OAK Validation workflow

odk/odk.py

@@ -369,6 +369,40 @@ class ReportConfig(JsonSchemaMixin):
     sparql_test_on: List[str] = field(default_factory=lambda: ['edit'])
     """Chose which file to run the custom sparql checks. Supported 'edit', any release artefact."""
 
+
+@dataclass_json
+@dataclass
+class OAKProfile(JsonSchemaMixin):
+    id: str
+    """profile identifier."""
+
+    filename: Optional[str] = None
+    """Filename of the profile. """
+
+    description: Optional[str] = None
+    """Description of the profile. """
+
+    mirror_from: Optional[str] = None
+    """URL where the profile is located and will be downloaded"""
+
+
+@dataclass_json
+@dataclass
+class OAKValidationConfig(JsonSchemaMixin):
+    """
+    A configuration section that consists of list of `OAKProfile` descriptions
+    Run reports into "reports/" directory
+    """
+
+    profiles: Optional[List[OAKProfile]] = None
+    """all OAK profiles"""
+
+    def _add_stub(self, filename: str):
+        if self.profiles is None:
+            self.profiles = []
+        self.profiles.append(OAKProfile(id=id))
+
+
 @dataclass_json
 @dataclass
 class DocumentationGroup(JsonSchemaMixin):
@@ -683,6 +717,9 @@ class OntologyProject(JsonSchemaMixin):
 
     release_diff : bool = False
     """When enabled, a diff is generated between the current release and the new one"""
+
+    oak_validation: Optional[OAKValidationConfig] = None
+    """Block that includes profiles to be used to validate the ontology"""
 
     def fill_missing(self):
         """

template/src/ontology/Makefile.jinja2

@@ -304,6 +304,30 @@ $(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR)
 $(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR)
 	$(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) {% if project.robot_report.use_base_iris %}{% if project.namespaces is not none %}{% for iri in project.namespaces %}--base-iri {{ iri }} {% endfor %}{% else %}--base-iri $(URIBASE)/{{ project.id.upper() }}_ --base-iri $(URIBASE)/{{ project.id }} {% endif %}{% endif -%} --print 5 -o $@
 
+{% if project. oak_validation %}
+# ----------------------------------------
+# OAK Validation
+# ----------------------------------------
+
+$(ONT)-simple.db: $(ONT)-simple.owl
+	semsql make $@
+	rm $(ONT)-simple-relation-graph.tsv.gz
+
+{% for profile in project.oak_validation.profiles %}
+$(TMPDIR)/{{ profile.id }}.yaml:
+	{% if profile.mirror_from %}wget {{ profile.mirror_from }} -O $@{% else %}cp {{ profile.filename }} $@
+{% endif %}
+
+$(REPORTDIR)/{{ profile.id }}.tsv: $(ONT)-simple.db $(TMPDIR)/{{ profile.id }}.yaml
+	runoak validate-multiple $< --schema $(TMPDIR)/{{ profile.id }}.yaml --output $@ --cutoff 5000
+	awk 'NR==1 {print} NR!=1 && $$2~/{{ project.id.upper() }}:/' $@ > [email protected] && mv [email protected] $@
+{% endfor%}
+
+.PHONY: oak_validation
+oak_validation: 
+	$(MAKE_FAST) {% for profile in project.oak_validation.profiles %} $(REPORTDIR)/{{ profile.id }}.tsv{% endfor %}
+{%- endif %}
+
 # ----------------------------------------
 # Release assets
 # ----------------------------------------