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Job request: 11577

Organisation:
University of Manchester
Workspace:
broad-spectrum-its
ID:
2ntavtp3deqngmm2
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 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: 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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:02:52

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
94408d3
Requested actions
  • generate_measures

Code comparison

Compare the code used in this Job Request