Merge pull request #224 from mcwdsi/omrse-qc-level

ODK update and stronger QC

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for omrse
 # Generated using ontology-development-kit
-# ODK Version: v1.4.1
+# ODK Version: v1.4.3
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use omrse.Makefile instead
 
@@ -43,13 +43,14 @@ SCRIPTSDIR=                 ../scripts
 UPDATEREPODIR=              target
 SPARQLDIR =                 ../sparql
 COMPONENTSDIR =             components
-REPORT_FAIL_ON =            None
-REPORT_LABEL =              -l true
-REPORT_PROFILE_OPTS =       
+ROBOT_PROFILE =             profile.txt
+REPORT_FAIL_ON =            ERROR
+REPORT_LABEL =              
+REPORT_PROFILE_OPTS =       --profile $(ROBOT_PROFILE)
 OBO_FORMAT_OPTIONS =        
-SPARQL_VALIDATION_CHECKS =  owldef-self-reference iri-range label-with-iri multiple-replaced_by 
+SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference iri-range 
 SPARQL_EXPORTS =            basic-report class-count-by-prefix edges xrefs obsoletes synonyms 
-ODK_VERSION_MAKEFILE =      v1.4.1
+ODK_VERSION_MAKEFILE =      v1.4.3
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -154,7 +155,7 @@ all_mappings: $(MAPPING_FILES)
 # QC Reports & Utilities
 # ----------------------------------------
 
-OBO_REPORT =  $(SRC)-obo-report
+OBO_REPORT =  omrse-base.owl-obo-report $(SRC)-obo-report
 REPORTS = $(OBO_REPORT)
 REPORT_FILES = $(patsubst %, $(REPORTDIR)/%.tsv, $(REPORTS))
 
@@ -186,10 +187,11 @@ validate_profile_%: $(REPORTDIR)/validate_profile_owl2dl_%.txt
 
 SPARQL_VALIDATION_QUERIES = $(foreach V,$(SPARQL_VALIDATION_CHECKS),$(SPARQLDIR)/$(V)-violation.sparql)
 
-sparql_test:  $(EDIT_PREPROCESSED) catalog-v001.xml | $(REPORTDIR)
+sparql_test:  omrse-base.owl catalog-v001.xml | $(REPORTDIR)
 ifneq ($(SPARQL_VALIDATION_QUERIES),)
 
-	$(ROBOT) verify  --catalog catalog-v001.xml -i $(EDIT_PREPROCESSED) --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR)
+
+	$(ROBOT) verify  --catalog catalog-v001.xml -i omrse-base.owl --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR)
 endif
 
 # ----------------------------------------

src/ontology/omrse-odk.yaml

@@ -62,6 +62,7 @@ import_group:
     #- filename: language/omrse-language.owl
     #- filename: omrse-core.owl
 #    - filename: import_terms.owl
+
 use_custom_import_module: TRUE
 robot_java_args: '-Xmx8G'
 custom_makefile_header: |
@@ -76,4 +77,18 @@ custom_makefile_header: |
   # 3. [Update repo to latest ODK](update_repo)
 create_obo_metadata: FALSE
 documentation:
-  documentation_system: mkdocs
+  documentation_system: mkdocs
+robot_report:
+  use_base_iris: True
+  fail_on : ERROR
+  use_labels : False
+  custom_profile : True
+  report_on :
+    - omrse-base.owl
+    - edit
+  sparql_test_on:
+    - omrse-base.owl
+  custom_sparql_checks :
+    - equivalent-classes
+    - owldef-self-reference
+    - iri-range

src/ontology/profile.txt

@@ -0,0 +1,25 @@
+WARN	annotation_whitespace
+ERROR	deprecated_boolean_datatype
+ERROR	deprecated_class_reference
+ERROR	deprecated_property_reference
+ERROR	duplicate_definition
+WARN	duplicate_exact_synonym
+WARN	duplicate_label_synonym
+ERROR	duplicate_label
+WARN	duplicate_scoped_synonym
+WARN	equivalent_pair
+WARN	invalid_xref
+ERROR	label_formatting
+ERROR	label_whitespace
+INFO	lowercase_definition
+WARN	missing_definition
+ERROR	missing_label
+WARN	missing_obsolete_label
+ERROR	missing_ontology_description
+ERROR	missing_ontology_license
+ERROR	missing_ontology_title
+INFO	missing_superclass
+ERROR	misused_obsolete_label
+ERROR	multiple_definitions
+ERROR	multiple_equivalent_classes
+ERROR	multiple_labels