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Job request: 11309

Workspace:
disect_uk_india_covid
ID:
72hujcqmbz7kxsy4
View repo View project.yaml

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

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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: 1000

actions:

  generate_study_population_w1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_w1
    outputs:
      highly_sensitive:
        cohort: output/input_w1.csv


  generate_study_population_w2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_w2
    outputs:
      highly_sensitive:
        cohort: output/input_w2.csv

  
  generate_study_population_w3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_w3
    outputs:
      highly_sensitive:
        cohort: output/input_w3.csv
  

  generate_study_population_w4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_w4
    outputs:
      highly_sensitive:
        cohort: output/input_w4.csv


  generate_study_population_full:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_full
    outputs:
      highly_sensitive:
        cohort: output/input_full.csv



  analyse_w1_long:
    run: r:latest analysis/analysis_wave1_long.R
    needs: [generate_study_population_w1]
    outputs:
      moderately_sensitive:
        table1a_long: output/table1a_w1_long.csv
        table1b_long: output/table1b_w1_long.csv
        long_incidence: output/long_incidence_w1.csv
        long_incidence_strata: output/long_incidence_strata_w1.csv
        long_incidence_indian: output/long_incidence_indian_w1.csv
        unadjusted_long: output/unadjusted_long_w1.csv


  analyse_w1_severe:
    run: r:latest analysis/analysis_wave1_severe.R
    needs: [generate_study_population_w1]
    outputs:
      moderately_sensitive:
        table1a: output/table1a_w1.csv
        table1b: output/table1b_w1.csv
        severe_incidence: output/severe_incidence_w1.csv
        severe_incidence_strata: output/severe_incidence_strata_w1.csv
        severe_incidence_indian: output/severe_incidence_indian_w1.csv
        unadjusted_long: output/unadjusted_severe_w1.csv
  
  data_check_w1:
    run: r:latest analysis/analysis_wave1_checks.R
    needs: [generate_study_population_w1]
    outputs:
      moderately_sensitive:
        sample_size_table: output/sample_size_table_w1.csv
        missing_nums: output/missing_nums_w1.csv
        long_dates: output/long_covid_dates_w1.csv
        covid_admit_dates: output/covid_admit_dates_w1.csv
        dereg_dates: output/dereg_dates_w1.csv
        died_dates: output/died_dates_w1.csv
        long_dates_15: output/long_covid_dates_15_w1.csv
        long_filter_check: output/long_filter_check_w1.csv
        long_covid_surv_time: output/long_covid_surv_time_w1.csv
        long_covid_surv_flag: output/long_covid_surv_flag_w1.csv
        severe_covid_surv_time: output/severe_covid_surv_time_w1.csv
        severe_covid_surv_flag: output/severe_covid_surv_flag_w1.csv
        continuous_checks: output/continuous_checks_w1.csv
        dates_dmy: output/dates_dmy_w1.csv
        dates_my: output/dates_my_w1.csv
        binary_checks: output/binary_checks_w1.csv
        eth_tab: output/ethnicity5_w1.csv
        eth16_tab: output/ethnicity16_w1.csv
        ethcross_tab: output/ethnicity_cross_w1.csv
        sex_tab: output/sex_w1.csv
        smoke_tab: output/smoke_w1.csv
        imd_tab: output/imd_w1.csv
        stp_tab: output/stp_w1.csv
        region_tab: output/region_w1.csv
        diabetes_tab: output/diabetes_w1.csv
        carehome_tab: output/carehome_w1.csv




  analyse_w2_long:
    run: r:latest analysis/analysis_wave2_long.R
    needs: [generate_study_population_w2]
    outputs:
      moderately_sensitive:
        table1a_long: output/table1a_w2_long.csv
        table1b_long: output/table1b_w2_long.csv
        long_incidence: output/long_incidence_w2.csv
        long_incidence_strata: output/long_incidence_strata_w2.csv
        long_incidence_indian: output/long_incidence_indian_w2.csv
        unadjusted_long: output/unadjusted_long_w2.csv


  analyse_w2_severe:
    run: r:latest analysis/analysis_wave2_severe.R
    needs: [generate_study_population_w2]
    outputs:
      moderately_sensitive:
        table1a: output/table1a_w2.csv
        table1b: output/table1b_w2.csv
        severe_incidence: output/severe_incidence_w2.csv
        severe_incidence_strata: output/severe_incidence_strata_w2.csv
        severe_incidence_indian: output/severe_incidence_indian_w2.csv
        unadjusted_long: output/unadjusted_severe_w2.csv
  
