lydata/dvc.lock at main · lycosystem/lydata · GitHub

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schema: '2.0'
stages:
  lyproxify@0:
    cmd: "uvx --with-requirements 2021-clb-oropharynx/requirements.in lyscripts data
      lyproxify --input-file 2021-clb-oropharynx/raw.csv --output-file 2021-clb-oropharynx/_lyproxified.csv
      --mapping-file 2021-clb-oropharynx/mapping.py --num-header-rows 1\n"
    deps:
    - path: 2021-clb-oropharynx/mapping.py
      hash: md5
      md5: 3899c25337b7e94976745a745fea1227
      size: 21345
    - path: 2021-clb-oropharynx/raw.csv
      hash: md5
      md5: f57bb69fbd20f558858b07f7e305721b
      size: 96522
    outs:
    - path: 2021-clb-oropharynx/_lyproxified.csv
      hash: md5
      md5: 8821a34c32f730de9ec02963d89ec992
      size: 93324
  lyproxify@1:
    cmd: "uvx --with-requirements 2023-clb-multisite/requirements.in lyscripts data
      lyproxify --input-file 2023-clb-multisite/raw.csv --output-file 2023-clb-multisite/_lyproxified.csv
      --mapping-file 2023-clb-multisite/mapping.py --num-header-rows 3 --drop-rows
      439\n"
    deps:
    - path: 2023-clb-multisite/mapping.py
      hash: md5
      md5: c9d25a46c10a391302519b7e0ddce3fe
      size: 28283
    - path: 2023-clb-multisite/raw.csv
      hash: md5
      md5: 07fb62f160142252fe11e1738de6331f
      size: 211635
    outs:
    - path: 2023-clb-multisite/_lyproxified.csv
      hash: md5
      md5: 9964f661050023367ba311a4a6de458c
      size: 113643
  lyproxify@2:
    cmd: "uvx --with-requirements 2023-isb-multisite/requirements.in lyscripts data
      lyproxify --input-file 2023-isb-multisite/raw.csv --output-file 2023-isb-multisite/_lyproxified.csv
      --mapping-file 2023-isb-multisite/mapping.py --num-header-rows 1\n"
    deps:
    - path: 2023-isb-multisite/mapping.py
      hash: md5
      md5: bdb387a20c6e3bcdc68913cc526d345a
      size: 53450
    - path: 2023-isb-multisite/raw.csv
      hash: md5
      md5: a715c9e179685c5874364087f9d95d40
      size: 167129
    outs:
    - path: 2023-isb-multisite/_lyproxified.csv
      hash: md5
      md5: 32e3df1c4dc994a9a514feb8a850bd29
      size: 204527
  format-dates-insert-institution-and-remove-spaces:
    cmd: "sed 's/\\([0-9]\\{2\\}\\)\\/\\([0-9]\\{2\\}\\)\\/\\([0-9]\\{4\\}\\)/\\3-\\\
      2-\\1/g' 2025-hvh-oropharynx/raw.csv | sed 's/,dataset,/,institution,/g' | sed
      \"s/,2023_HVH_OROPHARYNX,/,Vall d'Hebron Barcelona Hospital,/g\" | sed 's/,\\\
      s,/,,/g' | sed 's/,\\([0-3]\\)[A-C]*,/,\\1,/g' | sed 's/,N\\sVI,/,FALSE,/g'
      | sed 's/\"C05,1\"/C05.1/g' | sed 's/\\(FEMALE\\)/\\L&/g' | sed 's/\\(MALE\\\
      )/\\L&/g' | sed 's/\\(OROPHARYNX\\)/\\L&/g' | sed -E '2s/(#|1|info)/core/g'
      > 2025-hvh-oropharynx/_tmp.csv\n"
    deps:
    - path: 2025-hvh-oropharynx/raw.csv
      hash: md5
      md5: 536e399533a13327aaed658056b0eb7d
      size: 80516
    - path: scripts/drop_cols.py
      hash: md5
      md5: dc4bbeffb5e69044ae1d46851920cc02
      size: 1033
    outs:
    - path: 2025-hvh-oropharynx/_tmp.csv
      hash: md5
      md5: 15934ba0569f80112602ab36335574d8
      size: 82624
  join:
    cmd: "lyscripts data join --inputs='[{\"source\": \"2021-clb-oropharynx/data.csv\"\
      }, {\"source\": \"2023-isb-multisite/data.csv\"}, {\"source\": \"2023-clb-multisite/data.csv\"\
      }]' --output=joined.csv\n"
    deps:
    - path: 2021-clb-oropharynx/data.csv
      hash: md5
      md5: af05aeaa3fea122dd718b3dd9c6a22b1
      size: 92744
    - path: 2023-clb-multisite/data.csv
      hash: md5
      md5: 0ee586c452452c781e8b6c22b5e5ef71
      size: 111721
    - path: 2023-isb-multisite/data.csv
      hash: md5
      md5: 24c25eedd6a832e595b12bd6b822a25c
      size: 204462
    outs:
    - path: joined.csv
      hash: md5
      md5: a5a0b1371a7f0a23c88652124f69a6d0
      size: 508523
  enhance:
    cmd: "lyscripts data enhance --configs=modalities.ly.yaml --method=max_llh --input.source=joined.csv
      --output-file=enhanced.csv\n"
    deps:
    - path: joined.csv
      hash: md5
      md5: a5a0b1371a7f0a23c88652124f69a6d0
      size: 508523
    params:
      modalities.ly.yaml:
        modalities:
          CT:
            spec: 0.76
            sens: 0.81
          MRI:
            spec: 0.63
            sens: 0.81
          PET:
            spec: 0.86
