test(utils): test loading of referenced morph/biophs

neuroml/test/test_utils.py

@@ -7,14 +7,17 @@
 Copyright 2023 NeuroML contributors
 """
 
+import os
 import unittest
 
 import neuroml
 from neuroml.utils import (
     component_factory,
+    fix_external_morphs_biophys_in_cell,
     get_relative_component_path,
     print_hierarchy,
 )
+from neuroml.writers import NeuroMLWriter
 
 
 class UtilsTestCase(unittest.TestCase):
@@ -55,3 +58,129 @@ def test_networkx_hier_graph(self):
         path, graph = get_relative_component_path("Input", "Instance")
         self.assertIsNotNone(graph)
         self.assertEqual(path, "../Population/Instance")
+
+    def test_fix_external_morphs_biophys_in_cell(self):
+        """Test fix_external_morphs_biophys_in_cell function"""
+        # document that includes cell and morphology with cell referring to
+        # morphology
+        nml_doc = component_factory("NeuroMLDocument", id="testdoc")
+        nml_doc.add("Morphology", id="test_morph_1", validate=False)
+        test_cell_1 = nml_doc.add(
+            "Cell", id="test_cell_1", morphology_attr="test_morph_1"
+        )
+        test_cell_1.morphology = None
+
+        fix_external_morphs_biophys_in_cell(nml_doc)
+        self.assertIsNotNone(nml_doc.cells[0].morphology)
+        self.assertIsNone(nml_doc.cells[0].morphology_attr)
+        self.assertEqual(nml_doc.cells[0].morphology.id, "test_morph_1")
+        print(nml_doc)
+
+        # check that a key error is raised if the referenced morph cannot be
+        # found
+        nml_doc_2 = component_factory("NeuroMLDocument", id="testdoc")
+        nml_doc_2.add("Morphology", id="test_morph_5", validate=False)
+        test_cell_2 = nml_doc_2.add(
+            "Cell", id="test_cell_1", morphology_attr="test_morph_1"
+        )
+        test_cell_2.morphology = None
+
+        with self.assertRaises(KeyError):
+            fix_external_morphs_biophys_in_cell(nml_doc_2)
+            print(nml_doc_2)
+
+    def test_fix_external_morphs_biophys_in_cell_2(self):
+        """Test fix_external_morphs_biophys_in_cell function"""
+        # document that includes cell and biophysical properties with cell
+        # referring to biophysical properties
+        nml_doc = component_factory("NeuroMLDocument", id="testdoc")
+        nml_doc.add("BiophysicalProperties", id="test_biophys_1", validate=False)
+        test_cell_1 = nml_doc.add(
+            "Cell", id="test_cell_1", biophysical_properties_attr="test_biophys_1"
+        )
+        test_cell_1.biophysical_properties = None
+
+        fix_external_morphs_biophys_in_cell(nml_doc)
+        self.assertIsNotNone(nml_doc.cells[0].biophysical_properties)
+        self.assertIsNone(nml_doc.cells[0].biophysical_properties_attr)
+        self.assertEqual(nml_doc.cells[0].biophysical_properties.id, "test_biophys_1")
+        print(nml_doc)
+
+        # check that a key error is raised if the referenced biophysical
+        # property cannot be found
+        nml_doc_2 = component_factory("NeuroMLDocument", id="testdoc")
+        nml_doc_2.add("BiophysicalProperties", id="test_biophys_5", validate=False)
+        test_cell_2 = nml_doc_2.add(
+            "Cell", id="test_cell_1", biophysical_properties_attr="test_biophys_1"
+        )
+        test_cell_2.biophysical_properties = None
+        print(nml_doc_2)
+
+        with self.assertRaises(KeyError):
+            fix_external_morphs_biophys_in_cell(nml_doc_2)
+
+    def test_fix_external_morphs_biophys_in_cell_3(self):
+        """Test fix_external_morphs_biophys_in_cell function"""
+        filename = "nml_morph_doc.nml"
+        nml_doc = component_factory("NeuroMLDocument", id="testdoc")
+        nml_doc.add("Morphology", id="test_morph_1", validate=False)
+        NeuroMLWriter.write(nml_doc, file=filename)
+
+        # doc that includes
+        nml_doc_2 = component_factory("NeuroMLDocument", id="testdoc")
+        nml_doc_2.add("IncludeType", href=filename)
+        test_cell_1 = nml_doc_2.add(
+            "Cell", id="test_cell_1", morphology_attr="test_morph_1"
+        )
+        test_cell_1.morphology = None
+
+        fix_external_morphs_biophys_in_cell(nml_doc_2)
+        self.assertIsNotNone(nml_doc_2.cells[0].morphology)
+        self.assertIsNone(nml_doc_2.cells[0].morphology_attr)
+        self.assertEqual(nml_doc_2.cells[0].morphology.id, "test_morph_1")
+        print(nml_doc_2)
+        os.unlink(filename)
+
+        # doc that does not include, and should fail
+        nml_doc_3 = component_factory("NeuroMLDocument", id="testdoc")
+        test_cell_2 = nml_doc_3.add(
+            "Cell", id="test_cell_1", morphology_attr="test_morph_1"
+        )
+        test_cell_2.morphology = None
+        print(nml_doc_3)
+        with self.assertRaises(KeyError):
+            fix_external_morphs_biophys_in_cell(nml_doc_3)
+
+    def test_fix_external_morphs_biophys_in_cell_4(self):
+        """Test fix_external_morphs_biophys_in_cell function"""
+        # document that includes cell and biophysical properties with cell
+        # referring to biophysical properties
+        filename = "nml_biophys_doc.nml"
+        nml_doc = component_factory("NeuroMLDocument", id="testdoc")
+        nml_doc.add("BiophysicalProperties", id="test_biophys_1", validate=False)
+        NeuroMLWriter.write(nml_doc, file=filename)
+
+        # doc that includes
+        nml_doc_2 = component_factory("NeuroMLDocument", id="testdoc")
+        nml_doc_2.add("IncludeType", href=filename)
+        test_cell_1 = nml_doc_2.add(
+            "Cell", id="test_cell_1", biophysical_properties_attr="test_biophys_1"
+        )
+        test_cell_1.biophysical_properties = None
+
+        fix_external_morphs_biophys_in_cell(nml_doc_2)
+        self.assertIsNotNone(nml_doc_2.cells[0].biophysical_properties)
+        self.assertIsNone(nml_doc_2.cells[0].biophysical_properties_attr)
+        self.assertEqual(nml_doc_2.cells[0].biophysical_properties.id, "test_biophys_1")
+        print(nml_doc_2)
+        os.unlink(filename)
+
+        # doc that does not include, and should fail
+        nml_doc_3 = component_factory("NeuroMLDocument", id="testdoc")
+        test_cell_2 = nml_doc_3.add(
+            "Cell", id="test_cell_1", biophysical_properties_attr="test_biophys_1"
+        )
+        test_cell_2.biophysical_properties = None
+        print(nml_doc_3)
+        with self.assertRaises(KeyError):
+            fix_external_morphs_biophys_in_cell(nml_doc_3)