  data_check_w2:
    run: r:latest analysis/analysis_wave2_checks.R
    needs: [generate_study_population_w2]
    outputs:
      moderately_sensitive:
        sample_size_table: output/sample_size_table_w2.csv
        missing_nums: output/missing_nums_w2.csv
        long_dates: output/long_covid_dates_w2.csv
        covid_admit_dates: output/covid_admit_dates_w2.csv
        dereg_dates: output/dereg_dates_w2.csv
        died_dates: output/died_dates_w2.csv
        long_dates_15: output/long_covid_dates_15_w2.csv
        long_filter_check: output/long_filter_check_w2.csv
        long_covid_surv_time: output/long_covid_surv_time_w2.csv
        long_covid_surv_flag: output/long_covid_surv_flag_w2.csv
        severe_covid_surv_time: output/severe_covid_surv_time_w2.csv
        severe_covid_surv_flag: output/severe_covid_surv_flag_w2.csv
        continuous_checks: output/continuous_checks_w2.csv
        dates_dmy: output/dates_dmy_w2.csv
        dates_my: output/dates_my_w2.csv
        binary_checks: output/binary_checks_w2.csv
        eth_tab: output/ethnicity5_w2.csv
        eth16_tab: output/ethnicity16_w2.csv
        ethcross_tab: output/ethnicity_cross_w2.csv
        sex_tab: output/sex_w2.csv
        smoke_tab: output/smoke_w2.csv
        imd_tab: output/imd_w2.csv
        stp_tab: output/stp_w2.csv
        region_tab: output/region_w2.csv
        diabetes_tab: output/diabetes_w2.csv
        carehome_tab: output/carehome_w2.csv



  analyse_w3_long:
    run: r:latest analysis/analysis_wave3_long.R
    needs: [generate_study_population_w3]
    outputs:
      moderately_sensitive:
        table1a_long: output/table1a_w3_long.csv
        table1b_long: output/table1b_w3_long.csv
        long_incidence: output/long_incidence_w3.csv
        long_incidence_strata: output/long_incidence_strata_w3.csv
        long_incidence_indian: output/long_incidence_indian_w3.csv
        unadjusted_long: output/unadjusted_long_w3.csv


  analyse_w3_severe:
    run: r:latest analysis/analysis_wave3_severe.R
    needs: [generate_study_population_w3]
    outputs:
      moderately_sensitive:
        table1a: output/table1a_w3.csv
        table1b: output/table1b_w3.csv
        severe_incidence: output/severe_incidence_w3.csv
        severe_incidence_strata: output/severe_incidence_strata_w3.csv
        severe_incidence_indian: output/severe_incidence_indian_w3.csv
        unadjusted_long: output/unadjusted_severe_w3.csv
  
  data_check_w3:
    run: r:latest analysis/analysis_wave3_checks.R
    needs: [generate_study_population_w3]
    outputs:
      moderately_sensitive:
        sample_size_table: output/sample_size_table_w3.csv
        missing_nums: output/missing_nums_w3.csv
        long_dates: output/long_covid_dates_w3.csv
        covid_admit_dates: output/covid_admit_dates_w3.csv
        dereg_dates: output/dereg_dates_w3.csv
        died_dates: output/died_dates_w3.csv
        long_dates_15: output/long_covid_dates_15_w3.csv
        long_filter_check: output/long_filter_check_w3.csv
        long_covid_surv_time: output/long_covid_surv_time_w3.csv
        long_covid_surv_flag: output/long_covid_surv_flag_w3.csv
        severe_covid_surv_time: output/severe_covid_surv_time_w3.csv
        severe_covid_surv_flag: output/severe_covid_surv_flag_w3.csv
        continuous_checks: output/continuous_checks_w3.csv
        dates_dmy: output/dates_dmy_w3.csv
        dates_my: output/dates_my_w3.csv
        binary_checks: output/binary_checks_w3.csv
        eth_tab: output/ethnicity5_w3.csv
        eth16_tab: output/ethnicity16_w3.csv
        ethcross_tab: output/ethnicity_cross_w3.csv
        sex_tab: output/sex_w3.csv
        smoke_tab: output/smoke_w3.csv
        imd_tab: output/imd_w3.csv
        stp_tab: output/stp_w3.csv
        region_tab: output/region_w3.csv
        diabetes_tab: output/diabetes_w3.csv
        carehome_tab: output/carehome_w3.csv




  analyse_w4_long:
    run: r:latest analysis/analysis_wave4_long.R
    needs: [generate_study_population_w4]
    outputs:
      moderately_sensitive:
        table1a_long: output/table1a_w4_long.csv
        table1b_long: output/table1b_w4_long.csv
        long_incidence: output/long_incidence_w4.csv
        long_incidence_strata: output/long_incidence_strata_w4.csv
        long_incidence_indian: output/long_incidence_indian_w4.csv
        unadjusted_long: output/unadjusted_long_w4.csv


  analyse_w4_severe:
    run: r:latest analysis/analysis_wave4_severe.R
    needs: [generate_study_population_w4]
    outputs:
      moderately_sensitive:
        table1a: output/table1a_w4.csv
        table1b: output/table1b_w4.csv
        severe_incidence: output/severe_incidence_w4.csv
        severe_incidence_strata: output/severe_incidence_strata_w4.csv
        severe_incidence_indian: output/severe_incidence_indian_w4.csv
        unadjusted_long: output/unadjusted_severe_w4.csv
  