            sens: 0.79
          FNA:
            spec: 0.98
            sens: 0.8
          diagnostic_consensus:
            spec: 0.86
            sens: 0.81
          pathology:
            spec: 1.0
            sens: 1.0
          pCT:
            spec: 0.86
            sens: 0.81
          max_llh:
            spec: 1.0
            sens: 1.0
        version: 1
    outs:
    - path: enhanced.csv
      hash: md5
      md5: d9c0608bc2a827aefc0f51bf1bccb8c4
      size: 694603
  scenario-showcase:
    cmd: "python scripts/scenario_showcase.py --data enhanced.csv --mplstyle scripts/.mplstyle\n"
    deps:
    - path: enhanced.csv
      hash: md5
      md5: d9c0608bc2a827aefc0f51bf1bccb8c4
      size: 694603
    - path: scripts/.mplstyle
      hash: md5
      md5: 1dd8e65e1d2705d5c02ec977b8e7ca0d
      size: 2151
    - path: scripts/scenario_showcase.py
      hash: md5
      md5: d16498e9ce8a685f2c8bf7b8fc6d474e
      size: 6031
    outs:
    - path: scenario_showcase.png
      hash: md5
      md5: beafd10310cd876bb4077b447f75e01d
      size: 86382
  description-and-docs@2021-clb-oropharynx:
    cmd: "uv run scripts/render.py -m 2021-clb-oropharynx/mapping.py -d 2021-clb-oropharynx/data.csv
      -t 2021-clb-oropharynx/README.md.jinja -o 2021-clb-oropharynx/README.md\n"
    deps:
    - path: 2021-clb-oropharynx/README.md.jinja
      hash: md5
      md5: 167d94b07dce5980b1a897f5fb35947a
      size: 16665
    - path: 2021-clb-oropharynx/data.csv
      hash: md5
      md5: b39df5b5dbe9b99f3b7f7062530f3cda
      size: 88102
    - path: 2021-clb-oropharynx/mapping.py
      hash: md5
      md5: 3899c25337b7e94976745a745fea1227
      size: 21345
    - path: scripts/render.py
      hash: md5
      md5: 5ce21bd0d2137793d04c74008ae9fd87
      size: 2621
    outs:
    - path: 2021-clb-oropharynx/README.md
      hash: md5
      md5: 8a9f14c953113b33258a3cb67f03165b
      size: 25514
  description-and-docs@2023-clb-multisite:
    cmd: "uv run scripts/render.py -m 2023-clb-multisite/mapping.py -d 2023-clb-multisite/data.csv
      -t 2023-clb-multisite/README.md.jinja -o 2023-clb-multisite/README.md\n"
    deps:
    - path: 2023-clb-multisite/README.md.jinja
      hash: md5
      md5: c629b38333cf08dd8999f0765fabc463
      size: 3233
    - path: 2023-clb-multisite/data.csv
      hash: md5
      md5: c7122e540ab30ab014761100b173623e
      size: 108673
    - path: 2023-clb-multisite/mapping.py
      hash: md5
      md5: c9d25a46c10a391302519b7e0ddce3fe
      size: 28283
    - path: scripts/render.py
      hash: md5
      md5: 5ce21bd0d2137793d04c74008ae9fd87
      size: 2621
    outs:
    - path: 2023-clb-multisite/README.md
      hash: md5
      md5: d063e9578eb9105780d30dcb6301c502
      size: 14593
  description-and-docs@2023-isb-multisite:
    cmd: "uv run scripts/render.py -m 2023-isb-multisite/mapping.py -d 2023-isb-multisite/data.csv
      -t 2023-isb-multisite/README.md.jinja -o 2023-isb-multisite/README.md\n"
    deps:
    - path: 2023-isb-multisite/README.md.jinja
      hash: md5
      md5: 1f2d32a815921e9ba97825b661d992ad
      size: 3002
    - path: 2023-isb-multisite/data.csv
      hash: md5
      md5: 079ded521440c0cf66f16fe77dc00ef6
      size: 193281
    - path: 2023-isb-multisite/mapping.py
      hash: md5
      md5: bdb387a20c6e3bcdc68913cc526d345a
      size: 53450
    - path: scripts/render.py
      hash: md5
      md5: 5ce21bd0d2137793d04c74008ae9fd87
      size: 2621
    outs:
    - path: 2023-isb-multisite/README.md
      hash: md5
      md5: ca030a986c6ee20bf4c860aa4d939daa
      size: 19748
  plot-t-category@2021-usz-oropharynx:
    cmd: "uv run scripts/t_category.py 2021-usz-oropharynx/data.csv\n"
    deps:
    - path: 2021-usz-oropharynx/data.csv
      hash: md5
      md5: 6528695ea45b220e832a7120c773a76a
      size: 169719
    - path: scripts/t_category.py
      hash: md5
      md5: 533580c28a708f7ae40fff720b385452
      size: 2219
    outs:
    - path: 2021-usz-oropharynx/figures/t_category.png
      hash: md5
      md5: 5fc427aad233356674df964b56025acb
      size: 27174
  plot-t-category@2021-clb-oropharynx:
    cmd: "uv run scripts/t_category.py 2021-clb-oropharynx/data.csv\n"
    deps:
    - path: 2021-clb-oropharynx/data.csv
      hash: md5
      md5: b39df5b5dbe9b99f3b7f7062530f3cda
      size: 88102
    - path: scripts/t_category.py
