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Job request: 20302

Organisation:
The UK Renal Registry
Workspace:
renal-short-data-report
ID:
plbeglrafglmuxaf
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Louis Fisher 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_calculators:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_calculators
      --output-format csv.gz
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/input_calculators.csv.gz


  calculate_calculators:
    run: python:latest python analysis/scripts/calculate_calculators.py 
    needs: [generate_study_population_calculators]
    outputs:
      highly_sensitive:
        counts: output/input_calculators_calculated.csv.gz

  crcl_gault:
    run: python:latest python analysis/scripts/crcl_gault.py
    needs: [calculate_calculators]
    outputs:
      moderately_sensitive:
        plots: output/dist*.png
        venn: output/venn*.png
        counts: output/creatinine_vs_crlc.json

  generate_study_population:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition
      --index-date-range "2019-01-01 to 2023-07-01 by month"
      --output-format csv.gz
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/input*.csv.gz

  generate_study_population_ukrr_ethnicity:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition_ukrr_ethnicity
      --output-dir=output
      --output-format csv.gz
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/input_ukrr_ethnicity.csv.gz

  join_cohorts:
    run: >
      cohort-joiner:v0.0.46
        --lhs output/input_20*.csv.gz
        --rhs output/input_ukrr_ethnicity.csv.gz
        --output-dir output/joined
    needs: [generate_study_population, generate_study_population_ukrr_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_20*.csv.gz

  generate_table_1:
    run: python:latest python analysis/scripts/table_1.py --study_def_paths="output/joined/input_*.csv.gz" --demographics="age_band,sex,region,imd,ethnicity"
    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        tables: output/table_1*.csv

  get_counts:
    run: python:latest python analysis/scripts/combine_operators.py
    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        counts: output/*_count.csv
        operator_counts: output/*_count_*.csv

  generate_top_5_tables:
    run: python:latest python analysis/scripts/top_codes.py
    needs: [get_counts]
    outputs:
      moderately_sensitive:
        counts: output/top_5_code_table_*.csv

  generate_measures:
    run: cohortextractor:latest generate_measures 
      --study-definition study_definition
      --output-dir=output/joined
    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        measure_csv: output/joined/measure_*_rate.csv
  
  plot_ckd:
    run: python:latest python analysis/scripts/plot_ckd_over_time.py
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        plots: output/figures/plot_incident_ckd.jpeg
  
  generate_plots:
    run: python:latest python analysis/scripts/plot_measures.py
    needs: [generate_measures, join_cohorts]
    outputs:
      moderately_sensitive:
        counts: output/figures/plot_*.jpeg
        csv: output/figures/plot_*.csv

  generate_plots_numeric_values:
    run: python:latest python analysis/scripts/plot_numeric_values.py
    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        figures: output/*dis*.jpeg

  generate_upset_plots:
    run: python:latest python analysis/scripts/ckd_discrepancies.py
    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        figures: output/ckd_staging_*.png
        tables: output/ckd_staging_*.csv
        time: output/time_diff_ckd.jpeg
        dialysis: output/ckd_rrt_upset.csv
        dialysis45: output/biochem_4_5_not_coded.csv

  generate_study_population_ukrr_jul_22:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_ukrr
      --index-date-range "2022-07-01"
      --output-format csv.gz
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/ukrr/input_ukrr_2022-07-01.csv.gz

  generate_study_population_ukrr:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_ukrr
      --index-date-range "2020-01-01"
      --output-format csv.gz
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/ukrr/input_ukrr*.csv.gz

  generate_study_population_ukrr_1:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_ukrr_short
      --index-date-range "2021-01-01"
      --output-format csv.gz
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/ukrr/input_ukr*.csv.gz

  generate_study_population_ukrr_2:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_ukrr_short
      --index-date-range "2022-01-01"
      --output-format csv.gz
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/ukrr/input_uk*.csv.gz

  generate_study_population_paeds:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_paeds
      --output-format csv.gz
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/input_paeds.csv.gz


  

  generate_study_population_check_SC:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_check_SC
      --output-format csv.gz
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/input_check_SC.csv.gz

  

  # generate_notebook:
  #   run: jupyter:latest jupyter nbconvert /workspace/analysis/report.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
  #   needs: [generate_plots, get_counts]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/report.html

  # generate_ukrr_checks:
  #  run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-checks.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #  needs: [generate_study_population, generate_study_population_ukrr_ethnicity]
  #  outputs:
  #    moderately_sensitive:
  #      report: output/notebooks/ukrr-checks.html

  #generate_ukrr_report:
  #  run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-report.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #  needs: [join_acr]
  #  outputs:
  #    moderately_sensitive:
  #      report: output/notebooks/ukrr-report.html
       

