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Job request: 11707

Organisation:
University of Manchester
Workspace:
broad-spectrum-its
ID:
apopehtvll75b5gx
View repo View project.yaml

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

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

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

  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

  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

  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

  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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:24

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

Job request

Status
Succeeded
Backend
TPP
Workspace
broad-spectrum-its
Requested by
Billy Zhong
Branch
broad_ITS
Force run dependencies
No
Git commit hash
485991b
Requested actions
  • ITS_model_monthly_rest

Code comparison

Compare the code used in this job request