      hash: md5
      md5: 533580c28a708f7ae40fff720b385452
      size: 2219
    outs:
    - path: 2021-clb-oropharynx/figures/t_category.png
      hash: md5
      md5: 9a8fe1983b449413bf327adc6592d09f
      size: 30976
  plot-t-category@2023-clb-multisite:
    cmd: "uv run scripts/t_category.py 2023-clb-multisite/data.csv\n"
    deps:
    - path: 2023-clb-multisite/data.csv
      hash: md5
      md5: c7122e540ab30ab014761100b173623e
      size: 108673
    - path: scripts/t_category.py
      hash: md5
      md5: 533580c28a708f7ae40fff720b385452
      size: 2219
    outs:
    - path: 2023-clb-multisite/figures/t_category.png
      hash: md5
      md5: 8e970393d33eebf8f5351f6299e151b4
      size: 28442
  plot-t-category@2023-isb-multisite:
    cmd: "uv run scripts/t_category.py 2023-isb-multisite/data.csv\n"
    deps:
    - path: 2023-isb-multisite/data.csv
      hash: md5
      md5: 079ded521440c0cf66f16fe77dc00ef6
      size: 193281
    - path: scripts/t_category.py
      hash: md5
      md5: 533580c28a708f7ae40fff720b385452
      size: 2219
    outs:
    - path: 2023-isb-multisite/figures/t_category.png
      hash: md5
      md5: 0bc3c2da93b683d5c321f7174d2ae066
      size: 29019
  plot-t-category@2025-hvh-oropharynx:
    cmd: "uv run scripts/t_category.py 2025-hvh-oropharynx/data.csv\n"
    deps:
    - path: 2025-hvh-oropharynx/data.csv
      hash: md5
      md5: e239014a6d07c7b05aef6185b962a015
      size: 70816
    - path: scripts/t_category.py
      hash: md5
      md5: 533580c28a708f7ae40fff720b385452
      size: 2219
    outs:
    - path: 2025-hvh-oropharynx/figures/t_category.png
      hash: md5
      md5: 43ed1811b8e9d265b2474a13ff343a43
      size: 28660
  plot-age-and-sex@2021-usz-oropharynx:
    cmd: "uv run scripts/age_and_sex.py 2021-usz-oropharynx/data.csv\n"
    deps:
    - path: 2021-usz-oropharynx/data.csv
      hash: md5
      md5: 6528695ea45b220e832a7120c773a76a
      size: 169719
    - path: scripts/age_and_sex.py
      hash: md5
      md5: f261a84aa41ba6e270d36aae25ffc846
      size: 3700
    outs:
    - path: 2021-usz-oropharynx/figures/age_and_sex.png
      hash: md5
      md5: ddc422c92ac865f388f0ccc119aa5c09
      size: 48049
  plot-age-and-sex@2021-clb-oropharynx:
    cmd: "uv run scripts/age_and_sex.py 2021-clb-oropharynx/data.csv\n"
    deps:
    - path: 2021-clb-oropharynx/data.csv
      hash: md5
      md5: b39df5b5dbe9b99f3b7f7062530f3cda
      size: 88102
    - path: scripts/age_and_sex.py
      hash: md5
      md5: f261a84aa41ba6e270d36aae25ffc846
      size: 3700
    outs:
    - path: 2021-clb-oropharynx/figures/age_and_sex.png
      hash: md5
      md5: 74e5fa230e8cb1299eea8aaa31978920
      size: 46966
  plot-age-and-sex@2023-clb-multisite:
    cmd: "uv run scripts/age_and_sex.py 2023-clb-multisite/data.csv\n"
    deps:
    - path: 2023-clb-multisite/data.csv
      hash: md5
      md5: c7122e540ab30ab014761100b173623e
      size: 108673
    - path: scripts/age_and_sex.py
      hash: md5
      md5: f261a84aa41ba6e270d36aae25ffc846
      size: 3700
    outs:
    - path: 2023-clb-multisite/figures/age_and_sex.png
      hash: md5
      md5: bedc0cb0a125b64eee3c8ed80424ed97
      size: 50448
  plot-age-and-sex@2023-isb-multisite:
    cmd: "uv run scripts/age_and_sex.py 2023-isb-multisite/data.csv\n"
    deps:
    - path: 2023-isb-multisite/data.csv
      hash: md5
      md5: 079ded521440c0cf66f16fe77dc00ef6
      size: 193281
    - path: scripts/age_and_sex.py
      hash: md5
      md5: f261a84aa41ba6e270d36aae25ffc846
      size: 3700
    outs:
    - path: 2023-isb-multisite/figures/age_and_sex.png
      hash: md5
      md5: 9f6336b776b6ab9a57ac2022f48cedb2
      size: 49883
  plot-age-and-sex@2025-hvh-oropharynx:
    cmd: "uv run scripts/age_and_sex.py 2025-hvh-oropharynx/data.csv\n"
    deps:
    - path: 2025-hvh-oropharynx/data.csv
      hash: md5
      md5: e239014a6d07c7b05aef6185b962a015
      size: 70816
    - path: scripts/age_and_sex.py
      hash: md5
      md5: f261a84aa41ba6e270d36aae25ffc846
      size: 3700
    outs:
    - path: 2025-hvh-oropharynx/figures/age_and_sex.png
      hash: md5
      md5: 05b1b887f676bf3201558c0bc7e2b2f6
      size: 48305
  plot-subsite@2021-usz-oropharynx:
    cmd: "uv run scripts/subsite.py --data 2021-usz-oropharynx/data.csv\n"
    deps:
