Check annotation to be of type dict while reading it from the json

cobra/core/object.py

@@ -20,7 +20,7 @@ def __init__(self, id=None, name=""):
         self.name = name
 
         self.notes = {}
-        self.annotation = {}
+        self._annotation = {}
 
     @property
     def id(self):
@@ -40,6 +40,19 @@ def id(self, value):
     def _set_id_with_model(self, value):
         self._id = value
 
+    @property
+    def annotation(self):
+        return getattr(self, "_annotation", None)
+
+    @annotation.setter
+    def annotation(self, annotation):
+        if annotation == self.annotation:
+            pass
+        elif not isinstance(annotation, dict):
+            raise TypeError("Annotation must be a dict")
+        else:
+            self._annotation = annotation
+
     def __getstate__(self):
         """To prevent excessive replication during deepcopy."""
         state = self.__dict__.copy()

cobra/test/data/invalid_annotation_format.json

@@ -0,0 +1,24 @@
+{
+  "metabolites":[
+    {
+      "id":"4crsol_c",
+      "name":"",
+      "compartment":"c",
+      "annotation":[
+        [
+          "KEGG Compound",
+          "http://identifiers.org/kegg.compound/C01468"
+        ],
+        [
+          "CHEBI",
+          "http://identifiers.org/chebi/CHEBI:11981"
+        ]
+      ]
+    }
+  ],
+  "reactions":[],
+  "genes":[],
+  "id":"tesut",
+  "compartments":{},
+  "version": 1
+}

cobra/test/data/valid_annotation_format.json

@@ -0,0 +1,19 @@
+{
+  "metabolites":[
+    {
+      "id":"4crsol_c",
+      "name":"",
+      "compartment":"c",
+      "annotation": {
+        "bigg.reaction": [["is", "PFK26"]],
+        "kegg.reaction": [["is", "R02732"]],
+        "rhea": [["is", "15656"]]
+      }
+    }
+  ],
+  "reactions":[],
+  "genes":[],
+  "id":"tesut",
+  "compartments":{},
+  "version": 1
+}

cobra/test/data/valid_annotation_output.xml

@@ -0,0 +1,44 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" sboTerm="SBO:0000624" level="3" version="1" fbc:required="false">
+  <model metaid="meta_tesut" id="tesut" fbc:strict="true">
+    <listOfUnitDefinitions>
+      <unitDefinition id="mmol_per_gDW_per_hr">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
+          <unit kind="gram" exponent="-1" scale="0" multiplier="1"/>
+          <unit kind="second" exponent="-1" scale="0" multiplier="3600"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="c" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species metaid="meta_M_4crsol_c" id="M_4crsol_c" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+            <rdf:Description rdf:about="#meta_M_4crsol_c">
+              <bqbiol:is>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/PFK26"/>
+                  <rdf:li rdf:resource="https://identifiers.org/kegg.reaction/R02732"/>
+                  <rdf:li rdf:resource="https://identifiers.org/rhea/15656"/>
+                </rdf:Bag>
+              </bqbiol:is>
+            </rdf:Description>
+          </rdf:RDF>
+        </annotation>
+      </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter sboTerm="SBO:0000626" id="cobra_default_lb" value="-1000" constant="true"/>
+      <parameter sboTerm="SBO:0000626" id="cobra_default_ub" value="1000" constant="true"/>
+      <parameter sboTerm="SBO:0000626" id="cobra_0_bound" value="0" constant="true"/>
+      <parameter sboTerm="SBO:0000625" id="minus_inf" value="-INF" constant="true"/>
+      <parameter sboTerm="SBO:0000625" id="plus_inf" value="INF" constant="true"/>
+    </listOfParameters>
+    <fbc:listOfObjectives fbc:activeObjective="obj">
+      <fbc:objective fbc:id="obj" fbc:type="maximize"/>
+    </fbc:listOfObjectives>
+  </model>
+</sbml>

cobra/test/test_io/test_annotation_format.py

@@ -0,0 +1,25 @@
+import pytest
+from os.path import join
+from cobra.io import load_json_model, write_sbml_model
+
+
+def test_load_json_model_valid(data_directory):
+    """Testing valid annotation format"""
+    path_to_file = join(data_directory, "valid_annotation_format.json")
+    model = load_json_model(path_to_file)
+    dict = {
+        'bigg.reaction': [['is', 'PFK26']],
+        'kegg.reaction': [['is', 'R02732']],
+        'rhea': [['is', '15656']]
+    }
+    for x in model.metabolites:
+        assert x.annotation == dict, "Dictionary is not equal"
+    path_to_output = join(data_directory, 'valid_annotation_output.xml')
+    write_sbml_model(model, path_to_output)
+
+
+def test_load_json_model_invalid(data_directory):
+    """Testing invalid annotation format"""
+    path = join(data_directory, "invalid_annotation_format.json")
+    with pytest.raises(TypeError):
+        model = load_json_model(path)