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Merged
rdhyee merged 5 commits into from
Dec 11, 2025
Merged

Fix broken vocabulary links by restoring generation from TTL sources #46

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c8007d2
Initial plan
Copilot Dec 11, 2025
be529c8
Fix vocabulary generation script to use Python instead of vocab command
Copilot Dec 11, 2025
e74522a
Update vocabulary links in models/index.qmd to point to generated files
Copilot Dec 11, 2025
5794976
Fix vocabulary links to point to .html files instead of .qmd sources
Copilot Dec 11, 2025
27701f7
Remove generated files from git, update .gitignore, and clean up script
Copilot Dec 11, 2025
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7 changes: 7 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,13 @@ uv.lock
plantuml-images
docs

# Generated vocabulary documentation (but keep readme.md files)
models/generated/vocabularies/*.qmd
models/generated/vocabularies/*.md
!models/generated/vocabularies/readme.md
models/generated/extensions/*.md
!models/generated/extensions/readme.md

# Large data files
*.parquet

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2 changes: 1 addition & 1 deletion models/generated/extensions/readme.md
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@@ -1 +1 @@
this folder contains markdown output for extension vocabularies
this folder contains markdown output for extension vocabularies
6 changes: 3 additions & 3 deletions models/index.qmd
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Expand Up @@ -37,10 +37,10 @@ The iSamples taxonomies are used to characterize three fundamental concepts pert

Three taxonomies are currently defined :

[Material Sample (specimen) Type Vocabulary](https://isamplesorg.github.io/metadata/vocabularies/specimentype.html)
[Material Sample (specimen) Type Vocabulary](generated/vocabularies/material_sample_object_type.html)

[Materials Vocabulary](https://isamplesorg.github.io/metadata/vocabularies/materialtype.html)
[Materials Vocabulary](generated/vocabularies/material_type.html)

[Sampled Feature (context) Type vocabulary](https://isamplesorg.github.io/metadata/vocabularies/sampledfeature.html)
[Sampled Feature (context) Type vocabulary](generated/vocabularies/sampled_feature_type.html)


13 changes: 4 additions & 9 deletions scripts/generate_vocab_docs.sh
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Expand Up @@ -6,7 +6,6 @@

# get the core sample type vocabularies
SCRIPT_FOLDER="$(dirname ${0})"
#SOURCE_BASE="https://raw.githubusercontent.com/isamplesorg/metadata/develop/src/vocabularies/"

SOURCE_BASE="https://raw.githubusercontent.com/isamplesorg/vocabularies/main/vocabulary/"

Expand All @@ -16,8 +15,7 @@ mkdir -p "${DEST_FOLDER}"
for src in ${SOURCES[@]}; do
fname="${src%%.*}.qmd"
echo "Generating ${fname}..."
# python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
done

#
Expand All @@ -35,8 +33,7 @@ mkdir -p "${DEST_FOLDER}"
for src in ${SOURCES[@]}; do
fname="${src%%.*}.md"
echo "Generating ${fname}..."
# python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
done

SOURCE_BASE="https://raw.githubusercontent.com/isamplesorg/metadata_profile_archaeology/main/vocabulary/"
Expand All @@ -46,8 +43,7 @@ mkdir -p "${DEST_FOLDER}"
for src in ${SOURCES[@]}; do
fname="${src%%.*}.md"
echo "Generating ${fname}..."
# python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
done

SOURCE_BASE="https://raw.githubusercontent.com/isamplesorg/metadata_profile_biology/main/vocabulary/"
Expand All @@ -57,8 +53,7 @@ mkdir -p "${DEST_FOLDER}"
for src in ${SOURCES[@]}; do
fname="${src%%.*}.md"
echo "Generating ${fname}..."
# python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
vocab markdown "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
python "${SCRIPT_FOLDER}/vocab2md.py" "${SOURCE_BASE}${src}" > "${DEST_FOLDER}${fname}"
done

echo "Done."