dvc.yaml

stages:
  lyproxify:
    foreach:
      - folder: 2021-clb-oropharynx
        args: "-r 0"
      - folder: 2023-clb-multisite
        args: "-r 0 1 2 --drop-rows 439 --add-index"
      - folder: 2023-isb-multisite
        args: "-r 0"
    do:
      desc:
        Parse the `raw.csv` data using the `lyscripts` Python package and the
        `mapping.py` module to bring the original data into a format that the online
        interface LyProX understands.
      cmd: >
        lyscripts data lyproxify
        -i ${item.folder}/raw.csv
        -o ${item.folder}/data.csv
        -m ${item.folder}/mapping.py
        ${item.args}
      deps:
        - ${item.folder}/raw.csv
        - ${item.folder}/mapping.py
      outs:
        - ${item.folder}/data.csv:
            cache: false

  join:
    desc:
      Join together those datasets for which we want to create the showcase plot.
    deps:
      - 2021-clb-oropharynx/data.csv
      - 2023-isb-multisite/data.csv
      - 2023-clb-multisite/data.csv
    cmd: >
      lyscripts data join
      --inputs 2021-clb-oropharynx/data.csv 2023-isb-multisite/data.csv 2023-clb-multisite/data.csv
      --output joined.csv
    outs:
      - joined.csv

  enhance:
    desc:
      This stage fixes the super- and sub-level reporting for the LNLs and also creates
      new 'modalities' from combining existing ones, e.g. using the logical AND or
      estimating the most likely involvement based on the observations only.
    cmd: >
      lyscripts data enhance
      --consensus max_llh
      --params modalities.yaml
      joined.csv enhanced.csv
    deps:
      - joined.csv
    params:
      - modalities.yaml:
          - modalities
    outs:
      - enhanced.csv

  scenario-showcase:
    desc:
      Plot some involvement prevalences in the data for different scenarios, showcasing
      what is possible when data is reported in as much detail as we provide it.
    deps:
      - enhanced.csv
      - scripts/scenario_showcase.py
      - scripts/.mplstyle
    cmd: >
      python scripts/scenario_showcase.py
      --data enhanced.csv
      --mplstyle scripts/.mplstyle
    outs:
      - scenario_showcase.png

  description-and-docs:
    foreach:
      - 2021-clb-oropharynx
      - 2023-clb-multisite
      - 2023-isb-multisite
    do:
      desc:
        Generate the description of the `data.csv` columns from the `COLUMN_MAP` inside
        the `mapping.py` file, as well as the documentation of all the functions used
        in the `mapping.py` module. Insert these documentations into the
        `README.template` and create the `README.md` from it.
      deps:
        - scripts/render.py
        - ${item}/README.template
        - ${item}/mapping.py
        - ${item}/data.csv
      outs:
        - ${item}/README.md:
            cache: false
      cmd: >
        python scripts/render.py
        -m ${item}/mapping.py
        -d ${item}/data.csv
        -t ${item}/README.template
        -o ${item}/README.md

  plot-t-category:
    foreach:
      - 2021-usz-oropharynx
      - 2021-clb-oropharynx
      - 2023-clb-multisite
      - 2023-isb-multisite
    do:
      deps:
        - scripts/t_category.py
        - ${item}/data.csv
      cmd: >
        python scripts/t_category.py ${item}/data.csv

  plot-age-and-sex:
    foreach:
      - 2021-usz-oropharynx
      - 2021-clb-oropharynx
      - 2023-clb-multisite
      - 2023-isb-multisite
    do:
      deps:
        - scripts/age_and_sex.py
        - ${item}/data.csv
      cmd: >
        python scripts/age_and_sex.py ${item}/data.csv

  plot-subsite:
    foreach:
      - 2021-usz-oropharynx
      - 2021-clb-oropharynx
      - 2023-clb-multisite
      - 2023-isb-multisite
    do:
      deps:
        - scripts/subsite.py
        - ${item}/data.csv
      cmd: >
        python scripts/subsite.py --data ${item}/data.csv

  bar-plot:
    foreach:
      - 2021-clb-oropharynx
      - 2023-clb-multisite
      - 2023-isb-multisite
    do:
      deps:
        - scripts/bar_plot.py
        - ${item}/data.csv
      cmd:
        python scripts/bar_plot.py ${item}/data.csv