  data_check_w4:
    run: r:latest analysis/analysis_wave4_checks.R
    needs: [generate_study_population_w4]
    outputs:
      moderately_sensitive:
        sample_size_table: output/sample_size_table_w4.csv
        missing_nums: output/missing_nums_w4.csv
        long_dates: output/long_covid_dates_w4.csv
        covid_admit_dates: output/covid_admit_dates_w4.csv
        dereg_dates: output/dereg_dates_w4.csv
        died_dates: output/died_dates_w4.csv
        long_dates_15: output/long_covid_dates_15_w4.csv
        long_filter_check: output/long_filter_check_w4.csv
        long_covid_surv_time: output/long_covid_surv_time_w4.csv
        long_covid_surv_flag: output/long_covid_surv_flag_w4.csv
        severe_covid_surv_time: output/severe_covid_surv_time_w4.csv
        severe_covid_surv_flag: output/severe_covid_surv_flag_w4.csv
        continuous_checks: output/continuous_checks_w4.csv
        dates_dmy: output/dates_dmy_w4.csv
        dates_my: output/dates_my_w4.csv
        binary_checks: output/binary_checks_w4.csv
        eth_tab: output/ethnicity5_w4.csv
        eth16_tab: output/ethnicity16_w4.csv
        ethcross_tab: output/ethnicity_cross_w4.csv
        sex_tab: output/sex_w4.csv
        smoke_tab: output/smoke_w4.csv
        imd_tab: output/imd_w4.csv
        stp_tab: output/stp_w4.csv
        region_tab: output/region_w4.csv
        diabetes_tab: output/diabetes_w4.csv
        carehome_tab: output/carehome_w4.csv



  analyse_full_long:
    run: r:latest analysis/analysis_full_long.R
    needs: [generate_study_population_full]
    outputs:
      moderately_sensitive:
        table1a_long: output/table1a_full_long.csv
        table1b_long: output/table1b_full_long.csv
        long_incidence: output/long_incidence_full.csv
        long_incidence_strata: output/long_incidence_strata_full.csv
        long_incidence_indian: output/long_incidence_indian_full.csv
        unadjusted_long: output/unadjusted_long_full.csv


  analyse_full_severe:
    run: r:latest analysis/analysis_full_severe.R
    needs: [generate_study_population_full]
    outputs:
      moderately_sensitive:
        table1a: output/table1a_full.csv
        table1b: output/table1b_full.csv
        severe_incidence: output/severe_incidence_full.csv
        severe_incidence_strata: output/severe_incidence_strata_full.csv
        severe_incidence_indian: output/severe_incidence_indian_full.csv
        unadjusted_long: output/unadjusted_severe_full.csv
  
  data_check_full:
    run: r:latest analysis/analysis_full_checks.R
    needs: [generate_study_population_full]
    outputs:
      moderately_sensitive:
        sample_size_table: output/sample_size_table_full.csv
        missing_nums: output/missing_nums_full.csv
        long_dates: output/long_covid_dates_full.csv
        covid_admit_dates: output/covid_admit_dates_full.csv
        dereg_dates: output/dereg_dates_full.csv
        died_dates: output/died_dates_full.csv
        long_dates_15: output/long_covid_dates_15_full.csv
        long_filter_check: output/long_filter_check_full.csv
        long_covid_surv_time: output/long_covid_surv_time_full.csv
        long_covid_surv_flag: output/long_covid_surv_flag_full.csv
        severe_covid_surv_time: output/severe_covid_surv_time_full.csv
        severe_covid_surv_flag: output/severe_covid_surv_flag_full.csv
        continuous_checks: output/continuous_checks_full.csv
        dates_dmy: output/dates_dmy_full.csv
        dates_my: output/dates_my_full.csv
        binary_checks: output/binary_checks_full.csv
        eth_tab: output/ethnicity5_full.csv
        eth16_tab: output/ethnicity16_full.csv
        ethcross_tab: output/ethnicity_cross_full.csv
        sex_tab: output/sex_full.csv
        smoke_tab: output/smoke_full.csv
        imd_tab: output/imd_full.csv
        stp_tab: output/stp_full.csv
        region_tab: output/region_full.csv
        diabetes_tab: output/diabetes_full.csv
        carehome_tab: output/carehome_full.csv




  standardise_rates_full:
    run: r:latest analysis/poisson_standardization.R
    needs: [analyse_full_severe, analyse_full_long]
    outputs:
      moderately_sensitive:
        model_test_results: output/model_test_results.csv
        world_pop_standard: output/world_pop_standard.csv
        standard_rates: output/overall_standard_rates.csv
        world_pop_standard_Nb: output/world_pop_standard_nb.csv
        model_test_results_more: output/model_test_results_more.csv
        world_pop_more_standard: output/world_pop_more_standard.csv
        standard_rates_more: output/overall_standard_rates_more.csv
        world_pop_more_standard_Nb: output/world_pop_more_standard_nb.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job information

Status
Succeeded
Backend
TPP
Workspace
disect_uk_india_covid
Requested by
Nick Birk
Branch
main
Force run dependencies
No
Git commit hash
7207fd4
Requested actions
  • generate_study_population_full
  • analyse_full_long
  • analyse_full_severe
  • standardise_rates_full