Merge pull request #152 from BlueBrain/fix-endpoint

do not have endpoint hard-coded for ontology stuff

bluepyemodel/access_point/forge_access_point.py

@@ -895,14 +895,16 @@ def filter_resources(self, resources, filter):
         )
 
 
-def ontology_forge_access_point(access_token=None, forge_path=None):
+def ontology_forge_access_point(
+    access_token=None, forge_path=None, endpoint="https://bbp.epfl.ch/nexus/v1"
+):
     """Returns an access point targeting the project containing the ontology for the
     species and brain regions"""
 
     access_point = NexusForgeAccessPoint(
         project="datamodels",
         organisation="neurosciencegraph",
-        endpoint="https://bbp.epfl.ch/nexus/v1",
+        endpoint=endpoint,
         forge_path=forge_path,
         access_token=access_token,
     )
@@ -955,21 +957,29 @@ def raise_not_found_exception(base_text, label, access_point, filter, limit=30):
     raise AccessPointException(base_text)
 
 
-def check_resource(label, category, access_point=None, access_token=None, forge_path=None):
+def check_resource(
+    label,
+    category,
+    access_point=None,
+    access_token=None,
+    forge_path=None,
+    endpoint="https://bbp.epfl.ch/nexus/v1",
+):
     """Checks that resource is present on nexus and is part of the provided category
 
     Arguments:
         label (str): name of the resource to search for
         category (str): can be "etype", "mtype" or "ttype"
         access_point (str):  ontology_forge_access_point(access_token)
         forge_path (str): path to a .yml used as configuration by nexus-forge.
+        endpoint (str): nexus endpoint
     """
     allowed_categories = ["etype", "mtype", "ttype"]
     if category not in allowed_categories:
         raise AccessPointException(f"Category is {category}, but should be in {allowed_categories}")
 
     if access_point is None:
-        access_point = ontology_forge_access_point(access_token, forge_path)
+        access_point = ontology_forge_access_point(access_token, forge_path, endpoint)
 
     resource = access_point.resolve(label, strategy="exact")
     # raise Exception if resource was not found
@@ -1017,7 +1027,9 @@ def get_available_traces(species=None, brain_region=None, access_token=None, for
     return resources
 
 
-def get_brain_region(brain_region, access_token=None, forge_path=None):
+def get_brain_region(
+    brain_region, access_token=None, forge_path=None, endpoint="https://bbp.epfl.ch/nexus/v1"
+):
     """Returns the resource corresponding to the brain region
 
     If the brain region name is not present in nexus,
@@ -1027,10 +1039,11 @@ def get_brain_region(brain_region, access_token=None, forge_path=None):
         brain_region (str): name of the brain region to search for
         access_token (str): nexus connection token
         forge_path (str): path to a .yml used as configuration by nexus-forge.
+        endpoint (str): nexus endpoint
     """
 
     filter = "brain_region"
-    access_point = ontology_forge_access_point(access_token, forge_path)
+    access_point = ontology_forge_access_point(access_token, forge_path, endpoint)
 
     if brain_region in ["SSCX", "sscx"]:
         brain_region = "somatosensory areas"
@@ -1062,20 +1075,23 @@ def get_brain_region(brain_region, access_token=None, forge_path=None):
     return resource
 
 
-def get_brain_region_dict(brain_region, access_token=None, forge_path=None):
+def get_brain_region_dict(
+    brain_region, access_token=None, forge_path=None, endpoint="https://bbp.epfl.ch/nexus/v1"
+):
     """Returns a dict with id and label of the resource corresponding to the brain region
 
     Arguments:
         brain_region (str): name of the brain region to search for
         access_token (str): nexus connection token
         forge_path (str): path to a .yml used as configuration by nexus-forge.
+        endpoint (str): nexus endpoint
 
     Returns:
         dict: the id and label of the nexus resource of the brain region
     """
-    br_resource = get_brain_region(brain_region, access_token, forge_path)
+    br_resource = get_brain_region(brain_region, access_token, forge_path, endpoint)
 
-    access_point = ontology_forge_access_point(access_token, forge_path)
+    access_point = ontology_forge_access_point(access_token, forge_path, endpoint)
 
     # if no exception was raised, filter to get id and label and return them
     brain_region_dict = access_point.forge.as_json(br_resource)
@@ -1085,25 +1101,29 @@ def get_brain_region_dict(brain_region, access_token=None, forge_path=None):
     }
 
