Merge pull request #6 from luis-gonzalez-m/main

Clean objects and properties and German synonyms added.

.github/workflows/qc.yml

@@ -0,0 +1,33 @@
+# Basic ODK workflow
+
+name: CI
+
+# Controls when the action will run. 
+on:
+  # Triggers the workflow on push or pull request events but only for the main 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:
+  # This workflow contains a single job called "ontology_qc"
+  ontology_qc:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.2.29
+
+    # 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@v2
+
+      - name: Run ontology QC checks
+        env:
+          DEFAULT_BRANCH: main
+        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false
+

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for lepao
 # Generated using ontology-development-kit
-# ODK Version: v1.2.28
+# ODK Version: v1.2.29
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use lepao.Makefile instead
 
@@ -35,7 +35,7 @@ REPORT_PROFILE_OPTS =
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =   equivalent-classes owldef-self-reference
 SPARQL_EXPORTS =             basic-report class-count-by-prefix edges xrefs obsoletes synonyms
-ODK_VERSION_MAKEFILE =      v1.2.28
+ODK_VERSION_MAKEFILE =      v1.2.29
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -104,8 +104,7 @@ all_imports: $(IMPORT_FILES)
 SUBSETS = 
 
 SUBSET_ROOTS = $(patsubst %, subsets/%, $(SUBSETS))
-SUBSET_FORMATS = $(sort tsv owl)
-SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(foreach f,$(SUBSET_FORMATS), $(n).$(f)))
+SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(foreach f,$(FORMATS_INCL_TSV), $(n).$(f)))
 
 .PHONY: all_subsets
 all_subsets: $(SUBSET_FILES)
@@ -260,10 +259,15 @@ subsets/%.tsv: subsets/%.owl
 .PRECIOUS: subsets/%.tsv
 
 subsets/%.owl: $(ONT).owl
-	owltools --use-catalog $< --extract-ontology-subset --fill-gaps --subset $* -o $@.tmp.owl && mv $@.tmp.owl $@
+	owltools --use-catalog $< --extract-ontology-subset --fill-gaps --subset $* -o $@.tmp.owl && mv $@.tmp.owl $@ &&\
+	$(ROBOT) annotate --input $@ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@.tmp.owl && mv $@.tmp.owl $@
 .PRECIOUS: subsets/%.owl
 
 
+subsets/%.obo: subsets/%.owl
+	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
+
+
 # ----------------------------------------
 # Release
 # ----------------------------------------
@@ -330,6 +334,7 @@ $(ONT).obo: $(ONT).owl
 # -----------------------------------------------------
 # Release artefacts: variants (base, full, simple, etc)
 # -----------------------------------------------------
+SHARED_ROBOT_COMMANDS = 
 
 $(ONTOLOGYTERMS): $(SRC) $(OTHER_SRC)
 	touch $(ONTOLOGYTERMS) && \
@@ -346,7 +351,7 @@ $(ONTOLOGYTERMS): $(SRC) $(OTHER_SRC)
 $(ONT)-base.owl: $(SRC) $(OTHER_SRC)
 	$(ROBOT) remove --input $< --select imports --trim false \
 		merge $(patsubst %, -i %, $(OTHER_SRC)) \
-		annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \
+		 $(SHARED_ROBOT_COMMANDS) annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \
 		--ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
 		--output $@.tmp.owl && mv $@.tmp.owl $@
 
@@ -356,7 +361,7 @@ $(ONT)-full.owl: $(SRC) $(OTHER_SRC)
 		reason --reasoner ELK --equivalent-classes-allowed all --exclude-tautologies structural \
 		relax \
 		reduce -r ELK \
-		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@
+		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@