Generic hierarchy (#281)

* generic hierarchy method

* deduplicate

* action version

* upload-artifact-v3

.github/workflows/ci.yml

@@ -48,7 +48,7 @@ jobs:
         papermill doc/source/user_guide/AsynchronousAPI.ipynb doc/source/user_guide/AsynchronousAPI-output.ipynb
         jupyter nbconvert --to html doc/source/user_guide/AsynchronousAPI-output.ipynb
         
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v3
       with:
         name: AsynchronousAPI-output.html
         path: doc/source/user_guide/AsynchronousAPI-output.html

oda_api/ontology_helper.py

@@ -202,7 +202,7 @@ def parse_limits_annotations(self, graph, infer_datatype = True):
             graph.add((classuri, RDFS.subClassOf, bn))
 
     def _get_datatype_restriction(self, param_uri):
-        param_uri = f"<{param_uri}>" if param_uri.startswith("http") else param_uri
+        param_uri = self._normalize_uri(param_uri)
         query = """
             SELECT ?dt WHERE {
                 {
@@ -242,31 +242,37 @@ def parse_extra_triples(self, extra_triples, format='n3', parse_oda_annotations
             extra_triples = tmpg.serialize(format=format)
         self.g.parse(data = extra_triples, format = format)
 
-        
-    def get_parameter_hierarchy(self, param_uri):
-        param_uri_m = f"<{param_uri}>" if param_uri.startswith("http") else param_uri
+    def get_uri_hierarchy(self, uri, base_uri):
+        uri_m = self._normalize_uri(uri)
+        base_uri_m = self._normalize_uri(base_uri)
         query = """
         select ?mid ( count(?mid2) as ?midcount ) where { 
         %s  (rdfs:subClassOf|a)* ?mid . 
         
         ?mid rdfs:subClassOf* ?mid2 .
-        ?mid2 rdfs:subClassOf* oda:WorkflowParameter .
+        ?mid2 rdfs:subClassOf* %s .
         }
         group by ?mid
         order by desc(?midcount)
-        """ % ( param_uri_m )
+        """ % ( uri_m, base_uri_m )
 
         qres = self.g.query(query)
 
         hierarchy = [str(row[0]) for row in qres]
         if len(hierarchy) > 0:
             return hierarchy  
         else:
-            logger.warning("%s is not in ontology or not an oda:WorkflowParameter", param_uri)
-            return [ param_uri ]
-
+            logger.warning("%s is not in ontology or not an %s", uri, base_uri)
+            return [ uri ]
+
+    def get_parameter_hierarchy(self, param_uri):
+        return self.get_uri_hierarchy(param_uri, base_uri='oda:WorkflowParameter')
+
+    def get_product_hierarchy(self, prod_uri):
+        return self.get_uri_hierarchy(prod_uri, base_uri='oda:DataProduct')
+
     def get_parameter_format(self, param_uri, return_uri = False):
-        if param_uri.startswith("http"): param_uri = f"<{param_uri}>"
+        param_uri = self._normalize_uri(param_uri)
 
         query = """ SELECT ?format_uri WHERE { 
             %s (rdfs:subClassOf|a)* [
@@ -290,7 +296,7 @@ def get_parameter_format(self, param_uri, return_uri = False):
         return uri
 
     def get_parameter_unit(self, param_uri, return_uri = False):
-        if param_uri.startswith("http"): param_uri = f"<{param_uri}>"
+        param_uri = self._normalize_uri(param_uri)
 
         query = """SELECT ?unit_uri WHERE {
         %s (rdfs:subClassOf|a)* [
@@ -314,7 +320,7 @@ def get_parameter_unit(self, param_uri, return_uri = False):
         return uri
 
     def get_limits(self, param_uri):
-        if param_uri.startswith("http"): param_uri = f"<{param_uri}>"
+        param_uri = self._normalize_uri(param_uri)
 
         query = """  
             SELECT ?lim WHERE {
@@ -346,7 +352,7 @@ def get_limits(self, param_uri):
         return (ll, ul)
 
     def get_allowed_values(self, param_uri):
-        if param_uri.startswith("http"): param_uri = f"<{param_uri}>"
+        param_uri = self._normalize_uri(param_uri)
 
         query = """ SELECT ?item (count(?list) as ?midcount) WHERE {    
             
@@ -392,7 +398,7 @@ def get_oda_label(self, param_uri):
         return self.get_direct_annotation(param_uri, "label")
 
     def get_direct_annotation(self, param_uri, metadata, predicate="oda"):
-        if param_uri.startswith("http"): param_uri = f"<{param_uri}>"
+        param_uri = self._normalize_uri(param_uri)
 
         query = f"SELECT ?{metadata} WHERE {{{param_uri} {predicate}:{metadata} ?{metadata}}}"
 
@@ -405,7 +411,7 @@ def get_direct_annotation(self, param_uri, metadata, predicate="oda"):
         return metadata_value
 
     def is_data_product(self, owl_uri, include_parameter_products=True):
-        if owl_uri.startswith("http"): owl_uri = f"<{owl_uri}>"
+        owl_uri = self._normalize_uri(owl_uri)
 
         filt_param = 'MINUS{?cl rdfs:subClassOf* oda:ParameterProduct. }' if not include_parameter_products else ''
         query = """
@@ -464,6 +470,10 @@ def resources():
             yield dict(resource=str(resource).split('#')[-1], required=required, env_vars=env_vars)
 
     def is_optional(self, uri: str) -> bool:
-        if uri.startswith("http"): uri = f"<{uri}>"
+        uri = self._normalize_uri(uri)
         s_qres = self.g.query("ASK {%s rdfs:subClassOf? oda:optional .}" % uri )
         return cast(bool, list(s_qres)[0])
+
+    @staticmethod
+    def _normalize_uri(uri):
+        return f"<{uri}>" if uri.startswith("http") else uri