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Job request: 13108

Organisation:
University of Manchester
Workspace:
broad-spectrum-its
ID:
reexd3ihyyb66sc6
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Billy Zhong 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

  • Action:
    figure_3
    Status:
    Status: Succeeded
    Job identifier:
    vuzdyrcjf2n4zhl7

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 30000

actions:

  generate_study_population_patient_characteristics_2019:
      run: cohortextractor:latest generate_cohort 
        --with-end-date-fix
        --study-definition study_definition_patient_characteristics_2019
        --output-format=csv.gz
      outputs:
        highly_sensitive:
          cohort: output/input_patient_characteristics_2019.csv.gz

  generate_study_population_patient_characteristics_2020:
      run: cohortextractor:latest generate_cohort 
        --with-end-date-fix
        --study-definition study_definition_patient_characteristics_2020
        --output-format=csv.gz
      outputs:
        highly_sensitive:
          cohort: output/input_patient_characteristics_2020.csv.gz

  generate_study_population_patient_characteristics_2021:
      run: cohortextractor:latest generate_cohort 
        --with-end-date-fix
        --study-definition study_definition_patient_characteristics_2021
        --output-format=csv.gz
      outputs:
        highly_sensitive:
          cohort: output/input_patient_characteristics_2021.csv.gz

  table_1: 
    run: r:latest analysis/table_1.R
    needs: [generate_study_population_patient_characteristics_2019]
    outputs:
       moderately_sensitive:
        table1: output/table1_2019_overallcount.csv
        table2: output/table1_2019.csv

  table_1_2020: 
    run: r:latest analysis/table_1_2020.R
    needs: [generate_study_population_patient_characteristics_2020]
    outputs:
       moderately_sensitive:
        table1: output/table1_2020_overallcount.csv
        table2: output/table1_2020.csv

  table_1_2021: 
    run: r:latest analysis/table_1_2021.R
    needs: [generate_study_population_patient_characteristics_2021]
    outputs:
       moderately_sensitive:
        table1: output/table1_2021_overallcount.csv
        table2: output/table1_2021.csv

  generate_study_population:
    run: cohortextractor:latest generate_cohort
      --with-end-date-fix
      --study-definition study_definition 
      --index-date-range "2019-01-01 to 2021-12-31 by month" 
      --skip-existing 
      --output-dir=output/measures 
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv.gz

  generate_measures:
    run: cohortextractor:latest generate_measures 
      --study-definition study_definition 
      --skip-existing 
      --output-dir=output/measures
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_*.csv

  generate_study_population_covid:
    run: cohortextractor:latest generate_cohort
      --with-end-date-fix
      --study-definition study_definition_covid 
      --index-date-range "2019-01-01 to 2021-12-31 by month" 
      --skip-existing 
      --output-dir=output/measures 
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_covid_*.csv.gz

  generate_measures_covid:
    run: cohortextractor:latest generate_measures 
      --study-definition study_definition_covid 
      --skip-existing 
      --output-dir=output/measures
    needs: [generate_study_population_covid]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_allpopulation_*.csv

  figure_1A: 
    run: r:latest analysis/figure_1A.R
    needs: [generate_measures]
    outputs:
       moderately_sensitive:
        plot1: output/figure_1A.jpeg

  figure_1B: 
    run: r:latest analysis/figure_1B.R
    needs: [generate_measures,generate_measures_covid]
    outputs:
       moderately_sensitive:
        plot1: output/figure_1B.jpeg
        table1: output/figure_1B_table.csv

  figure_2: 
    run: r:latest analysis/figure_2.R
    needs: [generate_measures]
    outputs:
       moderately_sensitive:
        plot1: output/figure_2.1.jpeg
        plot2: output/figure_2.2.jpeg
        plot3: output/figure_2.3.jpeg
        table1: output/figure_2.1_table.csv

  generate_study_population_weekly:
    run: cohortextractor:latest generate_cohort
      --with-end-date-fix
      --study-definition study_definition_weekly 
      --index-date-range "2019-01-01 to 2021-12-31 by week" 
      --skip-existing 
      --output-dir=output/measures 
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_weekly_*.csv.gz

  generate_measures_weekly:
    run: cohortextractor:latest generate_measures 
      --study-definition study_definition_weekly 
      --skip-existing 
      --output-dir=output/measures
    needs: [generate_study_population_weekly]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_weekly_*.csv

  figure_1A_weekly: 
    run: r:latest analysis/figure_1A_weekly.R
    needs: [generate_measures_weekly]
    outputs:
       moderately_sensitive:
        plot1: output/figure_1A_weekly.jpeg

