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Job request: 20604

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
safety-sotrovimab-paxlovid-molnupiravir
ID:
laagtdktostyadd5
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 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

  • Action:
    cox_model
    Status:
    Status: Succeeded
    Job identifier:
    ks43ioblwn2p2knb
  • Action:
    preceed_rate
    Status:
    Status: Succeeded
    Job identifier:
    c3drrnx72so5kfxd
  • Action:
    redacted_table
    Status:
    Status: Succeeded
    Job identifier:
    nsy56i6ygbs32ivm

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/203_cox_model.do
    needs: [define_covariates_combine]
    outputs:
      moderately_sensitive:
        log: logs/cox_model.log 
        data: output/tables/cox_model_summary.csv 
        data1: output/tables/cox_model_disease.csv 
        data2: output/tables/cox_model_rates.csv 
        data3: output/tables/cox_model_rates_round.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_bronchospasm: output/figures/survrisk_ae_bronchospasm.svg
        survrisk_ae_contactderm: output/figures/survrisk_ae_contactderm.svg
        survrisk_ae_dizziness: output/figures/survrisk_ae_dizziness.svg
        survrisk_ae_nausea_vomit: output/figures/survrisk_ae_nausea_vomit.svg
        survrisk_ae_headache: output/figures/survrisk_ae_headache.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_bronchospasm: output/figures/survcur_ae_bronchospasm.svg
        survcur_ae_contactderm: output/figures/survcur_ae_contactderm.svg
        survcur_ae_dizziness: output/figures/survcur_ae_dizziness.svg
        survcur_ae_nausea_vomit: output/figures/survcur_ae_nausea_vomit.svg
        survcur_ae_headache: output/figures/survcur_ae_headache.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/303_ps_model.do
    needs: [define_covariates_combine]
    outputs:
      moderately_sensitive:
        log: logs/ps_model.log
        data: output/tables/cox_propensity.csv 
        data2: output/tables/cox_propensity_common.csv 
        histogram_sot_agesex: output/figures/histogram_sot_agesex.svg
        histogram_pax_agesex: output/figures/histogram_pax_agesex.svg
        histogram_mol_agesex: output/figures/histogram_mol_agesex.svg
        histogram_sot_adj: output/figures/histogram_sot_adj.svg
        histogram_pax_adj: output/figures/histogram_pax_adj.svg
        histogram_mol_adj: output/figures/histogram_mol_adj.svg
        histogram_sot_adj2: output/figures/histogram_sot_adj2.svg
        histogram_pax_adj2: output/figures/histogram_pax_adj2.svg
        histogram_mol_adj2: output/figures/histogram_mol_adj2.svg
        histogram_sot_adj3: output/figures/histogram_sot_adj3.svg
        histogram_pax_adj3: output/figures/histogram_pax_adj3.svg
        histogram_mol_adj3: output/figures/histogram_mol_adj3.svg
        match_sot_agesex: output/figures/sot_match_agesex.svg
        match_pax_agesex: output/figures/pax_match_agesex.svg
        match_mol_agesex: output/figures/mol_match_agesex.svg
        match_sot_adj: output/figures/sot_match_adj.svg
        match_pax_adj: output/figures/pax_match_adj.svg
        match_mol_adj: output/figures/mol_match_adj.svg
        match_sot_adj2: output/figures/sot_match_adj2.svg
        match_pax_adj2: output/figures/pax_match_adj2.svg
        match_mol_adj2: output/figures/mol_match_adj2.svg
        match_sot_adj3: output/figures/sot_match_adj3.svg
        match_pax_adj3: output/figures/pax_match_adj3.svg
        match_mol_adj3: output/figures/mol_match_adj3.svg
        histogram_sot_agesex_common: output/figures/histogram_sot_common_agesex.svg
        histogram_pax_agesex_common: output/figures/histogram_pax_common_agesex.svg
        histogram_mol_agesex_common: output/figures/histogram_mol_common_agesex.svg
        histogram_sot_adj_common: output/figures/histogram_sot_common_adj.svg
        histogram_pax_adj_common: output/figures/histogram_pax_common_adj.svg
        histogram_mol_adj_common: output/figures/histogram_mol_common_adj.svg
        histogram_sot_adj2_common: output/figures/histogram_sot_common_adj2.svg
        histogram_pax_adj2_common: output/figures/histogram_pax_common_adj2.svg
        histogram_mol_adj2_common: output/figures/histogram_mol_common_adj2.svg
        histogram_sot_adj3_common: output/figures/histogram_sot_common_adj3.svg
        histogram_pax_adj3_common: output/figures/histogram_pax_common_adj3.svg
        histogram_mol_adj3_common: output/figures/histogram_mol_common_adj3.svg
        match_sot_common_agesex: output/figures/sot_match_common_agesex.svg
        match_pax_common_agesex: output/figures/pax_match_common_agesex.svg
        match_mol_common_agesex: output/figures/mol_match_common_agesex.svg
        match_sot_common_adj: output/figures/sot_match_common_adj.svg
        match_pax_common_adj: output/figures/pax_match_common_adj.svg
        match_mol_common_adj: output/figures/mol_match_common_adj.svg
        match_sot_common_adj2: output/figures/sot_match_common_adj2.svg
        match_pax_common_adj2: output/figures/pax_match_common_adj2.svg
        match_mol_common_adj2: output/figures/mol_match_common_adj2.svg
        match_sot_common_adj3: output/figures/sot_match_common_adj3.svg
        match_pax_common_adj3: output/figures/pax_match_common_adj3.svg
        match_mol_common_adj3: output/figures/mol_match_common_adj3.svg

        
  preceed_rate:
    run: stata-mp:latest analysis/404_preceeding_rate.do
    needs: [define_covariates_combine]
    outputs:
      moderately_sensitive:
        log: logs/preceed_rate.log 
        data: output/tables/comparator_rates.csv 
        data1: output/tables/comparator_rates_round.csv 
  
  redacted_table:
    run: stata-mp:latest analysis/501_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: 02:23:13

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
Katie Bechman
Branch
main
Force run dependencies
No
Git commit hash
cbaaf0f
Requested actions
  • cox_model
  • preceed_rate
  • redacted_table

Code comparison

Compare the code used in this Job Request