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schema: '2.0'
stages:
lyproxify@0:
cmd: "lyscripts data lyproxify --input-file=2021-clb-oropharynx/raw.csv --output-file=2021-clb-oropharynx/data.csv
--mapping-file=2021-clb-oropharynx/mapping.py --num-header-rows=1\n"
deps:
- path: 2021-clb-oropharynx/mapping.py
hash: md5
md5: 82858134ab5f682a5e0baaf6940375cf
size: 21351
- path: 2021-clb-oropharynx/raw.csv
hash: md5
md5: ca6413b63f277e4f6bb40b50294b0ff0
size: 96789
outs:
- path: 2021-clb-oropharynx/data.csv
hash: md5
md5: af05aeaa3fea122dd718b3dd9c6a22b1
size: 92744
lyproxify@1:
cmd: "lyscripts data lyproxify --input-file=2023-clb-multisite/raw.csv --output-file=2023-clb-multisite/data.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: dc25188420e21de86f51034f6177b080
size: 28008
- path: 2023-clb-multisite/raw.csv
hash: md5
md5: 07fb62f160142252fe11e1738de6331f
size: 211635
outs:
- path: 2023-clb-multisite/data.csv
hash: md5
md5: 0ee586c452452c781e8b6c22b5e5ef71
size: 111721
lyproxify@2:
cmd: "lyscripts data lyproxify --input-file=2023-isb-multisite/raw.csv --output-file=2023-isb-multisite/data.csv
--mapping-file=2023-isb-multisite/mapping.py --num-header-rows=1\n"
deps:
- path: 2023-isb-multisite/mapping.py
hash: md5
md5: 077ee8c837b587e3fc5b5ee810d0265c
size: 52984
- path: 2023-isb-multisite/raw.csv
hash: md5
md5: 0546a71875f357e0210425407dedf426
size: 167129
outs:
- path: 2023-isb-multisite/data.csv
hash: md5
md5: 24c25eedd6a832e595b12bd6b822a25c
size: 204462
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' > 2025-hvh-oropharynx/data.csv
deps:
- path: 2025-hvh-oropharynx/raw.csv
hash: md5
md5: 536e399533a13327aaed658056b0eb7d
size: 80516
outs:
- path: 2025-hvh-oropharynx/data.csv
hash: md5
md5: 9dcad2ce5cacd103090c3abe9ce1920a
size: 82567
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: "python scripts/render.py -m 2021-clb-oropharynx/mapping.py -d 2021-clb-oropharynx/data.csv
-t 2021-clb-oropharynx/README.template -o 2021-clb-oropharynx/README.md\n"
deps:
- path: 2021-clb-oropharynx/README.template
hash: md5
md5: edf345ea5b29efcee0923cd7fcc43077
size: 16726
- path: 2021-clb-oropharynx/data.csv
hash: md5
md5: af05aeaa3fea122dd718b3dd9c6a22b1
size: 92744
- path: 2021-clb-oropharynx/mapping.py
hash: md5
md5: 82858134ab5f682a5e0baaf6940375cf
size: 21351
- path: scripts/render.py
hash: md5
md5: 097a0bf7d0a39981ee0b4f403bd534fc
size: 2096
outs:
- path: 2021-clb-oropharynx/README.md
hash: md5
md5: 8dc6c2dfcadc298fb6a6192a211bfc5f
size: 25546
description-and-docs@2023-clb-multisite:
cmd: "python scripts/render.py -m 2023-clb-multisite/mapping.py -d 2023-clb-multisite/data.csv
-t 2023-clb-multisite/README.template -o 2023-clb-multisite/README.md\n"
deps:
- path: 2023-clb-multisite/README.template
hash: md5
md5: 4fee1faf0a125c4dc6a9462a6a93fcc4
size: 3295
- path: 2023-clb-multisite/data.csv
hash: md5
md5: 0ee586c452452c781e8b6c22b5e5ef71
size: 111721
- path: 2023-clb-multisite/mapping.py
hash: md5
md5: dc25188420e21de86f51034f6177b080
size: 28008
- path: scripts/render.py
hash: md5
md5: 097a0bf7d0a39981ee0b4f403bd534fc
size: 2096
outs:
- path: 2023-clb-multisite/README.md
hash: md5
md5: f44a14e074db523a075f8e8796686e53
size: 14492
description-and-docs@2023-isb-multisite:
