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Job request: 18944

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
safety-sotrovimab-paxlovid-molnupiravir
ID:
7fb2d7lq7eppoxpa
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Millie Green requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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

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/001_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 


  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.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_combine]
    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_combine]
    outputs:
      moderately_sensitive:
        log: logs/preceed_rate.log 
        data: output/tables/comparator_rate_summary.dta

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:41:27

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

Job information

Status
Succeeded
Backend
TPP
Workspace
safety-sotrovimab-paxlovid-molnupiravir
Requested by
Millie Green
Branch
main
Force run dependencies
No
Git commit hash
57a103d
Requested actions
  • data_properties

Code comparison

Compare the code used in this Job Request