Minimal working sbml example

pgleeson · pgleeson · commit d65bc18b32df · 2023-09-18T15:48:17.000+01:00
Update a number of print statements
diff --git a/docs/sphinx/source/api/examples/document.xml b/docs/sphinx/source/api/examples/document.xml
@@ -1,5 +1,5 @@
-<?xml version="1.0" ?>
-<Document id="MyBook" title="My life in Python" ISBN="None">
+<?xml version="1.0" encoding="UTF-8"?>
+<Document id="MyBook" title="My life in Python">
     <Section id="Abstract">
         <Paragraph contents="Blah blah blah"/>
         <Paragraph contents="Blah2"/>
diff --git a/examples/document.xml b/examples/document.xml
@@ -1,5 +1,5 @@
-<?xml version="1.0" ?>
-<Document id="MyBook" title="My life in Python" ISBN="None">
+<?xml version="1.0" encoding="UTF-8"?>
+<Document id="MyBook" title="My life in Python">
     <Section id="Abstract">
         <Paragraph contents="Blah blah blah"/>
         <Paragraph contents="Blah2"/>
diff --git a/examples/neuroml2/TestNeuroML.xml b/examples/neuroml2/TestNeuroML.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" ?>
+<?xml version="1.0" encoding="UTF-8"?>
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="TestNeuroML" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd">
     <izhikevich2007Cell id="izh2007RS0" C="100pF" v0="-60mV" k="0.7nS_per_mV" vr="-60mV" vt="-40mV" vpeak="35mV" a="0.03per_ms" b="-2nS" c="-50.0mV" d="100pA"/>
     <pulseGenerator id="pulseGen_0" delay="100ms" duration="800ms" amplitude="0.07 nA"/>
diff --git a/examples/neuroml2/neuroml2_spec.py b/examples/neuroml2/neuroml2_spec.py
@@ -197,7 +197,7 @@ class neuroml(Base):
 
     with open("NeuroML2.specification.yaml", "w") as d:
         yy = yaml.dump(doc_dict, indent=4, sort_keys=False)
-        print(yy)
+        # print(yy)
         d.write(yy)
 
     from modelspec.utils import load_xml
diff --git a/examples/sbml/regenerateAndTest.sh b/examples/sbml/regenerateAndTest.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+set -ex
+
+python test_sbml3.py
+
+python sbml_validators.py example_sbml_minimal.xml
+python sbml_validators.py test_minimal_example.xml
diff --git a/examples/sbml/test_minimal_example.json b/examples/sbml/test_minimal_example.json
@@ -1,18 +1,11 @@
 {
-    "model": {
-        "substanceUnits": "mole",
-        "timeUnits": "second",
-        "extentUnits": "mole",
-        "listOfUnitDefinitions": [
-            {
-                "sid": "per_second",
-                "listOfUnits": [
-                    {
-                        "kind": "second",
-                        "exponent": -1.0
-                    }
-                ]
-            }
-        ]
+    "test_minimal_example": {
+        "level": "3",
+        "version": "2",
+        "model": {
+            "substanceUnits": "mole",
+            "timeUnits": "second",
+            "extentUnits": "mole"
+        }
     }
 }
diff --git a/examples/sbml/test_minimal_example.xml b/examples/sbml/test_minimal_example.xml
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" id="test_minimal_example" level="3" version="2">
+    <model substanceUnits="mole" timeUnits="second" extentUnits="mole"/>
+</sbml>
diff --git a/examples/sbml/test_minimal_example.yaml b/examples/sbml/test_minimal_example.yaml
@@ -0,0 +1,7 @@
+test_minimal_example:
+    level: '3'
+    version: '2'
+    model:
+        substanceUnits: mole
+        timeUnits: second
+        extentUnits: mole
diff --git a/examples/sbml/test_sbml3.py b/examples/sbml/test_sbml3.py
@@ -15,22 +15,27 @@
 def test_example_sbml_minimal():
     "aiming to match the xml file example_sbml_minimal.xml"
 
-    path = "test_minimal_example"
+    name = "test_minimal_example"
 
-    sbml_doc = SBML()
+    sbml_doc = sbml(id=name, version="2", level="3")
     # open(f"{path}.docs.json", "w").write(json.dumps(sbml_doc.generate_documentation(format="dict"), indent=4))
 
     model = Model(substanceUnits="mole", timeUnits="second", extentUnits="mole")
     sbml_doc.model = model
 