cmd: "python scripts/render.py -m 2023-isb-multisite/mapping.py -d 2023-isb-multisite/data.csv
-t 2023-isb-multisite/README.template -o 2023-isb-multisite/README.md\n"
deps:
- path: 2023-isb-multisite/README.template
hash: md5
md5: 289ed4bef464a64d84d93126403800a9
size: 3064
- path: 2023-isb-multisite/data.csv
hash: md5
md5: 24c25eedd6a832e595b12bd6b822a25c
size: 204462
- path: 2023-isb-multisite/mapping.py
hash: md5
md5: 077ee8c837b587e3fc5b5ee810d0265c
size: 52984
- path: scripts/render.py
hash: md5
md5: 097a0bf7d0a39981ee0b4f403bd534fc
size: 2096
outs:
- path: 2023-isb-multisite/README.md
hash: md5
md5: 5648913555b260ef67efaca4f9b7f331
size: 19642
plot-t-category@2021-usz-oropharynx:
cmd: "python scripts/t_category.py 2021-usz-oropharynx/data.csv\n"
deps:
- path: 2021-usz-oropharynx/data.csv
hash: md5
md5: a9e4043ed6a273c609fa16523bcae455
size: 166966
- path: scripts/t_category.py
hash: md5
md5: cf119e4a12ccd9a42cd55ac3bc863c4b
size: 1690
plot-t-category@2021-clb-oropharynx:
cmd: "python scripts/t_category.py 2021-clb-oropharynx/data.csv\n"
deps:
- path: 2021-clb-oropharynx/data.csv
hash: md5
md5: af05aeaa3fea122dd718b3dd9c6a22b1
size: 92744
- path: scripts/t_category.py
hash: md5
md5: cf119e4a12ccd9a42cd55ac3bc863c4b
size: 1690
plot-t-category@2023-clb-multisite:
cmd: "python scripts/t_category.py 2023-clb-multisite/data.csv\n"
deps:
- path: 2023-clb-multisite/data.csv
hash: md5
md5: 0ee586c452452c781e8b6c22b5e5ef71
size: 111721
- path: scripts/t_category.py
hash: md5
md5: cf119e4a12ccd9a42cd55ac3bc863c4b
size: 1690
plot-t-category@2023-isb-multisite:
cmd: "python scripts/t_category.py 2023-isb-multisite/data.csv\n"
deps:
- path: 2023-isb-multisite/data.csv
hash: md5
md5: 24c25eedd6a832e595b12bd6b822a25c
size: 204462
- path: scripts/t_category.py
hash: md5
md5: cf119e4a12ccd9a42cd55ac3bc863c4b
size: 1690
plot-t-category@2025-hvh-oropharynx:
cmd: "python scripts/t_category.py 2025-hvh-oropharynx/data.csv\n"
deps:
- path: 2025-hvh-oropharynx/data.csv
hash: md5
md5: 9dcad2ce5cacd103090c3abe9ce1920a
size: 82567
- path: scripts/t_category.py
hash: md5
md5: cf119e4a12ccd9a42cd55ac3bc863c4b
size: 1690
plot-age-and-sex@2021-usz-oropharynx:
cmd: "python scripts/age_and_sex.py 2021-usz-oropharynx/data.csv\n"
deps:
- path: 2021-usz-oropharynx/data.csv
hash: md5
md5: a9e4043ed6a273c609fa16523bcae455
size: 166966
- path: scripts/age_and_sex.py
hash: md5
md5: 9fc68d3a1f95e03d7262ef3225b28a32
size: 3252
plot-age-and-sex@2021-clb-oropharynx:
cmd: "python scripts/age_and_sex.py 2021-clb-oropharynx/data.csv\n"
deps:
- path: 2021-clb-oropharynx/data.csv
hash: md5
md5: af05aeaa3fea122dd718b3dd9c6a22b1
size: 92744
- path: scripts/age_and_sex.py
hash: md5
md5: 9fc68d3a1f95e03d7262ef3225b28a32
size: 3252
plot-age-and-sex@2023-clb-multisite:
cmd: "python scripts/age_and_sex.py 2023-clb-multisite/data.csv\n"
deps:
- path: 2023-clb-multisite/data.csv
hash: md5
md5: 0ee586c452452c781e8b6c22b5e5ef71
size: 111721
- path: scripts/age_and_sex.py
hash: md5
md5: 9fc68d3a1f95e03d7262ef3225b28a32
size: 3252
plot-age-and-sex@2023-isb-multisite:
cmd: "python scripts/age_and_sex.py 2023-isb-multisite/data.csv\n"
deps:
- path: 2023-isb-multisite/data.csv
hash: md5
md5: 24c25eedd6a832e595b12bd6b822a25c
size: 204462