  # generate_ukrr_discrepancies:
  #   run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-discrepancies.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #   needs: [join_acr]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/notebooks/ukrr-discrepancies.html

  ukrr_vs_prim_care_ckd:
    run: python:latest python analysis/scripts/ukrr_prim_care_crossover_ckd.py
    needs: [join_cohorts]
    outputs:
      moderately_sensitive:
        upset: output/*.png
        upset_csv: output/ukrr*overlap_stage.csv

  
  # generate_kidney_week:
  #   run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/kidney_week.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #   needs: [join_acr]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/notebooks/kidney_week.html
  
  # generate_ukrr_tables_figures:
  #   run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-tables-figures.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #   needs: [generate_study_population_ukrr]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/notebooks/ukrr-tables-figures.html

  generate_ukrr_tables_figures_1:
    run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-tables-figures-2021.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
    needs: [generate_study_population_ukrr_1]
    outputs:
      moderately_sensitive:
        report: output/notebooks/ukrr-tables-figures-2021.html

  generate_ukrr_tables_figures_2:
    run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-tables-figures-2022.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
    needs: [generate_study_population_ukrr_2]
    outputs:
      moderately_sensitive:
        report: output/notebooks/ukrr-tables-figures-2022.html

  generate_false_positives_ckd:
    run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/false-positives-ckd.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
    needs: [generate_study_population_ukrr]
    outputs:
      moderately_sensitive:
        report: output/notebooks/false-positives-ckd.html

  generate_agreement_by_eGFR:
    run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/agreement-by-eGFR.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
    needs: [generate_study_population_ukrr]
    outputs:
      moderately_sensitive:
        report: output/notebooks/agreement-by-eGFR.html

  # generate_pc_sc_codes1a:
  #   run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes1a.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #   needs: [generate_study_population_ukrr]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/notebooks/pc-sc-codes1a.html
  
  # generate_pc_sc_codes1b:
  #   run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes1b.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #   needs: [generate_study_population_ukrr]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/notebooks/pc-sc-codes1b.html

  # generate_pc_sc_codes2:
  #   run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes2.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #   needs: [generate_study_population_ukrr]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/notebooks/pc-sc-codes2.html

  # generate_pc_sc_codes3:
  #   run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes3.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #   needs: [generate_study_population_ukrr]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/notebooks/pc-sc-codes3.html

  # generate_pc_sc_codes4a:
  #   run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes4a.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #   needs: [generate_study_population_ukrr]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/notebooks/pc-sc-codes4a.html

  # generate_pc_sc_codes4b:
  #   run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes4b.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #   needs: [generate_study_population_ukrr]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/notebooks/pc-sc-codes4b.html

  # generate_pc_sc_codes4c:
  #   run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes4c.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #   needs: [generate_study_population_ukrr]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/notebooks/pc-sc-codes4c.html

  # generate_pc_sc_codes5a:
  #   run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes5a.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #   needs: [generate_study_population_ukrr]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/notebooks/pc-sc-codes5a.html
  
  # generate_pc_sc_codes5b:
  #   run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/pc-sc-codes5b.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #   needs: [generate_study_population_ukrr]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/notebooks/pc-sc-codes5b.html

  # generate_ukrr_tables_figures_paeds:
  #   run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/ukrr-tables-figures-paeds.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #   needs: [generate_study_population_paeds]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/notebooks/ukrr-tables-figures-paeds.html
  
  # generate_check_SC:
  #   run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/check-SC.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #   needs: [generate_study_population_check_SC, generate_study_population_ukrr_ethnicity]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/notebooks/check-SC.html

  # generate_modality_difference_table:
  #   run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/modality-difference-table.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #   needs: [generate_study_population_ukrr]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/notebooks/modality-difference-table.html

  # generate_incident_analysis:
  #   run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/incident-analysis.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #   needs: [generate_study_population_ukrr]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/notebooks/incident-analysis.html
        
  # generate_study_population_flowchart:
  #   run: cohortextractor:latest generate_cohort
  #     --study-definition study_definition_flowchart
  #     --output-format csv.gz
  #   outputs:
  #     highly_sensitive:
  #       cohort: output/input_flowchart.csv.gz
  
  # generate_median_age:
  #   run: r:latest -e 'rmarkdown::render("analysis/ukrr-analysis/median_age.Rmd", knit_root_dir = "/workspace", output_dir = "output/notebooks")'
  #   needs: [generate_study_population_ukrr]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/notebooks/median_age.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:07:11

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

Job information

Status
Succeeded
Backend
TPP
Workspace
renal-short-data-report
Requested by
Louis Fisher
Branch
main
Force run dependencies
No
Git commit hash
d50c49a
Requested actions
  • ukrr_vs_prim_care_ckd