diff --git a/examples/neuroml2/NeuroML2.md b/examples/neuroml2/NeuroML2.md
index aabfc643..405be412 100644
--- a/examples/neuroml2/NeuroML2.md
+++ b/examples/neuroml2/NeuroML2.md
@@ -13,7 +13,21 @@ Some description...
| xmlns |
str |
- Schema for NeuroML 2, usually http://www.neuroml.org/schema/neuroml2 |
+ Default namespace for the NeuroML file, usually http://www.neuroml.org/schema/neuroml2 |
+
+
+
+
+ | xmlns_xsi |
+ str |
+ Namespace for XMLSchema-instance |
+
+
+
+
+ | xmlns_loc |
+ str |
+ Specifies location of the main namespace |
@@ -24,14 +38,14 @@ Some description...
| izhikevich2007Cells |
izhikevich2007Cell |
- |
+ The izhikevich2007Cells |
| pulseGenerators |
pulseGenerator |
- |
+ The pulse current generators |
diff --git a/examples/neuroml2/NeuroML2.rst b/examples/neuroml2/NeuroML2.rst
index ee22286c..2a812b47 100644
--- a/examples/neuroml2/NeuroML2.rst
+++ b/examples/neuroml2/NeuroML2.rst
@@ -5,22 +5,24 @@ Some description...
**Allowed parameters**
-=============== =========== ====================================================================
+=============== =========== ======================================================================================
Allowed field Data Type Description
-=============== =========== ====================================================================
+=============== =========== ======================================================================================
**id** str The id of the NeuroML 2 document
-**xmlns** str Schema for NeuroML 2, usually http://www.neuroml.org/schema/neuroml2
-=============== =========== ====================================================================
+**xmlns** str Default namespace for the NeuroML file, usually http://www.neuroml.org/schema/neuroml2
+**xmlns_xsi** str Namespace for XMLSchema-instance
+**xmlns_loc** str Specifies location of the main namespace
+=============== =========== ======================================================================================
**Allowed children**
-======================= ============================================ ====================
+======================= ============================================ ============================
Allowed child Data Type Description
-======================= ============================================ ====================
-**izhikevich2007Cells** `izhikevich2007Cell <#izhikevich2007cell>`__
-**pulseGenerators** `pulseGenerator <#pulsegenerator>`__
+======================= ============================================ ============================
+**izhikevich2007Cells** `izhikevich2007Cell <#izhikevich2007cell>`__ The izhikevich2007Cells
+**pulseGenerators** `pulseGenerator <#pulsegenerator>`__ The pulse current generators
**networks** `network <#network>`__ The networks present
-======================= ============================================ ====================
+======================= ============================================ ============================
==================
izhikevich2007Cell
diff --git a/examples/neuroml2/NeuroML2.specification.json b/examples/neuroml2/NeuroML2.specification.json
index fe211575..8e39c0eb 100644
--- a/examples/neuroml2/NeuroML2.specification.json
+++ b/examples/neuroml2/NeuroML2.specification.json
@@ -8,17 +8,25 @@
},
"xmlns": {
"type": "str",
- "description": "Schema for NeuroML 2, usually http://www.neuroml.org/schema/neuroml2"
+ "description": "Default namespace for the NeuroML file, usually http://www.neuroml.org/schema/neuroml2"
+ },
+ "xmlns_xsi": {
+ "type": "str",
+ "description": "Namespace for XMLSchema-instance"
+ },
+ "xmlns_loc": {
+ "type": "str",
+ "description": "Specifies location of the main namespace"
}
},
"allowed_children": {
"izhikevich2007Cells": {
"type": "izhikevich2007Cell",
- "description": ""
+ "description": "The izhikevich2007Cells"
},
"pulseGenerators": {
"type": "pulseGenerator",
- "description": ""
+ "description": "The pulse current generators"
