Add qc

.github/workflows/qc.yml

@@ -0,0 +1,34 @@
+# Basic ODK workflow
+
+name: QC
+
+# Controls when the action will run. 
+on:
+  # Triggers the workflow on push or pull request events but only for the master branch
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  qc:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.5.4
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: make install
+      - name: Run ontology QC checks
+        env:
+          DEFAULT_BRANCH: main
+        run: make qc
+

.gitignore

@@ -3,3 +3,4 @@
 all_translations.zip
 crowdin_data/
 /site
+tmp/

Makefile

@@ -1,12 +1,16 @@
-##### Process translations
+BABELON_FILES := $(wildcard babelon/hp-*.babelon.tsv)
 
-install:
-	pip install -U babelon
+# Extract the variable part (e.g., pt)
+TRANSLATIONS := $(patsubst babelon/hp-%.babelon.tsv, %, $(BABELON_FILES))
 
+list-translations:
+	@echo $(TRANSLATIONS)
+
+##### Process translations
 
 sort-%: babelon/hp-%.babelon.tsv babelon/hp-%.synonyms.tsv
 	mkdir -p tmp
-	{ head -n 1 babelon/hp-$*.synonyms.tsv && tail -n +2 babelon/hp-$*.synonyms.tsv | sort; } > tmp/$*_synonyms_sorted.tsv
+	{ head -n 2 babelon/hp-$*.synonyms.tsv && tail -n +3 babelon/hp-$*.synonyms.tsv | sort; } > tmp/$*_synonyms_sorted.tsv
 	{ head -n 1 babelon/hp-$*.babelon.tsv && tail -n +2 babelon/hp-$*.babelon.tsv | sort; } > tmp/$*_babelon_sorted.tsv
 	mv tmp/$*_babelon_sorted.tsv babelon/hp-$*.babelon.tsv
 	mv tmp/$*_synonyms_sorted.tsv babelon/hp-$*.synonyms.tsv
@@ -22,8 +26,32 @@ sort-all:
 	$(MAKE) sort-pt sort-de sort-fr sort-pt sort-zh
 
 validate-%: babelon/hp-%.babelon.tsv babelon/hp-%.synonyms.tsv
-	tsvalid babelon/hp-$*.babelon.tsv --skip "W1"
-	tsvalid babelon/hp-$*.synonyms.tsv --skip "W1"
+	@output=$$(tsvalid babelon/hp-$*.synonyms.tsv --skip "W1"); \
+	if echo "$$output" | grep -Eq 'E[0-9]+:[ ]'; then \
+		echo "Error detected in hp-$*.synonyms.tsv: $$output"; \
+		exit 1; \
+	fi
+	@output=$$(tsvalid babelon/hp-$*.babelon.tsv --skip "W1"); \
+	if echo "$$output" | grep -Eq 'E[0-9]+:[ ]'; then \
+		echo "Error detected in hp-$*.babelon.tsv: $$output"; \
+		exit 1; \
+	fi
+	babelon convert babelon/hp-$*.babelon.tsv --output-format owl -o tmp/$*-babelon.owl
+	robot template --template babelon/hp-$*.synonyms.tsv --output tmp/$*-synonyms.owl
+
+validate-all:
+	$(MAKE) $(foreach lang, $(TRANSLATIONS), validate-$(lang))
+
+qc: validate-all
+	@echo "All translations are valid"
+
+update: babelon/hp-ja.babelon.tsv
+	$(MAKE) sort-all
+	$(MAKE) clean-all
+	$(MAKE) validate-all
+
+install:
+	pip install -U babelon==0.3.4 --break-system-packages
 
 ###
 prepare_data:
@@ -34,6 +62,9 @@ babelon/hp-%.babelon.tsv:
 	mkdir -p babelon/
 	babelon parse crowdin_data/$*/hpo_notes.xliff -o $@
 
+babelon/hp-ja.babelon.tsv:
+	wget "https://raw.githubusercontent.com/ogishima/HPO-Japanese/master/HPO-japanese.alpha.21Jul2023.tsv" -O $@
+
 LANGUAGES=cs nl tr
 HP_TRANSLATIONS=$(patsubst %, babelon/hp-%.babelon.tsv, $(LANGUAGES))
 

babelon/hp-ar.synonyms.tsv

@@ -1,2 +1,2 @@
 subject_id	translation_value	comment
-ID	AL oboInOwl:hasExactSynonym@ar	
+ID	AL oboInOwl:hasExactSynonym@ar