From b6f606ee268d371548b1e53d2d9ce3fceb0c185f Mon Sep 17 00:00:00 2001
From: pgleeson <p.gleeson@gmail.com>
Date: Fri, 31 May 2024 10:44:21 +0100
Subject: [PATCH] Add helper method fix_external_morphs_biophys_in_cell; use by
 default on XMLParser

---
 neuroml/hdf5/NeuroMLXMLParser.py | 17 +++++++++++++++--
 neuroml/utils.py                 | 16 ++++++++++++++++
 2 files changed, 31 insertions(+), 2 deletions(-)

diff --git a/neuroml/hdf5/NeuroMLXMLParser.py b/neuroml/hdf5/NeuroMLXMLParser.py
index fe1682bc..020a8991 100644
--- a/neuroml/hdf5/NeuroMLXMLParser.py
+++ b/neuroml/hdf5/NeuroMLXMLParser.py
@@ -27,8 +27,9 @@ class NeuroMLXMLParser:
     currentProjectionPostPop = ""
     currentSynapse = ""
 
-    def __init__(self, netHandler):
+    def __init__(self, netHandler, fix_external_morphs_biophys=True):
         self.netHandler = netHandler
+        self.fix_external_morphs_biophys = fix_external_morphs_biophys
 
         # For continued use with old API
         if not hasattr(self.netHandler, "handle_network") or hasattr(
@@ -91,6 +92,10 @@ def parse(self, filename):
         self.nml_doc = loaders.read_neuroml2_file(
             filename, include_includes=True, already_included=[]
         )
+        if self.fix_external_morphs_biophys:
+            from neuroml.utils import fix_external_morphs_biophys_in_cell
+            fix_external_morphs_biophys_in_cell(self.nml_doc)
+                
 
         print("Loaded: %s as NeuroMLDocument" % filename)
 
@@ -474,7 +479,11 @@ def parse(self, filename):
 
 
 if __name__ == "__main__":
-    file_name = "../examples/tmp/testh5.nml"
+    file_name = "../examples/tmp/testnet.nml"
+    
+    import sys 
+    if len(sys.argv)==2:
+        file_name = sys.argv[1]
 
     logging.basicConfig(
         level=logging.INFO, format="%(name)-19s %(levelname)-5s - %(message)s"
@@ -503,6 +512,10 @@ def parse(self, filename):
     nml_doc = nmlHandler.get_nml_doc()
 
     print(nml_doc.summary())
+    print(nml_doc.cells)
+
+    for cell in nml_doc.cells:
+        print('--- Cell: %s'%cell)
 
     nml_file = "../examples/tmp/testh5_2_.nml"
     import neuroml.writers as writers
diff --git a/neuroml/utils.py b/neuroml/utils.py
index b5998f43..526a7636 100644
--- a/neuroml/utils.py
+++ b/neuroml/utils.py
@@ -12,6 +12,7 @@
 import networkx
 
 import neuroml.nml.nml as schema
+from neuroml import NeuroMLDocument
 
 from . import loaders
 
@@ -305,6 +306,21 @@ def get_relative_component_path(src: str, dest: str, root: Type =
     return (path, graph)
 
 
+
+def fix_external_morphs_biophys_in_cell(nml2_doc: NeuroMLDocument) -> None:
+    """
+    Only used in the case where a cell element has a morphology (or biophysicalProperties) attribute, as opposed to a 
+    subelement morphology/biophysicalProperties. This will substitute the external element into the cell element for ease of access
+    """
+    for cell in nml2_doc.cells:
+        if cell.morphology_attr != None:
+            ext_morph = nml2_doc.get_by_id(cell.morphology_attr)
+            cell.morphology = ext_morph
+        if cell.biophysical_properties_attr != None:
+            ext_bp = nml2_doc.get_by_id(cell.biophysical_properties_attr)
+            cell.biophysical_properties = ext_bp
+
+
 def main():
     if len(sys.argv) != 2:
         print("Please specify the name of the NeuroML2 file...")