anaphylaxis: output/figures/survrisk_ae_anaphylaxis.svg
        survrisk_ae_severe_drug: output/figures/survrisk_ae_severe_drug.svg
        survrisk_ae_nonsevere_drug: output/figures/survrisk_ae_nonsevere_drug.svg
        survrisk_ae_ra: output/figures/survrisk_ae_ra.svg
        survrisk_ae_sle: output/figures/survrisk_ae_sle.svg
        survrisk_ae_psorasis: output/figures/survrisk_ae_psorasis.svg
        survrisk_ae_psa: output/figures/survrisk_ae_psa.svg
        survrisk_ae_axspa: output/figures/survrisk_ae_axspa.svg
        survrisk_ae_ibd: output/figures/survrisk_ae_ibd.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_ae_all: output/figures/survcur_ae_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
        survcur_ae_diverticulitis: output/figures/survcur_ae_diverticulitis.svg
        survcur_ae_diarrhoea: output/figures/survcur_ae_diarrhoea.svg
        survcur_ae_taste: output/figures/survcur_ae_taste.svg
        survcur_ae_rash: output/figures/survcur_ae_rash.svg
        survcur_ae_anaphylaxis: output/figures/survcur_ae_anaphylaxis.svg
        survcur_ae_severe_drug: output/figures/survcur_ae_severe_drug.svg
        survcur_ae_nonsevere_drug: output/figures/survcur_ae_nonsevere_drug.svg
        survcur_ae_ra: output/figures/survcur_ae_ra.svg
        survcur_ae_sle: output/figures/survcur_ae_sle.svg
        survcur_ae_psorasis: output/figures/survcur_ae_psorasis.svg
        survcur_ae_psa: output/figures/survcur_ae_psa.svg
        survcur_ae_axspa: output/figures/survcur_ae_axspa.svg
        survcur_ae_ibd: output/figures/survcur_ae_ibd.svg
        
  PS_model:
    run: stata-mp:latest analysis/300_ps_model.do
    needs: [define_covariates_combine]
    outputs:
      moderately_sensitive:
        log: logs/ps_model.log
        data: output/tables/cox_model_propensity_csv.csv 
        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_combine]
    outputs:
      moderately_sensitive:
        log: logs/preceed_rate.log 
        data: output/tables/comparator_rate_summary_csv.csv 
  
  redacted_table:
    run: stata-mp:latest analysis/500_redacted_table.do
    needs: [define_covariates_combine]
    outputs:
      moderately_sensitive:
        log1: logs/redacted_table.log   
        data: output/tables/baseline_table_redact_bydrug.csv   
        data1: output/tables/baseline_table_redact_mean.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 05:15:22

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

Job request

Status
Succeeded
Backend
TPP
Workspace
safety-sotrovimab-paxlovid-molnupiravir
Requested by
Katie Bechman
Branch
main
Force run dependencies
No
Git commit hash
dba3719
Requested actions
  • define_covariates_combine
  • baseline_characteristic
  • cox_model
  • PS_model
  • preceed_rate
  • redacted_table

Code comparison

Compare the code used in this job request