    - path: 2021-usz-oropharynx/data.csv
      hash: md5
      md5: 6528695ea45b220e832a7120c773a76a
      size: 169719
    - path: scripts/subsite.py
      hash: md5
      md5: 7904e25c43d20cd10b8ec090103417fc
      size: 5683
    outs:
    - path: 2021-usz-oropharynx/figures/subsite.png
      hash: md5
      md5: 70da624e5d11170132382ffd07cd286c
      size: 55851
  plot-subsite@2021-clb-oropharynx:
    cmd: "uv run scripts/subsite.py --data 2021-clb-oropharynx/data.csv\n"
    deps:
    - path: 2021-clb-oropharynx/data.csv
      hash: md5
      md5: b39df5b5dbe9b99f3b7f7062530f3cda
      size: 88102
    - path: scripts/subsite.py
      hash: md5
      md5: 7904e25c43d20cd10b8ec090103417fc
      size: 5683
    outs:
    - path: 2021-clb-oropharynx/figures/subsite.png
      hash: md5
      md5: 46e15670588e1fec404ca42c965eda7c
      size: 71982
  plot-subsite@2023-clb-multisite:
    cmd: "uv run scripts/subsite.py --data 2023-clb-multisite/data.csv\n"
    deps:
    - path: 2023-clb-multisite/data.csv
      hash: md5
      md5: c7122e540ab30ab014761100b173623e
      size: 108673
    - path: scripts/subsite.py
      hash: md5
      md5: 7904e25c43d20cd10b8ec090103417fc
      size: 5683
    outs:
    - path: 2023-clb-multisite/figures/subsite.png
      hash: md5
      md5: 950e6154bd354ce643a2246fba109336
      size: 131318
  plot-subsite@2023-isb-multisite:
    cmd: "uv run scripts/subsite.py --data 2023-isb-multisite/data.csv\n"
    deps:
    - path: 2023-isb-multisite/data.csv
      hash: md5
      md5: 079ded521440c0cf66f16fe77dc00ef6
      size: 193281
    - path: scripts/subsite.py
      hash: md5
      md5: 7904e25c43d20cd10b8ec090103417fc
      size: 5683
    outs:
    - path: 2023-isb-multisite/figures/subsite.png
      hash: md5
      md5: a92b8c78a5958eb3eda2f6a5d27a81e3
      size: 149033
  plot-subsite@2025-hvh-oropharynx:
    cmd: "uv run scripts/subsite.py --data 2025-hvh-oropharynx/data.csv\n"
    deps:
    - path: 2025-hvh-oropharynx/data.csv
      hash: md5
      md5: e239014a6d07c7b05aef6185b962a015
      size: 70816
    - path: scripts/subsite.py
      hash: md5
      md5: 7904e25c43d20cd10b8ec090103417fc
      size: 5683
    outs:
    - path: 2025-hvh-oropharynx/figures/subsite.png
      hash: md5
      md5: ceb1b099c37a2fbde4ddc1118469c383
      size: 73425
  bar-plot@2021-clb-oropharynx:
    cmd: uv run scripts/bar_plot.py 2021-clb-oropharynx/data.csv
    deps:
    - path: 2021-clb-oropharynx/data.csv
      hash: md5
      md5: b39df5b5dbe9b99f3b7f7062530f3cda
      size: 88102
    - path: scripts/bar_plot.py
      hash: md5
      md5: 42e4153d6b9dff871abe80b80753bfa5
      size: 2999
  bar-plot@2023-clb-multisite:
    cmd: uv run scripts/bar_plot.py 2023-clb-multisite/data.csv
    deps:
    - path: 2023-clb-multisite/data.csv
      hash: md5
      md5: c7122e540ab30ab014761100b173623e
      size: 108673
    - path: scripts/bar_plot.py
      hash: md5
      md5: 42e4153d6b9dff871abe80b80753bfa5
      size: 2999
  bar-plot@2023-isb-multisite:
    cmd: uv run scripts/bar_plot.py 2023-isb-multisite/data.csv
    deps:
    - path: 2023-isb-multisite/data.csv
      hash: md5
      md5: 079ded521440c0cf66f16fe77dc00ef6
      size: 193281
    - path: scripts/bar_plot.py
      hash: md5
      md5: 42e4153d6b9dff871abe80b80753bfa5
      size: 2999
  factors-diff@2021-usz-oropharynx-2025-hvh-oropharynx:
    cmd: "uv run scripts/factors_diff.py --first-dataset 2021-usz-oropharynx --second-dataset
      2025-hvh-oropharynx --commit ee15c4cabdd160a10783fcf85ffe1cbfeb5c4826 --repo
      lycosystem/lydata.private\n"
    deps:
    - path: 2021-usz-oropharynx/data.csv
      hash: md5
      md5: 6528695ea45b220e832a7120c773a76a
      size: 169719
    - path: 2025-hvh-oropharynx/data.csv
      hash: md5
      md5: e239014a6d07c7b05aef6185b962a015
      size: 70816
    - path: scripts/factors_diff.py
      hash: md5
      md5: fba11eb3b4af33b888c55c72886a5113
      size: 4094
  drop-cols:
    cmd: "uv run scripts/drop_cols.py --input-csv 2025-hvh-oropharynx/_tmp.csv --output-csv
      2025-hvh-oropharynx/data.csv --cols \"diagnostic_consensus,FNA,pCT\"\n"
    deps:
    - path: 2025-hvh-oropharynx/_tmp.csv
      hash: md5
      md5: 15934ba0569f80112602ab36335574d8
      size: 82624
    - path: scripts/drop_cols.py
      hash: md5
