Job request: 17739

### CTV3, PRIMIS, SNOMED analysis

version: '3.0'

expectations:
  population_size: 1000

actions:
  split_codelist:
    run: r:latest analysis/00_trim_snomed_codelist.r
    outputs:
      highly_sensitive:
        data: codelists/ethnicity_*.csv

  generate_study_population_5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_5 --output-file output/extract_5/input_5.feather --output-format feather
    needs: [split_codelist]
    outputs:
      highly_sensitive:
        cohort: output/extract_5/input_5.feather

  # dataset report from reusable action https://github.com/opensafely-actions/dataset-report
  generate_dataset_report_5:
    run: >
      dataset-report:v0.0.9
        --input-files output/extract_5/input_5.feather
        --output-dir output/extract_5
    needs: [generate_study_population_5]
    outputs:
      moderately_sensitive:
        dataset_report: output/extract_5/input_5.html

  generate_study_population_16:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_16 --output-file output/extract_16/input_16.feather --output-format feather
    needs: [split_codelist]
    outputs:
      highly_sensitive:
        cohort: output/extract_16/input_16.feather

  # dataset report from reusable action https://github.com/opensafely-actions/dataset-report
  generate_dataset_report_16:
    run: >
      dataset-report:v0.0.9
        --input-files output/extract_16/input_16.feather
        --output-dir output/extract_16
    needs: [generate_study_population_16]
    outputs:
      moderately_sensitive:
        dataset_report: output/extract_16/input_16.html

  generate_study_population_time:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_time --output-file output/extract_time/input_time.feather --output-format feather
    needs: [split_codelist]
    outputs:
      highly_sensitive:
        cohort: output/extract_time/input_time.feather

  # dataset report from reusable action https://github.com/opensafely-actions/dataset-report
  generate_dataset_report_time:
    run: >
      dataset-report:v0.0.9
        --input-files output/extract_time/input_time.feather
        --output-dir output/extract_time
    needs: [generate_study_population_time]
    outputs:
      moderately_sensitive:
        dataset_report: output/extract_time/input_time.html

  execute_simple_validation_analyses:
    run: python:latest python analysis/simple_validation_script.py
    needs: [generate_study_population_5]
    outputs:
      moderately_sensitive: 
        tables: output/simplified_output/5_group/tables/*.csv

  execute_simple_validation_analyses_16:
    run: python:latest python analysis/simple_validation_script_16.py
    needs: [generate_study_population_16]
    outputs:
      moderately_sensitive: 
        tables: output/simplified_output/16_group/tables/simpl*.csv


######## SUS
  execute_simple_validation_analyses_sus:
    run: python:latest python analysis/sus/simple_validation_script_sus.py
    needs: [generate_study_population_5]
    outputs:
      moderately_sensitive: 
        tables: output/sus/simplified_output/5_group/tables/*.csv
#        figures: output/sus/simplified_output/5_group/figures/*.png

  execute_simple_validation_analyses_16_sus:
    run: python:latest python analysis/sus/simple_validation_script_16_sus.py
    needs: [generate_study_population_16]
    outputs:
      moderately_sensitive: 
        tables: output/sus/simplified_output/16_group/tables/simpl*.csv


################## over time

  time_tables:
    run: r:latest analysis/time/times.R
    needs: [generate_study_population_time]
    outputs:
      moderately_sensitive:
        data: output/time/*.csv
        plots: output/time/*.png

##### draft report
  generate_draft_report:
    run: python:latest jupyter nbconvert /workspace/notebooks_jupyter/draft_report_ethnicity.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [execute_simple_validation_analyses,execute_simple_validation_analyses_16]
    outputs:
      moderately_sensitive:
        notebook: output/draft_report_ethnicity.html

#### move released files to output/released
###### run locally for manuscript
##### local notebook
  # generate_local_runs:
  #   run: python:latest jupyter nbconvert /workspace/notebooks_jupyter/local_runs.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
  #   needs: [execute_simple_validation_analyses,execute_simple_validation_analyses_16]
  #   outputs:
  #     moderately_sensitive:
  #       csvs: output/released/made_locally/*.csv

  # process_ons_census_data:
  #   run: r:latest analysis/local/ons_process.R
  #   outputs:
  #     moderately_sensitive:
  #       csvs: data/*.csv.gz

  # generate_local_ons_comparisons:
  #   run: r:latest analysis/local/combine_ons_sus.R
  #   needs: [process_ons_census_data]
  #   outputs:
  #     moderately_sensitive:
  #       csvs: output/released/made_locally/ethnic_group*.csv
  #       tests: output/tests/*.csv

## create outputs for the manuscript
  ## library(hrbrthemes) not currently available on the OS R image
  # generate_manuscript_plots:
  #   run: r:latest analysis/local/local_manuscript_plots.R
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/released/made_locally/*.png

## create outputs for the appendix
# `row_group.as_column = TRUE` option not currently available on the OS R image
  # generate_appendix:
  #   run: r:latest analysis/local/appendix.R
  #   needs: [generate_local_runs]
  #   outputs:
  #     moderately_sensitive:
  #       html: output/released/made_locally/*.html
  #       pdf: output/released/made_locally/*.pdf