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Job request: 11829

Organisation:
The UK Renal Registry
Workspace:
renal-short-data-report
ID:
vdhbmm2wu2aqnpjw
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher 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

  • Action:
    crcl_gault
    Status:
    Status: Succeeded
    Job identifier:
    vju7ws2ihvdva45t

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/violi*.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 2020-01-01 by month"
      --output-format csv.gz
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/input*.csv.gz

  generate_study_population_2:
   run: cohortextractor:latest generate_cohort
     --study-definition study_definition 
     --index-date-range "2020-02-01 to 2021-02-01 by month" 
     --output-format csv.gz
     --with-end-date-fix
   outputs:
     highly_sensitive:
       cohort: output/inpu*.csv.gz

  generate_study_population_3:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition 
      --index-date-range "2021-02-01 to 2022-01-01 by month" 
      --output-format csv.gz
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/inp*.csv.gz

  generate_study_population_4:
    run: cohortextractor:latest generate_cohort 
      --study-definition study_definition 
      --index-date-range "2022-02-01 to 2022-07-01 by month" 
      --output-format csv.gz
      --with-end-date-fix
    outputs:
      highly_sensitive:
        cohort: output/in*.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_2, generate_study_population_3, generate_study_population_4,generate_study_population_ukrr_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/joined/input_20*.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
      --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
      --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_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:
        counts: output/table_1.csv
        at_risk: output/table_1_at_risk.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_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_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
        
  
  generate_plots:
    run: python:latest python analysis/scripts/plot_measures.py
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        counts: output/figures/plot_*.jpeg

  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_upset_*.png
        time: output/time_diff_ckd.jpeg

  # 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_cohorts]
  #  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_cohorts]
  #   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/ukrr_overlap_stage.png
        violin: output/violin_*.png

  
  # 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_cohorts]
  #   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, generate_study_population_ukrr_1, generate_study_population_ukrr_2]
    outputs:
      moderately_sensitive:
        report: output/notebooks/ukrr-tables-figures.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, generate_study_population_ukrr_1, generate_study_population_ukrr_2]
    outputs:
      moderately_sensitive:
        report: output/notebooks/modality-difference-table.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:03:12

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

Job request

Status
Succeeded
Backend
TPP
Workspace
renal-short-data-report
Requested by
Louis Fisher
Branch
main
Force run dependencies
No
Git commit hash
4e9c4ae
Requested actions
  • crcl_gault

Code comparison

Compare the code used in this job request