      md5: dc4bbeffb5e69044ae1d46851920cc02
      size: 1033
    outs:
    - path: 2025-hvh-oropharynx/data.csv
      hash: md5
      md5: 9b517985d2c7d789bd41d750cd62c1da
      size: 69228
  clean@2025-hvh-oropharynx/tmp.csv:
    cmd: "rm -f 2025-hvh-oropharynx/tmp.csv\n"
  lyproxify-umcg@radiotherapy:
    cmd: "uvx --with-requirements 2025-umcg-hypopharynx-larynx/requirements.in lyscripts
      data lyproxify --input-file 2025-umcg-hypopharynx-larynx/raw_radiotherapy.csv
      --output-file 2025-umcg-hypopharynx-larynx/data_radiotherapy.csv --mapping-file
      2025-umcg-hypopharynx-larynx/mapping_radiotherapy.py\n"
    deps:
    - path: 2025-umcg-hypopharynx-larynx/mapping_radiotherapy.py
      hash: md5
      md5: 55a7aa89d8cf6a69c02543174109b418
      size: 18676
    - path: 2025-umcg-hypopharynx-larynx/raw_radiotherapy.csv
      hash: md5
      md5: e8f258bcccf744c91fabe4d62a3c1cc0
      size: 144440
    outs:
    - path: 2025-umcg-hypopharynx-larynx/data_radiotherapy.csv
      hash: md5
      md5: 9894de85425dadb493d9cc52822105e1
      size: 234135
  lyproxify-umcg@surgery:
    cmd: "uvx --with-requirements 2025-umcg-hypopharynx-larynx/requirements.in lyscripts
      data lyproxify --input-file 2025-umcg-hypopharynx-larynx/raw_surgery.csv --output-file
      2025-umcg-hypopharynx-larynx/data_surgery.csv --mapping-file 2025-umcg-hypopharynx-larynx/mapping_surgery.py\n"
    deps:
    - path: 2025-umcg-hypopharynx-larynx/mapping_surgery.py
      hash: md5
      md5: c828bfd6bb46e91d3ac1561dbbff7a8d
      size: 27026
    - path: 2025-umcg-hypopharynx-larynx/raw_surgery.csv
      hash: md5
      md5: ca7af4040dc364d036990369eda9c50c
      size: 64056
    outs:
    - path: 2025-umcg-hypopharynx-larynx/data_surgery.csv
      hash: md5
      md5: 988294cf66eb70d8732fecb41f5ffd1d
      size: 53628
  join-umcg-surgery-and-radiotherapy:
    cmd: "uvx --from \"lyscripts @ git+https://github.com/lycosystem/lyscripts@74551fed623356bc26f59e5cad9a532e5756da2e\"\
      \ lyscripts data join --inputs '{\"source\": \"2025-umcg-hypopharynx-larynx/data_surgery.csv\"\
      }' --inputs '{\"source\": \"2025-umcg-hypopharynx-larynx/data_radiotherapy.csv\"\
      }' --output-file 2025-umcg-hypopharynx-larynx/data.csv\n"
    deps:
    - path: 2025-umcg-hypopharynx-larynx/data_radiotherapy.csv
      hash: md5
      md5: 9894de85425dadb493d9cc52822105e1
      size: 234135
    - path: 2025-umcg-hypopharynx-larynx/data_surgery.csv
      hash: md5
      md5: 988294cf66eb70d8732fecb41f5ffd1d
      size: 53628
    outs:
    - path: 2025-umcg-hypopharynx-larynx/data.csv
      hash: md5
      md5: 004b5ac183509c0460987c14170fab3c
      size: 320558
  description-and-docs-umcg:
    cmd: "uv run scripts/render.py --mapping 2025-umcg-hypopharynx-larynx/mapping_surgery.py
      --template 2025-umcg-hypopharynx-larynx/README.md.jinja --data 2025-umcg-hypopharynx-larynx/data.csv
      --output /dev/stdout | sed 's/_surgery\\./_*\\./g' > 2025-umcg-hypopharynx-larynx/README.md\n"
    deps:
    - path: 2025-umcg-hypopharynx-larynx/README.md.jinja
      hash: md5
      md5: 8444485102312bb211e5002592b3e224
      size: 3156
    - path: 2025-umcg-hypopharynx-larynx/data.csv
      hash: md5
      md5: 004b5ac183509c0460987c14170fab3c
      size: 320558
    - path: 2025-umcg-hypopharynx-larynx/mapping_surgery.py
      hash: md5
      md5: c828bfd6bb46e91d3ac1561dbbff7a8d
      size: 27026
    - path: scripts/render.py
      hash: md5
      md5: 5ce21bd0d2137793d04c74008ae9fd87
      size: 2621
    outs:
    - path: 2025-umcg-hypopharynx-larynx/README.md
      hash: md5
      md5: e6a29eb10dcb191bcf650b2089130899
      size: 14101
  plot-t-category@2025-umcg-hypopharynx-larynx:
    cmd: "uv run scripts/t_category.py 2025-umcg-hypopharynx-larynx/data.csv\n"
    deps:
    - path: 2025-umcg-hypopharynx-larynx/data.csv
      hash: md5
      md5: 026dd7d406de4390e83a297be12dcd6e
      size: 279017
    - path: scripts/t_category.py
      hash: md5
      md5: 533580c28a708f7ae40fff720b385452
      size: 2219
    outs:
    - path: 2025-umcg-hypopharynx-larynx/figures/t_category.png
      hash: md5
      md5: 50c8e0210999f98b8ca89ee29140f429
      size: 29413
  plot-age-and-sex@2025-umcg-hypopharynx-larynx:
    cmd: "uv run scripts/age_and_sex.py 2025-umcg-hypopharynx-larynx/data.csv\n"