- path: scripts/age_and_sex.py
hash: md5
md5: 9fc68d3a1f95e03d7262ef3225b28a32
size: 3252
plot-age-and-sex@2025-hvh-oropharynx:
cmd: "python scripts/age_and_sex.py 2025-hvh-oropharynx/data.csv\n"
deps:
- path: 2025-hvh-oropharynx/data.csv
hash: md5
md5: 9dcad2ce5cacd103090c3abe9ce1920a
size: 82567
- path: scripts/age_and_sex.py
hash: md5
md5: 9fc68d3a1f95e03d7262ef3225b28a32
size: 3252
plot-subsite@2021-usz-oropharynx:
cmd: "python scripts/subsite.py --data 2021-usz-oropharynx/data.csv\n"
deps:
- path: 2021-usz-oropharynx/data.csv
hash: md5
md5: a9e4043ed6a273c609fa16523bcae455
size: 166966
- path: scripts/subsite.py
hash: md5
md5: 417c5dfd041e2bea130b5c7c76c34566
size: 4864
plot-subsite@2021-clb-oropharynx:
cmd: "python scripts/subsite.py --data 2021-clb-oropharynx/data.csv\n"
deps:
- path: 2021-clb-oropharynx/data.csv
hash: md5
md5: af05aeaa3fea122dd718b3dd9c6a22b1
size: 92744
- path: scripts/subsite.py
hash: md5
md5: 417c5dfd041e2bea130b5c7c76c34566
size: 4864
plot-subsite@2023-clb-multisite:
cmd: "python scripts/subsite.py --data 2023-clb-multisite/data.csv\n"
deps:
- path: 2023-clb-multisite/data.csv
hash: md5
md5: 0ee586c452452c781e8b6c22b5e5ef71
size: 111721
- path: scripts/subsite.py
hash: md5
md5: 417c5dfd041e2bea130b5c7c76c34566
size: 4864
plot-subsite@2023-isb-multisite:
cmd: "python scripts/subsite.py --data 2023-isb-multisite/data.csv\n"
deps:
- path: 2023-isb-multisite/data.csv
hash: md5
md5: 24c25eedd6a832e595b12bd6b822a25c
size: 204462
- path: scripts/subsite.py
hash: md5
md5: 417c5dfd041e2bea130b5c7c76c34566
size: 4864
plot-subsite@2025-hvh-oropharynx:
cmd: "python scripts/subsite.py --data 2025-hvh-oropharynx/data.csv\n"
deps:
- path: 2025-hvh-oropharynx/data.csv
hash: md5
md5: 9dcad2ce5cacd103090c3abe9ce1920a
size: 82567
- path: scripts/subsite.py
hash: md5
md5: 417c5dfd041e2bea130b5c7c76c34566
size: 4864
bar-plot@2021-clb-oropharynx:
cmd: python scripts/bar_plot.py 2021-clb-oropharynx/data.csv
deps:
- path: 2021-clb-oropharynx/data.csv
hash: md5
md5: af05aeaa3fea122dd718b3dd9c6a22b1
size: 92744
- path: scripts/bar_plot.py
hash: md5
md5: 16bb00580dbb46db7f52f6f9a3f59276
size: 2628
bar-plot@2023-clb-multisite:
cmd: python scripts/bar_plot.py 2023-clb-multisite/data.csv
deps:
- path: 2023-clb-multisite/data.csv
hash: md5
md5: 0ee586c452452c781e8b6c22b5e5ef71
size: 111721
- path: scripts/bar_plot.py
hash: md5
md5: 16bb00580dbb46db7f52f6f9a3f59276
size: 2628
bar-plot@2023-isb-multisite:
cmd: python scripts/bar_plot.py 2023-isb-multisite/data.csv
deps:
- path: 2023-isb-multisite/data.csv
hash: md5
md5: 24c25eedd6a832e595b12bd6b822a25c
size: 204462
- path: scripts/bar_plot.py
hash: md5
md5: 16bb00580dbb46db7f52f6f9a3f59276
size: 2628
factors-diff@2021-usz-oropharynx-2025-hvh-oropharynx:
cmd: "python scripts/factors_diff.py --first-dataset 2021-usz-oropharynx --second-dataset
2025-hvh-oropharynx --commit ee15c4cabdd160a10783fcf85ffe1cbfeb5c4826 --repo
rmnldwg/lydata.private\n"
deps:
- path: 2021-usz-oropharynx/data.csv
hash: md5
md5: a9e4043ed6a273c609fa16523bcae455
size: 166966
- path: 2025-hvh-oropharynx/data.csv
hash: md5
md5: 9dcad2ce5cacd103090c3abe9ce1920a
size: 82567
- path: scripts/factors_diff.py
hash: md5
md5: 182812f0fe01deba4fd1669153b88ae7
size: 3775