extract OntologyURI to fix circular imports

cmat/trait_mapping/ols.py

@@ -7,7 +7,7 @@
 
 from retry import retry
 
-from cmat.trait_mapping.oxo import OntologyUri
+from cmat.trait_mapping.ontology_uri import OntologyUri
 from cmat.trait_mapping.utils import json_request, ServerError
 
 OLS_SERVER = 'https://www.ebi.ac.uk/ols4'

cmat/trait_mapping/ontology_uri.py

@@ -0,0 +1,20 @@
+
+class OntologyUri:
+    db_to_uri_dict = {
+        "orphanet": "http://www.orpha.net/ORDO/Orphanet_{}",
+        "omim": "http://identifiers.org/omim/{}",
+        "efo": "http://www.ebi.ac.uk/efo/EFO_{}",
+        "mesh": "http://identifiers.org/mesh/{}",
+        "medgen": "http://identifiers.org/medgen/{}",
+        "hp": "http://purl.obolibrary.org/obo/HP_{}",
+        "doid": "http://purl.obolibrary.org/obo/DOID_{}",
+        "mondo": "http://purl.obolibrary.org/obo/MONDO_{}",
+    }
+
+    def __init__(self, id_, db):
+        self.id_ = id_
+        self.db = db
+        self.uri = self.db_to_uri_dict[self.db.lower()].format(self.id_)
+
+    def __str__(self):
+        return self.uri

cmat/trait_mapping/oxo.py

@@ -5,33 +5,13 @@
 
 from cmat.trait_mapping.ols import get_ontology_label_from_ols, is_in_ontology
 from cmat.trait_mapping.ols import is_current_and_in_ontology
+from cmat.trait_mapping.ontology_uri import OntologyUri
 from cmat.trait_mapping.utils import json_request
 
 
 logger = logging.getLogger(__package__)
 
 
-class OntologyUri:
-    db_to_uri_dict = {
-        "orphanet": "http://www.orpha.net/ORDO/Orphanet_{}",
-        "omim": "http://identifiers.org/omim/{}",
-        "efo": "http://www.ebi.ac.uk/efo/EFO_{}",
-        "mesh": "http://identifiers.org/mesh/{}",
-        "medgen": "http://identifiers.org/medgen/{}",
-        "hp": "http://purl.obolibrary.org/obo/HP_{}",
-        "doid": "http://purl.obolibrary.org/obo/DOID_{}",
-        "mondo": "http://purl.obolibrary.org/obo/MONDO_{}",
-    }
-
-    def __init__(self, id_, db):
-        self.id_ = id_
-        self.db = db
-        self.uri = self.db_to_uri_dict[self.db.lower()].format(self.id_)
-
-    def __str__(self):
-        return self.uri
-
-
 @total_ordering
 class OxOMapping:
     """