 
-def get_brain_region_notation(brain_region, access_token=None, forge_path=None):
+def get_brain_region_notation(
+    brain_region, access_token=None, forge_path=None, endpoint="https://bbp.epfl.ch/nexus/v1"
+):
     """Get the ontology of the brain location."""
     if brain_region is None:
         return None
 
     brain_region_resource = get_brain_region(
-        brain_region, access_token=access_token, forge_path=forge_path
+        brain_region, access_token=access_token, forge_path=forge_path, endpoint=endpoint
     )
 
     return brain_region_resource.notation
 
 
-def get_nexus_brain_region(brain_region, access_token=None, forge_path=None):
+def get_nexus_brain_region(
+    brain_region, access_token=None, forge_path=None, endpoint="https://bbp.epfl.ch/nexus/v1"
+):
     """Get the ontology of the brain location."""
     if brain_region is None:
         return None
 
     brain_region_from_nexus = get_brain_region_dict(
-        brain_region, access_token=access_token, forge_path=forge_path
+        brain_region, access_token=access_token, forge_path=forge_path, endpoint=endpoint
     )
 
     return {
@@ -1112,8 +1132,8 @@ def get_nexus_brain_region(brain_region, access_token=None, forge_path=None):
     }
 
 
-def get_all_species(access_token=None, forge_path=None):
-    access_point = ontology_forge_access_point(access_token, forge_path)
+def get_all_species(access_token=None, forge_path=None, endpoint="https://bbp.epfl.ch/nexus/v1"):
+    access_point = ontology_forge_access_point(access_token, forge_path, endpoint)
 
     resources = access_point.forge.search({"subClassOf": "nsg:Species"}, limit=100)
 

bluepyemodel/access_point/nexus.py

@@ -129,6 +129,7 @@ def __init__(
             self.emodel_metadata.brain_region,
             self.access_point.access_token,
             self.forge_ontology_path,
+            self.access_point.endpoint,
         )
 
         self.pipeline_settings = self.get_pipeline_settings(strict=False)
@@ -145,7 +146,7 @@ def download_directory(self):
     def check_mettypes(self):
         """Check that etype, mtype and ttype are present on nexus"""
         ontology_access_point = ontology_forge_access_point(
-            self.access_point.access_token, self.forge_ontology_path
+            self.access_point.access_token, self.forge_ontology_path, self.access_point.endpoint
         )
 
         logger.info("Checking if etype %s is present on nexus...", self.emodel_metadata.etype)
@@ -155,6 +156,7 @@ def check_mettypes(self):
             access_point=ontology_access_point,
             access_token=self.access_point.access_token,
             forge_path=self.forge_ontology_path,
+            endpoint=self.access_point.endpoint,
         )
         logger.info("Etype checked")
 
@@ -169,6 +171,7 @@ def check_mettypes(self):
                 access_point=ontology_access_point,
                 access_token=self.access_point.access_token,
                 forge_path=self.forge_ontology_path,
+                endpoint=self.access_point.endpoint,
             )
             logger.info("Mtype checked")
         else:
@@ -185,6 +188,7 @@ def check_mettypes(self):
                 access_point=ontology_access_point,
                 access_token=self.access_point.access_token,
                 forge_path=self.forge_ontology_path,
+                endpoint=self.access_point.endpoint,
             )
             logger.info("Ttype checked")
         else:
@@ -228,6 +232,7 @@ def build_ontology_based_metadata(self):
             self.emodel_metadata.brain_region,
             self.access_point.access_token,
             self.forge_ontology_path,
+            self.access_point.endpoint,
         )
 
     def get_nexus_subject(self, species):
@@ -573,7 +578,7 @@ def store_model_configuration(self, configuration, path=None):
 
         # set id to mechanisms by filtering with brain region, temperature, species, ljp correction
         ontology_access_point = ontology_forge_access_point(
-            self.access_point.access_token, self.forge_ontology_path
+            self.access_point.access_token, self.forge_ontology_path, self.access_point.endpoint
         )
         for mechanism in configuration.mechanisms:
             if mechanism.name in NEURON_BUILTIN_MECHANISMS:
@@ -891,7 +896,7 @@ def download_mechanisms(self, mechanisms, any_downloaded=False):
 
         mechanisms_directory = self.get_mechanisms_directory()
         ontology_access_point = ontology_forge_access_point(
-            self.access_point.access_token, self.forge_ontology_path
+            self.access_point.access_token, self.forge_ontology_path, self.access_point.endpoint
         )
 
         for mechanism in mechanisms:

tests/unit_tests/test_nexus_access_point.py

@@ -159,15 +159,17 @@ def test_check_mettypes(mock_nexus_access_point, mock_available_etypes, mock_ava
 
     mock_ontology_forge.assert_called_once_with(
         mock_nexus_access_point.access_point.access_token,
-        mock_nexus_access_point.forge_ontology_path
+        mock_nexus_access_point.forge_ontology_path,
+        mock_nexus_access_point.access_point.endpoint,
     )
 
     mock_check_resource.assert_any_call(
         "cAC",
         "etype",
         access_point=mock_ontology_forge.return_value,
         access_token=mock_nexus_access_point.access_point.access_token,
-        forge_path=mock_nexus_access_point.forge_ontology_path
+        forge_path=mock_nexus_access_point.forge_ontology_path,
+        endpoint=mock_nexus_access_point.access_point.endpoint,
     )