    deps:
    - path: 2025-umcg-hypopharynx-larynx/data.csv
      hash: md5
      md5: 026dd7d406de4390e83a297be12dcd6e
      size: 279017
    - path: scripts/age_and_sex.py
      hash: md5
      md5: f261a84aa41ba6e270d36aae25ffc846
      size: 3700
    outs:
    - path: 2025-umcg-hypopharynx-larynx/figures/age_and_sex.png
      hash: md5
      md5: 54ee411ef77387c65f4c7c1f481e3912
      size: 52843
  plot-subsite@2025-umcg-hypopharynx-larynx:
    cmd: "uv run scripts/subsite.py --data 2025-umcg-hypopharynx-larynx/data.csv\n"
    deps:
    - path: 2025-umcg-hypopharynx-larynx/data.csv
      hash: md5
      md5: 841769fcad20924408da2f5329928d86
      size: 324490
    - path: scripts/subsite.py
      hash: md5
      md5: 7904e25c43d20cd10b8ec090103417fc
      size: 5683
    outs:
    - path: 2025-umcg-hypopharynx-larynx/figures/subsite.png
      hash: md5
      md5: abc2c69fd9ede2150c036d3a1f3e8c1c
      size: 45953
  fix-tumor-side-add-linenumber-and-institution:
    cmd: sed 's/ambiguous/central/g' 2025-usz-hypopharynx-larynx/parsed.csv |
      sed 's/\([0-9]\{2\}\)\.\([0-9]\{2\}\)\.\([0-9]\{4\}\)/\3-\2-\1/g' | sed
      's/^,/University Hospital Zurich,/' | nl -v'-3' -n'rz' -s',' -w4 | sed
      's/^\-00[1-3],//' | sed 's/^id,/id,institution,/' | sed
      's/^patient,/patient,patient,/' | sed 's/^#,/#,#,/' | sed '4,$s/^/USZ/g' |
      sed -E '2s/(#|1|info)/core/g' > 2025-usz-hypopharynx-larynx/_tmp.csv
    deps:
    - path: 2025-usz-hypopharynx-larynx/parsed.csv
      hash: md5
      md5: 603a5a64adb33c564bacc2b9c69a297f
      size: 188471
    outs:
    - path: 2025-usz-hypopharynx-larynx/_tmp.csv
      hash: md5
      md5: ec327b4bc23fc70fdd738ac702725324
      size: 200957
  fix-involvement-info:
    cmd: "uv run scripts/fix_diagnoses.py 2025-usz-hypopharynx-larynx/_tmp.csv 2025-usz-hypopharynx-larynx/data.csv
      --delta-days 30\n"
    deps:
    - path: 2025-usz-hypopharynx-larynx/_tmp.csv
      hash: md5
      md5: ec327b4bc23fc70fdd738ac702725324
      size: 200957
    outs:
    - path: 2025-usz-hypopharynx-larynx/data.csv
      hash: md5
      md5: 2edf226426c8c9cab5b9322f1575c813
      size: 214032
  clean@2025-hvh-oropharynx/_tmp.csv:
    cmd: "rm -f 2025-hvh-oropharynx/_tmp.csv\n"
  plot-t-category@2025-usz-hypopharynx-larynx:
    cmd: "uv run scripts/t_category.py 2025-usz-hypopharynx-larynx/data.csv\n"
    deps:
    - path: 2025-usz-hypopharynx-larynx/data.csv
      hash: md5
      md5: 4e4b870e052e7081968f128ff88597db
      size: 218550
    - path: scripts/t_category.py
      hash: md5
      md5: 533580c28a708f7ae40fff720b385452
      size: 2219
    outs:
    - path: 2025-usz-hypopharynx-larynx/figures/t_category.png
      hash: md5
      md5: aaf8b7581d31b7b90a192c9b5c99b906
      size: 29605
  plot-age-and-sex@2025-usz-hypopharynx-larynx:
    cmd: "uv run scripts/age_and_sex.py 2025-usz-hypopharynx-larynx/data.csv\n"
    deps:
    - path: 2025-usz-hypopharynx-larynx/data.csv
      hash: md5
      md5: 4e4b870e052e7081968f128ff88597db
      size: 218550
    - path: scripts/age_and_sex.py
      hash: md5
      md5: f261a84aa41ba6e270d36aae25ffc846
      size: 3700
    outs:
    - path: 2025-usz-hypopharynx-larynx/figures/age_and_sex.png
      hash: md5
      md5: e73d8126d343467a01c4ba62ac9e5fab
      size: 49735
  plot-subsite@2025-usz-hypopharynx-larynx:
    cmd: "uv run scripts/subsite.py --data 2025-usz-hypopharynx-larynx/data.csv\n"
    deps:
    - path: 2025-usz-hypopharynx-larynx/data.csv
      hash: md5
      md5: c5a63befe10d9726ae9131824855c906
      size: 218686
    - path: scripts/subsite.py
      hash: md5
      md5: 7904e25c43d20cd10b8ec090103417fc
      size: 5683
    outs:
    - path: 2025-usz-hypopharynx-larynx/figures/subsite.png
      hash: md5
      md5: cfa99b654e4f076164073f1fd6bc2d4b
      size: 50973
  plot-ukf-conflicts:
    cmd: "uv run scripts/conflicts.py --input-file 2025-ukf-hypopharynx/data.csv --figure-dir
      2025-ukf-hypopharynx/figures\n"
    deps:
    - path: 2025-ukf-hypopharynx/data.csv
      hash: md5
      md5: 7bc2cc26acc6ecf4d50589be89c63463
      size: 36298
    - path: scripts/conflicts.py
      hash: md5
      md5: f0cbbabbef487d8466544271630f4791
      size: 6529
    outs:
    - path: 2025-ukf-hypopharynx/figures/conflicts.png
      hash: md5
      md5: cc9d09f686aa7464daa48e833c81f763
