Dom fix (#135)

* added extra converter test for JSON round trip
* fixed issue #134
* fixed issue #133
* fixed a bug where water was returned as a valid chemical

Author: terazus

ptmd/api/queries/core.py

@@ -28,7 +28,9 @@ def get_chemicals() -> tuple[Response, int]:
 
     :return: tuple containing a JSON response and a status code
     """
-    return jsonify({"data": [dict(chemical) for chemical in Chemical.query.filter(Chemical.ptx_code < 997).all()]}), 200
+    return jsonify({"data": [dict(chemical) for chemical in Chemical.query.filter(
+        Chemical.ptx_code < 997, Chemical.ptx_code > 0
+    ).all()]}), 200
 
 
 def get_organisations() -> tuple[Response, int]:

ptmd/api/queries/files/create.py

@@ -17,6 +17,7 @@
 from ptmd.database.queries.timepoints import create_timepoints_hours
 from ptmd.api.queries.utils import check_role
 from ptmd.database import get_shipped_file
+from ptmd.exceptions import TimepointValueError
 
 
 class CreateGDriveFile:
@@ -95,5 +96,7 @@ def create_gdrive_file() -> tuple[Response, int]:
         payload: CreateGDriveFile = CreateGDriveFile()
         response: dict = payload.generate_file(user=get_current_user().id)
         return jsonify({"data": response}), 200
+    except TimepointValueError as e:
+        return jsonify({"message": str(e)}), 400
     except Exception as e:
         return jsonify({"message": str(e)}), 400

ptmd/api/queries/files/isa.py

@@ -15,7 +15,7 @@ def convert_to_isa(file_id: int) -> tuple[Response, int]:
     :return: a tuple containing the response and the status code
     """
     try:
-        response: list[dict] = convert_file_to_isa(file_id)
+        response: dict = convert_file_to_isa(file_id)[0]
     except ValueError as e:
         return jsonify({'message': str(e)}), 400
     except FileNotFoundError as e:

ptmd/database/queries/timepoints.py

@@ -2,6 +2,7 @@
 """
 from ptmd.config import session
 from ptmd.database.models import Timepoint
+from ptmd.exceptions import TimepointValueError
 
 
 def create_timepoints_hours(values: list[int]) -> list[Timepoint]:
@@ -11,6 +12,8 @@ def create_timepoints_hours(values: list[int]) -> list[Timepoint]:
     """
     timepoints: list[Timepoint] = []
     for i, value in enumerate(values):
+        if not value or not isinstance(value, int):
+            raise TimepointValueError
         timepoint = Timepoint(value=value, unit='hours', label=f'TP{i + 1}')
         session.add(timepoint)
         timepoints.append(timepoint)

ptmd/exceptions.py

@@ -39,3 +39,11 @@ class TokenInvalidError(APIError):
     def __init__(self) -> None:
         """ Constructor """
         self.message: str = "Invalid token"
+
+
+class TimepointValueError(APIError):
+    """ Exception raised when a timepoint value is invalid """
+
+    def __init__(self) -> None:
+        """ Constructor """
+        self.message: str = "Timepoint value must be a positive integer"

ptmd/lib/isa/core.py

@@ -55,7 +55,8 @@ def convert(self) -> list[dict]:
         study: Study = Study(
             filename=self.filename,
             sources=[self.blank_source],
-            characteristic_categories=[ORGANISM_OA, SEX_OA, REPLICATE_OA, BOX_OA, POSITION_OA]
+            characteristic_categories=[ORGANISM_OA, SEX_OA, REPLICATE_OA, BOX_OA, POSITION_OA],
+            units=[HOURS_OA]
         )
         self.create_samples(study)
         study.factors = list(self.factors.values())

ptmd/lib/isa/ontologies.py

@@ -1,5 +1,6 @@
 """ Ontology annotations and sources to create the ISA investigations.
 """
+from uuid import uuid4
 
