new link system

links.yml

@@ -0,0 +1,7 @@
+name: "EnzymeML Links"
+module: "links"
+links:
+  - name: "sbml"
+    template: "sbml.toml"
+    script: "sbml.py"
+    function: "link"

links/sbml.py

@@ -0,0 +1,53 @@
+from typing import Dict
+from sdRDM import Linker
+
+
+def link(
+    dataset: "DataModel",  # type: ignore
+    template: Dict,
+):
+    """
+    Links the dataset to an SBML document based on the provided mapping template.
+
+    Args:
+        dataset: The dataset to be linked.
+        template: The mapping template specifying the link between the dataset and SBML.
+
+    Raises:
+        AssertionError: If the mapping template does not specify a 'SBML' source.
+
+    Returns:
+        None
+    """
+
+    linker = Linker(template)
+
+    assert (
+        "SBML" in linker.__sources__
+    ), "Not able to link to SBML. Please specify a 'SBML' source in the mapping template."
+
+    sbmldoc = linker.__sources__["SBML"]()
+    linker(dataset, sbmldoc)
+
+    for vessel in dataset.vessels:
+        linker(vessel, sbmldoc.model)
+
+    for protein in dataset.proteins:
+        linker(protein, sbmldoc.model)
+
+    for reactant in dataset.reactants:
+        linker(reactant, sbmldoc.model)
+
+    for reaction in dataset.reactions:
+        mapped = linker(reaction, sbmldoc.model)
+
+        for educt in reaction.educts:
+            linker(educt, mapped.reactions)
+
+        for product in reaction.products:
+            linker(product, mapped.reactions)
+
+        for modifier in reaction.modifiers:
+            linker(modifier, mapped.reactions)
+
+    return sbmldoc

links/sbml.toml

@@ -7,71 +7,71 @@ SBML = "https://github.com/JR-1991/sbml-specifications.git@Refactored-version"
 id = "SBML/model/id"
 name = "SBML/model/name"
 
-[vessels]
+["EnzymeMLDocument/vessels"]
 id = "SBML/model/compartments/id"
 name = "SBML/model/compartments/name"
 volume = "SBML/model/compartments/size"
 unit = "SBML/model/compartments/units"
 constant = "SBML/model/compartments/constant"
 
-[proteins]
+["EnzymeMLDocument/proteins"]
 id = "SBML/model/species/id"
 name = "SBML/model/species/name"
 vessel_id = "SBML/model/species/compartment"
 constant = "SBML/model/species/constant"
 init_conc = "SBML/model/species/initial_concentration"
 unit = "SBML/model/species/substance_units"
 
-[complexes]
+["EnzymeMLDocument/complexes"]
 id = "SBML/model/species/id"
 name = "SBML/model/species/name"
 vessel_id = "SBML/model/species/compartment"
 constant = "SBML/model/species/constant"
 init_conc = "SBML/model/species/initial_concentration"
 unit = "SBML/model/species/substance_units"
 
-[reactants]
+["EnzymeMLDocument/reactants"]
 id = "SBML/model/species/id"
 name = "SBML/model/species/name"
 vessel_id = "SBML/model/species/compartment"
 constant = "SBML/model/species/constant"
 init_conc = "SBML/model/species/initial_concentration"
 unit = "SBML/model/species/substance_units"
 
-[reactions]
+["EnzymeMLDocument/reactions"]
 id = "SBML/model/reactions/id"
 name = "SBML/model/reactions/name"
 reversible = "SBML/model/reactions/reversible"
 
-[global_parameters]
+["EnzymeMLDocument/parameters"]
 id = "SBML/model/parameters/id"
 name = "SBML/model/parameters/name"
 value = "SBML/model/parameters/value"
 unit = "SBML/model/parameters/units"
 
-["reactions/model"]
+["EnzymeMLDocument/reactions/model"]
 id = "SBML/model/reactions/kinetic_law/id"
 name = "SBML/model/reactions/kinetic_law/name"
 equation = "SBML/model/reactions/kinetic_law/math"
 
-["reactions/model/parameters"]
+["EnzymeMLDocument/reactions/model/parameters"]
 id = "SBML/model/reactions/kinetic_law/local_parameters/id"
 name = "SBML/model/reactions/kinetic_law/local_parameters/name"
 value = "SBML/model/reactions/kinetic_law/local_parameters/value"
 unit = "SBML/model/reactions/kinetic_law/local_parameters/units"
 
-["reactions/educts"]
+["EnzymeMLDocument/reactions/educts"]
 id = "SBML/model/reactions/reactants/id"
 species_id = "SBML/model/reactions/reactants/species"
 stoichiometry = "SBML/model/reactions/reactants/stoichiometry"
 constant = "SBML/model/reactions/reactants/constant"
 
-["reactions/products"]
+["EnzymeMLDocument/reactions/products"]
 id = "SBML/model/reactions/products/id"
 species_id = "SBML/model/reactions/products/species"
 stoichiometry = "SBML/model/reactions/products/stoichiometry"
 constant = "SBML/model/reactions/products/constant"
 
-["reactions/modifiers"]
+["EnzymeMLDocument/reactions/modifiers"]
 id = "SBML/model/reactions/modifiers/id"
-species_id = "SBML/model/reactions/modifiers/species"
+species_id = "SBML/model/reactions/modifiers/species"