},
"networks": {
"type": "network",
diff --git a/examples/neuroml2/NeuroML2.specification.yaml b/examples/neuroml2/NeuroML2.specification.yaml
index 0d4bb12a..df89cb5b 100644
--- a/examples/neuroml2/NeuroML2.specification.yaml
+++ b/examples/neuroml2/NeuroML2.specification.yaml
@@ -6,14 +6,20 @@ neuroml:
description: The id of the NeuroML 2 document
xmlns:
type: str
- description: Schema for NeuroML 2, usually http://www.neuroml.org/schema/neuroml2
+ description: Default namespace for the NeuroML file, usually http://www.neuroml.org/schema/neuroml2
+ xmlns_xsi:
+ type: str
+ description: Namespace for XMLSchema-instance
+ xmlns_loc:
+ type: str
+ description: Specifies location of the main namespace
allowed_children:
izhikevich2007Cells:
type: izhikevich2007Cell
- description: ''
+ description: The izhikevich2007Cells
pulseGenerators:
type: pulseGenerator
- description: ''
+ description: The pulse current generators
networks:
type: network
description: The networks present
diff --git a/examples/neuroml2/TestNeuroML.xml b/examples/neuroml2/TestNeuroML.xml
index 54ee04dc..70586cf6 100644
--- a/examples/neuroml2/TestNeuroML.xml
+++ b/examples/neuroml2/TestNeuroML.xml
@@ -1,5 +1,5 @@
-
+
diff --git a/examples/neuroml2/neuroml2_spec.py b/examples/neuroml2/neuroml2_spec.py
index 045931e9..6b07fda5 100644
--- a/examples/neuroml2/neuroml2_spec.py
+++ b/examples/neuroml2/neuroml2_spec.py
@@ -101,14 +101,26 @@ class neuroml(Base):
Args:
id: The id of the NeuroML 2 document
- xmlns: Schema for NeuroML 2, usually http://www.neuroml.org/schema/neuroml2
+ xmlns: Default namespace for the NeuroML file, usually http://www.neuroml.org/schema/neuroml2
+ xmlns_xsi: Namespace for XMLSchema-instance
+ xmlns_loc: Specifies location of the main namespace
+ izhikevich2007Cells: The izhikevich2007Cells
+ pulseGenerators: The pulse current generators
networks: The networks present
"""
id: str = field(validator=instance_of(str))
+
xmlns: str = field(
validator=instance_of(str), default="http://www.neuroml.org/schema/neuroml2"
)
+ xmlns_xsi: str = field(
+ validator=instance_of(str), default="http://www.w3.org/2001/XMLSchema-instance"
+ )
+ xmlns_loc: str = field(
+ validator=instance_of(str),
+ default="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd",
+ )
izhikevich2007Cells: List[izhikevich2007Cell] = field(factory=list)
pulseGenerators: List[pulseGenerator] = field(factory=list)
@@ -187,3 +199,8 @@ class neuroml(Base):
yy = yaml.dump(doc_dict, indent=4, sort_keys=False)
print(yy)
d.write(yy)
+
+ from modelspec.utils import load_xml
+
+ new_neuroml = load_xml("hello_world_neuroml.net.nml")
+ print(new_neuroml)
diff --git a/src/modelspec/base_types.py b/src/modelspec/base_types.py
index 7bb3f6a6..f4a81a9d 100644
--- a/src/modelspec/base_types.py
+++ b/src/modelspec/base_types.py
@@ -125,7 +125,6 @@ def to_xml(self) -> str:
)
from modelspec.utils import build_xml_element
- # root = ET.Element("modelspec")
root = build_xml_element(self)
xml_string = ET.tostring(
@@ -170,12 +169,38 @@ def from_bson(cls, bson_str: str) -> "Base":
@classmethod
def from_xml(cls, xml_str: str) -> "Base":
"""Instantiate a Base object from an XML string"""
- from modelspec.utils import element_to_dict, handle_id, convert_values
+ from modelspec.utils import (
+ elementtree_element_to_dict,
+ handle_xml_dict_id,
+ convert_xml_dict_values,
+ process_xml_namespace,
+ )
+ import re
+
+ # When the to_xml() method is used it messes up the string therefore,
+ # it is necessary to convert it into an elementree object then decode into a string.
+ xml_string_a = ET.fromstring(xml_str)
+ xml_string_b = ET.tostring(xml_string_a).decode()
+
+ # while trying to obtain a useable xml structure, using the conversion above it acquires
+ # some unusual string element that sometimes can be incremental from either :ns0 to :nsX or ns0: to nsX:.
+ # Using the regex expression pattern catches it in any form and removes it from the xml string structure.