### generate study cohort with the date of each prescriptions
  generate_study_population_ab_type_2019: 
    run: cohortextractor:latest generate_cohort
      --with-end-date-fix
      --study-definition study_definition_ab_type_2019
      --index-date-range "2019-01-01 to 2019-12-31"
      --skip-existing
      --output-dir=output/measures
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_ab_type_2019_*.csv.gz

  generate_study_population_ab_type_2020: 
    run: cohortextractor:latest generate_cohort 
      --with-end-date-fix
      --study-definition study_definition_ab_type_2020 
      --index-date-range "2020-01-01 to 2020-12-31" 
      --skip-existing 
      --output-dir=output/measures 
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_ab_type_2020_*.csv.gz

  generate_study_population_ab_type_2021: 
    run: cohortextractor:latest generate_cohort 
      --with-end-date-fix
      --study-definition study_definition_ab_type_2021 
      --index-date-range "2021-01-01 to 2021-12-31" 
      --skip-existing 
      --output-dir=output/measures 
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_ab_type_2021_*.csv.gz

  conversion_abtype_2019: 
    run: r:latest analysis/conversion_abtype_2019.R
    needs: [generate_study_population_ab_type_2019]
    outputs:
       highly_sensitive:
        rds1: output/measures/abtype_2019.rds

  conversion_abtype_2020: 
    run: r:latest analysis/conversion_abtype_2020.R
    needs: [generate_study_population_ab_type_2020]
    outputs:
       highly_sensitive:
        rds1: output/measures/abtype_2020.rds

  conversion_abtype_2021: 
    run: r:latest analysis/conversion_abtype_2021.R
    needs: [generate_study_population_ab_type_2021]
    outputs:
       highly_sensitive:
        rds1: output/measures/abtype_2021.rds

  figure_2B: 
    run: r:latest analysis/figure_2B.R
    needs: [conversion_abtype_2019,conversion_abtype_2020,conversion_abtype_2021]
    outputs:
       moderately_sensitive:
        plot1: output/figure_2B.jpeg
        table1: output/figure_2B_table.csv

  ITS_var: 
    run: r:latest analysis/ITS_var.R
    needs: [conversion_abtype_2019,conversion_abtype_2020,conversion_abtype_2021,generate_measures]
    outputs:
       moderately_sensitive:
        table1: output/mon_uti.csv
        table2: output/mon_cold.csv
        table3: output/mon_cough.csv
        table4: output/mon_copd.csv
        table5: output/mon_throat.csv
        table6: output/mon_lrti.csv
        table7: output/mon_urti.csv
        table8: output/mon_sinusitis.csv
        table9: output/mon_ot_media.csv
        table10: output/mon_ot_externa.csv
        table11: output/mon_all.csv
        table12: output/mon_all_coded.csv
        table13: output/mon_all_uncoded.csv

  describe_ITS_model_broad_mon_overall:
    run: r:latest analysis/itsmodel/ITS_model_monthly.R
    needs: [ITS_var]
    outputs:
        moderately_sensitive:
          plot1: output/mon_overall_predicted_plot.jpeg
          plot2: output/mon_overall_forest_C.jpeg
          plot3: output/mon_overall_forest_B.jpeg
          plot4: output/mon_overall_combined.jpeg
          table1: output/mon_overall_predicted_table.csv
          table2: output/mon_overall_forest_B_table.csv
          table3: output/mon_overall_forest_C_table.csv

  ITS_var_weekly: 
    run: r:latest analysis/ITS_var_weekly.R
    needs: [conversion_abtype_2019,conversion_abtype_2020,conversion_abtype_2021,generate_measures_weekly]
    outputs:
       moderately_sensitive:
        table1: output/week_uti.csv
        table2: output/week_cold.csv
        table3: output/week_cough.csv
        table4: output/week_copd.csv
        table5: output/week_throat.csv
        table6: output/week_lrti.csv
        table7: output/week_urti.csv
        table8: output/week_sinusitis.csv
        table9: output/week_ot_media.csv
        table10: output/week_ot_externa.csv
        table11: output/week_all.csv

  describe_ITS_model_broad_week_overall:
    run: r:latest analysis/itsmodel/ITS_model_weekly.R
    needs: [ITS_var_weekly]
    outputs:
        moderately_sensitive:
          plot1: output/week_overall_predicted_plot.jpeg
          plot2: output/week_overall_forest_C.jpeg
          plot3: output/week_overall_forest_B.jpeg
          plot4: output/week_overall_combined.jpeg
          table1: output/week_overall_predicted_table.csv
          table2: output/week_overall_forest_B_table.csv
          table3: output/week_overall_forest_C_table.csv