      size: 290396
    - path: 2025-ukf-hypopharynx/figures/total_conflicts.png
      hash: md5
      md5: 1a4a5cc1305fb16b9684b35e7f1b60ce
      size: 229802
  format-ukf-data:
    cmd: "sed -E '2s/(#|1|info)/core/g' 2025-ukf-hypopharynx/raw.csv | nl -v'-3' -n'rz'
      -s',' -w4 | sed '1s/^\\-003/patient/g' | sed '2s/^\\-002/info/g' | sed '3s/^\\\
      -001/id/g' | sed '4,$s/^/UKF/g' > 2025-ukf-hypopharynx/data.csv\n"
    deps:
    - path: 2025-ukf-hypopharynx/raw.csv
      hash: md5
      md5: 9aabf2cfa4342043b6f6ec8c587da99b
      size: 35790
    outs:
    - path: 2025-ukf-hypopharynx/data.csv
      hash: md5
      md5: 7bc2cc26acc6ecf4d50589be89c63463
      size: 36298
  fix-2025-usz-dates-and-add-institution:
    cmd: sed 's/ambiguous/central/g' 2025-usz-hypopharynx-larynx/parsed.csv |
      sed 's/^,/University Hospital Zurich,/' | sed
      's/^patient,/patient,patient,/' | sed 's/^core,/core,core,/' | sed
      's/^id,/id,institution,/' | sed '4,$s/^/,/g' >
      2025-usz-hypopharynx-larynx/_with_institution.csv
    deps:
    - path: 2025-usz-hypopharynx-larynx/parsed.csv
      hash: md5
      md5: eb3141c226db5c6e5bc293c41c3ea8ea
      size: 218529
    outs:
    - path: 2025-usz-hypopharynx-larynx/_with_institution.csv
      hash: md5
      md5: f031818bd163875b60a3de22d27951e3
      size: 218920
  fix-2025-usz-involvement-info:
    cmd: "uv run scripts/fix_diagnoses.py 2025-usz-hypopharynx-larynx/_with_institution.csv
      2025-usz-hypopharynx-larynx/_fixed_involvement.csv --delta-days 30\n"
    deps:
    - path: 2025-usz-hypopharynx-larynx/_with_institution.csv
      hash: md5
      md5: 2e5cb1bfc68329a600b0aa4ea868b1bd
      size: 200687
    outs:
    - path: 2025-usz-hypopharynx-larynx/_fixed_involvement.csv
      hash: md5
      md5: 26e65eeff8f1ede5b88e0e641d59e053
      size: 214158
  fix-2025-hvh-formatting:
    cmd: "sed 's/\\([0-9]\\{2\\}\\)\\/\\([0-9]\\{2\\}\\)\\/\\([0-9]\\{4\\}\\)/\\3-\\\
      2-\\1/g' 2025-hvh-oropharynx/raw.csv | sed 's/,dataset,/,institution,/g' | sed
      \"s/,2023_HVH_OROPHARYNX,/,Vall d'Hebron Barcelona Hospital,/g\" | sed 's/,\\\
      s,/,,/g' | sed 's/,\\([0-3]\\)[A-C]*,/,\\1,/g' | sed 's/,N\\sVI,/,FALSE,/g'
      | sed 's/\"C05,1\"/C05.1/g' | sed 's/\\(FEMALE\\)/\\L&/g' | sed 's/\\(MALE\\\
      )/\\L&/g' | sed 's/\\(OROPHARYNX\\)/\\L&/g' | sed -E '2s/(#|1|info)/core/g'
      > 2025-hvh-oropharynx/_fixed.csv\n"
    deps:
    - path: 2025-hvh-oropharynx/raw.csv
      hash: md5
      md5: 4eb858529c35ce9876decd4c7166c8c5
      size: 80520
    - path: scripts/drop_cols.py
      hash: md5
      md5: dc4bbeffb5e69044ae1d46851920cc02
      size: 1033
    outs:
    - path: 2025-hvh-oropharynx/_fixed.csv
      hash: md5
      md5: 5518d3424dfcc275f2fd7f26e1b7a43f
      size: 82628
  drop-2025-hvh-cols:
    cmd: "uv run scripts/drop_cols.py --input-csv 2025-hvh-oropharynx/_fixed.csv --output-csv
      2025-hvh-oropharynx/_reduced.csv --cols \"diagnostic_consensus,FNA,pCT\"\n"
    deps:
    - path: 2025-hvh-oropharynx/_fixed.csv
      hash: md5
      md5: 5518d3424dfcc275f2fd7f26e1b7a43f
      size: 82628
    - path: scripts/drop_cols.py
      hash: md5
      md5: dc4bbeffb5e69044ae1d46851920cc02
      size: 1033
    outs:
    - path: 2025-hvh-oropharynx/_reduced.csv
      hash: md5
      md5: d4b65fe9a15ae7dde2fe9a98eb5db9bf
      size: 69232
  assign-unique-ids@0:
    cmd: "uv run scripts/assign_ids.py 2021-clb-oropharynx --input-csv _lyproxified.csv
      --output-csv _to_cast.csv\n"
    deps:
    - path: 2021-clb-oropharynx/_lyproxified.csv
      hash: md5
      md5: 8821a34c32f730de9ec02963d89ec992
      size: 93324
    - path: scripts/assign_ids.py
      hash: md5
      md5: c0fbab360f3b10166bc62913ea6562e9
      size: 2611
    outs:
    - path: 2021-clb-oropharynx/_to_cast.csv
      hash: md5
      md5: da43b1cfc151ae902a6ec05abd654f2d
      size: 95428
  assign-unique-ids@2:
    cmd: "uv run scripts/assign_ids.py 2023-clb-multisite --input-csv _fixed_location.csv
      --output-csv _to_cast.csv\n"
    deps:
    - path: 2023-clb-multisite/_fixed_location.csv
      hash: md5
      md5: 82e099f807e233b7b2f79f99f24e9216
      size: 117178
    - path: scripts/assign_ids.py
      hash: md5
      md5: c0fbab360f3b10166bc62913ea6562e9
      size: 2611
    outs:
