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Job request: 7429

Organisation:
King's College London
Workspace:
early-inflammatory-arthritis
ID:
d6xgb52t3nbyc5bg
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Mark Russell 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: 700000

actions:

  generate_study_population_allpts:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_allpts
    outputs:
      highly_sensitive:
        cohort: output/input_allpts.csv
                  
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv
  
  create_cohorts_allpts:
    run: stata-mp:latest analysis/001_define_covariates_allpts.do
    needs: [generate_study_population_allpts]
    outputs:
      highly_sensitive:
        log1: logs/cleaning_dataset_allpts.log 
        data1: output/data/file_eia_allpts.dta        

  create_cohorts:
    run: stata-mp:latest analysis/000_define_covariates.do
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        log1: logs/cleaning_dataset.log 
        data1: output/data/file_eia_all.dta

  run_baseline_tables_allpts:
    run: stata-mp:latest analysis/101_baseline_characteristics_allpts.do
    needs: [create_cohorts_allpts]
    outputs:
      moderately_sensitive:
        log1: logs/descriptive_tables_allpts.log      
        doc1: output/tables/baseline_allpts.csv      

  run_baseline_tables:
    run: stata-mp:latest analysis/100_baseline_characteristics.do
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/descriptive_tables.log   
        doc1: output/tables/baseline_bydiagnosis.csv   
        doc2: output/tables/baseline_byyear.csv 
        doc3: output/tables/referral_bydiag_nomiss.csv   
        doc4: output/tables/referral_bydiag_miss.csv 
        doc5: output/tables/referral_byyear_nomiss.csv   
        doc6: output/tables/referral_byyear_miss.csv 
        doc7: output/tables/referral_byregion_nomiss.csv   
        doc8: output/tables/referral_byregion_miss.csv 
        doc9: output/tables/drug_bydiag_miss.csv 
        doc10: output/tables/drug_byyear_ra_miss.csv   
        doc11: output/tables/drug_byyear_psa_miss.csv
        doc12: output/tables/drug_byyear_undiff_miss.csv
        doc13: output/tables/biol_bydiag_miss.csv 
        doc14: output/tables/biol_byyear_ra_miss.csv 
        doc15: output/tables/biol_byyear_psa_miss.csv   
        doc16: output/tables/biol_byyear_axspa_miss.csv 
        doc17: output/tables/biol_byyear_undiff_miss.csv
  
  run_itsa_models:
    run: stata-mp:latest analysis/200_itsa_models.do
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/itsa_models.log   
        figure1:  output/figures/ITSA_referral_delay_newey_median.svg
        figure2:  output/figures/ITSA_referral_delay_prais_median.svg
        figure3:  output/figures/ITSA_referral_delay_newey_mean.svg
        figure4:  output/figures/ITSA_referral_delay_prais_mean.svg
        figure5:  output/figures/ITSA_diagnostic_delay_newey.svg
        figure6:  output/figures/ITSA_diagnostic_delay_prais.svg
        figure7:  output/figures/ITSA_diagnostic_delay_newey_2cuts.svg
        figure8:  output/figures/ITSA_diagnostic_delay_prais_2cuts.svg
        figure9:  output/figures/ITSA_diagnostic_delay_GP_newey.svg
        figure10:  output/figures/ITSA_diagnostic_delay_GP_prais.svg
        figure11:  output/figures/ITSA_diagnostic_delay_GPref_newey.svg
        figure12:  output/figures/ITSA_diagnostic_delay_GPref_prais.svg
        doc1: output/tables/referral_delay_GP_to_ref.csv
        doc2: output/tables/diagnostic_delay_ref_rheum_appt.csv
        doc3: output/tables/diagnostic_delay_GP_rheum_appt.csv
        doc4: output/tables/diagnostic_delay_GPref_rheum_appt.csv
  
  run_itsa_models_drugs:
    run: stata-mp:latest analysis/201_itsa_models_drugs.do
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/itsa_models_drugs.log   
        figure1:  output/figures/ITSA_csDMARD_delay_newey_raandpsa.svg
        figure2:  output/figures/ITSA_csDMARD_delay_prais_raandpsa.svg
        doc1: output/tables/csDMARD_delay_raandpsa.csv

  run_box_plots:
    run: stata-mp:latest analysis/300_box_plots.do
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/box_plots.log
        figure 1: output/figures/regional_qs1_bar.svg
        figure 2: output/figures/regional_qs2_bar.svg 
        figure 3: output/figures/regional_qs2_bar_GP.svg     
        figure 4: output/figures/regional_csdmard_bar.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:05:39

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

Job information

Status
Succeeded
Backend
TPP
Workspace
early-inflammatory-arthritis
Requested by
Mark Russell
Branch
main
Force run dependencies
Yes
Git commit hash
34381fc
Requested actions
  • generate_study_population
  • create_cohorts
  • run_baseline_tables
  • run_itsa_models
  • run_itsa_models_drugs
  • run_box_plots

Code comparison

Compare the code used in this Job Request