Minor fixes

pyenzyme/enzymeml/core/enzymemldocument.py

@@ -71,10 +71,10 @@ class EnzymeMLDocument(EnzymeMLBase):
         3,
         description="SBML evel of the EnzymeML XML.",
         inclusiveMinimum=1,
-        exclusiveMaximum=3,
+        inclusiveMaximum=3,
     )
 
-    version: str = Field(
+    version: int = Field(
         2,
         description="SBML version of the EnzymeML XML.",
     )
@@ -1094,7 +1094,7 @@ def addReaction(self, reaction: EnzymeReaction, use_parser: bool = True) -> str:
             # Reset temperature for SBML compliance to Kelvin
             reaction.temperature = (
                 reaction.temperature + 273.15
-                if re.match(r"^K|kelvin", reaction.temperature_unit)
+                if re.match(r"^c|celsius", reaction.temperature_unit.lower())
                 else reaction.temperature
             )
 
@@ -1345,6 +1345,7 @@ def _updateReplicateMeasurementIDs(
     ):
         """Updates the measurement IDs of replicates."""
         for measurement_data in measurement_data_dict.values():
+            measurement_data.measurement_id = measurement_id
             replicates = measurement_data.replicates
             for replicate in replicates:
                 replicate.measurement_id = measurement_id

pyenzyme/enzymeml/core/enzymereaction.py

@@ -180,6 +180,17 @@ def set_meta_id(cls, id: Optional[str], values: dict):
 
         return id
 
+    @validator("temperature_unit")
+    def convert_temperature_unit(cls, unit, values):
+        """Converts celsius to kelvin due to SBML limitations"""
+
+        if unit:
+            if unit.lower() in ["celsius", "c"]:
+                values["temperature"] = values["temperature"] + 273.15
+                return "K"
+
+        return unit
+
     # ! Getters
     def getEduct(self, id: str) -> ReactionElement:
         """

pyenzyme/enzymeml/core/measurement.py

@@ -16,7 +16,7 @@
 
 from typing import List, Dict, Tuple, Optional, TYPE_CHECKING, Union
 from dataclasses import dataclass
-from pydantic import validate_arguments, Field, PrivateAttr
+from pydantic import validate_arguments, Field, PrivateAttr, validator
 
 from pyenzyme.enzymeml.core.enzymemlbase import EnzymeMLBase
 from pyenzyme.enzymeml.core.measurementData import MeasurementData
@@ -94,6 +94,18 @@ class Measurement(EnzymeMLBase):
     _temperature_unit_id: str = PrivateAttr(None)
     _global_time_unit_id: str = PrivateAttr(None)
 
+    # ! Validators
+    @validator("temperature_unit")
+    def convert_temperature_unit(cls, unit, values):
+        """Converts celsius to kelvin due to SBML limitations"""
+
+        if unit:
+            if unit.lower() in ["celsius", "c"]:
+                values["temperature"] = values["temperature"] + 273.15
+                return "K"
+
+        return unit
+
     # ! Utility methods
     def __repr__(self):
         return self.printMeasurementScheme(stdout=False)

pyenzyme/enzymeml/tools/enzymemlreader.py

@@ -36,9 +36,8 @@
 )
 
 from libsbml import SBMLReader
-from enum import Enum
 from libcombine import CombineArchive
-from io import StringIO, BytesIO
+from io import StringIO
 
 # ! Factories
 
@@ -105,6 +104,11 @@ def readFromFile(self, path: str) -> EnzymeMLDocument:
                          folder destination for plain .xml
         """
 
+        if not path.endswith(".omex"):
+            raise TypeError(
+                f"File {os.path.basename(path)} is not a valid OMEX archive"
+            )
+
         # Read omex archive
         self.path = path
         self.archive = CombineArchive()
@@ -253,7 +257,7 @@ def _getUnits(self, model: libsbml.Model) -> Dict[str, UnitDef]:
             name = unit.name
             id = unit.id
             meta_id = unit.meta_id
-            ontology = "NONE"  # TODO get unit ontology
+            ontology = None  # TODO get unit ontology
 
             # Create unit definition
             unitdef = UnitDef(name=name, id=id, ontology=ontology, meta_id=meta_id)
@@ -344,6 +348,10 @@ def _getSpecies(
                     "init_conc": init_conc,
                     "_unit_id": unit_id,
                     "unit": unit,
+                    # Some attributes need special care
+                    "ecnumber": param_dict.get("e_cnumber"),
+                    "uniprotid": param_dict.get("uniprot_id"),
+                    "participants": param_dict.get("participant"),
                 }
             )
 