    - path: 2023-clb-multisite/_to_cast.csv
      hash: md5
      md5: fd391100ac1d7204110281d50195dee2
      size: 119043
  assign-unique-ids@3:
    cmd: "uv run scripts/assign_ids.py 2023-isb-multisite --input-csv _lyproxified.csv
      --output-csv _to_cast.csv\n"
    deps:
    - path: 2023-isb-multisite/_lyproxified.csv
      hash: md5
      md5: 32e3df1c4dc994a9a514feb8a850bd29
      size: 204527
    - path: scripts/assign_ids.py
      hash: md5
      md5: c0fbab360f3b10166bc62913ea6562e9
      size: 2611
    outs:
    - path: 2023-isb-multisite/_to_cast.csv
      hash: md5
      md5: 5d7e7f6facbe593b2ef549b78efa08cf
      size: 206851
  lyproxify-2025-umcg@radiotherapy:
    cmd: "uvx --with-requirements 2025-umcg-hypopharynx-larynx/requirements.in lyscripts
      data lyproxify --input-file 2025-umcg-hypopharynx-larynx/raw_radiotherapy.csv
      --output-file 2025-umcg-hypopharynx-larynx/_radiotherapy.csv --mapping-file
      2025-umcg-hypopharynx-larynx/mapping_radiotherapy.py\n"
    deps:
    - path: 2025-umcg-hypopharynx-larynx/mapping_radiotherapy.py
      hash: md5
      md5: 1e9a2f5cf85b28e3763fca4083c2e89d
      size: 17134
    - path: 2025-umcg-hypopharynx-larynx/raw_radiotherapy.csv
      hash: md5
      md5: a22ecda90aebcb8f85a9aeff059be629
      size: 144373
    outs:
    - path: 2025-umcg-hypopharynx-larynx/_radiotherapy.csv
      hash: md5
      md5: 69ea5bd564b4effb94958db02a8c119b
      size: 195758
  lyproxify-2025-umcg@surgery:
    cmd: "uvx --with-requirements 2025-umcg-hypopharynx-larynx/requirements.in lyscripts
      data lyproxify --input-file 2025-umcg-hypopharynx-larynx/raw_surgery.csv --output-file
      2025-umcg-hypopharynx-larynx/_surgery.csv --mapping-file 2025-umcg-hypopharynx-larynx/mapping_surgery.py\n"
    deps:
    - path: 2025-umcg-hypopharynx-larynx/mapping_surgery.py
      hash: md5
      md5: 610ce31b88668f04b755718bdac960a8
      size: 25250
    - path: 2025-umcg-hypopharynx-larynx/raw_surgery.csv
      hash: md5
      md5: a6da89499873a1ba6143e2aa1b432bde
      size: 64338
    outs:
    - path: 2025-umcg-hypopharynx-larynx/_surgery.csv
      hash: md5
      md5: 1af52faf3d5c7b7d0981984b2bd36860
      size: 47522
  join-2025-umcg-surgery-and-radiotherapy:
    cmd: "uvx --from \"lyscripts @ git+https://github.com/lycosystem/lyscripts@74551fed623356bc26f59e5cad9a532e5756da2e\"\
      \ lyscripts data join --inputs '{\"source\": \"2025-umcg-hypopharynx-larynx/_surgery.csv\"\
      }' --inputs '{\"source\": \"2025-umcg-hypopharynx-larynx/_radiotherapy.csv\"\
      }' --output-file 2025-umcg-hypopharynx-larynx/_joined.csv\n"
    deps:
    - path: 2025-umcg-hypopharynx-larynx/_radiotherapy.csv
      hash: md5
      md5: 69ea5bd564b4effb94958db02a8c119b
      size: 195758
    - path: 2025-umcg-hypopharynx-larynx/_surgery.csv
      hash: md5
      md5: 1af52faf3d5c7b7d0981984b2bd36860
      size: 47522
    outs:
    - path: 2025-umcg-hypopharynx-larynx/_joined.csv
      hash: md5
      md5: 2cbc6c56673f8c53d8bbc2b5fdd44236
      size: 276321
  assign-unique-ids@6:
    cmd: "uv run scripts/assign_ids.py 2025-umcg-hypopharynx-larynx --input-csv _joined.csv
      --output-csv _to_cast.csv\n"
    deps:
    - path: 2025-umcg-hypopharynx-larynx/_joined.csv
      hash: md5
      md5: 2cbc6c56673f8c53d8bbc2b5fdd44236
      size: 276321
    - path: scripts/assign_ids.py
      hash: md5
      md5: c0fbab360f3b10166bc62913ea6562e9
      size: 2611
    outs:
    - path: 2025-umcg-hypopharynx-larynx/_to_cast.csv
      hash: md5
      md5: a723493a77a6f4a0b64500bcbbe13290
      size: 280253
  render-2025-umcg-docs:
    cmd: "uv run scripts/render.py --mapping 2025-umcg-hypopharynx-larynx/mapping_surgery.py
      --template 2025-umcg-hypopharynx-larynx/README.md.jinja --data 2025-umcg-hypopharynx-larynx/data.csv
      --output /dev/stdout | sed 's/_surgery\\./_*\\./g' > 2025-umcg-hypopharynx-larynx/README.md\n"
    deps:
    - path: 2025-umcg-hypopharynx-larynx/README.md.jinja
      hash: md5
      md5: 90367dc08208e1e86e3aa92ca84ab570
      size: 3094
    - path: 2025-umcg-hypopharynx-larynx/data.csv
      hash: md5
      md5: 026dd7d406de4390e83a297be12dcd6e
      size: 279017
    - path: 2025-umcg-hypopharynx-larynx/mapping_surgery.py
      hash: md5
      md5: 610ce31b88668f04b755718bdac960a8
      size: 25250