Merge pull request #145 from BlueBrain/fix-ion-current

allow non-specific currents not starting with 'i'

bluepyemodel/access_point/access_point.py

@@ -284,9 +284,10 @@ def get_ion_currents_concentrations(self):
         mechs = self.get_available_mechanisms()
         if mechs is None:
             return None, None
-        ion_currents = list(chain.from_iterable([mech.get_current() for mech in mechs]))
+        # use list(set(...)) to only keep unique occurences
+        ion_currents = list(set(chain.from_iterable([mech.get_current() for mech in mechs])))
         ionic_concentrations = list(
-            chain.from_iterable([mech.ionic_concentrations for mech in mechs])
+            set(chain.from_iterable([mech.ionic_concentrations for mech in mechs]))
         )
         # append i_pas which is present by default
         ion_currents.append("i_pas")

bluepyemodel/access_point/forge_access_point.py

@@ -411,24 +411,27 @@ def retrieve(self, id_):
 
         return None
 
-    def fetch(self, filters):
+    def fetch(self, filters, cross_bucket=None):
         """Fetch resources based on filters.
 
         Args:
             filters (dict): keys and values used for the "WHERE". Should include "type" or "id".
+            cross_bucket (bool): whether to also fetch from other projects or not.
 
         Returns:
             resources (list): list of resources
         """
-
         if "type" not in filters and "id" not in filters:
             raise AccessPointException("Search filters should contain either 'type' or 'id'.")
 
+        if cross_bucket is None:
+            cross_bucket = self.cross_bucket
+
         logger.debug("Searching: %s", filters)
 
         resources = self.forge.search(
             filters,
-            cross_bucket=self.cross_bucket,
+            cross_bucket=cross_bucket,
             limit=self.limit,
             debug=self.debug,
             search_endpoint=self.search_endpoint,

bluepyemodel/access_point/nexus.py

@@ -1067,8 +1067,9 @@ def get_available_mechanisms(self, filters=None):
         filter = {"type": "SubCellularModelScript"}
         if filters:
             filter.update(filters)
-        resources = self.access_point.fetch(filter)
-
+        # do not look in other projects for these resources,
+        # because resources have 'full' metadata only in a few projects.
+        resources = self.access_point.fetch(filter, cross_bucket=False)
         if resources is None:
             logger.warning("No SubCellularModelScript mechanisms available")
             return None
@@ -1086,6 +1087,9 @@ def get_available_mechanisms(self, filters=None):
             stochastic = r.stochastic if hasattr(r, "stochastic") else None
 
             parameters = {}
+            ion_currents = []
+            non_specific_currents = []
+            ionic_concentrations = []
             if hasattr(r, "exposesParameter"):
                 exposes_parameters = r.exposesParameter
                 if not isinstance(exposes_parameters, list):
@@ -1094,33 +1098,26 @@ def get_available_mechanisms(self, filters=None):
                     if ep.type == "ConductanceDensity":
                         lower_limit = ep.lowerLimit if hasattr(ep, "lowerLimit") else None
                         upper_limit = ep.upperLimit if hasattr(ep, "upperLimit") else None
-                        if hasattr(r, "mod"):
-                            parameters[f"{ep.name}_{r.mod.suffix}"] = [
-                                lower_limit,
-                                upper_limit,
-                            ]
+                        # resource name is the mech SUFFIX
+                        parameters[f"{ep.name}_{r.name}"] = [lower_limit, upper_limit]
+                    elif ep.type == "CurrentDensity":
+                        if not hasattr(ep, "ionName"):
+                            logger.warning(
+                                "Will not add %s current, "
+                                "because 'ionName' field was not found in %s.",
+                                ep.name,
+                                r.name,
+                            )
+                        elif ep.ionName == "non-specific":
+                            non_specific_currents.append(ep.name)
                         else:
-                            parameters[f"{ep.name}_{r.nmodlParameters.suffix}"] = [
-                                lower_limit,
-                                upper_limit,
-                            ]
+                            ion_currents.append(ep.name)
+                            ionic_concentrations.append(f"{ep.ionName}i")
+                    elif ep.type == "IonConcentration":
+                        ionic_concentrations.append(ep.name)
 
-            ion_currents = []
-            ionic_concentrations = []
-            # technically, also adds non-specific currents to ion_currents list,
-            # because they are not distinguished in nexus for now, but
-            # the code should work nevertheless
-            ions = []
-            if hasattr(r, "mod") and hasattr(r.mod, "ion"):
-                ions = r.mod.ion if isinstance(r.mod.ion, list) else [r.mod.ion]
-            elif hasattr(r, "ion"):
-                ions = r.ion if isinstance(r.ion, list) else [r.ion]
-
-            for ion in ions:
-                if hasattr(ion, "label"):
-                    ion_name = ion.label.lower()
-                    ion_currents.append(f"i{ion_name}")
-                    ionic_concentrations.append(f"{ion_name}i")
+            # remove duplicates
+            ionic_concentrations = list(set(ionic_concentrations))
 
             mech = MechanismConfiguration(
                 r.name,

bluepyemodel/emodel_pipeline/plotting.py

@@ -1495,12 +1495,13 @@ def get_ordered_currentscape_keys(keys):
 
             if curr_name == "v":
                 ordered_keys[prot_name][loc_name]["voltage_key"] = name
-            elif curr_name[0] == "i":
-                ordered_keys[prot_name][loc_name]["current_keys"].append(name)
-                ordered_keys[prot_name][loc_name]["current_names"].append(curr_name)
             elif curr_name[-1] == "i":
                 ordered_keys[prot_name][loc_name]["ion_conc_keys"].append(name)
                 ordered_keys[prot_name][loc_name]["ion_conc_names"].append(curr_name)
+            # assumes we don't have any extra-cellular concentrations (that ends with 'o')
+            else:
+                ordered_keys[prot_name][loc_name]["current_keys"].append(name)
+                ordered_keys[prot_name][loc_name]["current_names"].append(curr_name)
 
     return ordered_keys
 

bluepyemodel/evaluation/evaluator.py

@@ -1020,7 +1020,7 @@ def add_recordings_to_evaluator(cell_evaluator, vars, use_fixed_dt_recordings=Fa
     """Add a recording for each new variable for each protocol in cell evaluator."""
     # add recording for each protocol x new variable combination
     for prot in cell_evaluator.fitness_protocols["main_protocol"].protocols.values():
-        if prot.name not in PRE_PROTOCOLS:
+        if prot.name == "SearchThresholdCurrent" or prot.name not in PRE_PROTOCOLS:
             base_rec = prot.recordings[0]
             for var in vars:
                 location = base_rec.location

bluepyemodel/tools/mechanisms.py

@@ -129,8 +129,10 @@ def get_mechanism_currents(mech_file):
                 ionic_concentrations.append(ion_var_name)
         elif "NONSPECIFIC_CURRENT" in line:
             var_name = line.split("NONSPECIFIC_CURRENT ")[1].rstrip("\n").split(" ")[0]
-            if var_name[0] == "i":
-                nonspecific_currents.append(var_name)
+            # here, we do not check if first letter is i, because
+            # NONSPECIFIC_CURRENT should indicate a current,
+            # and some special current do no start with i, e.g. 'lk'
+            nonspecific_currents.append(var_name)
 
     return ion_currs, nonspecific_currents, ionic_concentrations