@@ -399,11 +407,19 @@ def camel_to_snake(name):
         param_dict = {}
 
         for enzymeMLAnnot in speciesAnnot:
-            key = enzymeMLAnnot.tag.split("}")[-1].lower()
+            key = enzymeMLAnnot.tag.split("}")[-1]
             key = camel_to_snake(key)
-
             attribute = enzymeMLAnnot.text
 
+            if key in param_dict:
+                # Take care of list attributes
+                try:
+                    param_dict[key].append(attribute)
+                except AttributeError:
+                    param_dict[key] = [param_dict[key], attribute]
+
+                continue
+
             param_dict[key] = attribute
 
         return param_dict
@@ -623,9 +639,10 @@ def _parse_parameter(self, parameter, enzmldoc):
             value=value,
             unit=param_dict.get("unit"),
             ontology=self._sboterm_to_enum(parameter.getSBOTerm()),
-            initial_value=param_dict.get("initialvalue"),
+            initial_value=param_dict.get("initial_value"),
             upper=param_dict.get("upperbound"),
             lower=param_dict.get("lowerbound"),
+            stdev=param_dict.get("stdev"),
             constant=constant,
         )
 

pyenzyme/enzymeml/tools/enzymemlwriter.py

@@ -308,6 +308,7 @@ def appendMultiAttributes(
         for key, value in objectMapping.items():
             # "value" --> 10.00
             if hasattr(object, value):
+
                 attribute = getattr(object, value)
                 if attribute:
                     node.addAttr(key, str(attribute))
@@ -432,6 +433,7 @@ def _addProteins(
             "enzymeml:ECnumber": "ecnumber",
             "enzymeml:uniprotID": "uniprotid",
             "enzymeml:organism": "organism",
+            "enzymeml:organismTaxID": "organism_tax_id",
         }
 
         for protein in protein_dict.values():
@@ -473,7 +475,11 @@ def _addReactants(self, model: libsbml.Model, reactant_dict: Dict[str, Reactant]
         """
 
         # EnzymeML attributes
-        reactantAttributes = {"enzymeml:inchi": "inchi", "enzymeml:smiles": "smiles"}
+        reactantAttributes = {
+            "enzymeml:inchi": "inchi",
+            "enzymeml:smiles": "smiles",
+            "enzymeml:chebiID": "chebi_id",
+        }
 
         for reactant in reactant_dict.values():
             self._addSpecies(
@@ -645,6 +651,9 @@ def _addReactions(
                     annotationNode=conditionsAnnotation,
                 )
 
+            if conditionsAnnotation.getNumChildren() > 0:
+                reactionAnnotation.addChild(conditionsAnnotation)
+
             if reactionAnnotation.getNumChildren() > 0:
                 reaction.appendAnnotation(reactionAnnotation)
 
@@ -696,6 +705,7 @@ def _addModelToReaction(
                 "enzymeml:initialValue": "initial_value",
                 "enzymeml:upperBound": "upper",
                 "enzymeml:lowerBound": "lower",
+                "enzymeml:stdev": "stdev",
             }
 
             for attributeName, objectName in optional_parameters.items():

pyenzyme/enzymeml/tools/unitcreator.py

@@ -23,7 +23,6 @@ def __init__(self):
 
         self.__functionDict = {
             "M": self.__Molar,
-            "m": self.__Mole,
             "mole": self.__Mole,
             "l": self.__Volume,
             "liter": self.__Volume,
@@ -36,13 +35,11 @@ def __init__(self):
             "seconds": self.__Seconds,
             "min": self.__Minutes,
             "mins": self.__Minutes,
-            "minute": self.__Minutes,
             "minutes": self.__Minutes,
             "h": self.__Hours,
             "hour": self.__Hours,
             "hours": self.__Hours,
             "C": self.__Celsius,
-            "c": self.__Celsius,
             "celsius": self.__Celsius,
             "Celsius": self.__Celsius,
             "K": self.__Kelvin,

pyenzyme/enzymeml/tools/unitparser.py

@@ -113,7 +113,7 @@ def __getPrefix(self, string, exponent):
 
             try:
                 unit = re.findall(regex, string)[0][0]
-                return ("NONE", unit, exponent)
+                return (None, unit, exponent)
             except IndexError:
                 supportedUnits = regex.split()
                 raise KeyError(