 from isatools.model import OntologyAnnotation, OntologySource
 
@@ -68,7 +69,8 @@
 SEX_OA: OntologyAnnotation = OntologyAnnotation(term_source=PATO, term='biological sex', term_accession='PATO:0000047')
 EXPOSURE_OA: OntologyAnnotation = OntologyAnnotation(term_source=NCIT, term='Exposure', term_accession='NCIT:C17941')
 SAMPLING_OA: OntologyAnnotation = OntologyAnnotation(term_source=NCIT, term='Sampling', term_accession='NCIT:C25662')
-HOURS_OA: OntologyAnnotation = OntologyAnnotation(term_source=UO, term='hour', term_accession='UO:0000032')
+HOURS_OA: OntologyAnnotation = OntologyAnnotation(term_source=UO, term='hour', term_accession='UO:0000032',
+                                                  id_=f"#unit/{uuid4()}")
 ORGANISM_NA_OA: OntologyAnnotation = OntologyAnnotation(term_source=NCIT, term='N/A', term_accession='NCIT:C48660')
 BOX_OA: OntologyAnnotation = OntologyAnnotation(term_source=NCIT, term='Box', term_accession='NCIT:C43178')
 POSITION_OA: OntologyAnnotation = OntologyAnnotation(

tests/test_api/test_queries/test_files/test_create.py

@@ -7,6 +7,7 @@
 from ptmd.api import app
 from ptmd.const import ALLOWED_DOSE_VALUES
 from ptmd.database.models import Timepoint
+from ptmd.exceptions import TimepointValueError
 
 
 class MockGoogleAuth(GoogleAuth):
@@ -101,6 +102,13 @@ def test_create_gdrive_file(self, mock_get_shipped_file,
                                    data=dumps(data))
             self.assertEqual(response.json['data']['file_url'], 'a')
 
+            mock_timepoints.side_effect = TimepointValueError
+            data['timepoints'] = [None, 1]
+            response = client.post('/api/files', headers={'Authorization': f'Bearer {123}', **HEADERS},
+                                   data=dumps(data))
+            self.assertEqual(response.json, {'message': "Timepoint value must be a positive integer"})
+            self.assertEqual(response.status_code, 400)
+
     @patch('ptmd.api.queries.files.create.get_shipped_file', return_value=False)
     def test_create_gdrive_error(self,
                                  mock_get_shipped_file,

tests/test_api/test_queries/test_files/test_isa.py

@@ -36,7 +36,7 @@ def test_convert_success(self, mock_jwt_verify_flask, mock_jwt_verify_utils, moc
         mock_user().id = 1
         mock_user().role = 'admin'
         with patch('ptmd.api.queries.files.isa.convert_file_to_isa') as mock_convert:
-            mock_convert.return_value = {'message': 'SUCCESS'}
+            mock_convert.return_value = [{'message': 'SUCCESS'}]
             with app.test_client() as client:
                 response = client.get('/api/files/1/isa', headers=HEADERS)
                 self.assertEqual(response.json, {'message': 'SUCCESS'})

tests/test_database/test_queries/test_timepoints.py

@@ -3,6 +3,7 @@
 
 
 from ptmd.database.queries import create_timepoints_hours
+from ptmd.exceptions import TimepointValueError
 
 
 class TestCreateTimepointsHours(TestCase):
@@ -14,3 +15,8 @@ def test_create_timepoints_hours(self, mock_session):
         self.assertEqual(mock_session.add.call_count, 2)
         self.assertEqual(dict(timepoints[0]), {'value': 1, 'unit': 'hours', 'label': 'TP1', 'files': []})
         self.assertEqual(dict(timepoints[1]), {'value': 2, 'unit': 'hours', 'label': 'TP2', 'files': []})
+
+    def test_create_timepoint_errors(self):
+        with self.assertRaises(TimepointValueError) as context:
+            create_timepoints_hours([None, 1])
+        self.assertTrue('Timepoint value must be a positive integer' in str(context.exception))