+ ns_prefix_pattern = r"(ns\d+:|:ns\d+)"
+ cleaned_xml = re.sub(ns_prefix_pattern, "", xml_string_b).strip()
+
+ # For the xml to be useable in modelspec unnecessary string elements which only serve as asthetics for the xml must
+ # be removed when converting to a dict, the process_xml_namespaes function does just that.
+ removed_namespaces = process_xml_namespace(cleaned_xml)
+
+ # process_xml_namespace function returns an elementtree object which can be directly worked upon by the elementtree_element_to_dict
+ # function, this returns a python dictionary
+ data_dict = elementtree_element_to_dict(removed_namespaces)
+
+ # This strips every instance of 'id' from the resulting dictionary structure
+ removed_id = handle_xml_dict_id(data_dict)
- root = ET.fromstring(xml_str)
- data_dict = element_to_dict(root)
- removed_id = handle_id(data_dict)
- converted_to_actual_val = convert_values(removed_id)
+ # XML conversions do not returns exact values, instead all values are returned as a string, this reassigns their actual values
+ converted_to_actual_val = convert_xml_dict_values(removed_id)
return cls.from_dict(converted_to_actual_val)
@@ -377,15 +402,38 @@ def from_xml_file(cls, filename: str) -> "Base":
Returns:
A modelspec Base for this XML.
"""
- from modelspec.utils import element_to_dict, handle_id, convert_values
+ from modelspec.utils import (
+ elementtree_element_to_dict,
+ handle_xml_dict_id,
+ convert_xml_dict_values,
+ process_xml_namespace,
+ )
+ import re
with open(filename) as infile:
- tree = ET.parse(infile)
- root = tree.getroot()
+ tree = ET.parse(infile) # Parse the XML file into an ElementTree object
+ root = tree.getroot() # Get the root element
+
+ # This defines regular expressions to match the namespace patterns to be removed
+ ns_prefix_pattern = r"(ns\d+:|:ns\d+)"
+
+ # Converts the loaded xml into a string and removes unwanted string values ':ns0' to :ns∞ and 'ns0:' to ns∞:
+ # They prevent the xml from loading correctly
+ xml_string = ET.tostring(root).decode()
+ cleaned_xml = re.sub(ns_prefix_pattern, "", xml_string).strip()
+
+ # Removes xmlns, xmlns:xsi and xsi:schemaLocation from the xml structure for conversion
+ # it passes an element tree object to the elementtree_element_to_dict function
+ removed_namespaces = process_xml_namespace(cleaned_xml)
+
+ # Converts the resulting xml stripped of xmlns, xmlns:xsi and xsi:schemaLocation into a dict
+ data_dict = elementtree_element_to_dict(removed_namespaces)
+
+ # Removes every key having 'id' and replaces it with it's value
+ removed_id = handle_xml_dict_id(data_dict)
- data_dict = element_to_dict(root)
- removed_id = handle_id(data_dict)
- converted_to_actual_val = convert_values(removed_id)
+ # Values are returned as strings after conversion, this corrects them to their actual values
+ converted_to_actual_val = convert_xml_dict_values(removed_id)
return cls.from_dict(converted_to_actual_val)
def get_child(self, id: str, type_: str) -> Any:
diff --git a/src/modelspec/utils.py b/src/modelspec/utils.py
index 7f0aabca..16844cb1 100644
--- a/src/modelspec/utils.py
+++ b/src/modelspec/utils.py
@@ -67,19 +67,35 @@ def load_xml(filename: str):
Args:
filename: The name of the XML file to load.
"""
+ import re
+
with open(filename, "rb") as infile:
tree = ET.parse(infile) # Parse the XML file into an ElementTree object
root = tree.getroot() # Get the root element
- # Convert the ElementTree object to a dictionary
- data = element_to_dict(root)
- removed_id = handle_id(data)
- converted_to_actual_val = convert_values(removed_id)
+ # This defines regular expressions to match the namespace patterns to be removed
+ ns_prefix_pattern = r"(ns\d+:|:ns\d+)"
+
+ # Converts the loaded xml into a string and removes unwanted string values ':ns0' to :ns∞ and 'ns0:' to ns∞:
+ # They prevent the xml from loading correctly
+ xml_string = ET.tostring(root).decode()
+ cleaned_xml = re.sub(ns_prefix_pattern, "", xml_string).strip()
+
+ # Removes xmlns, xmlns:xsi and xsi:schemaLocation from the xml structure for conversion
+ # it passes an element tree object to the elementtree_element_to_dict function
+ removed_namespaces = process_xml_namespace(cleaned_xml)
+
+ # Converts the resulting xml stripped of xmlns, xmlns:xsi and xsi:schemaLocation into a dict
+ data = elementtree_element_to_dict(removed_namespaces)
- return convert_values(converted_to_actual_val)
+ # Removes every key having 'id' and replaces it with it's value
+ removed_id = handle_xml_dict_id(data)
+ # Values are returned as strings after conversion, this corrects them to their actual values
+ return convert_xml_dict_values(removed_id)
-def element_to_dict(element):
+
+def elementtree_element_to_dict(element):
"""
This convert an ElementTree element to a dictionary.
