Merge pull request #106 from BlueBrain/special-chars

add use_ProbAMPANMDA_EMS setting

bluepyemodel/emodel_pipeline/emodel_metadata.py

@@ -180,6 +180,9 @@ def as_string(self, seed=None, use_allen_notation=True):
         if seed not in [None, "None"]:
             s += f"seed={seed}__"
 
+        # can have ':' in mtype. Replace this character.
+        s = s.replace(":", "_")
+
         return s[:-2]
 
     def check_emodel_name(self):

bluepyemodel/emodel_pipeline/emodel_settings.py

@@ -61,6 +61,7 @@ def __init__(
         validation_function="max_score",
         validation_threshold=5.0,
         plot_optimisation=True,
+        use_ProbAMPANMDA_EMS=False,
         compile_mechanisms=False,
         n_model=3,
         optimisation_batch_size=5,
@@ -204,6 +205,8 @@ def __init__(
                 building task done. Only used by the Luigi workflow.
             plot_optimisation (bool): should the e-models scores and traces be plotted. Only used
                 by the Luigi workflow.
+            use_ProbAMPANMDA_EMS (bool): True to link ProbAMPANMDA_EMS in EMC on nexus,
+                and download ProbAMPANMDA from nexus along with other mechanisms.
             compile_mechanisms (bool): should the mod files be copied in the local
                 mechanisms_dir directory. Only used by the Luigi workflow.
             path_extract_config (str): specify the path to the .json file containing the targets
@@ -358,5 +361,8 @@ def __init__(
         self.auto_targets = auto_targets
         self.auto_targets_presets = auto_targets_presets
 
+        # Settings used with nexus
+        self.use_ProbAMPANMDA_EMS = use_ProbAMPANMDA_EMS
+
     def as_dict(self):
         return vars(self)

bluepyemodel/emodel_pipeline/plotting.py

@@ -560,6 +560,10 @@ def dendritic_feature_plot(
 
     if write_fig:
         fname = model.emodel_metadata.as_string(model.seed) + f"__{feature.name}.pdf"
+        # can have '[', ']' and ',' in feature name. Replace those characters
+        fname = fname.replace("[", "_")
+        fname = fname.replace("]", "_")
+        fname = fname.replace(",", "_")
         save_fig(figures_dir, fname)
 
     return fig, ax

bluepyemodel/model/neuron_model_configuration.py

@@ -52,6 +52,7 @@ def __init__(
         available_mechanisms=None,
         available_morphologies=None,
         morph_modifiers=None,
+        extra_mech_ids=None,
     ):
         """Creates a model configuration, which includes the model parameters, distributions,
         mechanisms and a morphology.
@@ -89,6 +90,16 @@ def __init__(
                     .. code-block::
 
                         morph_modifiers = [["path_to_module", "name_of_function"], ...].
+            extra_mech_ids (list of 2-d tuples): extra nexus ids and types to add to
+                related nexus ids. Must have shape:
+
+                    .. code-block::
+
+                        extra_mech_ids = [
+                            ("id1", "type1"),
+                            ("id2", "type2"),
+                            ...
+                        ]
         """
 
         if isinstance(parameters, dict):
@@ -130,6 +141,7 @@ def __init__(
         self.available_morphologies = available_morphologies
 
         self.morph_modifiers = morph_modifiers
+        self.extra_mech_ids = extra_mech_ids
 
     @property
     def mechanism_names(self):
@@ -574,6 +586,12 @@ def get_related_nexus_ids(self):
                 uses.append({"id": m.id, "type": "SubCellularModelScript"})
                 mechs_ids.add(m.id)
 
+        if self.extra_mech_ids is not None:
+            for mech_id, mech_type in self.extra_mech_ids:
+                if mech_id not in mechs_ids:
+                    uses.append({"id": mech_id, "type": mech_type})
+                    mechs_ids.add(mech_id)
+
         return {"uses": uses}
 
     def as_dict(self):

tests/unit_tests/test_emodelmetadata.py

@@ -195,18 +195,18 @@ def test_for_resource(metadata):
 def test_as_string(metadata):
     """Test as_string method."""
     assert metadata.as_string(seed=42) == (
-        "emodel=L5_TPC__etype=cAC__ttype=245_L5 PT CTX__mtype=L5_TPC:B__"
+        "emodel=L5_TPC__etype=cAC__ttype=245_L5 PT CTX__mtype=L5_TPC_B__"
         "species=mouse__brain_region=SSCX__iteration=v0__seed=42"
     )
 
     metadata.allen_notation = "SS"
     assert metadata.as_string() == (
-        "emodel=L5_TPC__etype=cAC__ttype=245_L5 PT CTX__mtype=L5_TPC:B__"
+        "emodel=L5_TPC__etype=cAC__ttype=245_L5 PT CTX__mtype=L5_TPC_B__"
         "species=mouse__brain_region=SS__iteration=v0"
     )
 
     assert metadata.as_string(use_allen_notation=False) == (
-        "emodel=L5_TPC__etype=cAC__ttype=245_L5 PT CTX__mtype=L5_TPC:B__"
+        "emodel=L5_TPC__etype=cAC__ttype=245_L5 PT CTX__mtype=L5_TPC_B__"
         "species=mouse__brain_region=SSCX__iteration=v0"
     )