-    unit_def = UnitDefinition(sid="per_second")
+    unit_def = unitDefinition(sid="per_second")
+    """
     model.listOfUnitDefinitions.append(unit_def)
-
     unit = Unit(kind="second", exponent=-1.0)
-    unit_def.listOfUnits.append(unit)
+    unit_def.listOfUnits.append(unit)"""
+
+    print("------------------------------------------------")
+    print(sbml_doc)
+    print("------------------------------------------------")
 
-    sbml_doc.to_json_file(f"{path}.json")
-    sbml_doc.to_xml_file(f"{path}.xml")
+    sbml_doc.to_json_file(f"{name}.json")
+    sbml_doc.to_yaml_file(f"{name}.yaml")
+    sbml_doc.to_xml_file(f"{name}.xml")
 
 
 if __name__ == "__main__":
diff --git a/examples/test/test.md b/examples/test/test.md
@@ -12,20 +12,20 @@ A model....
 
   <tr>
     <td><b>float_like_req</b></td>
-    <td>int</td>
+    <td>float</td>
     <td><i>name says it all...</i></td>
  </tr>
 
 
   <tr>
     <td><b>float_like_optional</b></td>
-    <td>int</td>
+    <td>float</td>
     <td><i>name also says it all...</i></td>
  </tr>
 
 
   <tr>
-    <td><b>float_like_optional2</b></td>
+    <td><b>int_like_optional</b></td>
     <td>int</td>
     <td><i>name also says it all...</i></td>
  </tr>
@@ -54,7 +54,7 @@ A model....
 
   <tr>
     <td><b>str_val</b></td>
-    <td>int</td>
+    <td>str</td>
     <td><i>name says it all...</i></td>
  </tr>
 
diff --git a/examples/test/test.py b/examples/test/test.py
@@ -10,14 +10,23 @@
 
 
 def convert2float(x: Any) -> float:
-    print("Converting {} ({})".format(x, type(x)))
+    print("convert2float {} ({})".format(x, type(x)))
     """Convert to float if not None"""
     if x is not None:
         return float(x)
     else:
         return None
 
 
+def convert2int(x: Any) -> int:
+    print("convert2int {} ({})".format(x, type(x)))
+    """Convert to int if not None"""
+    if x is not None:
+        return int(x)
+    else:
+        return None
+
+
 @modelspec.define
 class MidClassNoId(Base):
     """
@@ -29,7 +38,7 @@ class MidClassNoId(Base):
     """
 
     int_val: int = field(default=None, validator=instance_of(int))
-    str_val: int = field(default=None, validator=optional(instance_of(str)))
+    str_val: str = field(default=None, validator=optional(instance_of(str)))
 
 
 @modelspec.define
@@ -41,18 +50,18 @@ class TopClass(Base):
         id: The unique id of the thing
         float_like_req: name says it all...
         float_like_optional: name also says it all...
-        float_like_optional2: name also says it all...
+        int_like_optional: name also says it all...
     """
 
     id: str = field(validator=instance_of(str))
-    float_like_req: int = field(
+    float_like_req: float = field(
         default=None, validator=instance_of(float), converter=convert2float
     )
-    float_like_optional: int = field(
+    float_like_optional: float = field(
         default=None, validator=optional(instance_of(float)), converter=convert2float
     )
-    float_like_optional2: int = field(
-        default=None, validator=optional(instance_of(float)), converter=convert2float
+    int_like_optional: int = field(
+        default=None, validator=optional(instance_of(int)), converter=convert2int
     )
 
     mid: MidClassNoId = field(
@@ -66,8 +75,8 @@ class TopClass(Base):
 
