fixing #332

ISA-tools · Jan 21, 2021 · 15f33c7 · 15f33c7
1 parent e2ef151
commit 15f33c7
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Showing 5 changed files with 20 additions and 17 deletions.
diff --git a/isatools/create/model.py b/isatools/create/model.py
@@ -527,7 +527,7 @@ def loads_ontology_annotation(ontology_annotation_dict):
         if isinstance(ontology_annotation_dict.get("termSource", None), dict):
             term_source = OntologySource(**ontology_annotation_dict["termSource"])
         return OntologyAnnotation(
-            term=ontology_annotation_dict["term"], term_accession=ontology_annotation_dict["termAccession"],
+            term=ontology_annotation_dict["term"], term_accession=ontology_annotation_dict.get("termAccession", ''),
             term_source=term_source
         )
 

diff --git a/isatools/isajson.py b/isatools/isajson.py
@@ -1645,15 +1645,14 @@ def get_source(obj):
             )
 
         def get_characteristic(obj):
-            res = clean_nulls(
+            return clean_nulls(
                 {
                     "category": {"@id": id_gen(obj.category)} if obj.category else None,
                     # "category": get_value(o.category) if o.category else None,
                     "value": get_value(obj.value),
                     "unit": {"@id": id_gen(obj.unit)} if obj.unit else None
                 }
             )
-            return res
 
         def get_characteristics(obj):
             return list(map(lambda x: get_characteristic(x), obj))
@@ -1667,11 +1666,10 @@ def get_value(obj):
                 raise ValueError("Unexpected value type found: " + type(obj))
 
         def get_characteristic_category(obj):  # TODO: Deal with Material Type
-            ont_ann = OntologyAnnotation(term=obj) if isinstance(obj, str) else obj
             res = clean_nulls(
                 {
-                    "@id": id_gen(ont_ann),
-                    "characteristicType": get_ontology_annotation(ont_ann)
+                    "@id": id_gen(obj),
+                    "characteristicType": get_ontology_annotation(obj)
                 }
             )
             return res

diff --git a/isatools/model.py b/isatools/model.py
@@ -102,7 +102,8 @@ def value(self):
     def value(self, val):
         if isinstance(val, str):
             self.__value = val
-        raise ISAModelAttributeError('Comment.value must be a string')
+        else:
+            raise ISAModelAttributeError('Comment.value must be a string')
 
     def __repr__(self):
         return "isatools.model.Comment(name='{comment.name}', " \
@@ -2690,7 +2691,8 @@ def __init__(self, category=None, value=None, unit=None, comments=None):
         self.__value = None
         self.__unit = None
 
-        self.category = category
+        if category is not None:
+            self.category = category
         self.value = value
         self.unit = unit
 
@@ -2702,12 +2704,14 @@ def category(self):
 
     @category.setter
     def category(self, val):
-        if val is not None and not isinstance(val, (str, OntologyAnnotation)):
-            raise ISAModelAttributeError(
+        if isinstance(val, OntologyAnnotation) or val is None:
+            self.__category = val
+        elif isinstance(val, str):
+            self.__category = OntologyAnnotation(term=val)
+        else:
+            raise AttributeError(
                 'Characteristic.category must be either a string ot an OntologyAnnotation,'
                 ' or None; got {0}:{1}'.format(val, type(val)))
-        else:
-            self.__category = val
 
     @property
     def value(self):

diff --git a/tests/test_create_models_json.py b/tests/test_create_models_json.py
@@ -374,7 +374,9 @@ def test_with_strings(self):
         # log.info('Characteristic is {0}'.format(characteristic))
         actual_json_characteristic = json.loads(json.dumps(characteristic, cls=CharacteristicEncoder))
         expected_json_characteristic = {
-            'category': characteristic.category,
+            'category': {
+                'term': characteristic.category.term
+            },
             'value': characteristic.value
         }
         self.assertEqual(ordered(actual_json_characteristic), ordered(expected_json_characteristic))

diff --git a/tests/test_isajson.py b/tests/test_isajson.py
@@ -454,7 +454,6 @@ def test_isajson_with_strings_as_characteristic_category(self):
         self.assertIsInstance(isa_j, str)
         with open(os.path.join(utils.JSON_DATA_DIR, 'ISA-1', 'isa-test2.json'), 'w') as out_fp:
             out_fp.write(isa_j)
-        # FIXME fix this
-        # with open(os.path.join(utils.JSON_DATA_DIR, 'ISA-1', 'isa-test2.json')) as in_fp:
-        #     reverse_test_isa_investigation = isajson.load(in_fp)
-        #     self.assertIsInstance(reverse_test_isa_investigation, Investigation)
+        with open(os.path.join(utils.JSON_DATA_DIR, 'ISA-1', 'isa-test2.json')) as in_fp:
+            reverse_test_isa_investigation = isajson.load(in_fp)
+            self.assertIsInstance(reverse_test_isa_investigation, Investigation)