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Job request: 9053

Organisation:
King's College London
Workspace:
early-inflammatory-arthritis
ID:
mmrv7dj4ii3yp5b6
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

  • Action:
    generate_study_population
    Status:
    Status: Failed
    Job identifier:
    dqcgm4v7sjsn3gqj
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    run_baseline_tables
    Status:
    Status: Failed
    Job identifier:
    3mgwa3of2n3kh4dc
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    run_box_plots
    Status:
    Status: Failed
    Job identifier:
    zqgcwmbhjglxv4qn
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    run_itsa_models_drugs
    Status:
    Status: Failed
    Job identifier:
    trbamhhvu5vf7bo7
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    run_redacted_tables
    Status:
    Status: Failed
    Job identifier:
    arlg5olshzjrvr7w
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    create_cohorts
    Status:
    Status: Failed
    Job identifier:
    pejky4ahj6wkfeva
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    run_itsa_models
    Status:
    Status: Failed
    Job identifier:
    23xfvfqakedo4opn
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 400000

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_byyear_nomiss.csv   
        doc5: output/tables/referral_byregion_nomiss.csv   
        doc6: output/tables/drug_bydiag_miss.csv 
        doc7: output/tables/drug_byyear_miss.csv 
        doc8: output/tables/drug_byyear_ra_miss.csv   
        doc9: output/tables/drug_byyear_psa_miss.csv
        doc10: output/tables/drug_byyear_undiff_miss.csv
        doc11: output/tables/drug_byyearanddisease.csv
        doc12: output/tables/drug_byyearandregion.csv
        doc13: output/tables/diag_count_bymonth.csv
        doc14: output/tables/appt_count_bymonth.csv
        figure1: output/figures/incidence_twoway_rounded.svg
        figure2: output/figures/incidence_twoway_appt.svg
  
  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_diagnostic_delay_newey.svg
        figure2:  output/figures/ITSA_diagnostic_delay_prais.svg
        figure3:  output/figures/ITSA_diagnostic_delay_GP_newey.svg
        figure4:  output/figures/ITSA_diagnostic_delay_GP_prais.svg
        doc1: output/tables/gp_to_appt_ITSA_table.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.svg
        figure2:  output/figures/ITSA_csDMARD_delay_prais.svg
        figure3: output/figures/ITSA_csDMARD_delay_newey_sensitivity.svg
        figure4: output/figures/ITSA_csDMARD_delay_prais_sensitivity.svg
        doc1: output/tables/appt_to_csdmard_ITSA_table.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_overall.svg
        figure 2: output/figures/regional_qs1_bar_2019.svg 
        figure 3: output/figures/regional_qs1_bar_2020.svg       
        figure 4: output/figures/regional_qs2_bar_overall.svg  
        figure 5: output/figures/regional_qs2_bar_2019.svg 
        figure 6: output/figures/regional_qs2_bar_2020.svg    
        figure 7: output/figures/regional_qs2_bar_GP_overall.svg  
        figure 8: output/figures/regional_qs2_bar_GP_2019.svg     
        figure 9: output/figures/regional_qs2_bar_GP_2020.svg 
        figure 10: output/figures/regional_csdmard_bar_overall.svg  
        figure 11: output/figures/regional_csdmard_bar_2019.svg     
        figure 12: output/figures/regional_csdmard_bar_2020.svg  
 
  run_redacted_tables:
    run: stata-mp:latest analysis/400_redacted_tables.do
    needs: [create_cohorts]
    outputs:
      moderately_sensitive:
        log1: logs/redacted_tables.log   
        doc1: output/tables/table_1_rounded_bydiag.csv   
        doc2: output/tables/table_mean_bydiag_rounded.csv 
        doc3: output/tables/table_median_bydiag_rounded.csv   
        doc4: output/tables/table_median_bydiag_rounded_to21.csv   
        doc5: output/tables/ITSA_tables_appt_delay_rounded.csv   
        doc6: output/tables/ITSA_tables_csdmard_delay_rounded.csv 
        doc7: output/tables/drug_byyearanddisease_rounded.csv 
        doc8: output/tables/first_csdmard_rounded.csv   
        doc9: output/tables/drug_byyearandregion_rounded.csv
        doc10: output/tables/referral_byregion_rounded.csv

  run_redacted_tables_allpts:
    run: stata-mp:latest analysis/401_redacted_tables_allpts.do
    needs: [create_cohorts_allpts]
    outputs:
      moderately_sensitive:
        log1: logs/redacted_tables_allpts.log   
        doc1: output/tables/table_1_rounded_allpts.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 11:52:45

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

Job information

Status
Failed
Backend
TPP
Workspace
early-inflammatory-arthritis
Requested by
Mark Russell
Branch
main
Force run dependencies
Yes
Git commit hash
8c72f5a
Requested actions
  • generate_study_population
  • create_cohorts
  • run_baseline_tables
  • run_itsa_models
  • run_itsa_models_drugs
  • run_box_plots
  • run_redacted_tables

Code comparison

Compare the code used in this Job Request