 # tc.float_like_req = 2.01
 tc.float_like_optional = 44
-tc.float_like_optional2 = 66
-# tc.mid = MidClassNoId(int_val=4, str_val="three")
+# tc.float_like_optional2 = 66
+tc.mid = MidClassNoId(int_val=4, str_val="three")
 
 
 print(tc)
diff --git a/examples/test/test.specification.yaml b/examples/test/test.specification.yaml
@@ -5,12 +5,12 @@ TopClass:
             type: str
             description: The unique id of the thing
         float_like_req:
-            type: int
+            type: float
             description: name says it all...
         float_like_optional:
-            type: int
+            type: float
             description: name also says it all...
-        float_like_optional2:
+        int_like_optional:
             type: int
             description: name also says it all...
         mid:
@@ -23,5 +23,5 @@ MidClassNoId:
             type: int
             description: name says it all...
         str_val:
-            type: int
+            type: str
             description: name says it all...
diff --git a/examples/test/test_instance.json b/examples/test/test_instance.json
@@ -2,6 +2,9 @@
     "MyTest": {
         "float_like_req": 4.0,
         "float_like_optional": 44.0,
-        "float_like_optional2": 66.0
+        "mid": {
+            "int_val": 4,
+            "str_val": "three"
+        }
     }
 }
diff --git a/examples/test/test_instance.xml b/examples/test/test_instance.xml
@@ -1,2 +1,4 @@
-<?xml version="1.0" ?>
-<TopClass id="MyTest" float_like_req="4.0" float_like_optional="44.0" float_like_optional2="66.0" mid="None"/>
+<?xml version="1.0" encoding="UTF-8"?>
+<TopClass id="MyTest" float_like_req="4.0" float_like_optional="44.0">
+    <mid int_val="4" str_val="three"/>
+</TopClass>
diff --git a/examples/test/test_instance.yaml b/examples/test/test_instance.yaml
@@ -1,4 +1,6 @@
 MyTest:
     float_like_req: 4.0
     float_like_optional: 44.0
-    float_like_optional2: 66.0
+    mid:
+        int_val: 4
+        str_val: three
diff --git a/src/modelspec/base_types.py b/src/modelspec/base_types.py
@@ -57,11 +57,13 @@ def print_(text: str, print_it: bool = False):
     """
     Print a message preceded by modelspec, only if print_it=True
     """
+    if not print_it:
+        return
+
     prefix = "modelspec >>> "
     if not isinstance(text, str):
         text = ("%s" % text).decode("ascii")
-    if print_it:
-        print("{}{}".format(prefix, text.replace("\n", "\n" + prefix)))
+    print("{}{}".format(prefix, text.replace("\n", "\n" + prefix)))
 
 
 def print_v(text: str):
@@ -128,11 +130,14 @@ def to_xml(self) -> str:
         root = build_xml_element(self)
 
         xml_string = ET.tostring(
-            root, encoding="utf-8", xml_declaration=False, method="xml"
+            root, encoding="UTF-8", xml_declaration=True, method="xml"
         ).decode("utf-8")
 
         parsed_xml = xml.dom.minidom.parseString(xml_string)
         pretty_xml = parsed_xml.toprettyxml(indent=" " * 4)
+        pretty_xml = pretty_xml.replace(
+            '?xml version="1.0" ?', '?xml version="1.0" encoding="UTF-8"?'
+        )
         return pretty_xml
 
     @classmethod
@@ -318,14 +323,7 @@ def to_xml_file(
         if filename is None:
             filename = f"{self.id}.xml"
 
-        root = build_xml_element(self)
-
-        # Generate the XML string
-        xml_str = ET.tostring(root, encoding="utf-8", method="xml").decode("utf-8")
-
-        # Create a pretty-formatted XML string using minidom
-        parsed_xml = xml.dom.minidom.parseString(xml_str)
-        pretty_xml_str = parsed_xml.toprettyxml(indent=" " * 4)
+        pretty_xml_str = self.to_xml()
 
         # Write the XML data to the file
         with open(filename, "w", encoding="utf-8") as file:
diff --git a/src/modelspec/utils.py b/src/modelspec/utils.py

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-<?xml version="1.0" ?>`
	`1`	`+<?xml version="1.0" encoding="UTF-8"?>`
`2`	`2`	`<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="TestNeuroML" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd">`
`3`	`3`	`<izhikevich2007Cell id="izh2007RS0" C="100pF" v0="-60mV" k="0.7nS_per_mV" vr="-60mV" vt="-40mV" vpeak="35mV" a="0.03per_ms" b="-2nS" c="-50.0mV" d="100pA"/>`
`4`	`4`	`<pulseGenerator id="pulseGen_0" delay="100ms" duration="800ms" amplitude="0.07 nA"/>`