  ITS_overall_uti_plot:
    run: r:latest analysis/itsmodel/ITS_model_predict.R
    needs: [describe_ITS_model_broad_mon_overall]
    outputs:
        moderately_sensitive:
          plot1: output/overall_predicted.jpeg
          plot2: output/UTI_predicted.jpeg

  ITS_model_monthly_rest:
    run: r:latest analysis/itsmodel/ITS_model_monthly_rest.R
    needs: [ITS_var]
    outputs:
        moderately_sensitive:
          plot1: output/mon_overall_predicted_rest.jpeg

  Poisson_model_table:
    run: r:latest analysis/itsmodel/Poisson_model_table.R
    needs: [ITS_var]
    outputs:
        moderately_sensitive:
          plot1: output/table2.csv

  generate_study_population_2020_covid_window:
    run: cohortextractor:latest generate_cohort
      --with-end-date-fix
      --study-definition study_definition_2020_covid_window 
      --index-date-range "2020-01-01 to 2020-12-31 by month" 
      --skip-existing 
      --output-dir=output/measures 
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_2020_covid_window_*.csv.gz

  generate_measures_2020_covid_window:
    run: cohortextractor:latest generate_measures 
      --study-definition study_definition_2020_covid_window 
      --skip-existing 
      --output-dir=output/measures
    needs: [generate_study_population_2020_covid_window]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_covid_window_*.csv

  generate_study_population_2021_covid_window:
    run: cohortextractor:latest generate_cohort
      --with-end-date-fix
      --study-definition study_definition_2021_covid_window 
      --index-date-range "2021-01-01 to 2021-12-31 by month" 
      --skip-existing 
      --output-dir=output/measures 
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_2021_covid_window_*.csv.gz

  generate_measures_2021_covid_window:
    run: cohortextractor:latest generate_measures 
      --study-definition study_definition_2021_covid_window 
      --skip-existing 
      --output-dir=output/measures
    needs: [generate_study_population_2021_covid_window]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_21_covid_window_*.csv

  figure_3: 
    run: r:latest analysis/figure_3.R
    needs: [generate_measures_2020_covid_window,generate_measures_2021_covid_window]
    outputs:
       moderately_sensitive:
        plot1: output/figure_3.jpeg
        table1: output/figure_3_table.csv

  figure_3_bar: 
    run: r:latest analysis/figure_3_bar.R
    needs: [generate_measures_2020_covid_window,generate_measures_2021_covid_window]
    outputs:
       moderately_sensitive:
        plot1: output/figure_3_bar.jpeg
        table1: output/figure_3_bar_table.csv

  figure_3_2D: 
    run: r:latest analysis/figure_3_2D.R
    needs: [generate_measures_2020_covid_window,generate_measures_2021_covid_window]
    outputs:
       moderately_sensitive:
        plot1: output/figure_3_2D.jpeg
        table1: output/figure_3_2D_table.csv

  ab_type_table: 
    run: r:latest analysis/ab_type_table.R
    needs: [generate_measures_2020_covid_window,generate_measures_2021_covid_window]
    outputs:
       moderately_sensitive:
        table1: output/ab_type_table.csv
        table2: output/ab_type_table_2D.csv

  figure_Stype: 
    run: r:latest analysis/figure_Stype.R
    needs: [generate_measures]
    outputs:
       moderately_sensitive:
        plot1: output/figure_Stype.jpeg
        table1: output/figure_Stype_table.csv