@@ -94,35 +110,57 @@ def element_to_dict(element):
if attrs:
result.update(attrs)
+ children_by_tag = {}
for child_element in element:
- child_key = child_element.tag
- child_value = element_to_dict(child_element)
+ child_key = child_element.tag + "s"
+ child_value = elementtree_element_to_dict(child_element)
- if child_key in result:
- if not isinstance(result[child_key], list):
- result[child_key] = [result[child_key]]
- result[child_key].append(child_value)
- else:
+ # Check if the child element has an 'id' attribute
+ if "id" in child_element.attrib:
+ # If the child element has an 'id', add it to the result dictionary directly
result[child_key] = child_value
+ else:
+ # If the child element does not have an 'id', represent it as a list
+ children_by_tag.setdefault(child_key, []).append(child_value)
+
+ # Append the lists to the result dictionary
+ result.update(children_by_tag)
return result
-def handle_id(dictionary):
+def process_xml_namespace(xml_string):
+ # Remove ignored elements from the XML string
+ ignored_elements = [
+ 'xmlns="http://www.neuroml.org/schema/neuroml2"',
+ 'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"',
+ 'xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd"',
+ ]
+
+ # Loops through the xml string and removes every instance of the elements in the list named ignored_elements
+ for ignored_element in ignored_elements:
+ xml_string = xml_string.replace(ignored_element, "").strip()
+
+ # Parse the XML string into an ElementTree
+ root = ET.fromstring(xml_string)
+ return root
+
+
+def handle_xml_dict_id(dictionary):
if isinstance(dictionary, dict):
if "id" in dictionary:
nested_dict = {dictionary["id"]: dictionary.copy()}
del nested_dict[dictionary["id"]]["id"]
- return {k: handle_id(v) for k, v in nested_dict.items()}
+ return {k: handle_xml_dict_id(v) for k, v in nested_dict.items()}
else:
- return {k: handle_id(v) for k, v in dictionary.items()}
+ return {k: handle_xml_dict_id(v) for k, v in dictionary.items()}
elif isinstance(dictionary, list):
- return [handle_id(item) for item in dictionary]
+ return [handle_xml_dict_id(item) for item in dictionary]
else:
return dictionary
-def convert_values(value):
+def convert_xml_dict_values(value):
"""
This recursively converts values to their actual types.
@@ -146,9 +184,9 @@ def convert_values(value):
elif value.lower() == "none":
return None
elif isinstance(value, dict):
- return {key: convert_values(val) for key, val in value.items()}
+ return {key: convert_xml_dict_values(val) for key, val in value.items()}
elif isinstance(value, list):
- return [convert_values(item) for item in value]
+ return [convert_xml_dict_values(item) for item in value]
return value
@@ -219,11 +257,20 @@ def build_xml_element(data, parent=None):
for child in children:
child_element = build_xml_element(child)
parent.append(child_element)
- else:
+
+ # Filters name space and schemaLoacation attributes, only allows non name space attributes to be added as attributes
+ elif not isinstance(aattr.default, str):
attribute_name = aattr.name
attribute_value = data.__getattribute__(aattr.name)
parent.set(attribute_name, str(attribute_value))
+ # This defines the various namespaces and schemaLocation of the generated xml
+ if hasattr(data, "xmlns"):
+ parent.set("xmlns", data.xmlns)
+ if hasattr(data, "xmlns_xsi"):
+ parent.set("xmlns:xsi", data.xmlns_xsi)
+ if hasattr(data, "xmlns_loc"):
+ parent.set("xsi:schemaLocation", str(data.xmlns_loc))
return parent