  ITS_var_sen_2month: 
    run: r:latest analysis/ITS_var_sen_2month.R
    needs: [conversion_abtype_2019,conversion_abtype_2020,conversion_abtype_2021,generate_measures]
    outputs:
       moderately_sensitive:
        table1: output/sen_2mon_uti.csv
        table2: output/sen_2mon_cold.csv
        table3: output/sen_2mon_cough.csv
        table4: output/sen_2mon_copd.csv
        table5: output/sen_2mon_throat.csv
        table6: output/sen_2mon_lrti.csv
        table7: output/sen_2mon_urti.csv
        table8: output/sen_2mon_sinusitis.csv
        table9: output/sen_2mon_ot_media.csv
        table10: output/sen_2mon_ot_externa.csv
        table11: output/sen_2mon_all.csv
        table12: output/sen_2mon_all_coded.csv
        table13: output/sen_2mon_all_uncoded.csv

  ITS_var_sen_3month: 
    run: r:latest analysis/ITS_var_sen_3month.R
    needs: [conversion_abtype_2019,conversion_abtype_2020,conversion_abtype_2021,generate_measures]
    outputs:
       moderately_sensitive:
        table1: output/sen_3mon_uti.csv
        table2: output/sen_3mon_cold.csv
        table3: output/sen_3mon_cough.csv
        table4: output/sen_3mon_copd.csv
        table5: output/sen_3mon_throat.csv
        table6: output/sen_3mon_lrti.csv
        table7: output/sen_3mon_urti.csv
        table8: output/sen_3mon_sinusitis.csv
        table9: output/sen_3mon_ot_media.csv
        table10: output/sen_3mon_ot_externa.csv
        table11: output/sen_3mon_all.csv
        table12: output/sen_3mon_all_coded.csv
        table13: output/sen_3mon_all_uncoded.csv

  describe_ITS_model_broad_sen2mon:
    run: r:latest analysis/itsmodel/ITS_model_monthly_sen2mon.R
    needs: [ITS_var_sen_2month]
    outputs:
        moderately_sensitive:
          plot1: output/sen_2mon_overall_predicted_plot.jpeg
          plot2: output/sen_2mon_overall_forest_C.jpeg
          plot3: output/sen_2mon_overall_forest_B.jpeg
          plot4: output/sen_2mon_overall_combined.jpeg
          table1: output/sen_2mon_overall_predicted_table.csv
          table2: output/sen_2mon_overall_forest_B_table.csv
          table3: output/sen_2mon_overall_forest_C_table.csv

  describe_ITS_model_broad_sen3mon:
    run: r:latest analysis/itsmodel/ITS_model_monthly_sen3mon.R
    needs: [ITS_var_sen_3month]
    outputs:
        moderately_sensitive:
          plot1: output/sen_3mon_overall_predicted_plot.jpeg
          plot2: output/sen_3mon_overall_forest_C.jpeg
          plot3: output/sen_3mon_overall_forest_B.jpeg
          plot4: output/sen_3mon_overall_combined.jpeg
          table1: output/sen_3mon_overall_predicted_table.csv
          table2: output/sen_3mon_overall_forest_B_table.csv
          table3: output/sen_3mon_overall_forest_C_table.csv

  generate_study_population_2020_coinfection:
    run: cohortextractor:latest generate_cohort
      --with-end-date-fix
      --study-definition study_definition_2020_coinfection 
      --index-date-range "2020-01-01 to 2020-12-31 by month" 
      --skip-existing 
      --output-dir=output/measures 
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_2020_coinfection_*.csv.gz

  generate_measures_2020_coinfection:
    run: cohortextractor:latest generate_measures 
      --study-definition study_definition_2020_coinfection 
      --skip-existing 
      --output-dir=output/measures
    needs: [generate_study_population_2020_coinfection]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_infection_coded_*.csv

  generate_study_population_2021_coinfection:
    run: cohortextractor:latest generate_cohort
      --with-end-date-fix
      --study-definition study_definition_2021_coinfection 
      --index-date-range "2021-01-01 to 2021-12-31 by month" 
      --skip-existing 
      --output-dir=output/measures 
      --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_2021_coinfection_*.csv.gz

  generate_measures_2021_coinfection:
    run: cohortextractor:latest generate_measures 
      --study-definition study_definition_2021_coinfection 
      --skip-existing 
      --output-dir=output/measures
    needs: [generate_study_population_2021_coinfection]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_21_infection_coded_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:02:14

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

Job information

Status
Succeeded
Backend
TPP
Workspace
broad-spectrum-its
Requested by
Billy Zhong
Branch
broad_ITS
Force run dependencies
No
Git commit hash
72fc96d
Requested actions
  • figure_3